Biomarkers of IL7R modulator activity

Abstract

The present invention relates to a method of assessing or predicting a treatment response of a patient to treatment with an IL7R modulator, such as an IL7R antagonist or agonist, and more particularly to the identification of biomarkers for assessing or predicting whether an IL7R modulator can effectively treat a patient. The invention also relates to methods of screening for compounds effective in treating a patient.

Description

Technical Field

[0001] The present invention relates to a method for evaluating or predicting a patient's therapeutic response to treatment with an IL7R modulator (e.g., an IL7R antagonist or agonist), and more particularly to identifying biomarkers for evaluating or predicting whether an IL7R modulator is effective in treating a patient. The present invention also relates to a method for screening a compound that is effective in treating a patient. Background Art

[0002] IL-7 is the most important cytokine for the homeostasis, proliferation, differentiation and survival of naive and memory T cells. IL-7 signals through the IL-7 receptor (IL-7R), which consists of an α chain (IL-7Rα) (also known as CD127) and a cytokine receptor common γ chain (IL-2Rγ, CD132). IL-7R activation induces proliferation and anti-apoptotic signals mainly by activating the JAK-STAT pathway. Some studies have reported that the IL-7 channel also activates the PI3K or MAPK / ERK pathway, suggesting that IL-7 can use different signaling pathways depending on the cell type and the physiological state of the cell.

[0003] IL-7 and IL-7R are involved in the pathogenesis of different disease states mediated by lymphatic dysfunction, such as autoimmune diseases such as diabetes and multiple sclerosis (Lee, LF et al., Proc Natl Acad Sci USA 109, 12674-12679 (2012)), chronic inflammatory diseases such as rheumatoid arthritis, ankylosing spondylitis and inflammatory bowel disease (Churchman, SM & Ponchel, F. Rheumatology (Oxford) 47, 753-759 (2008); Krzystek-Korpacka, M. et al., Cancer Immunol Immunother 66, 171-179 (2017); Anderson, CA et al., Nat Genet 43, 246-252 (2011); Gracey, E. et al., Ann Rheum Dis 75, 2124-2132 (2016)) and hematological cancers (Oliveira, ML et al., Adv Biol Regul 71, 88-96 (2018)).

[0004] CD127 is fully expressed on naive T cells and memory T cells, but is lowly expressed on FoxP3+ regulatory T cells (Treg). This provides a unique opportunity to selectively target pathogenic effectors while retaining natural regulators (Liu W et al., J. Exp. Med. 2006; 203: 1701–1711; Seddiki N et al., J. Exp. Med. 2006; 203: 1693–1700; Michel L et al., J. Clin. Invest. 2008; 118: 3411–3419). Many IL7R antagonists are currently being developed. Although a number of studies have been conducted to analyze gene expression profiles and identify biomarkers for predicting or monitoring therapeutic responses (e.g., anti-PD1 antibodies) in cancer patients in vitro or in vivo, to the knowledge of the applicant, gene signatures associated with IL7R antagonist or agonist treatments are not yet known or publicly available. The IL7 signaling pathway is complex and involves multiple genes. In fact, 481 genes were differentially expressed in human PBMCs incubated with anti-human IL-7Rα monoclonal antibody compared to control conditions (Belarif L. et al., Nat Commun. 9(1):4483, October 26, 2018).

[0005] Therefore, there is a need to identify biomarkers of drug activity to accurately monitor patient responses to such drugs in clinical trials. Such markers will help in individualizing treatment for each patient. Summary of the invention

[0006] A method for analyzing gene expression profiles of subjects treated with anti-IL7R antagonist antibodies identified 41 differentially expressed genes. On the other hand, a method for analyzing gene expression profiles of human cells treated in vitro with IL7 cytokines identified 56 differentially expressed genes. Therefore, there is still a need to identify a limited number of drug-related biomarkers to easily assess the efficacy of anti-IL7R antagonists or agonists.

[0007] Furthermore, Applicants have previously shown that only a small proportion of IL7-induced transcriptional modifications are common to mice and humans, highlighting the poor translatability of mouse studies to humans when studying the IL7-IL7R signaling pathway. Therefore, in vitro gene signatures cannot be performed on mouse models to identify drug-related biomarkers that can be used in humans.

[0008] In order to solve these problems, the inventors of the present application have developed a new and efficient method in human peripheral blood mononuclear cells to identify highly correlated drug-related biomarkers (also referred to herein as gene signatures) to monitor the activity of IL7R agonists or antagonists (e.g., anti-IL7R antagonist antibodies). They used a comparative screening that can identify a very limited number of genes that can be used as efficient drug-related biomarkers to accurately monitor the efficacy of IL7R antagonist or agonist treatment. By measuring the expression level of at least one of these 4-6 target genes, the efficiency of IL7R antagonist or agonist compounds can be evaluated more easily and at a lower cost, thereby avoiding risks in clinical trials. The application of these biomarkers can be expanded to assess the possibility of a therapeutic response to the IL7R modulator. Therefore, therapeutic compounds can be selected more selectively.

[0009] The present invention relates to an in vitro method for evaluating a human patient's therapeutic response to treatment with an IL7R modulator, such as an IL7R antagonist, such as an anti-IL7R antagonist antibody or an antigen-binding fragment thereof, or an IL7R agonist, such as IL7, comprising the following steps: determining the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, FLT3LG and SOCS2 genes in a patient sample, wherein the patient has received at least one dose of an IL7R antagonist, such as an anti-IL7R antagonist antibody or an antigen-binding fragment thereof, or an IL7R agonist, such as IL7; wherein a lower or higher gene expression profile of the genes in the patient sample compared to a control value indicates that the patient may respond to the antagonist or agonist treatment, respectively. This group of genes corresponds to a unique marker for monitoring the activity of an IL7R modulator.

