NL2035804B1

NL2035804B1 - Immune modulating inhibitory receptors

Info

Publication number: NL2035804B1
Application number: NL2035804A
Authority: NL
Inventors: Meyaard Linde; Singh Akashdip; Juliette Von Richthofen Helen; Van Der Vlist Michiel; Herbert Ernst Kuball Jürgen; Kesmir Can; Inês Pascoal Martins Ramos Maria; Miranda Bedate Alberto
Original assignee: Umc Utrecht Holding Bv; Univ Utrecht Holding Bv
Priority date: 2023-09-15
Filing date: 2023-09-15
Publication date: 2025-03-25
Also published as: WO2025058519A1

Abstract

A B S T R A C T The present invention relates to a method for screening for compounds which modulate the expression and/or activity of a ITIM and/or ITSM comprising modulatory immune receptor expressed in an immune cell, in which a ITIM and/or ITSM comprising modulatory immune receptor or biologically active portion thereof with a test compound is contacted with a test compound; and the effect of the test compound on the expression and/or activity of the a ITIM and/or ITSM comprising modulatory immune receptor or biologically active portion thereof is determined. The invention also includes methods that relate to the inventive concept of using the ITIM and/or ITSM comprising modulatory immune receptor expressed in an immune cell to test compounds. lmmune cell wherein a gene encoding the ITIM and/or ITSM comprising modulatory immune receptor has been knocked-out is also disclosed.

Description

Title: Immune modulating inhibitory receptors

FIELD OF THE INVENTION

[001] This invention pertains in general to immune modulating receptors, (also referred to herein as modulatory immune receptors) and methods for screening for, identifying, and/or testing compounds/drugs that may modulate the expression and/or activity of such immune modulating receptors.

[002] In particular the invention relates to the identification of ITIM and/or ITSM comprising proteins that are expressed in various immune cells, and under different conditions.

BACKGROUND OF THE INVENTION

[003] The background description includes information that may be useful in understanding the present invention. It is not an admission that any of the information provided herein is prior art or relevant to the presently claimed invention, or that any publication specifically or implicitly referenced is prior art.

[004] Blocking modulatory receptors like PD-1 and CTLA-4 has revolutionized cancer treatment in recent years. However, despite major successes in melanoma and lung cancer, the majority of cancer types are not responsive to these immunotherapies. As such, there is an ongoing need for the identification of novel modulatory receptors as drug targets, and compounds that can target these novel modulatory receptors and thereby modulate the expression and/or activity of such immune modulatory receptors.

[005] In light of this, new products, compositions, methods and uses for in the treatment of conditions that involve such modulatory receptors would be highly desirable but are not yet readily available. In particular, there is a clear need in the art for reliable, efficient, and reproducible products, compositions, methods and uses that allow to be used in the treatment of such conditions. Accordingly, the technical problem underlying the present invention can been seen in the provision of such products, compositions, methods and uses for complying with any of the aforementioned needs, or at least providing the public with a useful choice. The technical problem is solved by the embodiments characterized in the claims and herein below.

SUMMARY OF THE INVENTION

[006] As embodied and broadly described herein, the present invention is directed to the surprising identification of modulatory receptors that are expressed across a wide variety of immune cells, and show cell type-specific patterns in expression, for example depending of the cell state (resting, activated), and also in relation to the function of the subset or subtype or its environment. For example, the inventors surprisingly determined immune modulatory receptors are expressed differentially in

CD4+ and CD8+ T cell subsets, including exhausted CD8+ T cells and CD4+ memory

T cells, which may allow for subset-specific targeting.

[007] All this results from an analysis by means of a novel bioinformatics pipeline, which allowed to identify immune modulatory receptors as potential therapeutic targets.

[008] The invention refers in a first aspect to a method for screening for compounds which modulate the expression and/or activity of a ITIM and/or ITSM comprising modulatory immune receptor expressed in an immune cell, more preferably wherein the ITIM and/or ITSM comprising modulatory immune receptor is i. a negative feedback modulatory immune receptor, preferably that is expressed in an activated immune cell; ii. a threshold modulatory immune receptor, preferably that is expressed on an immune cells in resting state; iii. a threshold-disinhibition modulatory immune receptor, preferably that is expressed on an immune cell in resting state and which expression is downregulated after activation of the immune cell; or iv. a threshold-negative feedback modulatory immune receptor, preferably expressed on an immune cell in resting state and which expression is upregulated after activation of the immune cell, comprising: (a) contacting the ITIM and/or ITSM comprising modulatory immune receptor or biologically active portion thereof with a test compound; and

(b) determining the effect of the test compound (which can also be a therapeutic element) on the expression and/or activity of the a ITIM and/or ITSM comprising modulatory immune receptor or biologically active portion thereof.

[008] Another aspect of the invention is a method for identifying a compound which modulates the expression and/or activity of a ITIM and/or ITSM comprising modulatory immune receptor expressed in an immune cell, more preferably wherein the ITIM and/or ITSM comprising modulatory immune receptor is i. a negative feedback modulatory immune receptor, preferably that is expressed in an activated immune cell; ii. a threshold modulatory immune receptor, preferably that is expressed on an immune cells in resting state; iii. a threshold-disinhibition modulatory immune receptor, preferably that is expressed on an immune cell in resting state and which expression is downregulated after activation of the immune cell; or iv. a threshold-negative feedback modulatory immune receptor, preferably expressed on an immune cell in resting state and which expression is upregulated after activation of the immune cell, comprising: (a) contacting the ITIM and/or ITSM comprising modulatory immune receptor or biologically active portion thereof with a test compound; and (b) determining the effect of the test compound on the expression and/or activity of the ITIM and/or ITSM comprising modulatory immune receptor or biologically active portion thereof to thereby identify a compound which modulates the activity of the polypeptide or biologically active portion thereof.

[010] Yet another aspect of the invention is a method for testing a drug for modulating the expression and/or activity of a ITIM and/or ITSM comprising modulatory immune receptor expressed in an immune cell, more preferably wherein the ITIM and/or ITSM comprising modulatory immune receptor is i.a negative feedback modulatory immune receptor, preferably that is expressed in an activated immune cell;

ii.a threshold modulatory immune receptor, preferably that is expressed on an immune cells in resting state; iii.a threshold-disinhibition modulatory immune receptor, preferably that is expressed on an immune cell in resting state and which expression is downregulated after activation of the immune cell; or iv.a threshold-negative feedback modulatory immune receptor, preferably expressed on an immune cell in resting state and which expression is upregulated after activation of the immune cell, comprising: (a) contacting the ITIM and/or ITSM comprising modulatory immune receptor or biologically active portion thereof with the drug; and (b) determining the effect of the drug on the expression and/or activity of the ITIM and/or ITSM comprising modulatory immune receptor or biologically active portion thereof.

[011] The invention also relates in another aspect to a method for screening for compounds which modulate the expression and/or activity of a polypeptide encoded by a gene listed in Table 1 or biological active portion thereof comprising: (a) contacting the polypeptide or biologically active portion thereof with a test compound; and (b) determining the effect of the test compound on the expression and/or activity of the polypeptide or biologically active portion thereof.

[012] Table 1 can be found in the Detailed Description section of this document.

[013] Another aspect of the invention is a method for identifying a compound which modulates the expression and/or activity of a polypeptide encoded by a gene listed in Table 1 or biological active portion thereof comprising: (a) contacting the polypeptide or biologically active portion thereof with a test compound; and (b) determining the effect of the test compound on the expression and/or activity of the polypeptide or biologically active portion thereof to thereby identify a compound which modulates the activity of the polypeptide or biologically active portion thereof.

[014] Yet another aspect of the invention is a method for testing a drug for 5 modulating the expression and/or activity of a polypeptide encoded by a gene listed in Table 1 or biological active portion thereof comprising: (a) contacting the polypeptide or biologically active portion thereof with the drug; and (b) determining the effect of the drug on the expression and/or activity of the polypeptide or biologically active portion thereof./nlp

[015] Another aspect of the invention is an immune cell wherein a gene encoding the ITIM and/or ITSM comprising modulatory immune receptor or a gene encoding the polypeptide encoded by a gene listed in Table 1 has been knocked-out.

[018] The invention also relates in another aspect to an expression vector comprising a nucleotide sequence encoding the ITIM and/or ITSM comprising modulatory immune receptor or encoding the polypeptide encoded by a gene listed in Table 1, operably linked with a promoter.

[017] Another aspect of the invention is a host cell comprising the vector of the previous aspect, or recombinantly expressing the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide encoded by a gene listed in Table 1.

[018] The invention also relates in another aspect to a method of determining the copy number, level of expression, or level of activity of the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide encoded by a gene listed in Table 1 in a cell comprising: (a) providing the cell; and (b) determining the copy number, level of expression, or level of activity of the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide encoded by a gene listed in Table 1 in the cell, preferably wherein the cell is an immune cell.

[019] Another aspect of the invention is a method for identifying a binding partner to a ITIM and/or ITSM comprising modulatory immune receptor or a polypeptide encoded by a gene listed in Table 1 or biological active portion thereof comprising:

(a) contacting the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide or biologically active portion thereof, or a cell expressing the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide, or biologically active portion thereof, with a test compound; and (b) determining whether the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide or biologically active portion thereof binds to the test compound.

BRIEF DESCRIPTION OF THE DRAWINGS

[020] Embodiments of the invention are further described hereinafter with reference to the accompanying drawings, in which:

[021] Figure 1: A novel bioinformatics approach for the identification of predicted modulatory receptors. Schematic overview of the bioinformatics pipeline with the number of unique genes and corresponding proteins remaining at every step. All amino acid sequences corresponding to a protein-coding transcript were retrieved from

Ensembl.

[022] Figure 2: Known and predicted single-spanning modulatory receptors are expressed in different cell types in the resting state and after activation. A. Novel and known receptors were classified into different functional categories based on changes, or lack thereof, in expression after stimulation. Threshold receptors were expressed at resting state, and did not change after activation (i.e., change in expression < 0.5 log2 fold change). Threshold-negative feedback and threshold-disinhibition receptors were defined by > 0.5 log2 fold change up or downregulation, respectively, in expression after activation. Negative feedback receptors were absent in the resting state, but were expressed after activation. Categories indicated from left to right are shown from top to bottom in the figure. B. Upset plot showing the number of single- spanning receptors that are expressed uniquely by individual immune cell subsets , or shared between subsets as indicated by connected circles. Sixty-four genes are expressed in all cell types (not depicted).

[023] Figure 3: Single-spanning predicted modulatory receptors are expressed across a wide variety of tumor infiltrating T cell subsets. Number of modulatory receptor genes expressed by different CD4+ (A) and CD8+ (B) T cell subsets.

Categories indicated from top to bottom are shown from left to right in the figure.

[024] Figure 4: Known and predicted multi-spanning modulatory receptors are expressed in different cell types in the resting state and after activation. A. Known and predicted multi-spanning receptors were classified into different functional categories based on changes, or lack thereof, in expression after stimulation. Threshold receptors were expressed at resting state, and did not change after activation (i.e., change in expression < 0.5 log2 fold change). Threshold-negative feedback and threshold- disinhibition receptors were defined by > 0.5 log2 fold change up or downregulation, respectively, in expression after activation. Negative feedback receptors were absent in the resting state, but expressed after activation. Categories indicated from left to right are shown from top to bottom in the figure. B. Upset plot showing the number of multi-spanning receptors that are expressed uniquely by individual immune cell subsets , or shared between subsets as indicated by connected circles. Seventy-five genes are expressed in all cell types (not depicted). Cell subsets without uniquely expressed putative modulatory receptors, i.e., B cells and T cells, were excluded from the panel for clarity.

[025] Figure 5: Multi-spanning predicted modulatory receptors are expressed across a wide variety of tumor infiltrating T cell subsets. Number of modulatory receptor genes expressed by different CD4+ (A) and CD8+ (B) T cell subsets. Categories indicated from left to right are shown from left to right in the figure.

DESCRIPTION Definitions

[026] A portion of this disclosure contains material that is subject to copyright protection (such as, but not limited to, diagrams, device photographs, or any other aspects of this submission for which copyright protection is or may be available in any jurisdiction.). The copyright owner has no objection to the facsimile reproduction by anyone of the patent document or patent disclosure, as it appears in the Patent Office patent file or records, but otherwise reserves all copyright rights whatsoever.

[027] Various terms relating to the methods, compositions, uses and other aspects of the present invention are used throughout the specification and claims. Such terms are to be given their ordinary meaning in the art to which the invention pertains, unless otherwise indicated. Other specifically defined terms are to be construed in a manner consistent with the definition provided herein. Although any methods and materials similar or equivalent to those described herein can be used in the practice for testing of the present invention, the preferred materials and methods are described herein.

[028] For purposes of the present invention, the following terms are defined below.

[029] As used herein, the singular form terms “a,” “an,” and “the” include plural referents unless the content clearly dictates otherwise. Thus, for example, reference to “a cell” includes a combination of two or more cells, and the like.

[030] As used herein, “about” and “approximately”, when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of £20% or £10%, more preferably 15%, even more preferably £1%, and still more preferably £0.1% from the specified value, as such variations are appropriate to perform the disclosed invention. Unless otherwise clear from context, all numerical values provided herein include numerical values modified by the term “about.”

[031] As used herein, “and/or” refers to a situation wherein one or more of the stated cases may occur, alone or in combination with at least one of the stated cases, up to with all of the stated cases.

[032] As used herein, "at least" a particular value means that particular value or more.

For example, "at least 2" is understood to be the same as "2 or more" i.e., 2, 3, 4, 5, 6,7,8,9 10, 11,12, 13, 14, 15, ..., etc. As used herein, the term “at most" a particular value means that particular value or less. For example, "at most 5" is understood to be the same as "5 or less" i.e, 5, 4, 3, ....-10, -11, etc.

[033] As used herein, “comprising” or “to comprise” is construed as being inclusive and open ended, and not exclusive. Specifically, the term and variations thereof mean the specified features, steps or components are included. These terms are not to be interpreted to exclude the presence of other features, steps or components. It also encompasses the more limiting “to consist of”.

[034] As used herein, “conventional techniques” or “methods known to the skilled person” refer to a situation wherein the methods of carrying out the conventional techniques used in methods of the invention will be evident to the skilled worker. The practice of conventional techniques in molecular biology, biochemistry, cell culture, genomics, sequencing, medical treatment, pharmacology, immunology and related fields are well-known to those of skill in the art and are discussed, in various handbooks and literature references.

[035] Throughout this disclosure, various aspects of the invention can be presented in a range format. It should be understood that the description in range format is merely for convenience and should not be construed as a limitation on the scope of the invention. The description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range including both integers and non-integers. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, 6 etc. This applies regardless of the breadth of the range.

[038] As used herein, “agonist”, refers to a compound or agent having the ability to initiate or enhance a biological function of a target protein or polypeptide, such as increasing the activity or expression of the target protein or polypeptide. Accordingly, "agonist" is defined in the context of the biological role of the target protein or polypeptide. While some agonists herein may specifically interact with (e.g., bind to) the target, compounds and/or agents that initiate or enhance a biological activity of the target protein or polypeptide by interacting with other members of the signal transduction pathway of which the target polypeptide is a member are in embodiments specifically included within this definition.

[037] As used herein, "antagonist" and/or "inhibitor" are used interchangeably, and they refer to a compound or agent having the ability to reduce ar inhibit a biological function of a target protein or polypeptide, such as by reducing or inhibiting the activity or expression of the target protein or polypeptide. Accordingly, the terms "antagonist" and "inhibitor" are defined in the context of the biological role of the target protein or polypeptide. While some antagonists herein may specifically interact with (e.g., bind to) the target, compounds that inhibit a biological activity of the target protein or polypeptide by interacting with other members of the signal transduction pathway of which the target protein or polypeptide are in embodiment also included within this definition.

[038] As used herein a “compound for screening”, “test compound”, “candidate agent” or “agent,” refers to a molecule that may be screened for, or be identified as,

modulating activity of a target activity (e.g. a compound directly or indirectly interacts with a ITIM and/or ITSM comprising immune receptor expressed in an immune cell as identified and disclosed herein). Such agent may, for example, be an inhibitor or enhancer of the activity or expression and may find use in a variety of applications, including as therapeutic agents, as agricultural chemicals, and so on. The screening methods will typically be assays which provide for qualitative/quantitative measurements of the activity in the presence of a particular candidate agent. For example, the assay could be an assay which measures the immune cell release of certain cytokines, the expression of certain markers or the immune cell viability. The screening method may be an in vitro or in vivo format, and both formats are readily developed by those of skill in the art according to conventional techniques. (Candidate) agents may be obtained from a wide variety of sources including libraries of synthetic or natural compounds. For example, numerous means are available for random and directed synthesis of a wide variety of organic compounds and biomolecules, including expression of randomized oligonucleotides and oligopeptides. Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts or purified compounds are available or may be produced. Additionally, natural or synthetically produced libraries and compounds can be prepared using conventional chemical, physical and biochemical means, and may be used to produce combinatorial libraries. Known pharmacological agents may be subjected to directed or random chemical modifications, such as acylation, alkylation, esterification, amidification, etc. to produce structural analogs or derivates. (Candidate) agents may also be biomolecules including peptides, antibodies, ligands, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof, preferably antibodies, ligands or antigen binding molecule (preferably the antigen being comprised in the immune modulating receptor according to the invention). In a preferred embodiment antibodies Within the context of the current invention, the agent used in the various methods of the invention may include cells such a modulates cells, including living cells).

[039] Using the above screening methods, a variety of different therapeutic agents may be identified. For example, such agents may target a ITIM and/or ITSM comprising immune receptor expressed in an immune cell as identified and disclosed herein. Such agents may be inhibitors or promoters of the targeted activity, where inhibitors are those agents that result in at least a reduction of activity as compared to a control and enhancers result in at least an increase in activity as compared to a control. Such agents may be find use in a variety of (therapeutic) applications.

[040] As used herein, the term “immune cell” encompasses any cell involved in the innate or adaptive immune response and includes one or more of macrophages, neutrophils, dendritic cells. lymphoid cells, mast cells, eosinophils, basophils, natural killer cells, granulocytes, T lymphocytes (including the killer T cell also known as CD8+

T cells, the helper T cell also known as CD4+ T cells, regulatory T cells, and ‘unconventional’ T cells exemplified by yò T cells and NKT cells), and B lymphocytes.

[041] As used herein, the term “modulatory immune receptor” or “immune modulatory receptor” or “madulatory receptor” or “immune modulating receptor” broadly refers to an immune cell receptor that may regulate (positively or negatively) immune cell function to (enhance or reduce) modulate immune reactions, for example, modulate autoimmune reactions and/or immunopathology. Only by way of example, and without limiting the invention disclosed herein, the most well-described modulatory receptor mechanism of action is the local and transient intracellular attenuation of positive signals from activating receptors, including antigen-receptors and co-stimulatory receptors. Most of the known modulatory receptors attenuate T-cell receptors (TCR) or B-cell receptors (BCR) signalling events by targeting these directly or their downstream signalling molecules. Modulatory receptors cause a broad, quantitative modulation, for example reduction, in activation-induced signal transduction and downstream gene expression. In some embodiments the modulatory immune receptor is a inhibitory immune receptor. In some embodiments the modulatory immune receptor is a stimulatory immune receptor.

[042] As used herein, the term “immunoreceptor tyrosine-based modulatory motif (ITIM)” refers to a conserved sequence of amino acids that is found in the cytoplasmic tails of many modulatory receptors of the immune system. The ITIM motif generally comprises a serine residue (S), a isoleucine residue (I), a valine residue (V) or a leucine residue (L), separated by any other amino acid residue (x) from a tyrosine residue (Y), separated by any two other amino acids from a isoleucine residue (1), valine residue (V) or leucine residue (L). The consensus signature is S/I/V/LxYxxI/V/L.

In vivo, ITIM-possessing modulatory receptors interact with their ligand, causing the

ITIM motif to become phosphorylated by enzymes of the Src kinases, allowing them to recruit other enzymes.

[043] As used herein, the term “immunoreceptor tyrosine-based switch motif (ITSM)” refers to a conserved sequence of amino acids that is found in the cytoplasmic tails of many modulatory receptors of the immune system. The ITSM motif generally comprises a threonine residue (T), separated by any other amino acid residue from a tyrosine residue (Y), separated by any other two amino acids from a valine residue (V) or an isoleucine residue (I). The consensus signature is TxYxxV/I. In vivo, ITSM.

[044] As used herein, a “negative feedback modulatory immune receptor” is an modulatory immune receptor, which is induced by cellular activation to ensure a timely resolution of the response and limit excessive immune response.

[045] As used herein, a “threshold modulatory immune receptor”, is an modulatory immune receptor, which is expressed on immune cells in the resting state and control the threshold for immune cell activation to provide context and prevent unnecessary or futile responses.

[046] As used herein, a “threshold-disinhibition modulatory immune receptor” is a threshold modulatory immune receptor, which preferably it is expressed on an immune cell in resting state and which expression is downregulated after activation of the immune cell.

[047] As used herein, a “threshold-negative feedback modulatory immune receptor”, is a threshold modulatory immune receptor, which expression is further induced upon cellular activation.

[048] As used herein, it is be understood that a cell, preferably an immune cell is in a resting state when it is quiescent and does, for example, not proliferate to perform their function. On the contrary, when a cell, in particular any immune cell is activated, this means that by stimulatory and co-stimulatory signals from outside or inside the cell may, for example, switch to the proliferating state to perform their function. Other examples of activation may include, for example, cytokine production, cytotoxicity and/or degranulation. The skilled person is well aware of such and other functions of activated immune cells.

[049] As used herein, a “modulator” refers to a compound that is either an agonist or an antagonist. As used herein, a “modulator” refers to a compound that alters the activity of a target activity, for example the activity of a target protein. The modulator may be an inhibitor (antagonist) or an enhancer (agonist). The modulator may alter the activity by modulation of, for example, the enzymatic activity of a target protein, by modulation the interaction of the target protein with a further factor, such as a further protein, by modulation of the activity of a regulator of the target protein, and/or by modulating expression of the target protein. In one example, the modulator is a ligand.

[050] As used herein, the terms “in vivo”, “ex vivo”, or “in vitro” take the meaning widely accepted. In vitro (Latin: in glass) studies in experimental biology are those that are conducted using components of an organism that have been isolated from their usual biological surroundings in order to permit a more detailed or more convenient analysis than can be done with whole organisms. In contrast, in vivo work is that which is conducted with living organisms in their normal, intact state, while ex vivo studies are conducted on functional organs that have been removed from the intact organism.

Ex vivo (Latin: "out of the living") means that which takes place outside an organism.

In science, ex vivo refers to experimentation or measurements done in or on tissue in an artificial environment outside the organism with the minimum alteration of natural conditions. Ex vivo conditions allow experimentation under more controlled conditions than is possible in in vivo experiments (in the intact organism), at the expense of altering the "natural" environment.

[051] As used herein, the term “expression vector” refers to a polynucleotide sequence, also known as plasmid or virus genome that comprises the sequence of a polynucleotide that is desired to be transcribed and translated in a cell. An expression vector, is used to introduce a specific gene into a target cell, and can commandeer the cell's mechanism for protein synthesis to produce the protein encoded by the gene.

The vector is engineered and contains regulatory sequences that act as enhancer and promoter regions and lead to efficient transcription of the gene carried on the expression vector. The promoter and enhancers are operably linked to the polynucleotide that wants to be expressed in the cell or by means of the cell.

[052] As used herein the term “nucleic acid” or “polynucleotide” refers to any polymers or oligomers of (contiguous) nucleotides. The nucleic acid may be DNA or

RNA, or a mixture thereof, and may exist permanently or transitionally in single- stranded or double-stranded form, including homoduplex, heteroduplex, and hybrid states. The present invention also contemplates any deoxyribonucleotide, ribonucleotide or peptide nucleic acid component, and any chemical variants thereof,

such as methylated, hydroxymethylated or glycosylated forms of these bases, and the like. The polymers or oligomers may be heterogeneous or homogenous in composition, and may be isolated from naturally occurring sources or may be artificially or synthetically produced.

[053] As used herein, “operably linked” refers to a linkage of polynucleotide elements in a functional relationship. A nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleotide sequence. For instance, a promoter, or rather a transcription regulatory sequence, is operably linked to a coding sequence if it affects the transcription of the coding sequence. Operably linked may mean that the

DNA sequences being linked are contiguous.

[054] As used herein, “protein” or “polypeptide” are used interchangeably and refer to molecules consisting of a chain of amino acids, without reference to a specific mode of action, size, 3 dimensional structure or origin. A “fragment” or “portion” of a protein may thus still be referred to as a “protein.” A protein as defined herein and as used in any method as defined herein may be an isolated protein. An “isolated protein” is used to refer to a protein which is no longer in its natural environment, for example in vitro or in a recombinant bacterial or plant host cell.

[055] As used herein, “sequence” or “nucleotide sequence” refers to the order of nucleotides of, or within a nucleic acid. In other words, any order of nucleotides in a nucleic acid may be referred to as a sequence or nucleotide sequence. The term “amino acid sequence” refers to the order of amino acids or, or within a polypeptide (or protein). In other words, any order of amino acids in a polypeptide may be referred to as a sequence of amino acid sequence.

Detailed description

[056] The invention is defined herein, and in particular in the accompanying claims.

Subject-matter which is not encompassed by the scope of the claims does not form part of the present claimed invention.

[057] It is contemplated that any method, use, or composition described herein can be implemented with respect to any other method, use or composition described herein. Embodiments discussed in the context of methods, use and/or compositions of the invention may be employed with respect to any other method, use or composition described herein. Thus, an embodiment pertaining to one method, use or composition may be applied to other methods, uses and compositions of the invention as well.