[0010] On the other hand, the present invention relates to an IL7R antagonist (e.g., an anti-IL7R antagonist antibody or an antigen-binding fragment thereof), which is used to treat a disease associated with IL7-induced enhancement of the IL7R signaling pathway in a human patient in need thereof, wherein the antagonist is administered to the patient after the patient is administered at least one dose of the antagonist (e.g., an anti-IL7R antagonist antibody or an antigen-binding fragment thereof) and when the patient is assessed as likely to respond to treatment with the antagonist (e.g., an anti-IL7R antagonist antibody or an antigen-binding fragment thereof) by the method as described above; preferably, the disease associated with IL7-induced enhancement of the IL7R signaling pathway is selected from autoimmune diseases, inflammatory diseases, allergic diseases, cancer diseases, infectious diseases, respiratory diseases, and transplantation-related diseases involving activation or proliferation of CD127-positive pathological cells, in particular autoimmune diseases or inflammatory diseases involving activation or proliferation of CD127-positive cells, more preferably chronic inflammatory diseases (e.g., Sjögren's syndrome) or inflammatory bowel diseases (e.g., ulcerative colitis).

[0011] On the other hand, the present invention relates to an IL7R agonist for use in treating a disease associated with impaired healthy T cell activity, preferably a disease requiring stimulation of an immune response, more preferably a cancer disease or an infectious disease whose own development is independent of the IL7R signaling pathway, in a human patient in need thereof; wherein the agonist is administered to the patient after the patient has been administered at least one dose of the agonist and when the patient is assessed as likely to respond to treatment with the agonist by the method as described above.

[0012] The present invention also relates to an in vitro method for assessing the likelihood of a human patient's response to treatment with an IL7R modulator (e.g., an IL7 receptor antagonist (e.g., an anti-IL7R antagonist antibody or antigen-binding fragment thereof) or agonist), comprising the steps of:

[0013] a) culturing a sample comprising cells previously collected from a patient prior to treatment with the IL7R modulator in the presence of the IL7R modulator (e.g., an IL7R antagonist (e.g., an anti-IL7R antagonist antibody or antigen-binding fragment thereof) or an IL7R agonist),

[0014] b) determining the gene expression profile of at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, FLT3LG and SOCS2 genes in the cultured sample, wherein a lower or higher gene expression profile of the genes in the cultured sample compared to the control value indicates that the patient may respond to antagonist (e.g., anti-IL7R antagonist antibody or antigen-binding fragment thereof) or agonist treatment.

[0015] On the other hand, the present invention relates to an IL7R antagonist (e.g., an anti-IL7R antagonist antibody or an antigen-binding fragment thereof), which is used to treat a disease associated with IL7-induced enhancement of the IL7R signaling pathway in a human patient in need thereof, wherein the patient is pre-evaluated as likely to respond to treatment with the antagonist (e.g., an anti-IL7R antagonist antibody or an antigen-binding fragment thereof) by the method as described above. Preferably, the disease associated with IL7-induced enhancement of the IL7R signaling pathway is selected from autoimmune diseases, inflammatory diseases, allergic diseases, cancer diseases, infectious diseases, respiratory diseases, and transplantation-related diseases involving activation or proliferation of CD127-positive pathological cells, in particular autoimmune diseases or inflammatory diseases involving activation or proliferation of CD127-positive cells, more preferably chronic inflammatory diseases (e.g., Sjögren's syndrome) or inflammatory bowel disease (e.g., ulcerative colitis).

[0016] On the other hand, the present invention relates to an IL7R agonist for use in treating a disease associated with impaired healthy T cell activity, preferably a cancer disease or an infectious disease whose development is independent of the IL7R pathway, in a human patient, wherein the patient is previously assessed as likely to respond to treatment with the IL7R agonist by the method described above, wherein the patient is previously assessed as likely to respond to treatment with the agonist (e.g., an anti-IL7R antagonist antibody or an antigen-binding fragment thereof) by the method described above.

[0017] The present invention also relates to an in vitro method for selecting an IL7R modulator (e.g., IL7R antagonist or IL7R agonist) compound, which is effective in treating a disease associated with an enhanced IL7R signaling pathway induced by IL7 or a disease associated with impaired activity of healthy T cells, the method comprising the following steps:

[0018] a) cultivating human cells in the presence of said compound,

[0019] b) determining the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in the cell, and

[0020] c) selecting an antagonist or agonist compound which induces a lower or higher gene expression profile, respectively, of said gene in said cell as compared to a control value.

[0021] On the other hand, the present invention relates to a kit comprising a set of reagents that specifically detect the gene expression profile of at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes, preferably, the reagents are primer pairs and / or probes specific for each gene. DETAILED DESCRIPTION

[0022] The term "biomarker" refers to a unique biological or biologically derived indicator (i.e., a cell, biochemical, molecule, gene, protein, metabolite, a specific post-translational modification, or a physiological or physical sign) of a process, event, or condition. According to the present disclosure, the biomarker may refer to a gene signature. A gene signature is a single or combined set of genes in a cell that has a unique characteristic gene expression profile that occurs due to an altered or unaltered biological process or a pathogenic medical condition.

[0023] The terms "subject" and "patient" are used interchangeably herein to refer to humans and non-human animals. As used herein, the term "patient" refers to mammals, such as rodents, felines, canines, and primates. Preferably, the patient of the present invention is a human.

[0024] The term "patient sample" refers to any biological sample derived from a patient. Examples of such samples include tissue samples, cell samples, organs, biopsy samples, preferably tumor tissue containing infiltrating immune cells from a cancer patient or a blood patient sample. A preferred biological sample is a cell sample, preferably a blood cell sample (e.g., isolated human peripheral blood mononuclear cells).

[0025] The term "likely responder" or "likely to respond to treatment" means that during or after treatment, the subject has the onset of at least one symptom of the disease being treated delayed or prevented, or has at least one symptom or symptoms stabilized, reduced or disappeared.

[0026] "Therapeutic response" refers to the effect of a medical treatment on a patient, the results of which are judged to be useful or beneficial. For example, a therapeutic response may be a delay or prevention of at least one symptom during or after treatment, or may be stabilization, alleviation or disappearance of a patient's symptoms or at least one of the symptoms.