[058] Any references in the description to methods of treatment refer to the compounds, pharmaceutical compositions, and medicaments of the present invention for use in a method for treatment of the human (or animal) body by therapy.

[059] As embodied and broadly described herein, the present invention is directed to the surprising identification of modulatory receptors that are expressed across a wide variety of immune cells, display cell type-specific patterns in expression depending of the cell state (resting, activated), and in relation to function of the subset or subtype of cells or its environment. For example, the inventors surprisingly identified immune modulatory receptors are expressed differentially in CD4+ and CD8+ T cell subsets, including exhausted CD8+ T cells and CD4+ memory T cells, which allows for subset- specific targeting.

[060] As previously indicated, the invention refers in a first aspect to a method for screening for compounds which modulate the expression and/or activity of a ITIM and/or ITSM comprising modulatory immune receptor expressed in an immune cell, more preferably wherein the ITIM and/or ITSM comprising modulatory immune receptor is i. a negative feedback modulatory immune receptor, preferably that is expressed in an activated immune cell; ii. a threshold modulatory immune receptor, preferably that is expressed on an immune cells in resting state; iii. a threshold-disinhibition modulatory immune receptor, preferably that is expressed on an immune cell in resting state and which expression is downregulated after activation of the immune cell, or iv. a threshold-negative feedback modulatory immune receptor, preferably expressed on an immune cell in resting state and which expression is upregulated after activation of the immune cell, comprising:

(a) contacting the ITIM and/or ITSM comprising modulatory immune receptor or biologically active portion thereof with a test compound; and (b) determining the effect of the test compound on the expression and/or activity of the a ITIM and/or ITSM comprising modulatory immune receptor or biologically active portion thereof.

[061] In another aspect, the invention relates to a method for identifying a compound which modulates the expression and/or activity of a ITIM and/or ITSM comprising modulatory immune receptor expressed in an immune cell, more preferably wherein the ITIM and/or ITSM comprising modulatory immune receptor is i. a negative feedback modulatory immune receptor, preferably that is expressed in an activated immune cell; ii. a threshold modulatory immune receptor, preferably that is expressed on an immune cells in resting state; iii. a threshold-disinhibition modulatory immune receptor, preferably that is expressed on an immune cell in resting state and which expression is downregulated after activation of the immune cell; or iv. a threshold-negative feedback modulatory immune receptor, preferably expressed on an immune cell in resting state and which expression is upregulated after activation of the immune cell, comprising: (a) contacting the ITIM and/or ITSM comprising modulatory immune receptor or biologically active portion thereof with a test compound; and (b) determining the effect of the test compound on the expression and/or activity of the ITIM and/or ITSM comprising modulatory immune receptor or biologically active portion thereof to thereby identify a compound which modulates the activity of the polypeptide or biologically active portion thereof.

[062] The skilled person will know the experimental and assays commonly used to determine the activity of a receptor, in particular of an immune receptor. For example, the assay could be an assay which measures the immune cell release of certain cytokines, which are known to be released in an activated state; the expression of certain markers; or the immune cell viability.

[083] Yet in another aspect, the invention relates to a method for testing a drug for modulating the expression and/or activity of a ITIM and/or ITSM comprising modulatory immune receptor expressed in an immune cell, more preferably wherein the ITIM and/or ITSM comprising modulatory immune receptor is i.a negative feedback modulatory immune receptor, preferably that is expressed in an activated immune cell; ii.a threshold modulatory immune receptor, preferably that is expressed on an immune cells in resting state; iii.a threshold-disinhibition modulatory immune receptor, preferably that is expressed on an immune cell in resting state and which expression is downregulated after activation of the immune cell; or iv.a threshold-negative feedback modulatory immune receptor, preferably expressed on an immune cell in resting state and which expression is upregulated after activation of the immune cell, comprising: (a) contacting the ITIM and/or ITSM comprising modulatory immune receptor or biologically active portion thereof with the drug; and (b) determining the effect of the drug on the expression and/or activity of the

ITIM and/or ITSM comprising modulatory immune receptor or biologically active portion thereof.

[064] In a particular embodiment of any one of the previous aspects, the ITIM and/or

ITSM comprising modulatory immune receptor expressed in an immune cell is encoded by a gene listed in Table 1.

[065] The invention also relates in another aspect to a method for screening for compounds which modulate the expression and/or activity of a polypeptide encoded by a gene listed in Table 1 or biological active portion thereof comprising: (a) contacting the polypeptide or biologically active portion thereof with a test compound; and (b) determining the effect of the test compound on the expression and/or activity of the polypeptide or biologically active portion thereof.

[066] Another aspect of the invention is a method for identifying a compound which modulates the expression and/or activity of a polypeptide encoded by a gene listed in

Table 1 or biclogical active portion thereof comprising: (a) contacting the polypeptide or biologically active portion thereof with a test compound; and (by determining the effect of the test compound on the expression and/or activity of the polypeptide or biologically active portion thereof to thereby identify a compound which modulates the activity of the polypeptide or biologically active portion thereof.

[067] Yet another aspect of the invention is a method for testing a drug for modulating the expression and/or activity of a polypeptide encoded by a gene listed in Table 1 or biological active portion thereof comprising: (a) contacting the polypeptide or biologically active portion thereof with the drug; and (b) determining the effect of the drug on the expression and/or activity of the polypeptide or biologically active portion thereof.

[068] In a particular embodiment of any of the methods of any of the aspects in this detailed description, the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide has the ability to modulate immunomodulatory function, modulate cytokine expression, modulate immune cell activation, modulate migration ability, modulate Killing ability, and/or modulate cellular proliferation.

[069] In another particular embodiment of any of the methods of any of the aspects in this detailed description, the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide is expressed in a cell, preferably an immune cell.

[070] In yet another particular embodiment of any of the methods of the aspects of the invention, the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide is expressed in a cell, preferably an immune cells, and wherein the contacting with the test compound or drug is performed in the presence of a target of the cell, preferably immune cell.

[071] In yet another particular embodiment of any of the methods of the aspects of the invention, the immune cell is a neutrophil, a monocyte, a myeloid cell, a lymphoid cell, aB cell, aT cell, a NK cell, a helper T cell, a follicular helper T cell, an effector memory T cell, a regulatory T cell, a macrophage.

[072] In yet another particular embodiment of any of the methods of the aspects of the invention, the T cell is a CD4+ T-cell, a CD8+ T cell, a tumor infiltrating T cell, an exhausted CD8+ T cell, a CD4+ memory T cell.

[073] In yet another particular embodiment of any of the methods of the aspects of the invention, determining the effect of the test compound or the drug on activity of the

ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide, comprises determining an effect of the test compound or the drug on the immune response of the cell, preferably the immune cell expressing the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide.

[074] In a more particular embodiment, the effect of the test compound or the drug on the immune response of the cell is modulating immunomodulatory function, modulating cytokine expression, modulating immune cell activation, modulating migration ability, modulating killing ability, and/or modulating cellular proliferation.

[075] In another particular embodiment of any of the methods of the aspects of the invention, the method comprises contacting the test compound or the drug with a cell expressing the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide and contacting the test compound or the drug with an identical cell but not expressing the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide or with an identical cell with reduced expression of the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide or the polypeptide, and comparing the effect of the test compound or the drug on the expression and/or activity of the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide.

[076] In another particular embodiment of any of the methods of the aspects of the invention, the cell is an immune cell and wherein the immune cell is activated prior to, during and/or subsequent to contacting the test compound or the drug with the cell.

[077] In another particular embodiment of any of the methods of the aspects of the invention, a further compound is contacted with the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide prior to, during and/or subsequent to contacting the test compound or the drug with the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide, preferably wherein the further compound is a known modulatory immune receptor modulator.

[078] In another particular embodiment of any of the methods of the aspects of the invention, the cell is a cell obtained from a subject, preferably wherein the cell is obtained from a subject suffering from cancer or suffering from an immune disease or suffering from inflammation. In one example, the subject are patients who enter or suspected to enter states of immune disease of inflammation due to iatrogenic intervention (e.g. checkpoint inhibitor treatment, allogenic stem cell transplantation .

[079] More particular embodiments relate to cells from a subject suffering from a cancer selected from bladder cancer, brain cancer, breast cancer, cervical cancer, ovarian cancer, colorectal cancer, esophageal cancer, head and neck cancer, kidney cancer, leukemia, liver cancer, lung cancer, lymphoma, melanoma, multiple myeloma, pancreatic cancer, prostate cancer, sarcoma, skin cancer, stomach cancer, endometrial cancer, among others.

[080] In another particular embodiment, the cell is obtained from a subject suffering from cancer or suffering from an immune disease selected from an autoimmune disease, for example, Multiple sclerosis, Myasthenia gravis, Pernicious anemia,

Reactive arthritis, Rheumatoid arthritis, Sjögren syndrome, Systemic lupus erythematosus, Systemic sclerosis, Type | diabetes. Other examples of immune disease include asthma, eczema, allergic rhinitis, severe combined immunodeficiency (SCID) and temporary acquired immune deficiencies.

[081] In some embodiments, the cells obtained from a subject are cells obtained from the tissue, organ or area that is affected by such conditions as indicated herein. In some embodiments, the cells are obtained from a tissue, organ or area that is not affected by such conditions as indicated herein. In some embodiments, the cells are obtained from blood obtained from the subject.

[082] In another particular embodiment of any of the methods of the aspects of the invention, optionally in combination with any of their embodiments, the step of contacting occurs in vivo, ex vivo, or in vitro.

[083] As indicated, another aspect of the invention relates to an immune cell wherein a gene encoding the ITIM and/or ITSM comprising modulatory immune receptor or a gene encoding the polypeptide encoded by a genes listed in Table 1 has been knocked-out.

[084] The invention also relates in another aspect to an expression vector comprising a nucleotide sequence encoding the ITIM and/or ITSM comprising modulatory immune receptor or encoding the polypeptide encoded by a gene listed in Table 1, operably linked with a promoter. Such expression vector and how to obtain them in the context of the current invention are well-known to the skilled person.

[085] Another aspect of the invention is a host cell comprising the vector of the previous aspect, or recombinantly expressing the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide encoded by a gene listed in Table 1.

[086] The invention also relates in another aspect to a method of determining the copy number, level of expression, or level of activity of the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide encoded by a gene listed in Table 1 in a cell comprising: (a) providing the cell; and (b) determining the copy number, level of expression, or level of activity of the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide encoded by a gene listed in Table 1 in the cell, preferably wherein the cell is an immune cell.

[087] In a particular embodiment of the method of determining the copy number, level of expression, or level of activity of the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide encoded by a gene listed in Table 1, the cell, prior to determining the copy number, level of expression, or level of activity of the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide encoded by a gene listed in Table 1, is contacted with a test compound or drug as defined or identified in any of the aspects and their embodiments and including: a method for screening for compounds which modulate the expression and/or activity of a ITIM and/or ITSM comprising modulatory immune receptor expressed in an immune cell; a method for identifying a compound which modulates the expression and/or activity of alTIM and/or ITSM comprising modulatory immune receptor expressed in an immune cell; a method for testing a drug for modulating the expression and/or activity of a ITIM and/or ITSM comprising modulatory immune receptor expressed in an immune cell; a method for screening for compounds which modulate the expression and/or activity of a polypeptide encoded by a gene listed in Table 1 or biological active portion thereof; a method for identifying a compound which modulates the expression and/or activity of a polypeptide encoded by a gene listed in Table 1 or biological active portion thereof; and a method for testing a drug for modulating the expression and/or activity of a polypeptide encoded by a gene listed in Table 1 or biological active portion thereof.

[088] As will be understood by the skilled person, any method of screening, identifying or testing as disclosed herein may be performed in an immune cell expressing the, or more than one, modulatory immune receptor, or in a non-immune cell expressing the, or more than one, modulatory immune receptor, for example, adapted to express the, or more than one, modulatory immune receptor as disclosed herein. Preferably, the cell is an immune cell, more preferably, the cell is an immune cell naturally (in vivo) expressing the, or more than one, modulatory immune receptor.

[089] In another particular embodiment of the method of determining the copy number, level of expression, or level of activity of the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide encoded by a gene listed in Table 1 in a cell, the copy number, level of expression, or level of activity of the ITIM and/or

ITSM comprising modulatory immune receptor or the polypeptide encoded by a gene listed in Table 1 is, preferably independently, determined in more than one cell type, preferably wherein the more than one cell type is obtained from a subject, preferably from a subject suffering from cancer or suffering from an immune disease or suffering from inflammation.

[090] Finally, the invention also relates in another aspect to a method for identifying a binding partner to a ITIM and/or ITSM comprising modulatory immune receptor or a polypeptide encoded by a gene listed in Table 1 or biological active portion thereof comprising: (a) contacting the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide or biologically active portion thereof, or a cell expressing the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide, or biologically active portion thereof, with a test compound; and (b) determining whether the ITIM and/or ITSM comprising modulatory immune receptor or the polypeptide or biologically active portion thereof binds to the test compound.

[091] Embodiments of the previous aspects in this descriptions relating to type of cells also apply to any other aspect according to the invention.

[092] As already described herein, the polypeptide according to the invention or the modulatory immune receptor according to the invention for use in the various aspects according to the invention as disclosed herein is in a preferred embodiment encoded by a gene listed in Table 1. In a more preferred embodiment, the polypeptide according to the invention/the modulatory immune receptor according to the invention/the gene according to the invention is selected from Table 2a, 2b, 2c, 2d, 3a, 3a”, 3b, 3b” or 4.

In an even more preferred embodiment, the polypeptide according to the invention/the modulatory immune receptor according to the invention/the gene according to the invention is at least expressed in one or more, preferably one of the immune cells indicated in Table 2a, 2b, 2c, 2d, 3a, 3a", 3b, 3b” or 4. For example, in one embodiment, the polypeptide according to the invention/the modulatory immune receptor according to the invention is one that is expressed in CD4 T cells, or one that is expressed in CD8 T cells, or expressed in B cells, or expressed in NK cells, or expressed in monocytes or expressed in neutrophils, either under resting or under stimulated conditions (see, for example Table 2, for example 2a, 2b), or is one that is expressed in a particular subset of CD4 T cells and/or CD8 cell, such as Th17 CD4 T cells or resident memory CD8 T cells, as indicated in Table 2c and/or 2d. In another example, the polypeptide according to the invention/the modulatory immune receptor according to the invention is one that is expressed in any on of the immune cells and is categorized to at least one of the categories as indicated in Table 3, in particular 3a, 3a”, 3b, and/or 3b”. In yet another preferred embodiment, the polypeptide according to the invention/the modulatory immune receptor according to the invention is one that is identified in Table 4. As will be understood by the skilled person, in a preferred embodiment, the polypeptide according to the invention/the modulatory immune receptor according to the invention is expressed in the corresponding immune cells, and/or under the corresponding conditions as indicated in any one of Table 2a, 2b, 2c, 2d, 3a, 3a”, 3b, 3b” or 4. In some embodiment, there is provided for a combination of the preferred embodiment described above.

[093] In yet another embodiment there is provided for the methods of the invention disclosed herein, wherein the method is for screening/identifying/testing/validating a compound for modulating the expression and/or activity of a ITIM and/or ITSM comprising modulatory immune receptor expressed in an immune cell as defined in any of table 2a, 2b, 2c, 2d, 3a, 3a”, 3b, 3b” or 4.

[094] The foregoing description of the specific embodiments will so fully reveal the general nature of the invention that others can, by applying knowledge within the skill of the art (including the contents of the references cited herein), readily modify and/or adapt for various applications such specific embodiments, without undue experimentation, without departing from the general concept of the present invention.

Therefore, such adaptations and modifications are intended to be within the meaning and range of equivalents of the disclosed embodiments, based on the teaching and guidance presented herein.

[095] All references cited herein, including journal articles or abstracts, published or corresponding patent applications, patents, or any other references, are entirely incorporated by reference herein, including all data, tables, figures, and text presented in the cited references. Additionally, the entire contents of the references cited within the references cited herein are also entirely incorporated by references.

[096] It is to be understood that the phraseology or terminology herein is for the purpose of description and not of limitation, such that the terminology or phraseology of the present specification is to be interpreted by the skilled artisan in light of the teachings and guidance presented herein, in combination with the knowledge of one of ordinary skill in the art.

[097] It will be understood that all details, embodiments, and preferences discussed with respect to one aspect of embodiment of the invention is likewise applicable to any other aspect or embodiment of the invention and that there is therefore not need to detail all such details, embodiments, and preferences for all aspect separately.

[098] Having now generally described the invention, the same will be more readily understood through reference to the following examples which is provided by way of illustration and is not intended to be limiting of the present invention. Further aspects and embodiments will be apparent to those skilled in the art.

[099] Table 1. All 320 modulatory receptor gene symbols, and corresponding matched Ensemble peptide IDs (release 105, December 2021, in hips www gnsemblorg/indey ntm).

Symbol

ENSP00000303960| ENSP0000037 4467] ENSP000004937 49

ENSP00000494101| ENSPO0000494321| ENSPO0000494450

ENSP00000494519| ENSP00000506935] ENSPO0000507768

ABHD16A ENSP00000410347| ENSP00000447498] ENSPO0000447549

ENSP00000447846| ENSPO0000448431| ENSPO0000448451

ENSP00000449579

HGNC Gene Ensembl Peptide ID

Symbol

ABI3BP ENSP00000435319

ACVR1 ENSP00000263640| ENSPO0000387127| ENSPO0000387273]

ENSP00000400767| ENSPO0000405004| ENSPO0000440091

ENSPO0000500109| ENSPO0O00500605| ENSPO0000507086

ENSP00000507102| ENSPO0000507113| ENSPO0000507597

ENSP00000507727| ENSPO0000507730| ENSPO0000508136]

ENSP00000508189

ACVRL1 ENSP00000373574| ENSP00000447884

ADAM22 ENSP00000265727| ENSPO0000381260| ENSPO0000381261

ENSP00000506730

ADGRB1 ENSP00000313046] ENSP00000430945| ENSP00000494563

ADGRB3 ENSP00000238918| ENSPO0000359630| ENSP00000441821

ADGRE2 ENSP00000319883| ENSP00000376692| ENSPO0000469277

ENSP00000470725| ENSPO0000471297| ENSPO0000472280

ENSP00000472735

ADGRE3 ENSP00000253673| ENSPO0000340758| ENSPO0000396208]

ENSP00000471853

ADGRL1 ENSP00000340688| ENSP00000355328| ENSPO0000500478

ADGRL2 ENSP00000501543

AFG3L2 ENSP00000269143| ENSP00000509010] ENSP00000510237

AGTRAP ENSP00000319713| ENSP00000365816

ANOS ENSP00000506069| ENSP00000506683

APOLD1 ENSP00000324277| ENSP00000348998

ARHGEF10 ENSP00000340297| ENSP00000381571| ENSPO0000427768

ENSP00000427909| ENSPO0000431012| ENSPO0000477988]

ENSP00000481974| ENSPO0000488343| ENSPO0000488344

ENSP00000488463

ATF6B ENSP00000293709| ENSP00000364347| ENSP00000364349

ENSP00000372642| ENSP00000391131| ENSPO0000393419]

ENSP00000399764| ENSP00000404725] ENSP00000404814

ATG9A ENSP00000394345| ENSP00000406785| ENSP00000413569]

ENSP00000416435

ATP2B1 ENSP00000261173| ENSPO0000392043| ENSP0O0000447096]

ENSP00000489171

ATP2B2 ENSP00000353414| ENSPO0000380267| ENSPO0000414854

ENSPO0000494004| ENSP00000494381] ENSP000004947 16

ATP2B3 ENSP00000263519| ENSPO0000343886

ATP2B4 ENSP00000340930| ENSP00000350310] ENSP00000356187

ATP5MC3 ENSP00000284727| ENSP00000376324| ENSP00000387317

ATP8A1 ENSP00000371084

ATP8B2 ENSP00000357475| ENSP00000500034

ATP10A ENSP00000480665

ATP13A2 ENSP00000423065

ENSP00000301178| ENSPO0000351995| ENSPO000047 1497

BDKRB1 ENSP00000452064

BEST3 ENSP00000446575

HGNC Gene Ensembl Peptide ID

Symbol

ENSP00000216115

Clorf162 ENSP00000344218| ENSP00000358732

C5orf15 ENSP00000231512

C60rf89 ENSP00000347322| ENSP00000362789

CABP7 ENSP00000216144

CACFD1 ENSP00000291722| ENSP00000317121| ENSP00000486098

ENSP00000486696

CACNA1D ENSP00000489769

CACNA1G ENSP00000422407| ENSPO0000426172

CACNATH ENSP00000334198

CACNG5 ENSP00000303092| ENSP00000436836

CATSPERB ENSP00000256343| ENSP00000478546

CBARP ENSP00000371917| ENSP00000465260] ENSP00000497208

CCKBR ENSP00000335544| ENSP00000432079] ENSP00000435534

CCPG1 ENSP00000311656| ENSP00000403400] ENSPO0000415128]

ENSP00000454456

CD1D ENSP00000357153| ENSP00000501010] ENSPO0000501066]

ENSP00000501100| ENSPO000050 1245

CD68 ENSP00000250092| ENSP00000369867

CD79A ENSP00000221972| ENSPO0000400605

CD81 ENSP00000370424| ENSPO0000432249| ENSPO0000433787

ENSP00000435633

CD84 ENSP00000312367| ENSP00000357027| ENSP00000357033]

ENSP00000442845

CD96 ENSP00000283285| ENSP00000342040

CD99L2 ENSP00000347275| ENSP00000359403| ENSP00000394858

ENSP00000417697| ENSPO0000480322| ENSP00000489166

CD164L2 ENSP00000363139| ENSP00000363142

CDH5 ENSP00000344115| ENSPO0000461880| ENSPO0000479381

ENSP00000497290

CDON ENSP00000263577| ENSP00000376458| ENSPO0000432901

ENSP00000507318

CEACAM3 ENSP00000349971

CEACAMZ0 ENSP00000480940| ENSPO0000481812| ENSPO0000481937

ENSP00000482943| ENSP00000483912

CERKL ENSP00000364108| ENSP00000364109

CHRNB4 ENSP00000416386

CKLF ENSP00000264003

CLCN1 ENSP00000339867| ENSP00000498052

CLCN7 ENSP00000262318| ENSP00000454845| ENSPO0000461009

CLDN18 ENSP00000183605| ENSP00000340939

CLDND1 ENSP00000425204

CLRN2 ENSP00000424711

CNIH2 ENSP00000310003| ENSP00000432177

Symbol

ENSP00000284878| ENSP00000383033

ENSP00000304414| ENSPO0000395704| ENSPO0000396218

ENSP00000396886

ENSP00000389745

ENSP00000389140| ENSPO0000397322| ENSP00000464582

ENSP00000216500] ENSP00000451882

ENSP00000400382

ENSP00000441068| ENSP00000442172

ENSP00000383303| ENSP00000385342| ENSPO0000478698

ENSP00000498769

ENSP00000498766

ENSP00000358850| ENSP00000358857| ENSP00000507533

ENSP00000472919

ENSP0000044677 1

ENSP00000418111

ENSP00000376068

FGFR3 ENSP00000231803

HGNC Gene Ensembl Peptide ID

Symbol

FLT1 ENSP00000282397

FLT4 ENSP00000261937| ENSPO0O00377016| ENSP00000426057

FURIN ENSP00000268171| ENSP00000483552] ENSPO0000484952

ENSP00000505303| ENSP00000506143

FZD8 ENSP00000363826

GABRB2 ENSP00000274547| ENSP00000377531

GABRP ENSP00000265294| ENSP00000430100

GGT6 ENSP00000301395] ENSPOO000370962| ENSP00000458307

GGT7 ENSP00000338964| ENSP00000394993

GHRHR ENSP00000320180| ENSP00000387113

GINM1 ENSP00000356389

GJB4 ENSP00000345868

GJC1 ENSP00000333193| ENSPOO000466339| ENSPO0000467201

ENSP00000468716

GLMP ENSP00000354553/ ENSP00000477187| ENSPO0000479149

ENSP00000480936

GPR82 ENSP00000303549

GPR149 ENSP00000374390

GPR157 ENSP00000366628

GPR182 ENSP00000311528| ENSPOOOO0399670| ENSPO0000475912

GPR183 ENSP00000365596

GRID1 ENSP00000330 148

GRID2 ENSP00000483084

GRM7 ENSP00000350348

HCRTR1 ENSP00000362809

HEPACAM2 ENSP00000340532| ENSPO0000377980| ENSPO0000390204

HEPHL1 ENSP0O0000313699

HLA-DMB ENSP00000372718| ENSP00000378723] ENSPO0000393646

ENSP00000398890| ENSP00000408453] ENSPO0000411321

ENSP00000413471| ENSP00000414817

HSD17B3 ENSP00000498039

ICAM3 ENSP00000160262| ENSP00000468230] ENSPO0000468333

IER3 ENSP00000259874/ ENSP00000373054] ENSPO0000397956]

ENSP00000398139| ENSP00000406245] ENSPO0000412283

IENAR2 ENSP00000403569

IGDCC4 ENSP00000319623

IGF1R ENSP00000496919

IGSF9 ENSP00000357073

IL1RAP ENSP00000072516| ENSPO0000390541| ENSPOO000401132

ENSP00000412053

IMPG2 ENSP00000193391

IRAG2 ENSP00000346442| ENSPO0000444056| ENSPO0000446496

ENSP00000450246] ENSP00000451048] ENSPOO000452116

HGNC Gene Ensembl Peptide ID

Symbol

ITGA3 ENSP00000007722

ITM2B ENSP00000498127

ITPR1 ENSP00000497999

ITPRIPL1 ENSP00000408336

KCNA2 ENSP00000314520] ENSPOO000433109| ENSPO0000487785

ENSP00000491613| ENSP00000491627| ENSPO0000491647

ENSP00000491977| ENSPOOO00492716| ENSPO0000502642

KCNB2 ENSP00000430846

KCNK5 ENSP00000352527

KCNK17 ENSP00000401271

KCNQ5 ENSP00000359419

KCNS3 ENSP00000305824| ENSP00000385968

KIAA0319 ENSP00000367459| ENSP00000401086] ENSPO0000442403]

ENSP00000483665

KIAA0319L ENSP00000318406| ENSP00000362363] ENSPO0000395883

KIDINS220 ENSP00000256707| ENSP00000418974| ENSPO0000419232

ENSP00000419964/ ENSPO00000420364| ENSPO0000508455

ENSP0O0000508523| ENSPOO000508907| ENSPO0000509014

ENSP00000509856| ENSP00000510148| ENSPO0000510486]

ENSP00000510510] ENSP00000510537

KIR2DL5A ENSP00000479384| ENSP00000480340] ENSPO0000483324

ENSP00000483518| ENSP00000484057] ENSP00000484296

ENSP00000484937

KIR2DL5B ENSP00000478053| ENSPO0000479965| ENSPO0000480935]

ENSP00000483362| ENSP00000483776] ENSPO0000484782

ENSP00000492850| ENSP00000495717] ENSPOO000500824

ENSP00000500868

KIR2DP1 ENSP00000484356

KIR2DS1 ENSP00000481519

KIR2DS2 ENSP00000481124| ENSP00000482387

KIR2DS3 ENSP00000490994| ENSP00000495002| ENSPO0000500588

ENSP00000500689

KIR2DS4 ENSP00000481757| ENSP00000491824

KIR2DS5 ENSP00000491079| ENSP00000491352] ENSP0O0000495310]

ENSP00000496435| ENSP00000500091| ENSP0O0000500428

ENSP00000500575| ENSP00000500722

KTN1 ENSP00000378719| ENSP00000378720] ENSPO0000378722

ENSP00000378725| ENSP00000391964] ENSPO0000394992

ENSP00000451641| ENSP00000451878

LAMP2 ENSPO0000408411

LAMP3 ENSP00000265598| ENSP00000418912

LAX1 ENSP00000356186| ENSP00000406970

LDHA ENSP00000486249| ENSP00000500733

LDLR ENSP00000252444| ENSP00000453557

LEMD1 ENSP00000356120

LEPR ENSP00000330393

HGNC Gene Ensembl Peptide ID

Symbol

LIFR ENSP00000263409| ENSP00000398368

LILRA6 ENSP00000484147| ENSPO0000484396| ENSPO0000484822

LMTK2 ENSP00000297293

LRIT1 ENSP00000361177

LRRC8A ENSP00000259324| ENSP0000036 1680] ENSPO0000361682

LRRC8B ENSP00000332674| ENSPO0000400704| ENSPO0000491377

ENSP00000492151

LRRC19 ENSP00000369395

LRRC25 ENSP00000340983| ENSP00000472290

LST1 ENSP0000036526 1] ENSP00000372978| ENSP00000383123]

ENSP00000387560| ENSPO0000388956| ENSPO0000391929]

ENSP00000392949| ENSPO0000394614| ENSPO0000395409]

ENSP00000398179| ENSPO0000396181| ENSPO0000396378]

ENSP00000396533| ENSPO0000398685| ENSPO0000399411

ENSP00000403097| ENSPO0000404051| ENSPO0000406455

ENSP00000409163| ENSPO0000409229| ENSPO0000412276]

ENSP00000414173| ENSPO0000416283

LY9 ENSP00000263285| ENSP00000357014| ENSPO0000357016]

ENSP00000376039

MACO1 ENSP00000382668

MAPKAPK2 ENSP00000356070

MAPKAPK3 ENSP00000350639| ENSPO0000396467| ENSP0O0000478922

MCHR1 ENSP00000370841

MEGF11 ENSP00000378976

MFSD6L ENSP00000330051

MFSD8 ENSP00000296468| ENSP00000425000| ENSPO0000492966)

ENSP00000492989| ENSPO0000493133| ENSPO0000493197

ENSP00000493218] ENSP00000493347| ENSPO0000493459

MFSD11 ENSP00000337240| ENSP00000348225| ENSP00000464932)]

ENSP00000466813| ENSPO0000466782| ENSPO0000468309]

ENSP00000485005| ENSP00000508960

ENSP00000432943| ENSP00000488104| ENSPO0000500814

MPZL1 ENSP00000352513

MRAP ENSP00000343661| ENSP00000382684

MS4A3 ENSP00000278865] ENSP00000350872| ENSPO0000434117

MS4A4E ENSP00000499123

MUCH ENSP00000338983| ENSP00000339690] ENSP0O0000342814]

ENSP00000343482| ENSP00000357375] ENSPO0000357377

ENSP00000357383| ENSPO0000389098| ENSPO0000481231

ENSP00000483473| ENSP00000483482

MUC22 ENSP00000455906

NALCN ENSP00000251127| ENSPO0000501603| ENSPO0000501955

ENSP00000502680

NALF1 ENSP00000365080

NAT 14 ENSP00000205194

HGNC Gene Ensembl Peptide ID

Symbol

NCLN ENSP00000246117| ENSP00000466844

NDC1 ENSP00000360483

NDFIP2 ENSP00000218652| ENSP00000480798| ENSPO0000480881

NFAM1 ENSP00000333680

NIPAL2 ENSP00000407087

NIPAL3 ENSP00000003912] ENSP00000363520

NKAIN1 ENSP00000433225

NNT ENSP00000264663| ENSP00000343873| ENSPO0000426343]

ENSP00000499249| ENSPO0000499281| ENSPOO000499494/

ENSP00000499527| ENSPO0000499611| ENSPOO000499839]

ENSP00000499670

NPC1 ENSP00000468438

NPIPA1 ENSP00000410814

NPIPA2 ENSP00000432767

NPIPA3 ENSP00000434172] ENSP00000488574

NPIPA5 ENSP00000435611

NPIPA9 ENSP00000437314

NPIPB15 ENSP00000411140| ENSPO0000508772

OR1R1P ENSP00000492889

OR2H1 ENSP00000366336| ENSP00000366337| ENSPO0000366340

ENSP00000373042] ENSP00000373140] ENSPO00003800 10

ENSP00000383527| ENSP00000383530] ENSPO0000383547

ENSP00000383548| ENSP00000383549] ENSPO0000389230

ENSP00000392619] ENSPOO000394698| ENSP00000395567

ENSP00000395850] ENSP00000396414] ENSPO0000397171

ENSP00000398695| ENSP000004057 14] ENSPO0000407739

ENSP00000408584| ENSP00000409651] ENSPO0000410401

ENSP00000411617] ENSP00000412463] ENSP00000413910

OR2K2 ENSP00000363550

OR2W1 ENSP00000366380| ENSPO0000373150| ENSPO0000388144/

ENSP00000389825| ENSPO0000392635| ENSPO000040 1866]

ENSP00000405025] ENSP00000412537

ORSD16 ENSP00000367649

OR13C3 ENSP00000493076

OR13C4 ENSP00000277216

OR13J1 ENSP00000367219

PACC1 ENSP00000261455

PANX2 ENSP00000159647

PARM1 ENSP00000370224| ENSP00000424276

PCDH8 ENSP00000341350] ENSPO0000367177

PCDH12 ENSP00000231484

PCDHGC3 ENSP00000481219

PCDHGCS ENSP00000252087| ENSP00000482569

PCNX2 ENSP00000258229

HGNC Gene Ensembl Peptide ID

Symbol

PDGFRB ENSP00000261799

PEX13 ENSP00000295030

PEX14 ENSP00000349016

PGRMC1 ENSP00000442821

PHTF1 ENSP00000416810

PIEZO2 ENSP00000463589

PIGW ENSP00000480475] ENSP00000488539

PIK3CB ENSP00000289153| ENSPO0000417869| ENSP00000418143

ENSP00000501150

PLD3 ENSP00000348901] ENSP00000352220] ENSPO0000375886

ENSP00000386293] ENSPO0000386938| ENSPO0000387022

ENSP00000387050| ENSPO0000468898| ENSPOO000468999]

ENSP00000469675| ENSP00000471838

PLPP1 ENSP00000264775] ENSP00000302229

PLPPR3 ENSP00000430297

PLXDC1 ENSP00000323927

PLXNA3 ENSP00000358696

PLXNA4 ENSP00000323194| ENSP00000352882

POPDC2 ENSP00000264231| ENSP00000417250] ENSPO0000420715

PRLR ENSP00000231423] ENSPO0000309008| ENSPO0000422556

ENSP00000441813] ENSP00000482689] ENSP00000482954

ENSP00000484768

PRRG3 ENSP00000394121

PTPRCAP ENSP00000325589

PTPRD ENSP00000489923| ENSPO0000490377

PTPRH ENSP00000263434| ENSP00000365528

PTPRM ENSP00000462176

PTPRO ENSP00000343434| ENSPO0000437571| ENSPO0000439234

PVRIG ENSP00000316675

PXMP2 ENSP00000398708

QRFPR ENSP00000377948

RABSIF ENSP00000362958

REEPS ENSP00000261482

RER1 ENSP00000302088] ENSPO0000464222| ENSPO0000475168

RFESD ENSP00000369341] ENSP00000413592

RHBDL1 ENSP00000219551| ENSPO0000344206

RHEX ENSP00000356093| ENSP00000463990] ENSPO0000474759]

ENSP00000474994

RMDN3 ENSP00000453978

RNF121 ENSP00000433574

RNF128 ENSP00000255499| ENSP00000316127

ROBO1 ENSP00000406043| ENSP00000417992| ENSPO0000420321

ENSP00000420637| ENSP00000482448

HGNC Gene Ensembl Peptide ID

Symbol

ROBO4 ENSP00000304945| ENSP00000437129

ROS1 ENSP00000357493| ENSPO0000357494

RRBP1 ENSP00000246043| ENSPO0000367044

ENSP00000419122| ENSP00000478721| ENSP00000485095

SCARB1 ENSP00000343795| ENSP00000505605| ENSPO0000505757

SCN1B ENSP00000262631| ENSPO0000468848| ENSPO0000492022

ENSP00000492247| ENSP00000502395

SCN3B ENSP00000299333| ENSP00000376523| ENSPO0000432785

ENSP00000499439| ENSP00000499755

SGMS1 ENSP00000354829| ENSP00000355235| ENSP0O0000479633

SGSM3 ENSP00000248929

SIAE ENSP00000263593

SIGLEC12 ENSP00000291707| ENSP00000472873

SIGLEC15 ENSP00000374125| ENSPO0000443509

SLAMF1 ENSP00000306190

SLAMF7 ENSP00000352281| ENSP00000357021| ENSPO0000357022

ENSP00000483774

SLC2A8 ENSP00000389070| ENSPO0000404893| ENSPO0000411726

SLC2A10 ENSP00000352216

SLC2A11 ENSP00000385949

SLC5A6 ENSP00000310208| ENSP00000384265| ENSP00000384853

ENSP00000411536

SLCBA1 ENSP00000493779

SLC6A6 ENSP00000481625

SLC6A11 ENSP00000404120

SLC7A8 ENSP00000391577| ENSPO0000416398| ENSPO0000434345

SLCBA1 ENSP00000383886| ENSP00000385188| ENSP00000385535

ENSP00000385678| ENSP00000385811

SLC8A2 ENSP00000236877| ENSP00000437536

SLC9A2 ENSP00000233969

SLC9A4 ENSP00000295269

SLC10A4 ENSP00000273861

SLC10A7 ENSP00000421275

SLC11A1 ENSP00000233202

SLC12A9 ENSP0000040857 1

SLC19A1 ENSP00000411345

SLC19A3 ENSP00000386298

SLC22A1 ENSP00000355930| ENSP00000409557

SLC22A3 ENSP00000275300

SLC24A3 ENSP00000333519

SLC24A5 ENSP00000389966

SLC26A5 ENSP00000377330

HGNC Gene Ensembl Peptide ID

Symbol

SLC33A1 ENSP00000494846

SLC35A2 ENSP00000365698| ENSP00000402726

SLC35B1 ENSP00000424367

SLC35C2 ENSP00000397142

SLC35D3 ENSP00000333591

SLC35F3 ENSP00000355577

SLC37A2 ENSP00000384407

SLC38A2 ENSP00000256689

SLC38A6 ENSP00000434543

SLC38A7 ENSP00000454646

SLC39A13 ENSP00000432302| ENSP00000432499| ENSP00000437186

SLC39A14 ENSP00000240095| ENSP00000289952| ENSP00000370635

ENSP00000427981

SLC41A2 ENSP00000258538

SLC44A3 ENSP00000271227| ENSP00000431836

SLC45A2 ENSP00000421100

SLC45A4 ENSP00000024061| ENSPO0000428137| ENSPO0000429059

SLC46A2 ENSP00000363345

SLC49A3 ENSP00000307545| ENSP00000320234| ENSPO0000384616)

ENSP00000423204

SLC66A3 ENSP00000416170

SLITRK3 ENSP00000241274| ENSP00000420091

SLITRK4 ENSP00000336627| ENSPO0000349400| ENSPO0000469205

SMIM31 ENSP00000493952

SMIM34A ENSP00000397039

SMIM34B ENSP00000490209

ENSP00000249373

SPAG4 ENSP00000505928

SPG7 ENSP00000268704| ENSP00000495473

SPNS1 ENSP00000456119

SPRY1 ENSP00000343785| ENSP00000377871] ENSPO0000480540

ENSPO0000481675| ENSPO0000498292

SPTLC1 ENSP00000509096| ENSPO0000509481

SSPN ENSP00000242729| ENSPO0000396087| ENSP00000442893

SSR1 ENSP00000417290

ST3GAL3 ENSP00000333494| ENSP00000355201| ENSP00000434378

ENSP00000435603| ENSP00000439634

ST3GAL5 ENSP00000366549| ENSP00000377394| ENSP00000377397

ENSP00000401375| ENSPO0000491316| ENSPO0000491564

ENSP00000491828| ENSPO0000491853| ENSP00000492045

ENSP00000492098| ENSPO0000492103| ENSP00000492244

ENSP00000492299| ENSP00000492753

SUN2 ENSP00000383992| ENSP00000385740] ENSPO0000508608

HGNC Gene Ensembl Peptide ID

Symbol

SYNE4 ENSP00000316130

SYPL1 ENSP00000417473

SYT3 ENSP00000340914| ENSP00000468982] ENSPO0000469398

TACR2 ENSP00000362404

TACR3 ENSP00000303325

TFR2 ENSP00000223051| ENSPO0000413905| ENSPO0000420525

TGOLN2 ENSP00000366603| ENSP00000381312] ENSPO0000386443

ENSP00000387035| ENSP00000391190

TIMM21 ENSP00000169551| ENSP00000462028

TIMM22 ENSP00000320236| ENSPO0000478463| ENSP00000482204

TIMM23 ENSP00000464522

TMCO3 ENSP00000481060

TMEM39A ENSP00000326063

TMEM44 ENSP00000333355| ENSPO000037 1402] ENSPO0000376227

ENSP00000414333| ENSP00000418674

TMEM52 ENSP0O0000311122| ENSP00000367865

TMEM59 ENSP00000234831

TMEM104 ENSP00000334849| ENSPO0000397676| ENSPO0000461922

ENSP00000463205

TMEM123 ENSP00000355285| ENSP00000381204| ENSPO0000434976]

ENSP00000435331

TMEM128 ENSP0O0000254742| ENSP00000372201

TMEM130 ENSP00000330262| ENSPO0000341256| ENSPO0000390200]

ENSP00000413163

TMEM132E ENSP0O0000316532| ENSP00000487800

TMEM134 ENSP00000312615] ENSP00000377455

TMEM151B ENSP00000409337

TMEM168 ENSP00000323068| ENSPOOOO0390696| ENSPOO000412462

TMEM169 ENSP00000295658| ENSP00000384100] ENSPO0000401305

ENSP00000412524

TMEM179B ENSP00000333697

TMEM209 ENSP00000380747| ENSP00000419697

TMEM222 ENSP00000419292

TMEM230 ENSP00000202834| ENSP00000341364| ENSPO0000368578]

ENSP00000368579| ENSPOO000368581| ENSPO0000368585

ENSP00000368588| ENSPOO000368601| ENSPO0000478112

ENSP00000478841

TMEM247 ENSP00000388684

TMEM251 ENSP00000283534| ENSP00000388431] ENSPO0000478917

ENSP00000486678

TMEM253 ENSP00000451229| ENSP00000453962

TMEM259 ENSP00000331423

TMEM271 ENSP00000493161

TPCN2 ENSP00000294309| ENSP00000445551

HGNC Gene Ensembl Peptide ID

Symbol

TRHR ENSPG0000309818] ENSPO00004307 11

TRIB2 ENSP00000384260

TRPC3 ENSP00000368966] ENSPO0000426899

TRPC6 ENSP00000340913| ENSPO0000343672

TRPCY ENSP00000367720| ENSPO0000424854

TSPAN7 ENSP00000286824

TSPAN16 ENSP00000319486] ENSPO0000466751

TYROBP ENSP00000262629| ENSPO0000402371| ENSPOO000445332

ENSP00000468447| ENSPO0000468608

VIPR1 ENSP00000327246| ENSPO0000394950| ENSP00000415371

ENSP00000445701

VIPR2 ENSP00000262178] ENSPO00O0366860| ENSPO0000384497

VSTM4 ENSP00000331062

VTI1B ENSP00000450731

ENSP00000262348| ENSP00000346829] ENSP00000360015

XKR3 ENSPC0000331704| ENSPO0000507478

XKR6 ENSP0000037 1900

XKR7 ENSP00000477059

YIPF3 ENSP00000361499| ENSPO0000423544| ENSP00000425494

YME1L1 ENSP00000365184

ZDHHC5 ENSP00000287 169] ENSPO0000432202

ZDHHC8 ENSP00000317804| ENSPOO000334490| ENSP000003847 16

ZDHHC13 ENSP00000382288

EXAMPLES Example

Identification of ITIM/ITSM-bearing immune modulatory receptors

[100] All the materials and methods for the performance of the examples are listed at the end of this section.

RESULTS

Putative ITIM/ITSM-bearing immune modulatory receptors can be found in the human genome

[101] To identify putative novel modulatory receptors, we first retrieved the protein sequences of all 96,457 protein-coding transcripts, corresponding to 19,353 individual human genes, annotated in the Ensembl database (release 105, December 2021)[13].

We retrieved all deposited isoforms, as certain proteins might only contain an ITIM in a specific isoform. We then screened the entire protein sequence for the presence of an ITIM or ITSM, based on the consensus sequence (V|L|I|S|T)xYxx(l|L|V), resulting in 40,063 protein sequences from the initial 96,457. We next used the TOPCONS server, which is based on a consensus of several prediction tools[14], to determine the membrane topology of all proteins with an ITIM/ITSM motif. TOPCONS predicted 12,576 out of the 40,056 input proteins to be integral membrane proteins, of which 7,445 contained multiple transmembrane domains and the remaining 5,131 are single- pass membrane proteins.

[102] We next filtered proteins for the presence of the ITIM or ITSM sequence in an intracellular domain of the protein based on the predicted topology. This yielded with 4,613 protein sequences bearing one or more intracellular ITIMs or ITSMs, which correspond to 1,562 genes (Figure 1). To assess how well our pipeline reflects previously documented modulatory receptors, we confirmed that all the 52 proteins known for their ITIM-mediated immune modulatory effects, such as PD-1 or leukocyte- associated immunoglobulin-like receptor 1 (LAIR-1) (Table A)[7], were recalled successfully, with the exception of MPIG6B, encoding for the inhibitory receptor G6B on platelets and megakaryocytes[15], due to an incorrect prediction of its transmembrane domain.

Table A. Genes encoding previously described ITIM-bearing inhibitory ce

BTLA CLEC4A KIR3DL2 NCR2 SIGLEC11

CD22 FCGR2B KIR3DL3 PDCD1 SIRPA

CD244 FCRL2 KLRC1 PECAM1 SIT1

CD300A FCRL3 KLRG1 PILRA SLAMFG

CD300LF FCRL4 LAIR1 PVR TIGIT

CD33 FCRL5 LILRB1 SIGLECS TREML1

CD5 KiR2DL1 LILRB2 SIGLECG VSIG4

CD72 KIR2DL2 LILRB3 SIGLEC7 VSTM1

CEACAM1 KIR2DL3 LILRB4 SIGLEC8

CLEC12A KIR2DL4 LILRBS SIGLEC9

CLEC12B KIR3DL1 MPIG6B SIGLEC10

[103] The composition of an ITIM/ITSM sequence is highly variable, as only 3 out of 6 amino acids positions are limited to specific amino acids. As a result of this, large proteins or proteins containing many tyrosines and hydrophobic residues are more likely to contain an ITIM/ITSM by chance (Data not shown). We therefore determined the likelihood of encountering an ITIM/ITSM by chance in the intracellular region of the putative targets. To this end, we randomly permutated the amino acid sequences of the intracellular domains by shuffling their order using the Fisher-Yates algorithm. We did this 10,000 times for each receptor and assessed how often the permutated sequence contained more or an equal amount of ITIM/ITSMs compared to the original sequence. For 41 out of 51 known receptors, these odds were low (< 5%). However, for 10 out of 51, we observed ITIM/ITSM sequences in the permutated sequence up to ~25% of the time. Based on these findings, we decided to exclude novel targets when they were above this threshold of 25%. After this statistical filtering, we were left with 837 modulatory receptor genes. As expected, the average length of the intracellular domains of the excluded proteins was much higher than that of the remaining targets.

AlphafFold structure predictions can assist in identifying likely functional ITIM/ITSMs

[104] Protein interaction motifs are most commonly found in intrinsically disordered regions within proteins[16], as structured regions are less accessible to binding with interacting partners. We therefore hypothesized that ITIM/ITSM sequences locate in disordered regions to allow for interaction with phosphatases and kinases. We therefore leveraged AlphaFold to infer three-dimensional structure predictions of the remaining modulatory receptor candidates to determine where the ITIM/ITSM sequences were located in three dimensional space[17].

[105] For 832 of the 837 remaining modulatory receptor genes, we were able to retrieve the predicted structures using AlphaFold. For every residue in the three- dimensional model, AlphaFold defines a confidence score (pLDDT). Low scores indicate reduced confidence, and regions with a low score are more likely to be intrinsically disordered[18]. We determined the average pLDDT of all six residues encompassing the ITIM/ITSM sequence, what resulted in an overall confidence score for each intracellular ITIM/ITSM in all targets.

[106] We found that 99 out of 101 ITIM/ITSMs of the 51 known receptors had low confidence scores, i.e., less than 80 pLDDT, with an average confidence score of 49.3 pLDDT. 64 of the ITIMs even had pLDDT values below 50, which means they are particularly likely to be intrinsically disordered[18]. This result confirmed the hypothesis that ITIM/ITSMs are likely to be located in disordered regions in the protein and indicates that the AlphaFold confidence score can be a valuable asset to determine the potential functionality of an ITIM sequence in predicted targets.

[107] Based on the known receptors, we determined a threshold of 80 pLDDT and were left with 390 out of 832 putative ITIM-bearing modulatory receptor genes likely to contain a functional ITIM/ITSM. Among these genes, 54.6% consisted of multi- spanning proteins, while the remaining 177 single transmembrane domain targets consisted of 145 (37.2%) type | and 32 (8.2%) type II receptors. In some cases, a single gene was predicted to have both single-spanning and multi-spanning isoforms.

Most putative modulatory receptors (275) were based on the canonical transcript, as annotated by Ensembl, while 115 were identified as a non-canonical isoform of the gene.

Putative modulatory receptors are expressed across immune cell subsets

[108] To better characterize these receptors, we studied the expression patterns of the retrieved known and putative modulatory receptor genes in various immune cells.

We collected publicly available bulk RNA sequencing data of various immune cell subsets, both at resting state and after in vitro stimulation[19,20] (Table B). We included all putative modulatory receptors, including those that were identified in a non-canonical transcript of the gene. For this analysis, we considered a receptor as expressed when the expression was above the median overall gene expression in the sample, in either resting or activated state. From our set of modulatory receptor genes, 2/51 known and 41/390 predicted genes were not detected in these datasets.

Table B. Number of samples for different resting and activated immune cell subsets

Celitype _ subsets Testing activated stimulation duration

Neutrophils 3 10 TSLP / S. 4h / 24h aureus

Monocytes 4 8 LPS 24h

NK cells 6 6 IL-2 24h

B cells naïve, memory, 13 10 anti-lgG/M + 24h plasmablast IL-4

D4 T cells naive, effector, memory, 37 0 dynabeads + Sah regulatory, Tfh IL-2

CD8 Tcells naive, effector, memory 15 16 dynabeads + 24h iL-2

[109] Almost all functionally characterized immune modulatory receptors are type transmembrane proteins, while only six are type Il single-spanners. So far, no multi- spanning receptors have been described to have an modulatory function in the immune system. Also, many genes encoding multi-spanning proteins only showed very limited expression across immune cell subsets in the datasets we used for our analysis.

Therefore, we analyzed the multi-spanning targets (Figure 4) separately from the single-spanning novel targets (Figure 2).