[0027] According to the present disclosure, "therapeutic response of a patient treated with an IL7R modulator" or "IL7R modulator therapeutic response" refers to the step of administering an IL7R modulator (e.g., an IL7R antagonist (e.g., an anti-IL7R antagonist antibody or antigen-binding fragment thereof) or an IL7R agonist (e.g., IL7)) resulting in an improvement in the clinical condition of an animal or human patient in need thereof, wherein the animal or human patient suffers from a disease associated with an enhancement of the IL7R signaling pathway induced by IL7 (i.e., a signaling pathway induced by the IL7-IL7 receptor interaction, also referred to herein as the IL7-IL7R pathway) or a disease associated with impaired healthy T cell activity, respectively, wherein the disease associated with an enhancement of the IL7R signaling pathway induced by IL7 involves activation and / or proliferation of CD127-positive cells. Such treatment is intended to improve the clinical condition of an animal or human patient by eliminating or reducing the symptoms associated with a disease associated with IL-7 or TSLP (thymic stromal lymphopoietin), and in a preferred embodiment, by eliminating or reducing the symptoms associated with a disease associated with the IL7R signaling pathway induced by IL7 or a disease associated with impaired healthy T cell activity.

[0028] In a specific embodiment, the therapeutic response of a patient treated with an IL7R antagonist (e.g., an anti-IL7R antagonist antibody or an antigen-binding fragment thereof) refers to an improvement in the clinical condition of a patient suffering from a disease associated with enhanced IL-7-induced IL7R signaling pathway, such as autoimmune diseases, inflammatory diseases, allergic diseases, cancer diseases, infectious diseases, respiratory diseases, and transplantation-related diseases involving activation or proliferation of CD127-positive diseased cells, in particular autoimmune diseases or inflammatory diseases involving activation or proliferation of CD127-positive cells, more preferably chronic inflammatory diseases (e.g., Sjögren's syndrome) or inflammatory bowel disease (e.g., ulcerative colitis).

[0029] In another specific embodiment, a therapeutic response in a patient treated with an IL7R agonist (e.g., IL7) refers to an improvement in the clinical condition of a patient resulting from administration of an IL7R agonist, wherein the patient suffers from a disorder or disease associated with impaired healthy T cell activity, preferably a disorder requiring stimulation of an immune response, more preferably a cancer disease or an infectious disease that develops independently of the IL7R pathway.

[0030] Typical IL7R modulators may be compounds that have IL7R antagonist or agonist properties towards IL7-IL7 receptor interaction and modulate (increase or decrease) IL7 / IL7R-mediated signaling (IL7R signaling pathway induced by IL7).

[0031] In a preferred embodiment, the IL7R modulator (e.g., an IL7R antagonist or an IL7R agonist) can be selected from: protein, polypeptide or peptide modulators, for example, components of the IL7-IL7R signaling pathway (e.g., IL7), variants or derivatives thereof (fragments, fusion proteins, soluble proteins, dominant negative mutants), antibodies against components of the IL7-IL7R signaling pathway (including fragments and expressible derivatives thereof and antigen-binding antibody mimetics).

[0032] Binding of IL-7 to IL-7R triggers activation of multiple signaling pathways, including Janus kinase (JAK)-1 and -3, signal transducer and activator of transcription 5 (STAT5), and phosphatidylinositol 3-kinase (PI3-k). STAT1 and STAT3 pathways have been reported to be activated, although they do not appear to be the primary pathways. Activation of the STAT5 pathway is required for the induction of the anti-apoptotic protein Bcl-2 and for preventing the pro-apoptotic protein Bax from entering the mitochondria and, therefore, for the survival of developing T-cell precursors in the thymus. Activation of the PI3-k pathway leads to the phosphorylation and cytoplasmic retention of the pro-apoptotic protein Bad.

[0033] In a specific embodiment, the IL7-R signaling pathway induced by IL7 can be identified by measuring STAT5 phosphorylation, as described in the examples of WO2018 / 104483. IL7-induced STAT5 phosphorylation is a hallmark of IL7-R activation. Compounds that antagonize IL7-IL7-R interactions are expected to reduce IL7-induced STAT5 phosphorylation, and compounds that stimulate IL7-IL7-R interactions are expected to increase IL7-induced STAT5 phosphorylation.

[0034] In a specific embodiment, the IL7-R antagonists of the present disclosure inhibit IL7-induced STAT5 phosphorylation. In a preferred embodiment, when the IL7R antagonist concentration is as low as 55 ng / ml, the inhibition of STAT5 phosphorylation is greater than 50%, and / or, when the antibody concentration is as low as 100 ng / ml, the inhibition of STAT5 phosphorylation is greater than 80%. The inhibition of STAT5 phosphorylation can be evaluated by methods known to the skilled person, in particular by methods such as those described in Example 5 and / or paragraphs

[69] and

[70] on page 21 of WO2018 / 104483 and Example 3 of WO2015 / 189302. The IL7-R agonists of the present disclosure increase IL7-induced STAT5 phosphorylation.

[0035] The IL7R modulators (e.g., IL7R antagonists (particularly antibodies, antigen-binding fragments thereof) or agonists) disclosed herein can be identified by measuring the activation of the PI3-K and / or ERK (extracellular signal-regulated kinase) signaling pathway. In a specific embodiment, the IL7R antagonist inhibits the activation of the PI3-k and / or ERK (extracellular signal-regulated kinase) signaling pathway and / or does not activate the PI3-k and / or ERK (extracellular signal-regulated kinase) signaling pathway or does not enhance the activation of the PI3-k and / or ERK (extracellular signal-regulated kinase) signaling pathway, in particular, inhibits the phosphorylation of PI3-k and / or ERK 1 and / or ERK 2 and / or does not induce or increase the phosphorylation of PI3-k and / or ERK 1 and / or ERK 2. In particular, the IL7R antagonists provided herein do not induce activation of the PI3-k and / or ERK pathway (preferably the PI3-k and ERK pathway), in particular, do not induce phosphorylation of PI3-k and / or ERK 1 and / or ERK 2, and more particularly do not induce phosphorylation of PI3-k and ERK 1 and ERK 2. In particular, the IL7R antagonists inhibit activation of the PI3-k and / or ERK pathway, in particular, inhibit phosphorylation of PI3-k and / or ERK 1 and / or ERK 2, and more particularly inhibit phosphorylation of PI3-k and ERK 1 and ERK 2. Activation of the pathway and / or phosphorylation of the protein can be achieved by methods known to the skilled person (in particular, by methods described in WO2018 / 104483). Figure 7 and Western blot as shown in Example 8), preferably by inhibiting the activation of PI3-k and / or ERK.

[0036] In another specific embodiment, the IL7R agonist induces or increases the activation of the PI3-k and / or ERK (extracellular signal-regulated kinase) signaling pathway, in particular induces or increases the phosphorylation of PI3-k and / or ERK 1 and / or ERK 2.

[0037] The IL7R antagonists (particularly antibodies, antigen binding fragments thereof) or agonists disclosed herein can also be identified by measuring the internalization of CD127. In a specific embodiment, the IL7R antagonists provided herein inhibit IL7-induced CD127 internalization, and the IL7R agonists increase IL7-induced CD127 internalization. The internalization of CD127 can be measured by measuring the cell surface expression level of CD127 in cells incubated with IL7R modulators (e.g., IL7R antagonists or agonists) compared to control values ​​(e.g., cells not incubated with IL7R modulators).

[0038] In a specific embodiment, when incubated with the IL7R antagonist, the presence of IL7 does not induce a decrease in the cell surface expression of CD127, or the intensity of the cell surface expression of induced CD127 is less than that of cells not incubated with the antagonist. In a specific embodiment, when incubated with the antagonist, when cells are incubated with 5ng / mL IL7 at 37°C for 15 minutes, the cell surface expression level of CD127 is at least 80%, preferably at least 90% of the cell surface expression level in cells not incubated with IL7. Preferably, cell surface expression is measured in vitro after the above-defined time. In addition, since most cell internalization processes are inhibited at low temperatures, the effect observed at physiological temperature, particularly at 37°C, is generally the best. However, it is also possible to consider incubating cells at low temperatures (especially at 4°C).

[0039] In another preferred embodiment, the IL7R antagonists provided herein do not induce the internalization of CD127. Therefore, relative to the cell surface expression in the cells incubated under the same other conditions but without antagonists, the CD127 cell surface expression in the cells incubated under the presence of the IL7R antagonist does not decrease or does not decrease significantly. In a specific embodiment, when incubated at 37 ° C for 30 to 45 minutes in the presence of 50ng / mL antagonists, the CD127 cell surface expression level is at least 80%, preferably at least 90% of the CD127 cell surface expression level in the cells incubated in the absence of antagonists. The antagonist effect can be observed in the absence of IL7 (in cells treated with antibodies and without antibody treatment), in the presence of IL7 and / or in two situations.

[0040] The above two characteristics related to CD127 internalization (i.e., inhibition of IL7-induced internalization or no induction of internalization) can also be defined and / or tested as described in WO2015 / 189302 (especially paragraphs

[59] -

[63] on pages 19-20 and Figure 16 and Example 5).

[0041] For example, the IL7R modulators of the present disclosure can be identified by the following method, which comprises the following steps:

[0042] a) providing a plurality of cells expressing CD127 on their surface,

[0043] b) incubating the cells with a candidate compound,

[0044] c) determining whether the candidate compound binds to and reduces or increases the biological activity of CD127 as described above (e.g., STAT5 phosphorylation, activation of phosphatidylinositol 3-kinase and / or ERK signaling pathways, CD127 internalization), and

[0045] d) selecting candidate compounds that decrease or increase the biological activity of CD127 (e.g., STAT5 phosphorylation, activation of phosphatidylinositol 3-kinase and / or ERK signaling pathways, CD127 internalization).

[0046] In a preferred embodiment, the IL7R modulators of the present disclosure are IL7R antagonists.

[0047] As used herein, "IL7 receptor antagonist (e.g., anti-IL7R antagonist antibody or antigen binding fragment thereof)" refers to a compound (e.g., anti-IL7R antagonist antibody or antigen binding fragment thereof) that has antagonistic properties against IL7-IL7 receptor interaction and impairs IL7 / IL7R-mediated signal transduction cells. According to a specific embodiment, the IL7R antagonist of the present disclosure also has antagonistic properties against interleukin 7 (IL7), thereby antagonizing the approach of IL7 to CD127 on CD127-positive cells (i.e., the binding of IL7 to CD127 on CD127-positive cells).

[0048] "Antagonistic properties for IL7-IL7-R interactions" refers to IL7R antagonists (e.g., IL7R antagonist antibodies or antigen-binding fragments thereof) targeting IL7-Rα, which have the effect of preventing the IL7 receptor expressed on CD127 cells (especially human effector T cells, especially human memory T cells) from approaching its binding partner IL7 (especially human IL7). Due to the antagonistic binding of IL7, IL7R antagonists cause lymphopenia by preventing the production of IL7-dependent thymic T cells. Antagonist properties can be, in particular, antagonism of IL7-R signaling induced by IL7.

[0049] In a preferred embodiment, the IL7R antagonists provided herein do not bind to CD127 in the TSLP (thymic stromal lymphopoietin) receptor (i.e., when CD127 forms a complex with CRLF2 (forming a TSLP receptor), it does not bind to CD127). Therefore, the antagonists provided herein do not interfere with TSLP-induced and / or TSLP receptor-mediated signal transduction. In another preferred embodiment, the IL7R antagonist cannot bind to non-T cells in whole blood; (d) cannot bind to CD127IL-7Ra expressed on non-T cells (e.g., monocytes) in whole blood (e.g., human whole blood).

[0050] In a specific embodiment, the IL7R antagonist can be an anti-IL7R antagonist antibody or an antigen-binding fragment thereof, preferably a monoclonal antibody or an antigen-binding fragment thereof that specifically binds to the IL-7 receptor α chain (preferably the human IL-7 receptor α chain). The α chain of the interleukin 7 (IL-7) receptor is named CD127 or p90 IL-7R, IL-7R alpha or IL-7Rα (NCBI accession number: XP_005248356.1, updated on November 22, 2021). According to the present disclosure, the IL7R antagonist is preferably an IL7Rα antagonist, more preferably an anti-IL7Rα antagonist antibody or an antigen-binding fragment thereof.