[110] We investigated the expression of 215 single-spanning receptor genes in these immune cell subsets and found that neutrophils (137 genes) and monocytes (120 genes) expressed the highest number of modulatory receptor genes. Lymphoid cells expressed fewer modulatory receptor genes compared to myeloid cells, with B and NK cells expressing 111 genes, followed by CD8+ (106 genes) and CD4+ (89 genes) T cells (Figure 2A). The relative contribution of known and novel targets in each subset varied between different immune cells. We found more novel targets being expressed in CD4+ (86/99 genes, 86.9%) and CD8+ T cells (88/106 genes, 84.3%), compared to neutrophils (98/137 genes, 71.5%). Neutrophils and monocytes uniquely expressed 9 and 3 modulatory receptor genes respectively, but the vast majority were shared between two or more immune cell subsets (Figure 2B).

[111] Compared to the single-spanners, we found slightly fewer multi-spanning modulatory receptor genes expressed in the different immune cell subsets. Out of 197 predicted genes, neutrophils expressed the most multi-spanning modulatory receptor genes {118 genes), while the other subsets expressed a similar number: Monocytes expressed 100 modulatory receptor genes, followed by B cells (95 genes), CD4+ (90 genes) and CD8+ (90 genes) T cells, and NK cells (89 genes) (Figure 4B). Neutrophils (14 genes) expressed the most unique set of multi-spanning modulatory receptors, while most other genes were shared between all subsets (Figure 4B).

Known and novel immune modulatory receptors of different functional categories can be identified in immune cells

[112] We next assigned the putative modulatory receptor into the previously described functional categories by comparing the expression in the resting state versus after activation in the available data from different cell types[7] (Table C). We defined negative feedback receptors as below median expression in the resting state, but expressed after activation. Threshold receptors were defined as being expressed in the resting state and having less than 0.5 log2 fold change after activation, while threshold-disinhibition and threshold-negative feedback receptors were defined by more than 0.5 log2 fold decrease or increase in expression upon activation, respectively. Using this functional classification system, we found that all immune cell subsets, except B cells, expressed receptors of all four categories, although all subsets primarily expressed threshold receptors.

Table C. Number of single-spanning receptors in different functional categories for each immune cell subset cell type not negative ee threshold- threshold expressed feedback feedback disinhibition

Neutrophils 78 6 3 4 124

Monocytes 95 26 1 21 72

NK cells 104 17 2 11 81

B cells 104 10 0 16 85

CDA T cells 116 8 2 16 73

CD8 T cells 109 9 4 15 78

[113] We did not observe many changes in modulatory receptor gene expression after activation in neutrophils. Six receptor genes, such as SLAMF1, were absent on resting neutrophils, but expression was induced after stimulation, categorizing them as negative feedback receptors. We identified 124 receptors as threshold receptors, while 4 and 3 genes were identified as threshold-disinhibition and threshold-negative feedback receptors, respectively (Figure 2A).

[114] In contrast, in monocytes 26 genes, including SIGLEC8 or SIGLEC11, had the expression pattern of negative feedback receptors. We found 72 receptors, e.g.,

SIGLEC10 or PILRA, that maintained their expression after activation, while 21 were downregulated, such as VSTM1 or CLEC12A. Only a single receptor, SLAMF7, was categorized as a threshold-negative feedback receptor. Of note, a cluster of 14 receptors was shared exclusively between monocytes and neutrophils (Figure 2B) and thus could be indicative of a set of conserved myeloid-specific checkpoints.

[115] We observed expression of 17 negative feedback receptors, e.g., SIGLEC15 and VSTM4, and 81 threshold receptors, such as CD244 and CD300A on NK cells.

Additionally, 11 genes were classified as threshold-disinhibition receptors, e.g.,

FCRLS, while 2 were determined to be threshold-negative feedback receptors.

[118] B cells expressed 111 predicted modulatory receptor genes, of which 10, like

SIRPA and SIGLEC6, were negative feedback receptors. We found 85 threshold receptors, such as BTLA, as well as 16 threshold-disinhibition receptors, e.g., PILRA and LST1. B cells were the only subset that are not predicted to express threshold- negative feedback receptors. B cells also shared expression of 6 receptors with monocytes and neutrophils, while 2 genes were uniquely expressed by B cells.

[117] CD4+ and CD8+ T cells expressed 8 and 9 negative feedback receptors, respectively, such as PDCD1, in addition to 73 (on CD4+ T cells) and 78 (on CD8+ T cells) threshold receptors, e.g., CEACAM1 and SIT1. In addition, we found 16 threshold-disinhibition receptors on CD4+ T cells and 15 on CD8+ T cells, such as

LAIR1 on CD4+ T cells and AXL on both subsets, as well as 2 threshold-negative feedback receptors on CD4+ and 4 on CD8+ T cells.

[118] Allimmune cell subsets expressed fewer multi-membrane spanning modulatory receptor genes compared to single-spanners. When we assigned these multi-spanning targets to the different functional categories, a similar picture emerged as for the single-spanners, where most receptors categorized as threshold receptors in all immune cell types. Whereas monocytes, B cells, CD4+ and CD8+ T cells expressed more single-spanning threshold-disinhibition receptors than negative feedback receptors, the opposite was observed for multi-spanning modulatory receptor genes.

NK cells had less dynamic gene regulation of multi-spanning targets than of single- spanners, while categorization for neutrophils was similar between multi- and single- spanners (Figure 4A). Interestingly, the multi-spanning targets were shared between three or more subsets more often than was the case for the single-spanners (Figure 4B).

[119] In summary, we identified 398 known and putative modulatory receptors being expressed across a variety of immune cell subsets, with mostly overlapping expression patterns. We classified these receptors into different functional categories based on their expression in the resting and activated states. We found that all immune cells expressed mostly threshold receptors. Among the receptors that changed expression after activation, monocytes and NK cells mainly expressed negative feedback receptors, while the T cells and B cells expressed more threshold-disinhibition receptors. Neutrophils did not have very dynamic gene expression patterns.

Known and putative modulatory receptors are expressed on tumour infiltrating T cells

[120] To further translate our findings to a disease context, we explored the expression of putative modulatory receptor genes in tumour infiltrating lymphocytes.

We used publicly available single cell RNA sequencing data of CD4+ and CD8+ T cells from 21 types of cancer and determined modulatory receptor gene expression in the different T cell subsets identified by Zheng et al. (2021)[21] (Figure 3A). After quality control and filtering, the expression of 133/215 single-spanners, and 111/197 of the multi-spanners could be assessed in this dataset.

[121] Among T cell subsets, expression of single-spanning modulatory receptor genes was variable (Data not shown). We found 27 and 46 modulatory receptor genes in naive CD4+ and CD8+ T cells, respectively, while T cells with a more differentiated phenotype, e.g., regulatory CD4+ T cells (68 genes) and exhausted CD8+ T cells (83 genes) expressed a wider array of known and predicted modulatory receptor genes (Figure 3A-B).

[122] When we assessed expression of multi-spanning modulatory receptor genes, we found similar variable expression across T cell subsets as for the single-spanners.

Naive CD4+ T cells expressed 21 multi-spanning receptor genes, while many more were found in the other subsets (Figure 5A). Resident memory CD8+ T cells expressed 87 multi-spanning modulatory receptor genes, while CD8+ memory and effector memory expressed 9 and 26 genes, respectively (Figure 5B).

[123] Overall, this shows that the putative modulatory immune receptors we identified are expressed on tumor infiltrating T cells and differ between cellular subsets. Further investigation into differences and similarities between these populations in different cancer types could assist in targeting these receptors for therapy.

[124] In conclusion, we designed a novel, combined bioinformatics approach to predict around 400 immune modulatory receptors in the human genome, including both single and multi-spanning targets. Our list of novel targets will assist drug target selection in diseases where modulatory receptor targeting is warranted.

[125] At the end of the Discussion, Tables 2a, 2b, 2c, 2d, 3a, 3a”, 3b, 3b” and 4 show the expressed modulatory immune receptors (IIR) in the different settings disclosed in this Example.

DISCUSSION

[126] This study introduces some major improvements over previous attempts at predicting novel modulatory receptors in the human genome. In 2004, Staub et al., performed a search limited to type | membrane receptors containing an annotated extracellular domain and a restricted ITIM sequence. They identified a total of 94 genes encoding modulatory receptors, of which 32 had been previously described to rely on their ITIM to inhibit immune function[22]. A later study by Daéron et al. (2008), performed a more extensive analysis of ITIM-bearing receptors across multiple species, including chickens and Drosophila[12]. In humans, they identified 613 predicted type | and type Il single-spanners and 992 multi-spanning transmembrane proteins, corresponding to around 1500 genes. This number agrees with what we retrieved in the initial steps of our bioinformatics pipeline, where we identified 1,562 genes. Our efforts to reduce this number to candidates with a high probability of functioning as modulatory receptors resulted in 390 novel targets. Compared to the previous studies, our method has key advantages. Firstly, the TOPCONS algorithm we used is superior to TMHMM and Philius, which have been used previously, at predicting membrane topology[14,23,24]. Most importantly, we excluded many potential false positives by filtering out proteins that are likely to contain an ITIM by chance and used three-dimensional structure predictions to enrich the remaining targets for those containing ITIMs in unstructured regions. Furthermore, our expression analysis and functional categorization of the putative modulatory receptors can assist in gaining a better understanding of their relevance in different contexts.

[127] An important component of our pipeline is the use of AlphaFold[17]. Our approach was exceptionally goad at filtering out many proteins in the olfactory receptor family, for which almost all ITIMs identified were found in highly structured regions.

We determined a threshold of 80 pLDDT based on the average prediction scores of the ITIM/ITSMs in known modulatory receptors. However, this excluded ITIMs in CD5 (Y402) and BTLA (Y282), with confidence scores of 85.2 and 81.5, respectively. Of note, studies have suggested that this particular ITIM in CD5 might not be functional or essential for CD5 function[25]. It is important to highlight that the AlphaFold structure predictions are based on the proteins being in isolation. It is possible that

ITIMs become available after conformational changes following ligand binding, or that

ITIMs in disordered regions are not functional when the proteins are found in complexes[26,27].

[128] We focused our search on receptors bearing ITIM or ITSM sequences, while modulatory receptors have been described that function independent of these short sequences. We previously reported that CD200R has a unique signaling motif that is not shared with any other protein[31]. Also, TIM-3 contains multiple tyrosine residues that are not part of any known signaling motif[32]. A small number (26 genes) of putative modulatory receptors contained an ITIM embedded in an ITAM sequence, i.e.,

Yxx(I|L)x6-12Yxx(I|L). Although some ITAM-bearing molecules are capable of mediating modulatory signals in an ITIM-independent manner, these receptors may not all be modulatory[33].

[129] Until now, no known functional multimembrane spanning immune modulatory receptors have been reported, although some ITIM-bearing multi-spanners, e.g.,

SSTR2 and HCRTR1, were shown to recruit SHP-2[34,35]. It is possible that multi- spanning modulatory receptors have not yet been fully characterized due to their size and limited targetability, making them difficult to study. Of interest, in our analysis multi-spanning receptors were often expressed by multiple immune cell subsets. This may suggest that multi-spanning modulatory receptors would be capable of inhibiting a broad array of immune responses.

[130] We previously argued how different functional categories of modulatory receptors might serve distinct purposes[7]. Here, we grouped known and putative modulatory receptors in different functional categories based on their expression in isolated immune cell subsets in resting and stimulated state and show that a large number of them is expressed and regulated in a cell type-specific manner. However, as we categorized these receptors based on in vitro activation with limited stimuli, expression must be further validated in in vivo settings.

[131] We found that the highest number of target genes are expressed in neutrophils, which fits the need to control and precisely regulate their potentially damaging effector functions[36]. However, modulatory receptor gene expression on these cells did not change much after activation. This does not exclude regulation of receptor expression at the protein level, which would fit with the more short-lived nature of these cells. For instance, LAIR-1 protein is stored in intracellular granules which results in rapid membrane expression on activated granulocytes[36]. On monocytes, we found many negative feedback receptors. Considering that monocytes (especially macrophages) play a central role in orchestrating the overall immune response, timely resolution of their activation is key to successful resolution of inflammation, which could be achieved by these receptors.

[132] For the functional categorization of novel modulatory receptor genes, we collected multiple publicly available datasets containing different isolated immune cell subsets in the resting state and after cell type-specific activation. For 115 genes, we predicted a non-canonical isoform, but not the canonical sequence, as a putative modulatory receptor. This means that our expression analyses for these modulatory receptor genes might not be fully reflective of the expression of individual isoforms of those genes, considering that isoform usage can vary widely between different cells and activation states, as has been well described for CEACAM1[37,38]. In the present study, we also did not consider the ligand expression of these known and putative receptors. Regulation of modulatory receptors does not only occur at the level of the receptor itself, but the presence or absence of ligands, decoy receptors, and other interactions all add additional layers of regulation of control to the immune system[7].

[133] As proof-of-concept, we assessed expression of both known and novel targets in various tumor infiltrating T cell subsets. This helps understanding how these drug targets are differentially expressed in a disease context. As many receptors we identified were shared across immune cell subsets, it would be particularly interesting to block those that are enriched in, e.g., effector CD8+ T cell subsets. In contrast, receptors expressed in subsets that can have pro-tumorigenic properties, such as

CD4+ Treg or Th17 cells[39,40], should not be activated; these targets could instead benefit from agonist therapy. Furthermore, these receptors are also attractive in autoimmune diseases, where immune checkpoints are increasingly being explored as targets for therapy[41,42].

[134] Taken together, we have designed a bioinformatic pipeline to identify a key list of 390 predicted modulatory receptors to be used as a starting point for further research into novel targets for targeting in diseases.

Tables 2a, 2b, 2c, 2d, 3a, 3a”, 3b, 3b” and 4 show the expressed modulatory immune receptors (IR) in the different settings disclosed in this Example.

CDATcells | CD8Tcells _ Beels | NKcells [Monocytes | Neutrophils on [Ln [ge oom poe To ome To

P 1 P 1 Pp EF10 | EF10 |P EF10 |P 1 1

EE [ara [EE [E39 | 82 | we on TEE on [9 en ro.

EF10 | ATF6B | EF10 | EF10 | EF10 | ATG9A | ATGOA | EF10 | ATG9A | EF10 | ATGSA | ATG9A yom ii srs Lose [£7 (3 ss [an [17

PE cl PPV OR PS FO PP [on

AXL BTLA | AXL BIK BTLA [5 5 62 5 62 BIK BIK lee a [en

Fi li PO Fl Poe Po Pa dF 9 1 9 9 1 CD68 | A CD22 | CD22 | CD22 19 9 il PP lil PP PP Pil Fi 1 cD5 1 1 CD1D | CD72 | CD72 | CD244 | CD244 | CD33 11 1 co con leger Ton [eoa oe | [3 Leon on Leon

CD22 | CD68 | CD244 | CD5 CD22 | CD79A | CD84 | A A CD68 | CDID | CD1D neon [1 [ou Les Jeo [com Lam [2 [cont [em cD5 CD84 | A CD68 | CD5 CD84 | CD96 | CD68 | LF CD84 | CD22 | CD22

CD99L oge [5 con Leon om [age [cn [£7 30 [3 cD96 | 2 CD84 | CD84 _CD72 |2 L CD96 | CD68 | 2 A A

AM1 L AM1 AM1 cDs4 |L A L CDS6 | AM3 CD33 | CD33 ee een oe |E or Jeon

L A L L CD96 |A CYB5B | B4 L L CD5 CD68

Faa ETE EE

A R A A 2 6 7 CLCN7 | 2A B4 CD68 | CD72 £2 Toma [2 TT ee [EE ou Lem

R CYB5B | R R AM1 CYB5B | DZIP3 | A 28 2A CD72 | CD79A

Pp SE Ee on 6 7 6 CYB5B | L 7 8 6 A A CD79A | CD84 gee [oy owe [7 [5 Los an oee [SST on [og

Te ee ee ee g g ated : : g g ron [ir | ele pr ae ee EE

FF Fn [en [|E [ns 3

EXTL3 | FCRL5 | EXTL3 | FCRL3 { EMD 2B FCRL6 | EXTL3 | EXTL3 | ERBB2 | 2A 2B

El Ll oo OL PY li 7 GINM1 | 7 FCRLS | ERBB2 | FCRL2 | GINM { 7 2B EXTL3 | 2B A oe gs Bene [ [EET

FCRL5 | IER3 FCRL3 | ICAM3 {7 FCRLS | ICAM3 | FCRL3 | GINM1 | FCRL2 | A1 R

FEN dP FP Ean POL Fl sal

PE Fc LF PO PeE

PP EF ck Py og pe py [enn

EL [EE Ton [S00 Fr ER E

P ITPR1 | DMB ITM2B | DMB p L1 2 P IER3 9 DZIP3

Ed PP SE APP ad FPR Lh

ITPR1 | 319L 2 L1 2 ITPR1 | Lt p ITPR1 IGFIR | ERBB2 | EMD

Fl FP Pl Pl Pa a PO Py

Ell FE ll PE LP 319L KTN1 Pp KLRC1 | P 319L L4 ITM2B | KTN4 ITGA3 | 7 EXTL3 ee on Lm ma ETE

Le rem 00 EL

LAIR1 LAX1 ITPR1 | LAIR1 ITPR1 | LAIR KLRC1 | 319L LDHA 319L FCRL3 | FCRL3 eo [0 27 Le me

LAMP3 | LDLR 319L LAMP3 | 319L LAMP3 | KTN1 L3 6 KTN1 FURIN | FCRL6

Lae name EE

LAX1 LMTK2 | KLRC1 | LAX1 KLRG1 | LAX1 LAIR1 L4 1 LAIR1 GGT6 FURIN

Jur [area [a Lm [ar on Ter {DHA LST1 KLRG1 | LDHA KTN1 LDHA LAMP2 | L1 2 LAMP2 | GGT7 GGT6

Le inom PP IE

LDLR LYS KTN1 {DLR LAIR LDLR LAX1 L2 3 LAMP3 | GINM1 | GGT7 [a Tee [| [Tan

LMTK2 | APK2 LAIR1 LMTK2 | LAMP2 | 1 LDHA KLRC1 | 4 LAX1 2 GINM1

PE FP VPRO FO [en 0

LST APK3 LAMP2 | LST1 LAX1 2 LDLR KLRG1 | LMTK2 | LDHA DMB 2 oral Jo 1 om [Ean [eas

LY9 MPZL14 | LAMP3 | LY9 LDHA 3 LEPR KTN1 5 LDLR ICAM3 | DMB

FO OR [an [OE 0 PP (eg [en

APK2 NCLN LAX1 APK2 LDLR 4 1 LAIR1 LSTH LEPR IER3 ICAM3

El a

APK3 1 LDHA | APK3 LEPR LST1 LMTK2 | LAMP2 | LYS 6 2 IER3

Fi Fn Rl PY

NCLN 1 LDLR MPZL1 | 1 LY9 LST LAX1 APK2 1 IGFIR | 2

Ee Te [ior Br TH or 1 PEX14 | 1 NCLN 2 APK2 LY9 LDHA | APK3 2 p IGF1R

PEP eli aL

PEX14 | C1 LMTK2 | 1 3 APK3 APK2 LDLR MPZL1 | 3 ITM2B | P aL [PE rm Bg Le eT

C1 PLD3 LST1 1 4 MPZL1 | APK3 LEPR NCLN 4 ITPR1 | ITM2B

En Te mm 0 0

PLD3 C1 LY9 PEX14 | LMTK2 | NCLN MPZL4 ! 1 1 LMTK2 | L1 ITPR1

FS Fl Ee a

C1 3 APK2 C1 5 1 NCLN 3 1 5 319 L1

CAP D 1 3 APK3 C1 C1 LY9 PILRA | APK2 L3 L1 eer eg rar yg [an [Ee

M 3 PEX14 | CAP MPZL4 | PLD3 PLD3 APK2 PLD3 APK3 L2 L3

Fu Lda PRE eea

PVRIG | 1 C1 M NCLN C1 C1 APK3 3 MPZL1 | KLRC1 | L1

Lng ae or aa 3 RYK PLD3 PVRIG | 1 3 3 1 PRLR 1 KLRG14 | L2 bl FP el PO dF oy 1 SIT1 C1 D 1 CAP 4 2 PVR 1 KTN1 KLRC1

PIE PP ld aa

RYK F1 3 3 1 M CAP PLD3 3 C1 LAIR1 KLRG1

Fadl ld POP [ee [a ee

B F6 4 1 PEX14 | PVRIG | M C1 1 PILRA | LAMP2 | KTN1 a EET a Be [elan

SIAE F7 CAP 1 PILRA | 3 PVRIG | 3 RYK PLD3 LAMP3 | LAIR1 eea ET age Pel [EE an [a

SIT1 SPG7 M RYK PLD3 1 3 4 SIAE C1 LAX1 LAMP2 ee age ee ae EEE [a an

F4 SPRY1 | PVRIG | SIAE C1 1 1 CAP C10 3 LDHA | LAMP3

Ee EE [Pa [an

F6 1 D SIT 3 RYK RYK M C15 3 LDLR LAX1

FR Nl ee PL al PR en

SPG7 SSR1 3 F1 3 SIAE SIAE PVRIG | C5 M LEPR LDHA ee ee a

SPRY1 | L5 1 F6 CAP C10 C7 3 C7 PVR 6 LDLR ee ee Ge Bf 1 N2 RYK F7 Q C6 C9 1 C9 1 1 LEPR so Ln La Lo Lvs Bo La 1

SSR1 TIGIT SIAE SPG7 PVRIG | SIRPA | F6 RYK SIRPA | 1 2 6

Fld PR Pl Gl al ON id Fl £3 1 SIT1 SPRY1 | 3 F4 F7 B F7 RYK 3 1 er a a EE

L5 123 F4 1 1 F6 SPG7 SIAE K4 B 4 2

Fl a Pa AP [ana

N2 230 F6 SSR1 RYK F7 1 C10 SPG7 B LMTK2 | 3 a EE ee en EET ST

TIGIT 59 F7 L5 SIAE SPG7 SSR1 C15 1 SIAE 5 4 eo re ee ae 1 TRIB2 | SPG7 N2 C10 1 L5 C7 SSR1 C10 LST1 LMTK2 ee ee pe Ge fT 123 VT1B | SPRY1 | TIGIT SIT SSR1 TFR2 C9 L5 C11 LYS 5 fo Rr Br Br J or or 130 1 1 1 F1 L5 N2 F6 N2 C15 APK2 LST1 ar] [om or fo Be Shr 230 SSR1 123 F6 N2 TIGIT F7 1 C5 APK3 LY9 or do [EET en [EE 59 L5 230 F7 TIGIT 1 SPG7 123 C7 MPZ APK2

Fd ee

TRIB2 N2 59 SPG7 1 123 1 230 C8 MPZL1 | APK3 ea PE Tr 4 TIGIT TRIB2 11 123 230 SSR1 59 C9 NCLN MPZ a |e TE oe PE Tes

TRIB2 123 4 1 123 1 1 PILRA | PEX14

CE Tea

BP 130 VTi1B 130 SSR1 PLD3 C1

Tl a A

VT1B 230 1 230 N2 C1 PILRA ee 1 59 59 1 3 PLD3 ee EE

TRIB2 TRIB2 123 CAP C1

RTE

BP BP 130 PVR 3

B a

VTHB 4 230 PVRIG | 4

B

1 VT1B 59 3 CAP

SO OE ER

1 BP 1 PVR rr ee 4 RYK PVRIG ri

VT1B | B 3

Fn mi. 1 C10 1

TP ee ee [Te RT g g ated : : g g

Le en

C11 RYK

Ee

C12 B

C5 C10

C7 C11

Ee

C8 C12

Ee

C9 C5

Ln

SIRPA | C7

Ee

F6 C8

Ee

F7 C9 ood bo Lseor | sirea

I I I tee 1 F4

EE rea

SSR1 F6

L5 F7

De

N2 SPG7

Der

TIGIT 1

Dg 1 SSR1

LE

123 L5 ae 230 N2

I ae 59 TIGIT

Le

TRIB2 | 1

EE

BP 123

SO NE A OE LE

1 230

SO NE OO

4 59

Lt Lvs [Re 1 BP

OD

C8 1

E

4

LL

Table 2a. lIRs expressed in immune cell subsets, subdivided by activation state, single-spanners only

CD4Tcells _ CD8Tcells Beels | NKcells | Monocytes | Neutrophils _ stimul | restin restin restin restin (J J ated Q J 0 J 1

ZDHH

C8

CD4Tcells | CD8Tcells Beels | NKcells | Monocytes | Neutrophils m= ome nome d ated a La [ge 16A BA 18A BA 1 GA 16A 6A 1 6A 1 ABCD 2 2 2 2 16A 2 2 2 16A 2 164 GA

AP AP AP AP 2 AP AP AP 2 AP 2 2 ei PE

ANO6 | ANO6 | ANO6 | ANOS | AP ANOS | ANO6 | ANOB | AP ANOS | AP AP [TT a [Ee

D1 1 D1 4 ANOS | 1 D1 1 ANO6 | 1 ANOS | ANO6 en Pg Pel Po Pe i

A TT a a ee TE an

A A A A 1 A2 A A A A2 A ATG9A 1 A2 1 4 4 4 A2 1 A2 1 A A 4 4 4 4 1 4 1 4 4 4 A2 A2 1 4 1 4 2 2 4 1 4 2 4 1

ET oT LS ey [ 2 4 2 2 D1 CD84 | 1 2 4 A1G 4 4 am OV oo [eon Joon one VE ll ll cD8t | 2 CD81 | CD81 | CD81 | CKLF 12 A1G 2 ERB 4 1 our ou one leur loge 5° om [com [os Joos [5712

CKLF | CD81 | CKLF | CKLF | CKLF | D1 CD81 | CD81 | cD8% | cD81 | 2 2

EPE EE Lous [ous Lone [687 [0

Lo Le [oo Ly ee | [PT 2

L4 1A3 7 7 p FLT1 2 CXCR2 | 7 1A3 7 CLCN7

PLEA ala india Ea

GJCt 17 L4 L4 GJC1 | P 1A3 1A3 L4 L4 D1 D1

El Hl Pl a El lad Pon 57 L4 p 7 57 Gdct 17 7 D7 7 2 CNIH2 an ogen (go [Ly (oy 83 FLT4 GJC1 | FLT1 83 7 L4 L4 = FLT1 1A3 CXCR2

El PTL PR alii il Pu ll al 2 GJC1 157 GJct 12 3 p P GJC1 |P 7 1A3

IS I Loy oe eee 3M9L 17 83 3 5 5 GJC1 | GJC1 157 GJC1 | L4 7

EE eS a To oe oe 8220 | 3 319L | KCNK5 | 319L | 319L 57 7 83 7 D7 L4 me Ee a [57] 8A GPR82 | S220 | 5 S220 | 220 83 3 2 3 ELM | 7

ET a TR Lr I [0 Ton oer an 8B 319L 8A 319L 8A A 2 GPR82 | 319L | GPR82 | GJC1 | FLT

Kos | LARC Kos | LAR LRRC8 | KIAAQ KIAAO

LY9 220 8B 220 8B B 319L | 319L 8220 | 319L 57 GJC

EE EE SE ated ated g ated

Ell al PON lOO wlll ud lid 11 A LYS A LYS LY9 S220 220 8A 220 62 7 8 B 11 B 11 1 L4 L4 8B A 83 2

FPN al Tl PPPOE PO Fl lid

NDC1 LYS 8 LY9 8 MFSD8 | 8A A LY9 B 2 3

Re Hoi [iH 2 1 NDC1 1 2 NDC1 LY9 B 14 LYS 319L GPR82 [PL Ee 0 [EP 2 MFSD8 | 3 MFSD8 | 3 2 11 LYS 8 1 8220 KCNKS ee Tor Jy Lor ae TEE 3 NDC1 NNT NDC1 NNT 2 8 1 NDCA MFSD8 | 8A 319L

Ed Sd a a al

NNT 2 NPC1 2 NPC1 3 2 MFSD8 | 2 2 8B 220

FN PO PON Lil id Lal Pd

NPC 1 3 PEX13 13 PEX13 | NNT 3 2 2 3 LYS A

J Fy PPR ll

PEX13 | NNT PHTF1 | NNT PHTF1 | NPCH1 NNT 2 3 NNT 11 B

PO 3 PO oa [an [EE [an

PHTF1 | NPC4 B NPCA B PEX13 | NPC1 3 NNT NPC1 8 LYS es [ET Lor [2 Tn ren ore rs [TO

B PEX13 | C2 PEX13 | C2 PHTF1 PEX13 | NNT NPC1 PEX13 | 3 1

Ee Lo TE TB ens gp [ern

C2 PHTF1 2 PHTF1 5 B PHTF1 | NPC1 PEX13 | PHTF1 NAT14 | MFSD8

Fil al PO PO PP [en

B 5 B RER1 C2 B PEX13 PHTF1 |B NDC1 MS4A3

FPR FO OV FO Od 3

RER1 PXMP2 | RER1 PXMP2 | 1 PXMP2 15 PHTF1 B REEPS | 2 NAT14

Ee Fc [ann TE E27 og 7 Lg” 1 REEPS | 1 REEPS | Bt REEPS | RER1 B C2 RER1 3 NDC1 ee an Ee Too [THR 3 RER1 1 RER1 1 RER1 1 REEPS | 2 4 NNT 2

A7 1 3 1 3 1 1 RER1 5 B1 NPC1 3

A1 B1 A7 B1 A7 B1 3 1 RER1 1 2 NNT

A9 1 A1 1 At 1 A7 3 B1 A1 5 NPC1 11 3 A9 3 AS 3 At A7 1 A9 2 2 peer for Bono fe ar foie

A1 A7 11 A7 11 A7 AS A1 3 A1 PEX13 1 5 om rem fr de fe or eee on

A2 A1 A1 A1 At A1 A3 AS A7 A3 PHTF1 | PANX2

Ho ores or oe or er or er

B1 A9 B1 A9 A2 A9 | A1 A3 At A1 B PEX13 fo ov hes fo hoe fr dow for or fe he

G2 A1 C2 A1 B1 A1 | 11 A1 A9 11 C2 PHTF1

A2 A1 A2 11 C2 11 | A1 11 A1 A1 2 B

AS 14 AS A1 A2 A1 A2 A1 11 A2 R C2 eet Et TT ee Te

A7 A1 A7 A2 A2 A2 B1 B1 A1 B1 5 PXMP2

EE rE rE Ee ated ated g ated ee ese

A13 A2 A13 B1 A6 B1 C2 C2 A2 C2 RER1 R

Ho or for a Be oor ee 6 B1 A2 C2 A7 C2 A2 A2 B4 A2 L4 REEP5 ier oe foe or ore 8 C2 6 A2 A13 A2 A2 A2 C2 A2 1 RER1 po a [in fe Hf ef or or

SPG7 A2 8 A2 A2 A2 AB AB A2 AB B4 4 1 A2 4 AB 6 AB A7 A7 A2 A7 1 B4 eee

C1 A6 SPG7 A7 4 A7 A13 A13 AB A13 3 4 a ee

SUN2 A7 4 A13 4 A13 6 A14 A7 A14 A1 3 me en al Ld El dl

SYPL1 | A13 C1 A14 SPG7 A14 4 A2 A2 A2 AS A7 [hr [1 Thi her for for for 2 A14 SUN2 A2 1 A2 SPG7 6 6 1 A1 A1 re [re fo 88 for se for 3 A2 SYPL1 | 6 C1 6 1 4 1 4 A3 A9

Fill oe PP i 3 6 2 SPG7 SSPN SPG7 G1 SPG7 4 SPG7 A1 A1

FP OF gp gg EE 123 SPG7 3 SPNS1 | SUN2 SPNS1 | SUN2 SPNS1 | SPG7 SPNS1 11 A3 pL TS 1 TER TER TRE for 128 SPNS1 13 1 SYPL4 11 SYPL1 | 1 1 1 8 A1

ERE PH PE Pd 134 1 123 SUN2 2 SUN2 2 SUN2 C4 SUN2 A1 11 a Te TL TE To 168 SUN2 128 SYPL1 3 SYPL1 3 SYPL1 SUN2 SYPL1 A2 8 1798 SYPL1 134 2 3 2 3 2 SYPL{ | 2 B1 A1 209 2 168 3 123 3 123 3 2 3 C2 A2 222 3 179B 3 128 3 128 3 3 3 A2 B1 230 3 209 123 134 104 134 123 3 123 A2 C2 259 104 222 128 168 123 168 128 104 128 AG A2 39A 123 230 134 179B 128 179B 134 123 134 A7 A2 a re for

VIPR4 128 259 168 209 134 209 168 128 168 A13 AS ne fe fl fo fe

YIPF3 134 39A 179B 222 168 | 222 169 134 1798 A14 A7 en EE EE

C13 168 XKR6 209 230 179B | 230 179B 168 209 A2 A13 eH Be Br fe ff

G5 179B YIPF3 222 259 209 | 259 209 179B 222 A4 A14

ETE A eff 209 C13 230 39A 222 39A 222 209 230 6 A2

Ee eo Lo [BB 222 C5 251 YIPF3 230 VIPR2 | 230 222 251 6 A4

EE Er EEE ated ated g ated ee et Th fo 230 259 C13 251 YIPF3 251 230 259 8 6 ee ee 251 39A C5 259 C13 259 251 39A 1 6 a the 259 YIPF3 39A C5 39A 259 YIPF3 4 4

ET a 39A C13 TPCN2 VIPR2 390A C13 4 4 lees IBM me lve [EM eer | space,

YIPF3 C5 XKR6 YIPF3 2 C5 SPG7 SPAG4 eg Te | [le

C13 YIPF3 C13 VIPR4 1 SPG7

Ee |E ge c5 C13 C5 WLS C1 SPNS1

Em les] swe le

C5 YIPF3 SUN2 1

OO OO seen

C13 SYPL1 | SSPN

Cae

Ch 2 SUN2 ae] 3 SYPL1 ee Te 3 2 104 3 123 3 ee ma 128 104

CC mae 134 123

CC mae 168 128

CC mae 169 134

IEEE

1798 168 ee 208 169 222 179B 230 209

SO ee 251 222 ee 259 230

CL ee 39A 251 ee 2 259 ve de

VIPR1 39A

CD4Teele CORTesls Boole |e Henoeytes | Neutrophie _ cede wml

TT we ee es

Te ae een

C5 C13

C8 ch

C8 spanners onl m effec | follic reg KI | effec [ex |e resid tor ular me ula RT | tor ha im ent

EM | Th | mem | help | mo | nai tor cel | mem | ust | or | nai mem

RA | 17 | ory er ry |ve y | ory ed {y |ve ory

AD | AT AD | AD [AC | AC | AD | AC AC | AC | AC | AT

AM | P2 | ADAM | ATF6 | AM | AM | VR | VR | AM {VR | ATG9 {VR [VR | VR | P2 | ACVR 22 B1 22 B 22 22 1 1 22 1 A 1 1 1 B1 1

AR AR AR C1

AT | HG HG HG orf | AD

AT | AX | ATG9 | ATG9 | P2 EF | AT | EFM | AT | EFt ATF { 16 | AM | C50 | ARHG

F6B | L A A B1 10 F6B | 0 F6B 10 BIK 6B 2 22 15 | EF10

AR

AT C1 AT AT AT CX | HG

G9 AX |offt | G9 | ATF | P2 AT | CCPG | G8 | AD | EF | C6o | ATF6

A BIK | BIK AXL L 62 A 68 B1 F6B | 1 A R 10 89 |B

AT CX | AT | AT Cto | AT G AT

P2 Cho | CCPG AD | P2 G9 | rf16 | P2 CD30 | BTL | GT | P2 CD | ATG9

B1 15 | 1 BIK BIK | R B1 A 2 B1 0A A 6 B1 68 A

FA

CC Cto | M1

PG | C6o | CD24 rf16 | 71A BTL | C6o | AX C50 { IE | AX | CD | ATP2 1 rf89 | 4 BTLA | 2 1 BIK | A 89 IL CD5 15 | R3 |L 96 B1

CC cc KL CD

CD | PG | CD30 | Chorf | C6o | FLT | BTL | Cho | PG C6o | RC | BT | 99L 244 | 1 0A 15 189 | 4 A 15 11 BIK | CD84 {rf89 | 1 LA | 2 AXL

CE

CD | CD CD Cto Cto CC | LA | Ct AC 300 | 300 Céorf | 300 | GG | rf16 | C6o | CD | rf16 PG {IR | orft | AM

A A CD5 89 A 16 2 189 | 244 | 2 DZIP3 | 1 1 62 1 BIK

CC | CD CL

CD | CD CCPG | CD | GG | C5o | PG | 300 | Coo CD | LE | CD | EC 72 CD68 | 1 5 T7 rf15 | 1 A rf89 | EMD 244 1 PR | 5 12A | BTLA

CC LiL DH

CD | CD CD24 | CD | IER | C60 | CD | CD {PG | EXTL {CD | RA | CD | RS | Cöorft 68 96 CD72 | 4 96 3 rf89 | 5 5 1 3 68 6 79A | 7 5

CE

CD CE LIL | AC | EB

CD | 99L RK | IGF | CD [CD {CD {CD | FCGR | CD | RB | AM | AG | C6orf8 72 2 CD84 | CD72 |L IR 15 68 72 244 | 2B 72 3 1 9 9

CD | CL CL CD | CD CL 99L | CN CD78 | EC |LAl | CD | ECD | 99L {300 | FCRL | CD {LY | EC | EV | CCPG 2 7 CD96 | A 12A | R1 68 72 2 A 3 79A 19 4A | C2 1

FA

CE | CL CX | LR CE PC | CX | Mt

RK | EC | CLEC AD | RC (CD | CD {RK {CD | FCRL {CD | DH | AD | 71A | CD24

L 12A | 12A CD84 | R 25 84 79A 1 L 72 6 84 12 |R 1 4

CL | CX Cx CD | CD | DH PL | CX

EC | CLt1 | CLEC CL1 99L | 99L | RS | CD CD | XD | CL | FLT 12A | 6 4A CD96 | 6 LYS | 2 2 7 96 GGT6 | 96 C1 | 16 4 CD5 spanners onl m effec | follic reg KI | effec [ex |e resid tor ular | me ula RT | tor ha im ent

Th | mem | help | mo | nai tor cel | mem | ust { or | nai mem 17 | ory er ty | ve y | ory ed y |ve ory

CE | CE CE

CL | DH DH | ME | AC | AC | ER | AC CD | RF | EB

EC | RS | CXAD | CD99 | RS | GF | AM | AM | BB | AM 99L | ES | AG | FU 4A | 7 R L2 7 11 1 1 2 1 GGT7 {2 D 9 RIN | CD68

CE | SL | FA

DH | EB CE | CL CL AC | A M1

RS | AG | CXCL | CERK | EM | MP | RK | CN | EX | ON AM | MF | 71A | ICA 7 9 16 L D Z L 7 TL3 17 ITM2B | 1 1 1 M3 | CD72

FA

ER M1 NPP | CL | CL FB | CL CE {SP

BB | EM CLCN | 71A | PA | CN | EC { XL1 | EC | ITPRI | RK | RY | FLT | IER 2 D DZIP3 | 7 1 1 7 4A 17 12A | PLY L 1 4 3 CD96

PC |CL | CX | FC {CL CL Lt

EX | EV CLEC | FU | DH | EC | AD | GR | EC | KIAAO | CN GG | RA | CD99

TL3 | C2 | EMD 4A RIN | 12 12A |R 2B 4A | 319L 7 T7 p L2

FB PE | CL CX CL IEN

XL1 | EX DHRS | IER | CA | EC | DZ! { FC | CL1 | KLRG | EC AR | ITG | CEAC 7 TL3 | EvC2 | 7 3 M1 | 4A | P3 RL3 | 6 1 12A 2 A3 | AM1

FA

FC | M1 DH | EB DH CL

GR | 71A | EXTL ITM | PIL | RS | AG | FC | RS EC IGF | ITM | CLCN 2B 1 3 DZIP3 | 2B RA | 7 3 RL6 17 LAX1 4A 1R | 2B 7

FB ITP | PL 1

FC | XL1 | FBXL | EBAG | RIP | XD | DZI | ER | GG | DZ! DZ! RA | ITP | CLEC

RL3 | 7 17 9 L1 Ct P3 BB2 | T6 P3 LDHA | P3 P R1 12A

KIR | PT | EB EB ITP

FC | FU | FCGR 3DL | PR | AG | EX | ICA | EM AG ITM | RIP | CLEC

RL6 | RIN | 2B EMD 2 0 9 TL3 {M3 ID LDLR 19 2B L1 4A

KL RF FB KIA

FLT | GIN | FCRL | ERBB | RG | ES | EM | XL1 | {ER | EX | LMTK | EM LAL | AO3 | CXAD 4 Mt 13 2 1 D D 7 3 TL3 | 2 D R1 19L |R

FA

IFN | M1 KL

GG | IER | FCRL KT | RY | EV [FC | AR | 71A EV LE RG | CXCL

T6 3 6 EVC2 | Nt K C2 RL3 {2 1 LYS C2 PR | 1 16

FB LIL

[ER | ITM EXTL | LAI | SIA | EX | FU {IGF | XL1t | PCDH | EX RA | KT | DHRS 3 2B FLT4 3 R1 E TL3 | RIN [IR 17 12 TL3 6 N1 7

FA

Lt ST | M1 Lt { FC FB LIL

RA | ITP FBXL | LD | 3G | 71A | GG | RA | GR | PECA | XL4 RB | LAI

P R1 ITGA3 | 17 HA | AL3 | 1 17 p 2B M1 7 3 R1 DZIP3

KIR | ITP TIM | FB KIR FC LM | LA 2DL | RIP | ITPRE | FUR | LDL | M2 | XL1 | GIN | 2DL | FC | PGRM | GR TK | MP | EBAG 1 L4 PL4 N R 1 7 M1 1 RL3 | C1 28 2 2 9

MA

KIR KL LIL

3DL | LA} | KIR3D | ICAM | MP ICA | ITG | RG | IER | PTPR | GIN MP | RA | FBXL1 2 R1 L1 3 ZL4 M3 | A3 1 3 M M1 Zz 6 7

KL PL IFN | ITP {FN NF

KL PL KIR | LA IEN NPI

RG | LDL | KLRC XN ITG | 2DL | MP | ITG | RMDN | AR PA | LST | GINM 1 R 1 ITPR1 | A3 A3 | 4 2 A3 3 2 1 1 1

PT MA

PR LA KIR fL1 PK

KT | LE KLRG | KIAAO | CA ITM | MP | LA | 2DL | SLAM | RA PIL | AP

N4 PR 11 319L p 2B 2 Xl 1 F6 P RA | K2 ICAM3

MA

LIL PT LA KIR PK

LAI | RA KIR2 PR ITP | MP | LDL | 2DL | SLAM | ITG PL | AP | IFNAR

R1 6 KTN1 | DL3 M R1 3 R 3 F7 A3 D3 | K3 |2

LIL ITP KIR PL ME

HA | 3 2 DL4 RIG L1 1 PR 1 4 ALS R1 C1 11 ITGA3

LIL [LR RM KIA LIL | KIR ITP PT

LiL RR LIL | KIR KIA RF | NF

RB | LST KIR3 BP KT | LDL {RB | 3DL A03 ES | AM 1 1 LAX1 DL2 1 N1 R 3 2 TIGIT | 19L D 1 ITPR1

LIL KL KIR NPI

RB SIA LAI | LEP | LM {| RC 2DL RY | PA | ITPRI 3 LY9 | LDHA | KTN1 |E R1 R TK2 {1 4 K 1 PL4

MA

LR | PK SP LA LR IKL KL

RC | AP LAMP | RY MP | LM | RC | RG RC SIA | PE | KLRC

K2 LDLR | 2 1 2 TK2 | 25 1 1 E X14 | 1

ME LA SL

GF | LILRA ss MP | LST KT KT AM | PIL

LYS | 11 6 LDHA | Rt 3 1 LY9 | Ni N1 F4 RA | KTN1

MA MA | MA

PK PK | PK LA

AP | MP | LILRB | LMTK | TF LA | AP | AP {LA MP SP | PL

K2 ZL1 13 2 R2 Xl K2 K2 Xl 2 G7 | D3 | LAIRY

MA

ME ™ PK ME ST | PL

GF | NC { LRRC | LRRC | EM LD | AP | GF {LD LAX 3G | XN | LAMP 11 LN 125 25 123 HA | K3 11 HA 1 AL3 | A3 [2

NF VS TIM

MP | AM MAPK | TM LDL | NC | MP | LDL LM M2 | PT

ET p

PD | NPI YM LR TM

GF | PA | MEGF | MAPK | EL LE PE | NC | LE RC EM | PV

RB | 1 11 APK3 | 1 PR | X14 | LN PR 25 123 | RIG | LDHA

MA

PE | PC LIL | PG | NF | LIL PK YM | RF

CA | DH MPZL RA | RM | AM | RB AP EIL | ES

M1 12 NCLN | 1 6 C1 1 1 K2 1 D LDLR

PT MA

PR | PD LR PD {LR PK ZD | RM

CA | CD | NPIPA RC | PL GF {| RC AP HH | DN

P 1 1 NCLN 25 D3 RB 125 K3 C8 |3 LEPR

PT

PT | PG PR

PR | RM | PCDH | NFAM LST | CA | PE MP RY | LILRA

M Ct 12 1 1 p X14 | LYS Z K 6

MA MA

PK PK

PV | PIL | PDCD | NPIP AP | RR | PIL | AP MP SIA | LILRB

RIG | RA 11 At K3 BP1 | RA | K2 ZL4 E 3

MA

RM | PL ME | SIG PK SIG

DN | XN | PDGF | PCDH GF | LE PL | AP NC LE LRRC 3 A3 | RB 12 11 C10 | D3 K3 LN C9 | 25

PT

RR | PT SIG | PR NF SL

PT SL

RY | PV | PGRM | PECA MP | SIT | PR | NC NPI AM | MAPK

K R C1 M1 ZL1 | 1 M LN PA1 F6 APK2

SIG SLA | RM | NF PC

LE PV PEX1 NC | MF | DN | AM DH SP | MAPK

C10 | RIG | PILRA | 4 LN 1 3 1 12 G7 | APK3

SIG | RM NF RR IPD PD SP

C9 |3 C1 MC1 1 G7 1 RB 1 1 MPZ

SL SL PC | SP PE PD SP

AM | AM | PTPR | PILR DH | TLC | SIA | CA GF TL MPZL

F6 F1 CAP A 12 1 E M1 RB C1 1

SL SP PD SIG PE

AM | RY | PTPR CD | SS | LE PE CA SS

F7 1 M PLD3 1 R1 C10 | X14 M1 R1 NCLN

PE | ST3 | SIG | PG ST3

SS | SS | PVRI PLXN CA | GA | LE RM PE GA | NFAM

R1 R1 G A3 M1 | L3 C9 | Ct X14 L5 1

ST3 | ST3 ST3 | SL PG TG

GA | GA | RMDN | PTPR PE | GA | AM | PIL RM OL | NPIPA

ST3 PG | SY | SL TIM

GA | TF RRBP RM | NE | AM | PL PL M2 | PCDH

L5 R2 1 PVR C1 4 F7 D3 D3 1 12 ™ TG | SP IPL PLX ™

TF EM RRBP PIL | OL | TL XD NA EM | PDCD

R2 123 | RYK 1 RA | N2 Ct Ct 3 123 | 1

PT

TM | TM PL ST3 {PL PR TM

EM | EM | SIGLE XN | TIG | GA | XN CA EM | PECA 59 230 | C10 RYK A3 IT L3 A3 P 230 | M1

PT

TY | TM PR | TIM | ST3 ™

RO | EM | SIGLE | SIGL CA | M2 | GA | PV PV EM | PEX1

BP | 59 C9 EC10 p 1 LS RIG R 59 4

VS TM | SY | RM

VTE | TM | SLAM | SLAM PV | EM | NE | DN RR TRI | PGRM 1B 4 F6 F6 R 230 | 4 3 BP1 B2 C1

ZD | YM TM RR TY

HH | E1L | SLAM PV | EM | TF BP RY RO

C8 | 1 F7 SPG7 RIG | 59 R2 1 K BP | PLD3

ZD RF TG SIG VS

HH | ST3G | SPRY ES | TRI | OL | RY LE TM | PLXD

C8 | ALS 1 D B2 N2 K C10 4 C1

RM | VS | TIM | SIG SIG YM

SYNE | SPTL DN | TM | M2 {LE LE E1L | PLXN 4 C1 3 4 1 C10 C12 1 A3

RR TM | SIG

BP | VTI | EM {LE SIT PTPR

TFR2 | SSR4 1 1B 230 | C12 1 CAP

YM | TM | SL SLA

TIMM | ST3G SIA | E1L | EM | AM ME 21 AL3 E 1 59 F7 1 PVR

ZD TY SLA

TYRO | SYNE SIT | HH | RO | SP MF PVR!