[0051] As used herein, the term "specifically binds to" or "specific binding" refers to the binding of an antigen receptor to an antigen receptor with a specific binding affinity of at least about 1 x 10 -6 M, 1x 10 -7 M, 1x 10 -8 M, 1x 10 -9 M, 1x 10 -10 M, 1x 10 -11 M, 1x 10 -12 The ability of a target to bind to an antigen with an affinity of 54 or higher, and / or the ability to bind to a target with an affinity at least twice as high as its affinity for a non-specific antigen. Affinity can be determined by various methods well known to those skilled in the art. These methods include, but are not limited to, Biacore analysis, Blitz analysis, and Scatchard mapping.

[0052] In one embodiment, the KD value of the antibody or antigen-binding fragment thereof of the present invention for CD127 (particularly for human CD127) is less than or equal to 10 -8 M, preferably less than or equal to 10 -9 M, more preferably less than or equal to 1.10 -10 M, which can be determined by biosensor analysis, in particular by Biacore analysis.

[0053] As used herein, the term "antibody" refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen binding site that immunospecifically binds to an antigen. Therefore, the term antibody includes not only complete antibody molecules, but also antibody fragments and variants (including derivatives) of antibodies.

[0054] In natural antibodies of rodents and primates, two heavy chains are linked to each other by disulfide bonds, and each heavy chain is linked to a light chain by a disulfide bond. There are two types of light chains, lambda (λ) and kappa (κ). There are five major heavy chain types (or isotypes) that determine the functional activity of antibody molecules: IgM, IgD, IgG, IgA, and IgE. Each chain contains different sequence domains. In a typical IgG antibody, the light chain includes two domains, a variable domain (VL) and a constant domain (CL). The heavy chain includes four domains, a variable domain (VH) and three constant domains (CH1, CH2, and CH3, collectively referred to as CH). The variable regions of the light chain (VL) and heavy chain (VH) determine the binding recognition and specificity for the antigen. The constant regions of the light chain (CL) and heavy chain (CH) confer important biological properties, such as antibody chain binding, secretion, transplacental mobility, complement binding, and binding to Fc receptors (FcR).

[0055] The Fv fragment is the N-terminal portion of the immunoglobulin Fab fragment, which consists of one light chain and the variable portion of one heavy chain. The specificity of an antibody lies in the structural complementarity between the antibody binding site and the antigenic determinant. The antibody binding site consists of residues mainly from the hypervariable regions or complementary determining regions (CDRs). Sometimes, residues from non-hypervariable regions or framework regions (FRs) can participate in the antibody binding site or affect the overall domain structure and thus the binding site. The complementary determining regions or CDRs refer to amino acid sequences that together determine the binding affinity and specificity of the native Fv region of the natural immunoglobulin binding site. The light and heavy chains of immunoglobulins each have three CDRs, designated L-CDR1, L-CDR2, L-CDR3 and H-CDR1, H-CDR2, H-CDR3, respectively. Therefore, the antigen binding site usually includes 6 CDRs, including CDRs from each heavy and light chain V region. The framework region (FR) refers to the amino acid sequence inserted between the CDRs. Thus, the variable regions of the light and heavy chains typically include four framework regions and three CDRs in the following order: FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4.

[0056] The residues in the variable domains of antibodies are usually numbered according to the system designed by Kabat et al. The system is described in "Kabat et al., 1987, Sequences of Proteins of Immunological Interest, U.S. Department of Health and Human Services, NIH, USA (Kabat et al., 1992, hereinafter referred to as "Kabat et al.")". This numbering system is used in this specification. The Kabat residue nomenclature does not always correspond directly to the linear numbering of the amino acid residues in the SEQ ID sequence. The actual linear amino acid sequence may contain fewer or more amino acids than the strict Kabat numbering, which corresponds to the shortening or insertion of the structural components of the basic variable domain structure (whether framework or complementary determining region (CDR)). The correct Kabat numbering of a given antibody residue can be determined by aligning the homologous residues in the antibody sequence with the "standard" Kabat numbering sequence.

[0057] As used herein, the term "monoclonal antibody" refers to a preparation of antibody molecules with a single specificity. A monoclonal antibody exhibits a single binding specificity and affinity for a particular epitope. Thus, the term "human monoclonal antibody" refers to an antibody exhibiting a single binding specificity having variable and constant regions derived from or based on human germline immunoglobulin sequences or derived from completely synthetic sequences. The method for preparing the monoclonal antibody is independent of the binding specificity.

[0058] As used herein, the term "antigen binding fragment" (or simply "antibody fragment") of an antibody refers to one or more fragments of an antibody that retain the ability to specifically bind to an antigen (e.g., IL7R), particularly having antagonistic properties of IL7-IL7 receptor interactions, weakening IL7 / IL7R-mediated signal transduction (e.g., PI3K / Akt / mTOR and JAK / STAT pathways), and can exhibit cytotoxic activity against CD127-positive cells. It has been shown that the antigen binding function of an antibody can be achieved by a fragment of a full-length antibody.

[0059] Examples of binding fragments encompassed by the term "antigen-binding fragment" of an antibody include a Fab fragment (a monovalent fragment consisting of the VL, VH, CL and CH1 domains), a F(ab)2 fragment (a bivalent fragment comprising two Fab fragments linked by a disulfide bond in the hinge region), a Fd fragment consisting of the VH and CH1 domains, a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, a dAb fragment consisting of a VH domain (Ward et al., 1989 Nature 341:544-546), or any fusion protein comprising such an antigen-binding fragment. In addition, although the two domains (VL and VH) of the Fv fragment are encoded by different genes, they can be connected by synthetic linkers using recombinant methods to make them into single-chain proteins, in which the VL and VH regions are paired to form monovalent molecules (called single-chain Fv (scFv); see, for example, Bird et al., 1988 Science 242: 423-426; and Huston et al., 1988 Proc. Natl. Acad. Sci. 85: 5879-5883). Such single-chain antibodies are also intended to be encompassed within the term "antigen-binding fragment" of an antibody. These antibody fragments are obtained using conventional techniques known to those skilled in the art, and the utility of the fragments is screened in the same manner as intact antibodies.