BP 4 1 C8 BP | G7 6 G

SL VS | SP

AM TM | RY SP RFES

TFR2 F1 4 1 G7 D

SL SP

TGOL AM VTI | SS RY RMDN

N2 F6 1B R1 1 3

ZD | ST3 SP

SP HH | GA TLC RRBP

TIGIT G7 C8 {15 1 1

SP

TME TL TF ss

M123 C1 R2 R1 SIAE

TG ST3

TME SS OL GA SIGLE

SY SY

TME NE TIG NE

M59 4 IT 4 SIT

TM TG

VSTM TF EM OL SLAM

4 R2 123 N2 F1

TG TM

OL EM TIG SLAM

VT1B N2 230 IT F7

TIM TM TIM

YME1 M2 EM M2

L1 1 59 1 SPG7 ™ ™

EM TRI EM SPRY

123 B2 230 1 ™ TY ™

EM RO EM SPTL

230 BP 59 C1

TM

EM VTI TRI

59 1B B2 SSR1

YM

TRI EL VTI ST3G

B2 1 1B ALS

TY YM

RO EL SYNE

BP 1 4

ZD

VTI HH

1B C8 TFR2

YM

E1L TGOL 1 N2 zD

HH

C8 TIGIT 0 0 0 123 0 0 0 0 230 0 0 0 0 59

LL TL LLL | ee

LLL LLL LL |E] 4

Li LLL LL LLL vies

LLL

L1

CT rE

C8 spanners only m effect | follic reg KI | effect ex |e resid or ular | me ula RT or ha Im ent

EM | Th | mem | help | mo tor | EM | cel | mem | ust | or | nai mem

RA | 17 | ory er ry y RA | | ory ed |y |ve ory

AB

AB | AB AT | AB | AB HD | AB AB | AP | AP | AB

HD | CD | AFG3 | ABCD | AN | P10 | CD | HD | 16 CD | ABHD | CD | OL | OL {CD | ABCD 16A | 1 L2 1 O6 {A 1 16A | A 1 16A 1 D1 | Dt 1 1

AB

AF | AB AT {AT | AB | AF | AG | HD AB | AT | AT

G3 | HD | ATG9 | ABHD | P10 | P8 HD | G3L | TR | 16 ATGS | HD | P8 | P10 { AN | ABHD

L2 16A | A 16A A B2 16A | 2 AP | A A 16A | B2 | A O6 | 16A

CA DP

AG | AF AT | TS | AF | AG AF AF | Y1 | AT | AP

TR | G3 | ATP2 | AFG3 {P13 {PE | G3 | TR | AN | G3 | ATP8 | G3L | 9L | P2 OL | AFG3

AP | L2 B4 L2 A2 RB | L2 AP | 06 | L2 A1 2 4 B1 D1 L2

AT | DP | AG | AP | AT | AG GP | AT | AT

AN | AN | ATP8 P2 Y19 | TR | OL P1 TR | CATS | AN | Rt | P8 P13 | AGTR 06 | 06 | A1 ANO6 | B1 L4 AP | D1 OA | AP | PERB | 06 157 | B2 ! A2 AP

AT

AT | AT AT | GP AT P1 AP | GP | CA | AT

GY | P10 | CATS | ATG9 | P2 R15 | AN | G9 | 3A | AN OL | Rt | CF | P2

A A PERB | A B4 7 06 | A 2 O6 { CD81 | Dt 83 | D1 B1 ANO6

AT CA

AT | AT AT | GP | AP | AT | AT | Pt AT GP | TS | AT

P10 | P13 ATP1 | P8 R18 | OL | P13 | P2 | 3A | CLDN | G9 R8 | PE | P2 | APOL

A A2 CD81 | DA B2 3 D1 A2 B1 2 D1 A 2 RB | B4 D1

CA CA

AT | AT TS KC | AT | AT | AT | AT AT KC | CY | TS

P13 | P2 ATP2 {PE | NQ | GS | P8B | P2 | P2 | DHCR | P10 | NA | B56 | PE | ATG9

A2 B1 CKLF | B4 RB 15 A 2 B4 | Bi 7 A 2 1A IRB | A

AT | AT AT | CA AT AT DP

P2 P2 CLDN | ATP8 | CD P10 | CF | CD | P8 | GPR1 | P2B | LY | Y18 {| CK | ATP10

B1 B4 D1 At 81 LYS | A D1 81 At 83 4 9 L4 LF A

AT | AT AT CX | CA AT Pi CL

P2 P8 CXCR | CACF { CK | NIP | P13 | CK | CR | CF | KCNQ | PSA | K3 | FLT | DN | ATP13

B4 | AM 6 D1 LF AL3 | A2 LF 2 D1 5 1 CB | 1 D1 A2

CA CY

AT | TS DH | PIK | AT | CL B5 CA GP | CX

P8 PE | ENTP CR {3C P2 CN | 61 CK | KIAAO | CF R15 { CR | ATP2

At RB | D7 CD81 17 B B1 7 A3 | LF {319L D1 7 6 B1

CA DP | SC | AT | CL DP | CL GP | EN

CF | CD | KCNQ Y19 | AR | P2 DN | Yi CN | LRRC | CD R18 | TP | ATP2

D1 81 5 CKLF {14 B1 B4 D1 94 | 7 8A 81 3 D7 B4

EN {| SL | AT | CX | KID | DH GP

CD | CK | KIR2D | CLCN | TP | C19 | P8 CR | INS | CR CK GP | R15 | ATP8 81 LF L4 7 D7 | Al At 6 220 | 7 LY9 LF R82 | 7 At

CX | CL GP {SL | AT | CY | LR | EN CL LR | GP

CR | ON | LRRC | CYB5 | R15 | C2 P8 B5 | RC | TP CN RC | R18 | ATP8 2 7 8A 61A3 17 A11 | B2 1A3 | 8A | D7 | NDC1 17 8B 3 B2

DP | CL GP | SL EN GP CX

Y19 | DN DPYt | R18 | C38 | CA | TP | LY | Rt PIK3C | CR GP | CACF

L4 D1 LY9 9L4 3 Ab TS D7 9 57 B 6 LYS | R82 | D1 spanners onl m effect | follic reg KI | effect { ex |e resid or ular | me ula RT | or ha | m ent

Th | mem | help | mo tor cel { mem | ust | or | nai mem 17 | ory er ry y | ory ed |y |ve ory el

RB

KC | CX KC | st MF | GP MF | KC

NQ | CR | NATH ENTP | NA | C7 CD | FAL | SD | R8 | REEP | CYB561A | SD | NA | CATS 6 4 D7 2 A8 81 M2 | 11 2 5 3 8 2 PERB

KID | CY KiD MF | KC EN KIA

INS | B56 | PEX1 FAIM [INS | SY | CK | FLT | SD | NA | SCAR | TP NIP | AO3 220 | 1A3 | 3 2 220 | PL1 | LF 1 8 2 B1 D7 AL3 | 19L | CD81

KIR | DH LR | TM | CL NIP | KC ME 2D | CR | PIK3C RC | EM | CN | GP | AL | NQ | SGMS | FA! PIG | SD

L4 7 B FLT1 8A 123 | 7 R82 | 2 5 1 M2 W 11 CKLF

LR | EN TM | CL KID KID SG

RC | TP | REEP | KCNK EM | DN | INS | NN | INS | SLC3 | FLT SM | NA | CLCN 8A D7 5 5 LY9 | 168 | D1 220 |T 220 | 8A2 1 3 T14 {7

GP MF | TM | CY | KIR KIR KC SL

R18 | RNF1 | KCNQ { SD | EM | B56 | 2DL | NP | 2D | SLC3 | NK C11 { NP | CLDN

LYS | 3 21 5 11 251 | 1A3 | 4 C1 | L4 BA6 5 At C1 D1

MF PIK DP | LR KC SL

SD | GP | SCAR | KIAAD | 3C | VIP | Y19 | RC | PIG | LY | SLC4 | NQ C12 PE | CXCR 11 R82 | Bt 319L B Ri L4 8A |W 3 5A4 5 A9 1X13 16

MF | KIA RE EN | LR NIP SL

SD | A03 | SLC1 KIR2 EP | XK | TP | RC | RE | AL | SLC6 | KIAA0319 | C19 | PH | CYB5 8 19L | 2A9 DL4 5 R6 D7 | 8B R1 | 2 A6 L At TF1 | 61A3

SL

KID SC MF | C1 PE SL

NN | INS | SLC2 | LRRC | AR FLT | SD | OA | X1 SYPL | KIDINS22 | C2 PIG | DHCR

T 220 | A8 8B B1 1 11 7 3 1 0 A11 IW 7

SL

LR SL GP | MF | C1 PH KIR SL PIK

NP | RC | SLC3 | NAT | C11 Rig | SD | 1A | TF | TMEM | 2DL C35 | 3C | ENTP

Ct 8A | 3A1 4 At 3 8 1 1 39A 4 C2 B D7

SL

SL ND | C1 LR SL PO

PE SLC3 | NDFt | C19 GP | FIP | 2A | PIG RC C37 | PD | GPR4

X13 | LYS | 8A2 p2 At R82 | 2 9 W VIPR2 | 8B A2 C2 157

SL

MF SL KC C3 | RN MF SL RE

PIG | SD | SLC3 | NIPAL | C33 NA | NIP | 3A | F12 | ZDHH | SD C38 {| EP | GPR1

W 11 9A14 2 At 2 AL2 | 1 1 C13 8 A6 5 83

SL

RE SL KC C3 | SC SL

EP | NA | SLC6 | NIPAL | C38 NQ | NN | 5B | AR | ZDHH | NA C38 | RE | GPR8 5 T14 | A6 3 A2 5 T 1 B1 C5 T14 A7 R4 2

SL

SC SL KIA C3 | SG ND SL RN

AR | NP C45 A03 | NP | BC | MS FIP C39 | F12 | KCNA

B1 C1 SUN2 | NNT A4 19L | C1 2 1 2 A13 | 1 2

SL

SL SL KID C3 | SG SL SL

C1 PH | TMEM | PEX1 | C7 INS | PH | 7A | SM NIP C5 | C10 | KCNK 2A9 | TF1 | 251 3 A8 220 | TF1 | 2 3 AL2 A6 A7 5 spanners onl m effect | follic reg KI | effect { ex |e resid or ular | me ula RT | or ha | m ent

Th | mem | help | mo tor cel { mem | ust | or | nai mem 17 | ory er ry y | ory ed |y |ve ory

SL | SL

SL LR | PO | C3 | Ct SL SL

C2 | PIG | TMEM | PHTE | SU RC | PD | 8A | DA NIP C7 Cit | KIDIN

AB |W 39A 1 N2 8A C2 7 7 AL3 A8 | Al 5220

SL | SL

SL PIK LR [PX | C3 | Ct SL

C3 | 3C | TMEM SY RC | MP | 9A | 9A NN SP 1 C19 | MFSD 3A1 | B 44 PIGW | PL1 SB 2 13 1 T G7 | A1 11

SL

SL PX ME SP | C2 SP | SL

C3 | MP | TPCN | PXMP SD | RE | NS | At PE NS | C2 MFSD

B5A2 | 2 2 2 TMEM123 | 11 EPS | 1 1 X13 1 A11 18

SL

SL RE MF SP | C3 SL

C3 | EP SD | RE | TL | 3A PH SU | C33 | NATH 581 | 5 VIPR2 | RER1 | TMEM398A | 8 R1 Ct 1 TF1 N2 | At 4

SL SL

C3 RN C3 SL 5C | RE RNF1 | VIP NA | F12 | SU | 5B PIG SY | C35 | NDFIP 2 R1 XKR6 | 21 R1 T14 | 1 N2 | 1 W PL1 | A2 2

SL

SL SC ND | SG | TIM | C3 PO TM | SL

C3 | AR | ZDHH | SCAR | XK FIP | MS | M2 | 5C PD EM | C35 | NIPAL 8A7 | Bl C13 B1 R6 2 1 2 2 C2 123 | Bf 3

SL SL

C3 | SL ZD SG | TM | C3 PX TM ISL

SA1 | C11 SGS HH NIP | SM | CO | 7A MP EM | C35 3 Al M3 C5 AL2 | 3 3 2 2 128 | C2 | NNT

SL

SP | SL SL TM | C3 TM | SL

NS | C33 SLC1 NIP | C10 | EM | 8A RE EM | C38 1 Al 0A7 AL3 | A7 104 | 2 EPS 168 | A6 NPC1

SL

SL SL TM | C3 TM ISL

SU | C35 SLC1 NN | C12 | EM | 9A RE EM | C39 | PEX1

N2 | B1 2A9 T A9 168 | 13 R1 169 | A14 | 3

SL

TIM | SL SL TM | C3 RN TM | SL

M2 | C38 SLC2 PE | C19 | EM | SA F12 EM | C45 | PHTF 2 A2 A11 X13 | A1 169 | 14 1 251 | A4 1

SL

TM | SL SL TM | C4 SC SL

EM | C38 SLC2 PH | C2 EM | 5A AR VIP | C5 104 | A7 A8 TF1 | A11 | 209 | 4 B1 R1 A6 PIGW

TM

EM | SL SL TM | SL SG SL 179 | C39 SLC3 PIG | C2 EM | C5 MS XK {C6 | POPD

B A13 3A1 W AS 222 | A6 1 R6 | A6 C2

TM | SL PIK | SL TM | SL SG ZD ISL

EM | C39 SLC3 3C C35 | EM | C7 SM HH | C7 | PXMP 209 | A14 5A2 B A2 230 | A8 3 C8 | A8 2 spanners onl m effect | follic reg KI | effect { ex |e resid or ular | me ula RT | or ha | m ent

TM | SL PO | SL TM | SP SL

EM | C5 SLC3 PD | C35 | EM | AG C10 SP | REEP 222 | A6 5B1 C2 B1 251 | 4 A7 G7 [5

TM | SL PX | SL ™ SL SP

EM | C6 SLC3 MP | C35 | EM | SP C11 TL 251 | A6 7A2 2 C2 259 | G7 Al C1 RER1

SL RE | SL SL TIM

VIB | C7 SLC3 EP | C37 | VIP | SU C12 M2 | RNF1

R2 | A8 8AG 5 A2 R2 | N2 A9 2 21

SP SL SY SL ™

XK | AG SLC3 RE | C38 | WL | PL C2 EM | SCAR

R6 | 4 8A13 R1 A2 S 1 A11 123 | B1

ZD RN | SL TIM SL TM

HH | SU SLC3 F12 | C38 | YIP | M2 C2 EM | SGMS

C5 | N2 9A14 1 A6 F3 | 2 A8 128 | 1

ZD | TIM SC | SL ZD | TM SL TM

HH | M2 SLC4 AR | C38 | HH | CO C33 EM | SGSM

C8 | 2 1A2 B1 A7 C8 |3 Al 134 13

SG | SL SL TM

SLC4 MS | C41 C35 EM | SLC10

TMEM104 5A4 1 A2 TMEM123 A2 168 | A7

TM

SG | SL SL EM

SLC5 SM | C5 C35 179 | SLCH1

TMEM123 AB 3 Ab TMEM128 B1 B At

SL SL SL TM

SLC6 C10 | C6 C35 EM | SLC12

TMEM128 AG A7 A6 TMEM134 C2 222 | A9

SL SP SL ™

SPAG Ctt | AG C37 EM | SLC19

TMEM168 4 At 4 TMEM168 A2 230 | A1

SL SL TM

Ct2 | SP C38 EM | SLC2

TMEM209 SPG7 A9 G7 TMEM169 A2 259 | A8

SL SP SL

SPNS C19 | NS C38 VIP | SLC33

TMEM222 1 At 1 TMEM209 A7 R1 At

SL SP SL

SPTL C2 | TLC C39 XK | SLC35

TMEM230 Ct A8 1 TMEM230 A13 R6 | A2

SL | TIM SL

SYPL C35 | M2 C39 YIP | SLC35

TMEM39A 1 A2 2 TMEM258 A14 F3 B1

SL TM SL ZD

VIP TIMM C35 | CO C41 HH | SLC35

R2 22 B1 3 TMEM39A A2 C5 | C2

SL TM SL

XK TMC C35 EM C5 SLC38

R6 03 C2 | TMEM128 | 44 A6 A2 spanners onl m effect | follic reg KI | effect { ex |e resid or ular | me ula RT | or ha | m ent

ZD SL TP SL

HH C37 CN C6 SLC39

C5 TMEM104 A2 TMEM134 | 2 A6 A13

ZD SL SP

HH C38 VIP AG SLC39

C8 TMEM123 A2 TMEM169 | R2 4 A14

SL ZD

C38 | TMEM179 | HH SP SLC41

TMEM128 AB B C5 G7 A2

SL SP

C38 NS SLC45

TMEM134 A7 TMEM209 1 Ad

SL SP

C39 TLC SLCS

TMEM179B A13 | TMEM222 1 AG

SL TIM

C45 M2 SLC6

TMEM209 A4 | TMEM230 2 A6

SL TM

C5 co SPAG

TMEM222 A6 TMEM251 3 4

SL

C6

TMEM230 AB TMEM259 TMEM104 SPG7

SL TP

C7 CN SPNS

TMEM259 A8 2 TMEM128 1

TT fee [ [EET [ne EE

TMEM39A G7 |S TMEM134 C1

SP

TME NS | YIP

M44 1 F3 TMEM168 SUN2

SP | ZD

TPCN TL HH TMEM179 SYPL 2 Ct C13 B 1

ZD

SU | HH TIMM

VIPR2 N2 C8 TMEM209 22

CU fe ED TT en 2

YIPE3 PL1 TMEM222 3

TIM

ZDHH M2 TMEM

C13 2 TMEM230 104 ™

ZDHH CO TMEM

C5 3 TMEM251 123

IT fee | [fe]

TMEM104 TMEM259 128

LLL ne | a

TMEM123 TMEM39A 134 spanners onl m effect | follic reg KI | effect { ex |e resid or ular | me ula RT | or ha | m ent

Th | mem | help | mo tor cel { mem | ust | or | nai mem 17 | ory er ry y | ory ed |y |ve ory ™

DLL ll |] JE] ue

TMEM128 44 1798

DLL lee |] EL] ae

CN TMEM

TMEM134 2 209

LL eme

TMEM168 S 222

LLL IE EE LE A

TMEM169 R6 230

LLL Le a

B F3 251

LL ewe] || BL] ee

HH TMEM

TMEM209 C13 259

LL ee] || EL] ue

HH TMEM

TMEM222 C5 39A ll lee OE ue

HH TMEM

TMEM230 C8 44 bl Tees | LL

TMEM251 2

LLL wees | LLL LL wes

DLL ET ee 44 C13

LLL B ILL LIL me

CN ZDHH

2 C5

LLL EEE ri

R1 C8 rel LL LDL

R2 rer LLL LL

F3

DLL Le LL

HH

C13

DLL EL

HH

C5

LLL B LLL LL

HH

C8 onl

AR

AC AC | AC AD HG

VRL ABI3B | VR | VRL | ACV ABI3B | AM | AC | ATG | ABI3B | EF 1 BIK SLAMFt | P 1 1 R1 BTLA Pp 22 | VR1 | 9A Pp 10

AR AR

AD HG HG | AC AT

AT AT MAP AT

BES Clorft | F6 | CA F6 | BES | KAP P2

T3 JER3 62 B BP7 | CD68 | TIGIT CD244 |B T3 K2 AXL B1

AT | CD1 AT

CA | IGDC GY | 64L CD300 | G9 PGR BT

BP7 | C4 CD22 A 2 CD72 | TIMM21 | A A BIK | MC1 | CD1D | LA

C1

C1 orf | CD1 C5

CD1 | PDC FBXLt | BT | CD2 | IGDC FBXL1 | 16 | 64L | ROB orf

D D1 7 LA | 2 C4 7 2 2 01 ITGA3 | 15

C5 | CD3 C5 Cé

CD3 | SLA orf | CD3 | PDC off | CD3 | SIRP PG 00A | MF7 LAIR1 189 |3 D1 FCRL6 | 89 | 00A | A LMTK2 | 1

F LYS 1 9A Ot FLT4 1 F TIGIT | 5 22

LEE Ten |E 3 4 5 aL2 GGT7 | 5 3 M4 LSTI 68 > [ele [aas Tes 2 M 84 | H5 DMB 84 | H5 1 72

CD

CE

CD AC

CD 99 LILRB | AM PRRG | CD

H5 SIAE L2 | CEACAM3 1 1 CEACAM3 3 84

CE

AC | CH CE | CH

CD ST3G | AM | RN PLXNA | RK | RN PTPR | CD

ON AL3 1 B4 4 L B4 0 96 onl

CE CL CD

TMEM | RK | CLC TYRO | EC | CLC 99

CEACAM3 130 L N7 BP 4A | N7 SIT1 L2

CE

CH CL | CLE CX | CLE AC

RN VSTM | EC | C12 AD | C12 TYRO | AM

B4 4 4A | A R A BP 1

CX | CLE CY | CLE CE

CLC AD | C12 B5 | C12 RK

N7 R B B B L

CLE CY | CO DH | CO CL

C12 B5 | L17 RS | L17 EC

A B Al 7 A1 4A

CLE DH | CY CX CX

C12 RS | P4A DZ | AD CL

B 7 11 IP3 IR 16

CO EB | CY CY

L17 DZ | DC AG | P4A B5

At IP3 | C 9 11 B

CY EB DH

P4A AG | DC EM | DC RS 11 9 T D Cc 7

ER

DC EM | DD BB | DC DZ

C D R2 2 T IP3

ER EX EB

DC BB | DLL TL | DD AG

T 2 1 3 R2 9

EX FC

DD TL | DLL RL | DLL EM

R2 3 4 3 1 D

FC | DN FC ER

DLL RL | AJC RL | DLL BB 1 3 5G 5 4 2

FC | DS GI | DN EX

DLL RL | CA NM | AJC TL 4 5 M 1 5G 3

DN Gl | DS IC | DS FB

AJC NM | CA AM | CA XL 5G i ML1 3 M 17

DS ie IF | DS FC

CA AM | DS NA | CA GR

M 3 PP R2 | ML1 2B

DS IF IG FC

CA NA | EV F4 | DS RL

ML R2 | C2 R PP 2

IG | FA IL FC

DS Ft | M16 RA | EV RL

PP R 3B P C2 3 onl

EV RA M2 | M16 RL

C2 P FAM171A1 B 3B 5

FA IT Gl

M16 M2 | FCA ITP NM 3B B MR Rt | FAM171A1 1

ITP HL

FC Ri A-

ITP | GR PL | FCA DM

FAM171A1 Ri | 2B 1 MR B

Ki

ITP AA

Ri 03 IC

FCA PL | FC 18 | FC AM

MR 1 RL4 L RL4 3

KI

AA

FC 03 KL IF

GR 19 | FGF RC | FC NA 2B L R3 1 RL6 R2

KL KL IG

FC RG | FU RG | FGF F4

RL2 1 RIN 1 R3 R 4

FC KT | GG KT | FLT RA

RL4 Ni | T6 Nt 1 4 P

LA | GP IT

FC MP | R16 LAL | FU M2

RL6 2 2 Rt | RIN B

LA LA

FGF MP MP | GG ITP

R3 3 HEPACAM2 2 T6 R1

ITP

HE LA Ri

FLT LA | PHL MP | GG PL 4 Xt 11 3 T7 1

Ki

AA

GP 03

FU LD | IGS LA | R16 19

RIN HA | F9 X1 12 L

KL

GG LD | IMP LD RG

T6 LR | G2 HA | HEPACAM2 1

GP LM | KIA HE

R16 TK | A03 LD | PHL KT 2 2 19 LR | 1 N1

KIR LM

LS | 2DL TK | IER LA!

HEPACAM2 Tí | 1 2 3 R1 onl

MA

HE PK | KIR LA

PHL AP | 2DL LS | IGD MP 1 K2 13 T1 | CC4 2

HLA MA

- PK | KIR

DM AP | 2DL LY | IGS LA

B K3 | 4 9 F9 Xt

MA

KIR PK

IGS NC | 3DL AP | IMP LD

F9 LN | 1 K2 | G2 HA

NP | KIR KIA

IMP IP | 3DL NC | AO3 LD

G2 Al | 2 LN 119 LR

PE | KIR NP | KIR LiL

ITG X1 | 3DL IP | 2DL RB

A3 4 3 Al it 1

KIA PG | LE PE | KIR LiL

A03 RM | MD X1 | 2DL RB 19 Ci [1 4 3 2

KIR PG | KIR LiL 2DL PL | LEP RM | 2DL RB 1 D3 | R C1 1 4 3

KIR PL KIR LiL 2DL XD | LiL PL | 3DL RB 3 C1 | RAB D3 | 1 4

KIR PL PL | KIR 2DL XN | LIL XD | 3DL LY 4 A3 | RB2 Ct 12 9

PT MA

KIR PR PL | KIR PK 3DL CA | LIL XN | 3DL AP 1 P RB3 A3 3 K3

PT

KIR PV PR MP

3DL Ri | LiL CA | KLR ZL 2 G RB4 P C1 1

KIR RM PT | LE 3DL DN | LIL PR | MD NC 3 3 RB5 M 1 LN

RR PV NP

KLR BP | LR! Ri | LiL IP

C1 1 Ti G RAG At

LE RF PA

MD RY | LRR ES | LIL RM 1 K C19 D RB5 1

RM PE

LEP SIT | LRR DN | LR! xt

R 1 C25 3 T1 4 onl

SL | ME RR

LiL AM | GFt BP | LRR PL

RAG F6 | 1 1 C19 D3

ME PL

LiL SP | MP RY | GF1 xD

RB G7 |Z K 1 C1

SP PL

LiL RY | MR Si | MP XN

RB2 1 AP AE |Z A3

PT

SP PR

LiL TL | MU SIT | MR CA

RB3 C1 | C1 1 AP Pp

SL PV

LiL SS | MU AM | MU Ri

RB4 Rt | C22 F1 | Ct G

ST

3G SL RM

LiL AL | NC AM | MU DN

RB5 5 R2 F6 | C22 3

TG SL RR

LRI OL | NFA AM | NC BP

Th N2 | Mt F7 | R2 i

Ti

M PA PC

LRR M2 | RM SP | DH RY

C19 1 1 G7 12 K

TM

EM | PC SP

LRR 12 | DH1 RY | PC Si

C25 3 2 1 DH8 AE

TM PC Si

ME EM SP | DH GL

GF1 23 | PC TL | GC EC 1 0 DH8 Ct 13 10

PC PC

TM | DH DH SL

MP EM | GC SS | GC AM

Z 59 |3 R1 15 F4

PC ST

DH 3G SL

MR TR | GC AL | PD AM

AP B2 | 5 5 CD4 F6

PD TG | PD SL

MU VTE | GF OL | GF AM

C1 1B | RB N2 | RB F7 ™

Yi EM

MU Et | PIE 12 | PIE SP

C22 Lt | ZO2 3 Z02 G7 onl

EM SP

NC PIL 23 | PLX TL

R2 RA 0 NA4 C1 ™

NFA PRL EM | PRL SS

M1 R 59 IR R1

ST

PA PR 3G

RM RG TR | PTP AL 1 3 IB2 | RD 5

PC TG

DH1 PTP VTE | PTP OL 2 RD 1B | RH N2

TI

YM M

PC PTP Et | PV M2

DH8 RH Lt IR 1

PC TM

DH EM

GC PTP RFE 12 3 RO SD 3

PC TM

DH RN EM

GC PV F12 13

R 8 0

TM

PD RN EM

GF F12 RO 23

RB 8 BO4 0

TM

PIE RO RO EM

Z02 BO4 St 59

BE TT Ee

RA S1 N1B IB2

Le

R N1B N3B 1B

PR SiG YM

RG sc LEC Et 3 N3B 11 L1

SiG SiG

PTP LEC LEC

RD 10 12

SiG SIG

PTP LEC LEC

RH 11 15

SIG SIG

PTP LEC LEC

RO 12 5 onl

SIG SIG

PV LEC LEC

R 15 7

RN SiG SiG

F12 LEC LEC 8 5 8

SIG SIG

RO LEC LEC

BO1 6 9

SIG SL!