[0060] In a specific embodiment, the anti-IL7R antagonist antibody or antigen-binding fragment thereof of the present disclosure is N13B2h1, N13B2h2 or N13B2h3 antibody or antigen-binding fragment thereof as described in WO2015 / 189302, or N13B2-hVL3, N13B2-hVL4, N13B2-hVL5 or N13B2-hVL6 antibody or antigen-binding fragment thereof as described in WO2018 / 104483, and comprises: (a) a variable heavy chain comprising three CDRs, wherein VHCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 1, VHCDR2 comprises or consists of the amino acid sequence of SEQ ID NO: 2, and VHCDR3 comprises or consists of the amino acid sequence of SEQ ID NO: 3 or 11; (b) a variable light chain comprising three CDRs, wherein VLCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 4 or 12, VLCDR2 comprises NO: 5 or 13 or consist thereof, and VLCDR3 comprises or consists of the amino acid sequence of SEQ ID NO: 6.

[0061] In a more specific embodiment, the anti-IL7R antagonist antibody or antigen-binding fragment thereof of the present disclosure is the N13B2h3 antibody or antigen-binding fragment thereof as described in WO2015 / 189302, or the N13B2-hVL3, N13B2-hVL4, N13B2-hVL5 or N13B2-hVL6 antibody or antigen-binding fragment thereof as described in WO2018 / 104483 (preferably the N13B2-hVL6 antibody or antigen-binding fragment thereof as described in WO2018 / 104483), and comprises: (a) a variable heavy chain comprising three CDRs, wherein VHCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 1, VHCDR2 comprises or consists of the amino acid sequence of SEQ ID NO: 2, and VHCDR3 comprises or consists of the amino acid sequence of SEQ ID NO: 3; (b) a variable light chain comprising three CDRs, wherein VLCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: NO:4 or consist of the amino acid sequence, VLCDR2 comprises or consists of the amino acid sequence of SEQ ID NO:5, and VLCDR3 comprises or consists of the amino acid sequence of SEQ ID NO:6.

[0062] It is also possible to consider further screening or optimizing the affinity binding and / or antagonistic activity of antibodies or their antigen-binding fragments. In particular, it is expected that antibodies or their antigen-binding fragments can have 1, 2, 3, 4, 5, 6 or 6 CDR amino acid sequences of the monoclonal antibodies provided herein. 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids in the VJ or VDJ regions of the light chain or heavy chain variable domains of the expected antibodies, CDR1, CDR2, CDR3, CDR4, CDR5 or CDR6 may have insertions, deletions or substitutions with conservative or non-conservative amino acids. Such amino acids that can be substituted or constitute substitutions are disclosed above.

[0063] In some embodiments, the amino acid difference is a conservative substitution, i.e., one amino acid is substituted by another amino acid with similar chemical or physical properties (size, charge or polarity), and such substitutions generally do not adversely affect the biochemical, biophysical and / or biological properties of the antibody. In particular, the substitution does not disrupt the interaction and antagonistic properties of the antibody with the IL7R antigen. The conservative substitutions are advantageously selected within one of the following five groups: Group 1 - small aliphatic non-polar or weakly polar residues (A, S, T, P, G); Group 2 - polar, negatively charged residues and their amides (D, N, E, Q); Group 3 - polar, positively charged residues (H, R, K); Group 4 - large aliphatic non-polar residues (M, L, I, V, C); and Group 5 - large aromatic residues (F, Y, W).

[0064] In a specific embodiment, the anti-IL7R antagonist is an N13B2h1, N13B2h2 or N13B2h3 antibody or an antigen-binding fragment thereof as described in WO2015 / 189302, and comprises a heavy chain variable domain and a light chain variable domain, wherein the heavy chain variable domain comprises an amino acid sequence selected from SEQ ID NOs: 14-17 or consists of an amino acid sequence selected from SEQ ID NOs: 14-17, and the light chain variable domain comprises an amino acid sequence selected from SEQ ID NOs: 18-21 or consists of an amino acid sequence selected from SEQ ID NOs: 18-21. Preferably, the anti-IL7R antagonist is an N13B2h3 antibody or an antigen-binding fragment thereof as described in WO2015 / 189302, and comprises a heavy chain variable domain comprising or consisting of the amino acid sequence of SEQ ID NO: 17 and a light chain variable domain comprising or consisting of the amino acid sequence of SEQ ID NO: 21. More preferably, the antibody or antigen-binding fragment thereof comprises a complete heavy chain and a complete light chain, the complete heavy chain comprising or consisting of SEQ ID NO: 22, and the complete light chain comprising or consisting of SEQ ID NO: 23.

[0065] In another specific embodiment, the anti-IL7R antagonist is an N13B2-hVL3, N13B2-hVL4, N13B2-hVL5 or N13B2-hVL6 antibody or an antigen-binding fragment thereof as described in WO2018 / 104483, and comprises a heavy chain variable domain and a light chain variable domain, wherein the heavy chain variable domain comprises or consists of the amino acid sequence SEQ ID NO: 7, and the light chain variable domain comprises or consists of an amino acid sequence selected from SEQ ID NO: 8, 24-26.

[0066] In a more preferred embodiment, the anti-IL7R antagonist antibody or antigen-binding fragment thereof is an N13B2-hVL6 antibody or antigen-binding fragment thereof as described in WO2018 / 104483, and comprises a heavy chain variable domain and a light chain variable domain, the heavy chain variable domain comprising or consisting of the amino acid sequence SEQ ID NO: 7, and the light chain variable domain comprising or consisting of the amino acid sequence SEQ ID NO: 8. Preferably, the antibody or antigen-binding fragment thereof comprises a complete heavy chain and a complete light chain, the complete heavy chain comprising or consisting of SEQ ID NO: 9, and the complete light chain comprising or consisting of SEQ ID NO: 10.

[0067] Anti-IL7R antagonist antibodies or antigen-binding fragments thereof having an amino acid sequence that is at least 90% (e.g., at least 95%, 96%, 97%, 98% or 99%) identical to any of the amino acid sequences defined above are also part of the present disclosure. Generally, the antagonist activity of the anti-IL7R antagonist antibody or antigen-binding fragment thereof against IL7-IL7R interaction is at least the same as or higher than the above-mentioned anti-IL7R antagonist antibody or antigen-binding fragment thereof composed of the VH and VL (particularly the heavy chain and the light chain) of the N13B2-hVL6 antibody.

[0068] As used herein, the percent identity between two sequences is a function of the number of identical positions that the sequences have (i.e., % identity=number of identical positions / total number of positions × 100), taking into account the number of gaps and the length of each gap that need to be introduced for the best comparison of the two sequences. As described below, the comparison of sequences and the determination of percent identity between the two sequences can be accomplished using a mathematical algorithm.

[0069] The percent identity between two amino acid or nucleotide sequences can be determined using the algorithm of E. Meyers and W. Miller (Comput. Appl. Biosci., 4: 11-17, 1988) incorporated into the ALIGN program (version 2.0), a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4. Alternatively, the percent identity between two amino acid or nucleotide sequences can be determined using the algorithm of Needleman and Wunsch (J. Mol, Biol. 48: 444-453, 1970) incorporated into the GAP program in the GCG software package (available at http: / / www.gcg.com), a Blossom 62 matrix or a PAM250 matrix, a gap weight of 16, 14, 12, 10, 8, 6 or 4, and a length weight of 1, 2, 3, 4, 5 or 6. The percent identity between two nucleotide or amino acid sequences can also be determined using, for example, an algorithm (such as the BLASTN program for nucleic acid or amino acid sequences, using as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=4, and a comparison of both strands).

[0070] In another specific embodiment of the present disclosure, the IL7R antagonist (eg, an IL7R antagonist antibody or an antigen-binding fragment thereof) also has cytotoxic properties against human cells (particularly human T cells expressing the receptor).

[0071] According to a specific embodiment of the present disclosure, the cytotoxic IL7R antagonist is an antibody that also has the ability to increase the antibody-dependent cellular phagocytosis (ADCP) activity of macrophages on CD127-positive tumor cells, and does not have antibody-dependent cellular toxicity (ADCC) activity, especially antibody-dependent cellular toxicity (ADCC) activity on immune cells. In a specific embodiment of the present invention, the anti-IL-7R antagonist antibody or antigen-binding fragment thereof (especially anti-CD127 antibody or fragment thereof) used in the method of the present invention or the application of the present invention has the ability to increase the antibody-dependent cellular phagocytosis (ADCP) activity of macrophages on CD127-positive tumor cells, and preferably does not have antibody-dependent cellular toxicity (ADCC) activity, especially antibody-dependent cellular toxicity (ADCC) activity on immune cells.

[0072] In another embodiment, the IL7R modulator (i.e., IL7R antagonist or IL7R agonist) is an antigen-binding antibody mimetic. As used herein, the term "antigen-binding antibody mimetic" refers to artificial proteins, peptides, and any chemical compounds that have the ability to mimic antibody binding to antigen. Such mimics include affitins and anticalins, as well as aptamers (peptide aptamers and oligonucleotide aptamers).

[0073] In one embodiment, the IL7R modulator (i.e., antagonist or IL7R agonist) is an aptamer. Aptamers are a class of molecules that represent alternatives to antibodies in terms of molecular recognition. Aptamers are oligonucleotide or oligopeptide sequences that can recognize almost any class of target molecules with high affinity and specificity. Such ligands can be isolated by systematic evolution of ligands by exponential enrichment (SELEX) of random sequence libraries. Random sequence libraries can be obtained by combinatorial chemical synthesis of DNA. In this library, each member is a linear oligomer of a unique sequence that is ultimately chemically modified. Peptide aptamers consist of conformationally restricted antibody variable regions displayed by platform proteins (e.g., E. coli thioredoxin A selected from a combinatorial library by two hybridization methods).

[0074] In some embodiments, the IL7R modulator (i.e., IL7R antagonist or IL7R agonist) is a polypeptide. The term "polypeptide" herein refers to an amino acid polymer of no particular length. Therefore, peptides, oligopeptides, and proteins are included in the definition of "polypeptide", and these terms are used interchangeably throughout the specification and claims. The term "polypeptide" does not exclude post-translational modifications, including but not limited to phosphorylation, acetylation, glycosylation, etc.

[0075] In one embodiment, the length of the polypeptide of the present invention is 2 to 200 amino acids. In one embodiment, the length of the polypeptide of the present invention is 2 to 190, particularly 10 to 180, 10 to 170, 10 to 160, 10 to 150, 10 to 140, 10 to 130, 10 to 120, 10 to 110 amino acids. In one embodiment, the length of the polypeptide of the present invention is 10 to 100 amino acids. In one embodiment, the length of the polypeptide of the present invention is 50 to 100 amino acids. In one embodiment, the length of the polypeptide of the invention is 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100 amino acids.

[0076] In a specific embodiment, the polypeptide is a functional equivalent of IL7R. As used herein, a "functional equivalent" of IL7R is a compound that is capable of binding to at least one IL7 ligand, thereby preventing it from interacting with IL7R. The term "functional equivalent" includes fragments, mutants and mutant proteins of IL7R. Therefore, the term "functional equivalent" includes any equivalent of IL7R obtained by changing the amino acid sequence (e.g., by deleting, substituting or adding one or more amino acids so that the protein analog retains the ability to bind to its ligand). Amino acid substitutions can be performed, for example, by point mutations of the DNA encoding the amino acid sequence.