RO LEC TRK

BO4 7 3

SiG SLi

RO LEC TRK

$1 8 4

SIG

SC LEC SP

N1B 9 RY1

SIG ST3

LEC SIR GAL

10 PA 3

SiG SLi

LEC TRK SY

11 3 NE4

SIG SLI

LEC TRK SYT

12 4 3

SiG ST3

LEC GAL TFR

15 3 2

SiG

LEC SY

NE4 TMEM132E

SIG TM

LEC SYT EM

6 3 52

SiG

LEC TFR TRE

7 2 ML1

SIG

LEC VSI

8 TMEM130 G4

SiG

LEC VST

9 TMEM132E M1 ™ ZD

SIR EM HH

PA 52 C8 onl

SLI

TRK TRE

3 ML1

SLI

TRK VSI

4 G4

EE LLN

NE4 M1

ALLE LIE

3 M4

ZD

TFR HH

2 C8

Tee | rr rrr 52

Err rrr

ML1

TYR

OB p

SLI

G4

Err

M1

ZD

HH

C8

NKeells Monocytes I MNewophils neg | thresh neg | thresh neg | thresh ativ | old- thres ativ | old- thres ativ | old- thres not |e negati | hold- | thr | not |e negati | hold- not | e negati | hold- exp | feed | ve disin {es | exp | feed | ve disin exp | feed | ve disin res | bac | feedba | hibiti | ho | res | bac | feedba | hibiti res | bac | feedba | hibiti sed | k ck on ld | sed | k ck on sed | k ck on

A A

R R

H H A

AC G | AC G | ABI C

VR | ABI3 | ITPRIP EF | VR | ABI3 | SLAMF EF | 3B | CXA V

L4 BP L1 AXL 10 | L1 BP 7 AXL 10 | P DR CD22 CD1D | Rt

AD AT { AD AT | AC AT

AM | ACV F6 | AM | ACV Cort | F6 | VR | DLL F6 22 | Ri TIGIT cb72 [B (22 [Rt 162 B | L1 1 SCN1B | CD5 B

BE AT | BE AT | AD AT

ST | CD2 CD998 | G9 | ST | CD9 GY | AM | FCR | SLAMF | FCRL | G9 3 2 L2 A 13 9L2 CD1D | A 122 [15 7 2 A

AR

AT CEA AT | HG AT

CD6 FCGR | P2 CAM CD24 | P2 | EF | KIR3 MPZL | P2

BIK 18 2B B1 | BIK | 1 4 B1 110 | DL1 1 B1

C1 orf CEA C5 | CA

BT FCRL | 16 | BT | CAM CD30 | orf | BP | PLX AX

LA | CEACAMI 6 2 LA |3 0A 1517 NA4 L

CA C5 | CA C6 | CD BE

BP | CHR ICAM | orf | BP | CHR CD30 | off | 164 | SLA ST 7 NB4 3 15 17 NB4 OLF 89 {1 L2 | MF1 3

Cc cb C6 | CD Cc 164 | CXC MPZL | orf | 164 | CXA P {CD Bi

L2 {L186 1 89 {L2 | DR CD33 | G1 | H5 K

C

Cc Cc

CD | FBX P | CD | DLL CLEC | D2 | CD BT 1D 1L17 NCLN | G1 15 1 12A 2 ON LA

C1

CD Cc C ICE orf 300 | FCR PEX1 | D2 | CD | FCR CLEC | D6 | RK 16

LF | L2 4 44 172 |L2 12B 8 L 2

Cc

D3 | CD C | CH C5

CY c C | P4 C6

CD | LILR D8 | CD | ITG FCGR | D9 | A1 orf

B3 TFR2 14 H5 | A3 2B 6 1 89

C Cc

CD Cc E C 78 | PIEZ D9 | CD | KLR HLA- IR | DC P

A 02 6 ON | Gt DMB {KL IC G1

C CL

E | CL E C

CD | SCN R | CN | LAM [CAM | C4 | DC D2

H5 | 3B KL | 7 P3 3 A iT 44

Cc Cc

SIG CL | CO X D3

CD | LEC C | L17 | LAX CL | DD 00

ON 110 N7 | At | 1 NCLN | 16 | R2 A

CE CL | CY C

AC | SiG E P4 Cc D3

AM | LEC C4 | At | LEP PEXt | YB | DL 00 3 15 A 11 R 4 5B | L4 LF

CL D

EC c H | DS Cc 12 YB | DC | PLX R | CA D3

A TMEM130 5B |C DC1 PRLR 187 I M 3

CL D Ds

EC H EB | CA C 12 | VST R | DC | PRR RMD | A | ML Ds

B M4 ST LT G3 N3 G9 11 8

E co DZ R C

L17 IP | DD | PTP SLIT {BB | DS D7

A1 3 R2 | RM RK4 2 PP 2

Cx EB EX C

AD A {DL | ROB ST3G | TL | EV D7

R Go L4 | Of ALS 3 C2 9A

CY DN FA

P4 E | A FC | M1 C

A1 M | C5 | SCN VSIG | RL | 63 D8 1 DG 1B 4 5 B 4

E Gl

R | DS N C

DC BB | CA | SCN VSTM | M D9

C 2 M 3B 1 1 FAM171A1 6

DS C

EX | CA | SIG FC D9

DC TL [ML | LEC IE | AM aL

T 3 1 11 R3 IR 2

C

EA

IF Cc

FC SIG N | FC A

DD RL | DS | LEC A IRL M

R2 3 PP [8 R2 1 4 1

Cc

EA

C

FC IG | FG A

DL RL | DZI | SLA Ft | FR M

L1 5 P3 | MF1 R 13 3

Gl

N TME IL CL

DL M LEV | M13 IR | FL C

L4 1 C2 | 0 AP | T4 N7

DN FA CL

AJ HL | M1 IT E

C5 A- {63 | VST M | HEPACAM C1

G D IB M4 2B [2 2A

J LE LL

B

IF CL

DS N IT | HE E

CA A P | PH Ct

M R2 | FAM171A1 R{ Lt 2B

Ki

DS AA CL

CA IG | FB 03 {IG E

ML Ft | XL 19 | DC C4 1 R 117 L C4 A

C fb | FC OL

DS IR | AM KT | IGS 17

PP AP IR N1 | F9 At

C

IT | FC LA | IM X

EV M | RL IR | PG CL

C2 2B 13 1 2 16

FA

M1 IT | FC LA C 63 P {RL M [ITG YB

B R1 | 4 P2 | A3 5B

Ki

AA D

03 | FC LD | KIR H 19 | RL H 2D R

FAM171A1 L 6 A iL4 S7

D

Ki N

FC R2 | FG KIR AJ

AM DL | FR LD | 3D C5

R 1 3 LR | L3 G

KI

FC R2 LI | LE Dz

RL DL | FL LR | MD IP 4 3 T4 A6 | 1 3

Ki

FG R2 LE | LiL EB

FR DL | FU LR | RB A 3 4 RIN B1 15 G9

Ki

R3 Li E

FL DL | GG LR | LR! M

T4 1 T7 B2 | Tí D

Ki E

R3 | GP Lb {LR R

FU DL | Rt LR | RC BB

RIN 2 62 B3 {19 2

KL LI | ME EX

GG R | HEPACAM LR | GF TL

T6 C112 B4 | 11 3

L

KL | HE M FB

GG R | PH TK { MR XL

T7 G1 | L4 2 AP 17

LR FC

GP IG R G

R1 KT | DC C2 | MU R2 62 Nt | C4 5 C1 B

LA MU FC

HEPACAM IR | IGS LS | C2 RL 2 1 F9 Tt 12 3

HE LA | IM FC

PH M | PG LY | NC RL

L1 P2 | 2 9 R2 6

M

AP

ITP KA | PA FU

IER LA | RIP PK | RM Ri 3 Xt | L1 2 1 N

M

AP

IG LD | KIA KA | PC G

DC H | AO PK | DH G

C4 A 1319 3 12 16

KIR M | PC G

IGS LD | 2D PZ | DH G

F9 LR | L4 Lt 18 T7

NF | PC Gl

IM LE | KIR A | DH N

PG P {2D M | GC M 2 R | L3 1 3 1

N | PC G

KIA LE KIR Pi | DH P

AO LR | 2D PA | GC R1 319 Bt | L4 1 5 62

P HL

L G A

KIR M | KIR R LPD D 3D TK | 3D M | CD M

L3 2 L4 C111 B iC

LA KIR Pl | PD A

MP LS | 3D LR | GF M 3 Ti | L2 A | RB 3

LE KIR PIE

MD LY | 3D PL | ZO IE 1 9 L3 D3 12 R3

M

AP PL IF

LiL KA | KL X N

RA PK | RC N | PR A 6 2 1 A3 | LR R2

M

AP

LiL KA | LE PR IG

RB PK | MD PV | RG F4 2 3 1 R 13 R

N R

LiL P | LIL R | PT IL

RB PA | RB BP | PR IR 4 1 5 1 D AP

LiL PT IT

RB PL | LRI R | PR M

D3 | T1 YK { H 2B

PL

X {LR PT IT

LR} D {RC sf | PR P

Tt C1119 AE { M R1

Si IT

PL GL P

LR X | ME E PT Ri

RC N | GF Ct IPR PL 19 A3 11 0 0 1

Si

PL GL Ki

LR X E RF AA

RC N | MP C1 | ES 03

A 5 D 19

PT Ki

P Si AA

ME R GL | RN 03

GF C | MR E F12 19 11 AP | AP C518 L

PT Si Ki

P GL | RO R2

MP R | MU E BO DL

Z M | Ct C7 11 1

Si Ki

PV | MU GL | RO R2

MR RI | C2 E BO DL

AP G 12 C9 i 4 3

R Ki

M Si R3

MU D | NC R | RO DL

C1 N3 | R2 PA | S1 2

MU PA SC KL

C2 RM SP | N3 R 2 1 G7 | B Ct

LE LL

1

PC SP KL

NC R | DH TL | SIA R

R2 YK | 12 CLE G1

SiG

NF PC LE

AM St | DH SS | C1 KT 1 AE | 8 R115 N1

St | PC T

PA GL | DH G | SiG LA

RM E | GC OL | LE IR 1 C7 13 N2 | C6 1

St | PC Ti

PC GL | DH M LA

DH E | GC M | SIT M 12 C9 15 2111 P2

T

M

SL E

PC A | PD M | SLi LA

DH M | CD 12 | TR M 8 F6 | 1 3 K3 P3

T

M

PC SL E

DH A {PD M | SLI

GC M | GF 23 {TR LA 3 F7 | RB 0 K4 X1

T

PC M

DH PIE E SP LD

GC SP | ZO M | RY H

G7 {2 59 11 A

TY | ST

PD SP | PL R 13G

CD TL | XN 0 | AL LD 1 C1 | A4 BP 13 LR

PT

PD PR VT | SY LE

GF 8S | CA 1 | NE P

RB Ri | P B 14 R

ST Y

3G | PT M LI

PiL AL | PR Et | SY LR

RA 5 D Lt | T3 A6

T

G | PT Li

PR OL | PR TF LR

LR N2 | H R2 B1

Ti

PR M | PT Lt

RG M | PR LR 3 21 10 TMEM130 B2

T

M

E

PT M | PV Lt

PR 12 | RI LR

D 3 G TMEM132E B3

T

M

E

PT M | RF TM Lt

PR 23 | ES EM LR

H 0 D 52 B4

T

M L

PT E RN TR M

PR M | F12 EM TK 0 59 | 8 L1 2

LR

TR | RO R

PV IB | BO VSI C2

R 2 4 G4 5

TY

RF R

ES 0 | RO LS

D BP | S1 T1

SIG

RN VT { LE

F12 ft | Ct LY 8 B [2 9

M

Y AP

RO M | SIG KA

BO Et | LE PK 1 Lt | C6 2

M

AP

RO KA

BO SIT PK

4 1 3

SL

RO AM M

St F6 PZ sc SL! N

N14 TR CL

B K3 N

SiG NF

LE SP A

C1 RY M 1 1 1

SIG ST N

LE 3G Pi

C1 AL PA 2 3 1

SIG SY PE

LE NE X1

C5 4 4

Pp

G

SIG R

LE SY M

C6 73 C1

SIG Pi

LE TF LR

C8 R2 A

ELLE Ie

PA IT D3

PL

X

SIT D

1 TMEM132E Ct

PL

SL TM X

AM EM N

F1 52 A3

PT

P

SL! TR R

TR EM Cc

K3 L4 AP

SLI

TR TRI PV

K4 B2 R

SP ZD PV

RY HH Ri 1 C8 G

ST R

3G M

AL D

3 N3

R

SY R

NE BP

4 1 eo | | LO

T3 YK

Si

GL

E

C1

TMEM132E 0

Si

GL

TM E

EM C1 52 1

Si

GL

TR E

EM C1

L1 2

Si

GL

VSI E

G4 C5

Si

VS GL

TM E

1 C7

Si

ZD GL

HH E

C8 C8

Si

GL

E

C9

Si

R

PA

SL

A

M

F6

TILLE

G7

SP

TL

C1

LLL |E

R1

ST

3G

AL

LLL

G

CLT rT

N2

Ti

Gl

T

Ti

M

21 7

M

E

M

12 3

T

M

E

M

23 0 7

M

E

M

59

TR

IB

2

TY

R

0

BP

VS

T

M

1

VS

T

M

4

VT

I

B

Y

M

Et

L1 rrr Pre

H

CTT TTT

C8

AB AB AB

HD HD HD

CC8 | 3A2 NDC1 LYS A CC8 | PD7 NDC4 P A CC8 | A 1 A

AF AF AF

AB CXC NIPAL | G3 | AB SLC41A | GPR15 | G3 | ATP | ATP14 | ATP2B | G3

CD1 | R6 NDFIP2 {2 L2 | CD1 | FLT1 [2 7 L2 | 10A | 3A2 4 L2

AG | ATP AG AG

ATP POPD | TR | 13A | KCN POPD | TR | ATP | DHC | CACF | TR 2B2 | FLT1 C2 AP {2 K5 C2 AP 1 2B2 | RY D1 AP

EL EEE EE an ome 2B3 | P2 8 O6 | 2B2 | Q5 8 O6 | 2B3 | FLT1 | GPR82 | 06

BD AP AP | BD AP

KR | RNF1 OL | ATP | NDF SLCSA | OL IKR | NDC | SLCSA | OL

B1 21 VIPRT | D1 | 2B3 | P2 4 D1 | B1 1 4 D1

CA AT | BD AT | CA AT

CF SCA G9 | KR | SCA G9 | CN | NDF | SPAG | P2

D1 RB1 A B1 RB1 XKR6 | A A1D | P2 4 B1

CA AT { CA AT | CA AT

CN | SLC Pt | CF SLC4 Pt | CN | PXM P8

A1D | 9A1 OA | D1 9A1 0A | A1G | P2 SSPN | At

CA AT | CA AT | CA AT

CN | SLC2 P2 | CN | SLC3 P2 | CN | SLC2 P8

A1G | 2A1 B1 | A1D | 5A2 Bt | ATH | 2A1 B2

CA AT | CA AT | CA

CN | SLC3 P2 | CN | SLC3 P2 | CN | SLC3 CD

AH | 7A2 B4 | A1G | 7A2 B4 | G5 9A14 81

CA AT | CA AT | CAT

CN | SLC3 P8 | CN | SLC3 P8 | SPE CK

G5 9A14 Al | AH | 9A14 At | RB | TMEM104 LF

CAT AT | CA AT { CC CL

SPE | SLC4 P8 | CN P8 | KB DN

RB 1A2 B2 | G5 | TMEM251 B2 | R TMEM251 D1 cy

CC B5

KB CD CD | CLC | TPC 61

R TMEM104 81 | CATSPERB 81 | N1 N2 A3

DP

CC Y1

CLC CK | KB CK | CLC gL

N1 TMEM251 LF IR LF | N7 XKR6 4

CL CL GA

CLC DN | CLC DN | CLD BR

N7 Dt | Nt D1 | N18 Pp

CY

B5 CX

CLD 61 | CLC CR | CLR GJ

N18 A3 | N7 6 N2 C1

CY

DH B5 GP

CLR CR | CLD 61 | CNI R1

N2 7 N18 A3 | H2 57

DP

Y1 DH GP

CN! 9L | CLR CR | CX R1

H2 4 N2 7 CR2 83

DP

Y1 KC

CX GJ | CNI gL | CX NQ

CR2 C1 | H2 4 CR6 5

Ki

AA

GP 03

DR Rt | CX GJ | DR 19

D2 57 | CR2 Ct | D2 L

Ki

DI

GP GP NS

ENT Rt | DR R1 | ENT 22

PD7 83 | D2 83 | PD7 0

Ki

AA

ER GP | ER 03 | ER LR

VV- R8 | W- 19 | VV- RC 2 2 2 L 2 8A

Ki KI

AA Di 03 NS LR

FA! 19 | FAI 22 | FAI RC

M2 L M2 0 M2 8B

Ki

Di

NS LR

FCA 22 | FCA RC | FCA LY

MR 0 MR 8A | MR 9

LR LR MF

FZD RC | FZD RC | FZD SD 8 8A 18 8B [8 11

GA LR | GA GA MF

BR RC | BR LY | BR SD

B2 8B | B2 g B2 8

GA MF | GH MF | GH NI

BR SD | RH SD | RH PA

P 11 IR 11 IR L2

GH ME MF NI

RH SD | GJB SD | GJB PA

R 8 4 8 4 L3

Ni | GP NI | GP

GJB PA | R14 PA | R14 NN 4 L3 19 L3 19 T

GP GP GP

R14 NN | R16 NN | R16 NP 9 T 2 T 2 C1

GP PE

R16 NP | GP NP | GRI X1 2 C1 | R82 C1 | Dt 3

PE PE PH

GRI X1 | GRI X1 | ORI TF

D1 3 D1 3 D2 1

PH PH Pi

GRI TF | OR! TF | GR K3

D2 1 D2 1 M7 CB

Pi PL | HC PO

GR K3 | GR K3 | RT PD

M7 CB | M7 CB | R1 C2

HC RE | HC PX RE

RT EP | RT MP EP

R1 5 R1 2 HEPACAM2 5

RE | HS

RE EP | D17 RE

HEPACAM2 R1 | HEPACAM2 5 B3 R1

HS SG | HS RN

D17 MS | D17 RE | KC F4

B3 1 B3 R1 | NA2 21

SG RN sc

KC SM | KC Ft | KC AR

NA2 3 NA2 21 | NB2 B1

SL

C1 SG | KC SG

KC OA IKC MS | NK] MS

NB2 7 NB2 1 7 1

SL

KC Ct | KC SG SG

NK1 1A | NK1 SM | KC SM 7 1 7 3 NK5 3

SL SL SL

C1 Ct C1

KC 2A | KC OA | KC 0A

NKS 9 NS3 7 NS3 7

SL SL SL

KC C2 | KIR Ct | KIR C1

NQ At | 2DL 1A | 2DL 1A 1 4 1 4 1

SL SL SL

C3 Ct C1

KC 3A | LIF 2A | LIF 2A

NS3 1 R 9 R 9

SL SL SL

KIR C3 C2 C2 2DL 5A | MC Al | MC A1 4 2 HR1 1 HR1 1

SL SL SL

C3 | MF C3 | MF C3

LIF 5B | SD6 3A | SDs 3A

R 1 L 1 L 1

SL SL SL

C3 C3 C3

MC 5C | MS 5B | MS 5A

HR1 2 4A3 1 4A3 2

SL SL SL

MF C3 C3 C3

SD6 8A | NAL 5C | NAL 58

L 2 CN 2 CN 1

SL SL SL

C3 C3 C3

MS 8A | NAT 8A | NAT 5C 4A3 6 14 2 14 2

SL SL SL

C3 C3 | NK C3

NAL 8A | NIP 8A | AIN 7A

CN 7 AL2 6 1 2

SL SL SL

C3 | NK C3 C3

NAT 9A | AIN 8A | NPI 8A 14 13 {1 7 PA2 2

SL SL

NK SL C3 C3

AIN C5 | NPI SA | NPI BA 1 A6 | PA2 13 | PA3 6

SL

SL C3

NPI SP | NPI C5 | NPI 8A

PA2 G7 | PA3 AG | PAS 7

SL

SP OR C3

NPI NS | NPI SP | 13C GA

PA3 1 PAS G7 13 13

SL

SP | OR SP | OR C4

NP} TL | 13C NS | 13C 1A

PAS C113 1 4 2

OR OR SP | OR SL 13C SU | 13C TL | 134 C5 3 N2 1 4 Ct 11 A6

OR SY | OR 13C PL | 134 SU | OR SP 4 1 1 N2 | 2H1 G7

T

OR M SY SP

134 M2 | OR PL | OR NS 1 2 2H1 1 2K2 1

Ti Ti

M M OR SP

OR M2 | OR M2 | 2W TL 2H1 3 2K2 2 1 C1

T

TM | OR M OR

OR CO | 2W M2 | 5D1 SU 2K2 3 1 3 6 N2

TM

OR EM | OR TM SY 2W 12 | 5D1 CO | PA PL 1 3 6 3 NX2 1 ™ ™ Ti

OR EM EM M

5D1 12 | PA 12 | QR M2 6 8 NX2 3 FPR 2

TM TM Ti

EM EM | RH M

PA 13 | QR 12 | BDL M2

NX2 4 FPR 8 1 3

TM TM

EM | RH EM | SLC ™

QR 16 | BDL 13 | 10A CO

FPR 8 1 4 4 3 ™ ™ ™

RH EM | SLC EM | SLC EM

BDL 17 | 10A 16 | 19A 12 1 9B 1 4 8 1 3

TM TM TM

SLC EM | SLC EM | SLC EM 10A 20 | 19A 17 | 19A 12 4 9 3 9B 13 8 ™ ™ ™

SLC EM | SLC EM | SLC EM 19A 22 | 22A 20 | 22A 13 3 2 1 9 3 4

TM TM TM

SLC EM | SLC EM | SLC EM 22A 23 | 22A 22 | 24A 16 3 0 3 2 3 8

TM TM TM

SLC EM | SLC EM | SLC EM 24A 25 | 24A 23 | 24A 17 3 9 3 0 5 9B

SLC SLC SLC

24A TM | 24A TM | 26A TM

EM 15 EM 15 EM

LE TE

A 9 9

TM TM

SLC Yi | SLC EM | SLC EM 26A PF | 26A 39 | 2A1 22 3 5 A 0 2

ZD TM

SLC HH | SLC YI EM 2A1 Ct | 2A1 PF | SLC 23 0 3 0 3 2A8 0

ZD TM

ZD HH | SLC EM

SLC HH | SLC C1 | 35D 25 2A8 C5 | 2A8 3 3 9 ™

SLC SLC ZD | SLC EM 35D 35D HH | 35F 39 3 3 C5 13 A

SLC SLC SLC Yi 35F 35F 44A PF 3 3 3 3 zD

SLC SLC SLC HH

44A 44A 45A C1 3 3 2 3

SLC SLC SLC ZD

45A 45A 45A HH 2 2 4 C5

SLC SLC SLC

45A 45A 46A 4 4 2

SLC SLC

46A 48A SLC 2 2 GA1

SLC

SLC SLC GA1 6A1 6A1 1

SLC SLC

6A1 6A1 SLC 1 1 BAS

EE mT

GA6 GA6 7A8 a | de ne |] 8A1 8A1 8A1 wel | oem | ee 8A2 8A2 8A2 ee Le LL 9A2 GA2 9A2 wT Te LL 9A4 0 0

SL LEL IE [ 0 G4 R2

ELLE LE

G4 N R3

ET eee

N R2 TMEM151B

EL LIE [aen [

R2 R3 TMEM169

SL ee ee

R3 TMEM104 TMEM253

TM

EM

TMEM151B TMEM151B 44 ee tee

TMEM169 TMEM169 HR ee

TMEM253 TMEM253 C3 ™ TM

EM EM TRP

44 44 C6

EE ET

N2 N2 C7

TSP

TR TR AN1

HR HR 6

ELLE LE LL

C3 C3 AN7

ELLE LE LD

C6 C6 R1

EL DEE

C7 C7 R2

TSP TSP

AN1 AN1 WL 6 6 5

EDE En

AN7 AN7 R3

ETE

R2 R1 R7 zD

WL VIP HH

S R2 C8 aL LDA LIL LD

R3 S

Brrr

R6 R3

EL LEL LLL LL

R7 R7

ZD zD

HH HH

C8 C8 onl

AB AB

AB | CAC H | AB | CAC H | AB AB

CC | NA1 | SLC22 | ATP1 | D1 | CC | NA | TMEM2 | ABCD | D1 { CC | CNI | SLC38 | RHBD | C 8 G Al 3A2 GA | 8 G 51 1 GA | 8 H2 A7 L1 D1

AB

AB AF | AT | CAT AF | AT H

CD | LRR SGM | G3 | Pt | SPE | ZDHHC | AGTR | G3 | P2 | KCN SLC7 | D1 1 C8B St L2 | 0A | RB 13 AP L2 | B2 | K5 A8 BA

A

AT G | AT A | AT | SLC AF

P2 | NDF SLC3 {| TR | P2 | CLD ATP8 IN P2 | 10A VIPR | G3

B2 | IP2 5A2 AP | B2 | N18 At O6 {B3 | 7 1 L2

A

AT | SLC A | AT AP | BD G

P2 | 39A N P2 | FLT DHC OL | KR | SSP TR

B3 | 14 O6 | B3 {1 R7 D1 | B1 N AP

CA

BD | SLC AP | BD AT | CN A

KR | 41A OL | KR | RNF G9 | At N

Bt | 2 D1 | Bi 121 NDCt | A ID 08

AT | CA

CA AT | CA | SLC Pt | CN AP

CF G9 | CF | 198A NDFE | 3A | At OL

D1 | TMEM169 A D1 13 P2 2 G D1

CA CA CA

CN AT | CN | SLC AT | CN AT

At Pt | A1 | 22A POPD | P2 | At G9

D TMEM251 0A |D 1 C2 Bi IH A

CA CA

CN AT | CN | SLC AT | CA AT

At P2 | At | 39A PXMP | P2 | CN P1

H Bi | H 13 2 B4 | G5 0A

AT

CA AT | CA | SLC AT P1

CN P2 | CN | 39A SGS P8 3A

G5 B4 | G5 | 14 M3 B2 | CATSPERB 2

AT | CC | SLC C {CC AT

P8 | KB | 41A SLC4 | D8 | KB P2

CATSPERB Al | R 2 0A7 1 R B1

CC AT | CL C {CL AT

KB P8 | CN SLC4 | KL | CN P2

R B2 | 1 GA2 F 1 B4

CL

CL Cc CL D ICL AT

CN D8 | CN SLC5 | N DN P8 1 1 7 A6 Dt 1 18 At onl

Cc

YB

CL CG | CL 5 | CL AT

DN KL | RN TME 1A | RN Pg 18 F 2 M104 | 3 2 B2

D C

CL CL PY | CX A

RN C | CN! TPCN | 19 | CR CF 2 N7 | H2 2 L4 16 D1

CL E

D | CX NT C

CNI N | CR VIPR |P | DR D8

H2 D112 1 D7 | D2 1 c G

CX X | CX AB | ER Cc

CR C | CR R | W- KL 6 R2 | 6 WLS P 12 F

Cc

YB

56 CL

DR 1A | BR GJ | FA! C

D2 3 D2 C1 | M2 N7

D G CL

EN H ER P | FC D

TP C | W- R1 | AM N

D7 R7 | 2 57 IR D1

D G C

ER PY P X

W- 19 | FAI R1 | FZ C 2 L4 | M2 83 | D8 R2

C

G G YB

AB | FC P | GA 56

FAL R | AM R8 | BR 1A

M2 Pp R 2 B2 3

Ki

AA D

FC 03 | GA H

AM GJ | FZ 19 | BR C

R C1 | D8 L Pp R7

KI

G DI D

P | GA N | GH PY

FL R1 | BR $2 { RH 19

T1 57 | B2 20 IR L4

G LR E

P | GH R NT

FZ R1 | RH C8 | GJ Pp

D8 83 | R A | B4 D7 onl

G LR

GA Pp R | GP

BR R8 | GJ C8 | Ri FL

B2 2 B4 B 149 T1

Ki

AA

GH 03 | GP

RH 19 | Rt LY | GR GJ

R L 49 9 [D4 C1

Ki

DI M G

N GP FS P

GJ S2 | Rt D1 | GR R1

B4 20 | 62 1 [D2 57

Ki G

GP R2 M P

R1 DL | GR FS {| GR R1 49 4 {D1 D8 | M7 62

LR G

GP R Ni | HC P

R1 C8 | GR PA | RT R1 62 A 1D2 L2 | Ri 83

G

NI Pp

GR LY | GR PA | HEPACAM R8 (D1 9 M7 13 12 2

Ki

M HS AA

FS | HC D1 03

GR D1 | RT N {7B 19 {D2 1 R1 NT {3 L

Ki

Di

M N KC N

GR FS | HEPACAM P [NA 82

M7 D8 | 2 C112 20

HS LR

HC NI | D1 PE | KC R

RT PA | 7B Xt | NB C8

R1 L2 | 3 3 2 A

LR

NI | KC P KC R

HEPACAM PA | NA HT | NK C8 2 L3 | 2 F4 117 B

HS Pl

D1 KC K3 | KC 7B N NB C INQ LY 3 NT | 2 B 15 9 onl

M

KC N KC R | KC FS

NA P NK EE | NS D1 2 ct | 17 P5 13 1

KC PE | KC R | KIR M

NB Xt | NK E | 2D FS 2 3 5 R1 114 D8

S

Cc

KC P KC A M

NK HT | NQ R {LF S4 17 F1 | 5 B1 IR A3

Pi S

KC K3 | KC G | MC N

NK C | NS M | HR AT

B 3 St 11 14

SL

KC R | KIR Ct {| MF N

NQ EE | 2D 1A | SD D 5 PS | L4 1 6L C1

SL

KC R Ct | NA Ni

NS E LIF 2A {LC PA 3 R1 | R 9 N L2

R SL

NF | MC C1 IND Ni

LIF 12 | HR 9A | FIP PA

R 1 1 1 2 L3

S

G SL

MC S MF C2 | NK

HR M | SD Atl | AIN N 1 3 6L 1 1 NT

SL SL

MF Ct | MS C3 | NPI N

SD 0A | 4A 3A | PA Pp 6L 7 3 1 3 C1

SL SL N

MS Ct | NA C3 { OR Pi 4A 1A | LC 5A | 13 PA 3 1 N 2 C3 2

SL SL N

NA C1 C3 {| OR Pi

LC 2A | NA 5B | 13 PA

N 9 T14 1 C4 5

SL SL

C1 | NK C3 | OR PA

NA 9A | AIN 5C | 134 N

T14 3 1 2 1 x2 onl

SL SL

C2 | NPI C3 IOR PE

ND At | PA 7A | 2H X1

Ct 1 2 2 1 3

SL SL

NK C3 | NP! C3 | OR P

AÎN 3A | PA 8A | 2K HT 1 1 3 2 2 F1

SL SL Pi

NP} C3 | NPI C3 LOR K3

PA 58 | PA 8A | 2W C 2 1 5 6 1 B

P

SL SL 0

NP} C3 | OR C3 | OR Pp

PA 5C | 13 8A | 5D D 3 2 C3 7 16 C2

SL SL

NPI C3 | OR SL | C1 PX

PA TA | 13 C8 | DA M 2 C4 A1 1 4 P2

SL SL Q

OR C3 | OR SL | C2 RF 13 8A | 13J Cg | 2A Pp

C3 2 1 Ad 13 R

SL SL

OR C3 | OR C2 R 13 8A | 2H SP | 4A EE

C4 6 1 G7 13 P5

SL SL

OR C3 | OR SP | C2 R 13J 8A | 2K N | 4A E 1 7 2 S115 R1

SL SL R

OR C3 | OR SP | C2 NF 2H 9A | 2W TL | 6A 12 1 13 | 1 C115 1

S

SL C

OR SL | OR S {C2 A 2K C5 | 5D U | At R 2 A6 | 16 N2 10 B1

SL S

TI

OR QR M {SL 5 5D SP | FP M | C3 G 16 G7 | R 22 | 5F3 S onl

J 0 TE 3

TH | SL SL

PA SP | RH M | C4 C1

NX N BD M | 4A 1A 2 St | L1 23 13 1

SL T SL SL

PO SP | Ct M | C4 C1

PD TL | 0A C {5A 2A

C2 Ct ]4 03 {2 9

T

M

SL E SL SL

PX S C2 M | C4 C1

MP U | 2A 12 | 6A 9A 2 N2 | 3 3 2 1

T

M

SL E SL

QR SY | C2 M | SL C1

FP PL | 4A 12 | C6 9A

R 1 3 8 Al 3

T

M

TH | SL E SL SL

RH M | C2 M {C6 C2

BD M | 4A 13 | A1 2A

L1 22 | 5 4 1 1

T

M

Ti | SL E SL

SC M | C2 M | SL C2

AR M | BA 16 | C8 At

B1 2315 8 A2 1

T

M

SL T SL E

C1 M | C2 M SL SL 0A C | At 17 1 C9 C2 4 0310 9B | A2 A8

T T

M M

SL E E SL

C1 M | SL M C3 9A 12 | C2 20 | SM 3A 1 3 AS 9 0 1

SL T SL T SL

C2 M | C3 M | TA C3 2A E 5D E | CR 5A 3 M | 3 M 12 2 onl

LILLE ELL

8 2

T T

M M

SL E E SL

C2 M | SL M | TA C3 4A 13 | C3 23 {| CR 5B 3 4 5F3 0 3 1

T T

M M

SL E SL E SL

C2 M | C4 M C3 4A 16 | 4A 25 5C 8 3 9 TMEM151B 2

T T

M M

SL E SL E SL

C2 M | C4 M C3 6A 17 | BA 39 7A 5 98 | 2 A | TMEM253 2

T

M

SL E SL SL

C2 M | C4 Yi | TM C3

At 20 | BA PF | EM 8A 0 9 4 3 44 2

T

M

E ZD SL

SL M | SL H C3

C2 22 | CB H ITR 8A

A8 2 Al C5 | HR 6

T

M

SL E SL SL

C3 M | C6 TR C3 5D 23 | At PC 9A 3 0 1 3 13

T

M

E SL

SL M | SL TR C3

C3 25 | C6 PC 9A 5F3 9 A6 6 14

T

M

SL E SL

C4 M | SL TR C4 4A 39 | C7 PC 1A 3 A | A8 7 2 onl

SL TS SL

C4 vi | SL PA C4 5A P C8 N1 5A 2 R2 | A2 6 4

SL

C4 Yi | SL TS SL 5A PF | C9 PA C5 4 3 A2 N7 A6 zD

SL H

C4 H SL 6A Ct | SM XK C6 2 3 0 R6 A6 zD

SL H SP SL

C6 H | AG XK C8

Al C5 | 4 R7 At

SL

C6 SL

At SS C9 1 PN A4

SL TA SP

C6 CR A

A6 2 G4

SL TA

C7 CR SP

A8 3 G7

SL SP

C8 N

Al TMEM151B S4

SL SP

C8 TL

A2 TMEM169 C1

SL 5

C9 U

A2 TMEM253 N2

TM SY

SM EM PL

0 44 1

Ti

SP M

AG TR M

4 HR 22

TI

TR M

S$ PC M

PN 3 23

TA TR

CR PC T

2 6 M onl

LLL LLL

03

T

M

E

TA TR M

CR PC 10 3 7 4 7

M

TS E

PA M

N1 12

TMEM104 6 3 7

M

E

TS M

PA 12

TMEM151B N7 8 7

M

E

M

VIP 13

TMEM253 R2 4 7

M

E

™ M

EM XK 16 44 R3 8 7

M

E

TP M

CN XK 16 2 R6 9 7

M

E

M

TR XK 17

HR R7 9B

T

M

E

TR ZD M

PC HH 20 3 C8 9 onl

M

E

TR M

PC 22 6 2 7

M

E

TR M

PC 23 7 0 7

M

TS E

PA M

N1 25 6 1

T

M

E

TS M

PA 25

N7 9 7

M

E

M

VIP 39

R1 A

TP

WL Cc

N2

VI

XK P

R3 R2

LLL

R6 LS

LLT

R7 R3 zD YI

HH PF

C8 3 zD

H

C1 3

J

H onl

TL re rl

C5

ZD

H

Dea ware

Fr [oerier | wee

I rsa. rr Tuer eae rb zondes | meow

LL sco rr bb [stom

LL | tes

Lg

Ke EE

MATERIALS AND METHODS

Identification of putative modulatory receptors in the human genome

[135] To identify putative modulatory receptors in the human genome, amino acid sequences for 96,457 protein-coding, as annotated by Ensembl, transcripts were retrieved from Ensembl (release 105, December 2021)[13] using the biomaRt package[43] in R. Amino acid sequences were then filtered based on the presence of an ITIM or ITSM sequence, (VIL|I|S|T)xYxx(l|L|V). Seven out of 40,063 ITIM- containing proteins were larger than 10,000 amino acids, and were excluded because they are not feasible for membrane topology prediction using the TOPCONS method[14]. Topology results for the remaining 40,058 proteins were then retrieved, and proteins were further filtered based on the presence of a predicted transmembrane domain (12,576 out of 40,056 proteins). For the remaining proteins, we determined whether the identified ITIM or ITSM sequence corresponded to an intracellular section of the protein, which resulted in 4,613 protein sequences remaining, corresponding to 1,562 individual genes (Figure 1). A further 61 protein sequences were excluded as they could not be matched to a HUGO Gene Nomenclature Committee (HGNC) gene symbol[44].

Determining the likelihood of intracellular protein domain containing an ITIM by chance

[136] To determine the odds of finding an intracellular ITIM or ITSM sequence in a specific protein, all intracellular domains of the proteins were retrieved based on the

TOPCONS predictions. For each protein, the amino acids in the intracellular domain were then shuffled randomly, using the stringi package[45], and the number of identified ITIM or ITSM sequences in the permutated sequences was compared to the actual number of intracellular ITIM or ITSM sequences in the original protein. Each protein was permutated 10,000 times, and the number of occurrences of a permutated protein containing more or equal ITIM/ITSMs to the original sequence was counted and used as measure for the likelihood of finding an ITIM or ITSM by chance. A threshold was defined based on likelihood scores for the proteins corresponding to known modulatory receptors, and was set at 0.25+¢, with £ being a random number determined error between 0 and 0.01.

Determining AlphaFold model confidence scores for individual ITIMs

[137] Three-dimensional structure of protein sequences that passed the likelihood threshold were next determined using AlphaFold (v2.2.0) under default parameters with amber minimization (run_relax = True) using the pdb70, uniref980, mgnify (mgy_clusters_2018_12), uniclust30 (uniclust30_2018_08) and bfd (bfd_metaclust_clu_complete_id30_c90_final_seq) databases on a high-performance cluster[17,46]. AlphaFold was not able to determine the structure for 46 of these proteins, of which 6 were too long and 40 returned a run time error involving HHblits and the hh-suite. The three-dimensional prediction of 37 of these proteins was instead determined using ColabFold[47] (v1.5.2) using MMseqs2 and HHsearch under default parameters without using template information (template_mode = none) and using mmseq2_uniref_env as MSA mode. The top ranked prediction files were retrieved for each protein, and loaded into R using the bio3d package[48]. Prediction confidence scores (pLDDT) were retrieved, and the average pLDDT for all six amino acids encompassing the ITIM or ITSM sequence was used as the AlphaFold confidence score for that ITIM or ITSM. Proteins that had no ITIM or ITSM sequences with an average confidence score below 80 were used in further analysis.

Classification of receptor functional categories

[138] Based on the in vitro RNA sequencing dataset of immune cells in the resting state and after activation, functional categories were defined based on expression patterns as outlined previously[7]. Data was retrieved from Calderon et al. (2019) and

West et al. (2016)[19,20] Gene symbols were matched to Ensembl Gene IDs using biomaRt and Ensembl (release 108, October 2022)[13]. For the neutrophil data[19],

TPM values were retrieved and log2 scaled. For other immune cells, count matrix was normalized using the DESeq2 package[49]. Culture conditions for all immune cells were simplified to major immune cell subsets, and to resting and stimulated (Table 2).

Average expression for each modulatory receptor gene was determined for each sample. An modulatory receptor gene was considered expressed when it was above the median expression of all genes within the sample. Genes that were not expressed in the resting state, but were expressed in the stimulated state were considered negative feedback receptors. Genes expressed in the resting state were considered threshold, threshold-disinhibition, or threshold-negative feedback receptors if the log2 fold change in expression was between -0.5 and 0.5, below -0.5, or above 0.5, respectively. Genes expressed in the resting state, but not after activation were also considered threshold-disinhibition receptors.

Collection and normalization of immune cell RNAseg data

[139] For the analysis of tumour infiltrating T cells, a normalized expression matrix was retrieved from Zheng et al. (2021)[21,50]. The average Z score of all cells in a T cell subset was determined, weighted by the relative contribution of different subclusters identified in the study. Modulatory receptor genes were considered expressed in a T cell subset if the average Z score was above 0.

[140] Having now fully described this invention, it will be appreciated by those skilled in the art that the same can be performed within a wide range of equivalent parameters, concentrations, and conditions without departing from the spirit and scope of the invention and without undue experimentation.

[141] Reference to known method steps, conventional methods steps, known methods or conventional methods is not in any way an admission that any aspect, description, or embodiment of the present invention is disclosed, taught, or suggested in the relevant art.

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Claims

CONCLUSIONS

1. A method of screening for compounds that modulate the expression and/or activity of an ITIM and/or ITSM containing modulating immune receptor expressed in an immune cell, preferably wherein the ITIM and/or ITSM containing modulating immune receptor is i. a negative feedback modulating immune receptor, preferably expressed in an activated immune cell;

ii. a threshold-modulating immune receptor, preferably expressed in a resting immune cell;

iii. a threshold-disinhibitory immune receptor, preferably expressed in a resting immune cell and the expression of which is reduced upon activation of the immune cell; or iv. a threshold-negative feedback modulating immune receptor, preferably expressed in a resting immune cell and the expression of which is increased upon activation of the immune cell, comprising: (a) contacting the ITIM and/or ITSM containing modulating immune receptor or a biologically active portion thereof with a test compound; and (b) determining the effect of the test compound on the expression and/or activity of the ITIM and/or ITSM containing modulating immune receptor or a biologically active portion thereof.

2. A method for identifying a compound that modulates the expression and/or activity of an ITIM and/or ITSM containing modulatory immune receptor expressed in an immune cell, preferably wherein the ITIM and/or ITSM containing modulatory immune receptor is i. a negative feedback modulatory immune receptor, preferably expressed in an activated immune cell;

iii. a threshold-disinhibitory immune receptor, preferably expressed in a resting immune cell and the expression of which is reduced upon activation of the immune cell; or iv. a threshold-negative feedback modulating immune receptor, preferably expressed in a resting immune cell and the expression of which is increased upon activation of the immune cell, comprising: (a) contacting the ITIM and/or ITSM containing modulating immune receptor or a biologically active portion thereof with a test compound; and (b) determining the effect of the test compound on the expression and/or activity of the ITIM and/or ITSM containing modulating immune receptor or a biologically active portion thereof, so as to identify a compound that modulates the activity of the polypeptide or a biologically active portion thereof.

3. A method of testing a drug for modulating the expression and/or activity of an ITIM and/or ITSM containing modulatory immune receptor expressed in an immune cell, preferably wherein the ITIM and/or ITSM containing modulatory immune receptor isp i. a negative feedback modulatory immune receptor, preferably expressed in an activated immune cell;

iii. a threshold-disinhibitory immune receptor, preferably expressed in a resting immune cell and the expression of which is reduced upon activation of the immune cell; or iv. a threshold-negative feedback modulating immune receptor, preferably expressed in a resting immune cell and the expression of which is increased upon activation of the immune cell, comprising: (a) contacting the ITIM and/or ITSM modulating immune receptor or biologically active portion thereof with the medicinal product; and

(b) determining the effect of the drug on the expression and/or activity of the ITIM and/or ITSM modulating immune receptor or biologically active portion thereof.

4. The method according to any one of claims 1 to 3, wherein the ITIM and/or ITSM containing modulating immune receptor expressed in an immune cell is encoded by a gene listed in Table 1.

5. A method of screening for compounds that modulate the expression and/or activity of a polypeptide encoded by a gene listed in Table 1 or a biologically active portion thereof, comprising: (a) contacting the polypeptide or biologically active portion thereof with a test compound; and (b) determining the effect of the test compound on the expression and/or activity of the polypeptide or biologically active portion thereof.

6. A method for identifying a compound that modulates the expression and/or activity of a polypeptide encoded by a gene listed in Table 1 or a biologically active portion thereof, comprising: (a) contacting the polypeptide or biologically active portion thereof with a test compound; and (b) determining the effect of the test compound on the expression and/or activity of the polypeptide or biologically active portion thereof to identify a compound that modulates the activity of the polypeptide or biologically active portion thereof.

7. A method for testing a drug for modulating the expression and/or activity of a polypeptide encoded by a gene listed in Table 1 or a biologically active portion thereof, comprising: (a) contacting the polypeptide or biologically active portion thereof with the drug; and (b) determining the effect of the drug on the expression and/or activity of the polypeptide or biologically active portion thereof.

8. The method of any one of claims 1 to 7, wherein the ITIM and/or ITSM containing modulating immune receptor or polypeptide has the ability to modulate an immunomodulatory function, modulate cytokine expression, modulate immune cell activation, modulate migration ability, modulate killing ability and/or modulate cell proliferation.

9. The method according to any one of claims 1 to 8, wherein the ITIM and/or ITSM containing modulating immune receptor or the polypeptide is expressed in a cell, preferably an immune cell.

10. The method according to any one of claims 1 to 9, wherein the ITIM and/or ITSM containing modulating immune receptor or the polypeptide is expressed in a cell, preferably an immune cell, and wherein the contacting with the test compound or the drug is carried out in the presence of a target of the cell, preferably an immune cell.

1. The method according to any one of claims 1 to 10, wherein the immune cell is a neutrophil, a monocyte, a myeloid cell, a lymphoid cell, a B cell, a T cell, an NK cell, a helper T cell, a follicular helper T cell, an effector memory T cell, a regulatory T cell, an 'unconventional' T cell, a macrophage.

12. The method of any one of claims 1 to 11, wherein the T cell is a CD4+ T cell, a CD8+ T cell, a tumor infiltrating T cell, an exhausted CD8+ T cell, a CD4+ memory T cell, or an 'unconventional' T cell.

13. The method according to any one of claims 1 to 12, wherein determining the effect of the test compound or the drug on the activity of the ITIM and/or ITSM containing modulating immune receptor or the polypeptide comprises determining an effect of the test compound or the drug on the immune response of the cell, preferably the immune cell expressing the ITIM and/or ITSM containing modulating immune receptor or the polypeptide.

14. The method of claim 13, wherein the effect of the test compound or the drug on the immune response of the cell comprises modulating immunomodulatory function, modulating cytokine expression, modulating immune cell activation, modulating migration ability, modulating killing ability and/or modulating cell proliferation.

15. The method of any one of claims 1 to 14, the method comprising contacting the test compound or drug with a cell expressing the ITIM and/or ITSM containing modulating immune receptor or polypeptide and contacting the test compound or drug with an identical cell but not expressing the ITIM and/or ITSM containing modulating immune receptor or polypeptide or with an identical cell having reduced expression of the ITIM and/or ITSM containing modulating immune receptor or polypeptide, and comparing the effect of the test compound or drug on the expression and/or activity of the ITIM and/or ITSM containing modulating immune receptor or polypeptide.

16. The method of any of claims 1 to 15, wherein the cell is an immune cell and wherein the immune cell is activated prior to, during and/or after contact of the test compound or drug with the cell.

17. The method of any one of claims 1 to 16, wherein another compound is contacted with the ITIM and/or ITSM containing modulatory immune receptor or the polypeptide prior to, during and/or after contacting the test compound or the drug with the ITIM and/or ITSM containing modulatory immune receptor or the polypeptide, preferably wherein the other compound is a known modulatory immune receptor modulator.

18. The method of any of claims 1 to 17, wherein the cell is a cell obtained from a subject, preferably wherein the cell is obtained from a subject suffering from cancer or suffering from an immune disease or suffering from an inflammation.

19. The method of any one of claims 1 to 18, wherein the contacting step takes place in vivo, ex vivo or in vitro.

20. An immune cell in which a gene encoding the ITIM and/or ITSM containing modulating immune receptor or a gene encoding the polypeptide encoded by a gene listed in Table 1 has been knocked out.

21. An expression vector containing a nucleotide sequence encoding the ITIM and/or ITSM containing modulating immune receptor or the polypeptide encoded by a gene listed in Table 1, operably linked to a promoter.

22. A host cell containing the vector according to claim 21, or recombinantly expressing the modulating immune receptor containing ITIM and/or ITSM, or the polypeptide encoded by a gene included in Table 1.

23. A method for determining the copy number, expression level or activity level of the ITIM and/or ITSM containing modulating immune receptor or the polypeptide encoded by a gene listed in Table 1 in a cell, comprising: (a) providing the cell; and (b) determining the copy number, expression level or activity level of the ITIM and/or ITSM containing modulating immune receptor or the polypeptide encoded by a gene listed in Table 1 in the cell, preferably wherein the cell is an immune cell.

24. The method of claim 23, wherein, prior to determining the copy number, expression level or activity level of the ITSM and/or the ITSM-containing modulating immune receptor or the polypeptide encoded by a gene listed in Table ], the cell is contacted with a test compound or drug as defined in any one of claims 1 to 7.

25. The method according to any one of claims 23 to 24, wherein the copy number, expression level or activity level of the ITIM and/or ITSM containing modulating immune receptor or the polypeptide encoded by a gene listed in Table 1 is determined, preferably independently, in more than one cell type, preferably wherein the more than one cell type is obtained from a subject, preferably a subject suffering from cancer or suffering from an immune disease or suffering from an inflammation.

26. A method for identifying a binding partner for an ITIM and/or ITSM containing modulating immune receptor or a polypeptide encoded by a gene listed in Table 1, or biologically active portion thereof, comprising: (a) contacting the ITIM and/or ITSM containing modulating immune receptor or the polypeptide, or biologically active portion thereof, or a cell expressing the ITIM and/or ITSM containing modulating immune receptor or the polypeptide or biologically active portion thereof, with a test compound; and (b) determining whether the ITIM and/or ITSM containing modulating immune receptor or the polypeptide or biologically active portion thereof, binds to the test compound.