[0077] Functional equivalents include, but are not limited to, molecules that bind to an IL7R ligand and contain all or part of the extracellular domain of IL7R to form a soluble receptor capable of capturing an IL7R ligand. Thus, functional equivalents include soluble forms of IL7R. Suitable soluble forms of these proteins or their functional equivalents may include, for example, truncated forms of proteins in which the transmembrane domain has been removed by chemical, proteolytic or recombinant methods. In particular, functional equivalents are composed of sequences having at least 80% identity, more particularly at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% identity, and further more particularly at least 99% identity with the corresponding protein over the entire length of the corresponding protein. As used herein, the term "corresponding protein" refers to a protein with similar functions to a functional equivalent of the present invention. The identity percentages cited in the present statement are determined according to a global alignment of the sequences to be compared (that is, according to the alignment of the sequences over their entire length) using, for example, the algorithm of Needleman and Wunsch 1970. The sequence comparison can be performed, for example, using the needle software, with the parameter "gap opening" equal to 10.0, the parameter "gap extension" equal to 0.5, and the matrix "BLOSUM62" used. Needle and other software are available worldwide on the ebi.ac.uk website under the name "needle". As used herein, the term "functionally equivalent fragment" may also refer to any fragment or combination of fragments of IL7R that binds to IL7. Therefore, the present disclosure provides a polypeptide (particularly a functional equivalent) capable of inhibiting the binding of IL7R to IL7, the polypeptide comprising contiguous amino acids corresponding to the sequence of at least a portion of the extracellular domain of IL7R (which portion binds to IL7). In some embodiments, the polypeptide (particularly a functional equivalent) corresponds to the extracellular domain of IL7R.

[0078] In some embodiments, the functional equivalent of IL7R is fused to a heterologous polypeptide to form a fusion protein. As used herein, a "fusion protein" comprises all or part (usually biologically active) of a functional equivalent of the present disclosure operably linked to a heterologous polypeptide (i.e., a polypeptide other than the same polypeptide). In a fusion protein, the term "operably linked" is intended to mean that the functional equivalent of the present disclosure and the heterologous polypeptide are fused to each other in a reading frame-compliant manner. The heterologous polypeptide can be fused to the N-terminus or the C-terminus of the functional equivalent of the present disclosure.

[0079] In some embodiments, the functional equivalent of IL7R is fused to an immunoglobulin constant region (Fc region) to form an immunoadhesin. Immunoadhesins can have many important chemical and biological properties of human antibodies. Since immunoadhesins can be constructed from human protein sequences with desired specificity connected to appropriate human immunoglobulin hinge and constant domain (Fc) sequences, the target binding specificity can be achieved entirely using human components. Such immunoadhesins have minimal immunogenicity to patients and are safe for long-term or repeated use. In some embodiments, the Fc region is a native sequence Fc region. In some embodiments, the Fc region is a variant Fc region. In another embodiment, the Fc region is a functional Fc region. As used herein, the term "Fc region" is used to define the C-terminal region of an immunoglobulin heavy chain, including a native sequence Fc region and a variant Fc region. Although the boundaries of the immunoglobulin heavy chain Fc region may be different, the human IgG heavy chain Fc region is generally defined as extending from an amino acid residue at position Cys226 or from an amino acid residue at position Pro230 to its carboxyl terminus. The adhesion portion of the immunoadhesin and the immunoglobulin sequence portion can be connected by a minimal joint. The immunoglobulin sequence is usually (but not necessarily) an immunoglobulin constant domain. The immunoglobulin portion in the chimera of the present invention can be obtained from IgG1, IgG2, IgG3 or IgG4 subtypes, IgA, IgE, IgD or IgM, but is usually obtained from IgG1 or IgG4. In some embodiments, the functional equivalent of IL7R and the immunoglobulin sequence portion of the immunoadhesin are connected by a minimal joint. As used herein, the term "joint" refers to a sequence of at least one amino acid that connects the polypeptide of the present invention and the immunoglobulin sequence portion. Such joints can be used to prevent steric hindrance. In some embodiments, the joint has 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 amino acid residues. However, the upper limit is not important, but the upper limit is selected to facilitate the biopharmaceutical production of such polypeptides. The joint sequence can be a naturally occurring sequence or a non-naturally occurring sequence. If used for therapeutic purposes, the joint is usually non-immunogenic in the subject to which the immunoadhesin is applied. One group of useful joint sequences is a joint derived from the hinge region of a heavy chain antibody as described in WO 96 / 34103 and WO 94 / 04678. Other examples are polyalanine joint sequences.

[0080] According to the present disclosure, a patient may respond to treatment with an IL7R antagonist (e.g., an anti-IL7R antagonist antibody or an antigen-binding fragment thereof) when the antagonist (e.g., an anti-IL7R antagonist antibody or an antigen-binding fragment thereof) has an IL7R antagonist effect in the patient that can be associated with a therapeutic response to treatment with the antagonist.

[0081] In another specific embodiment, according to the present disclosure, a patient may be responsive to treatment with an IL7R agonist (eg, IL7) when there is an effect of the IL7R agonist in the patient that can be correlated with a therapeutic response to treatment with the agonist.

[0082] According to different methods of the present disclosure, gene expression profiling of at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in patient samples previously treated with IL7R modulators (e.g., IL7R antagonists (e.g., anti-IL7R antagonist antibodies or antigen-binding fragments thereof) or IL7R agonists) in vitro or in vivo can be used as biomarkers to determine the efficacy of IL7R modulators (e.g., IL7R antagonists (e.g., anti-IL7R antagonist antibodies or antigen-binding fragments thereof) or IL7R agonists) in patients, and to assess the therapeutic response or assess the likelihood of the patient's therapeutic response to the antagonist (e.g., anti-IL7R antagonist antibody or antigen-binding fragment thereof) or agonist treatment or to select IL7R antagonist or agonist compounds that may be effective in the treatment.

[0083] Therefore, various methods disclosed herein comprise determining the expression level of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 and 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in a patient sample.

[0084] The term "determining the expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes" refers to evaluating the expression level of at least 1, 2, 3 or 4 of the genes. In a specific embodiment, the expression level of each of all the genes is evaluated.

[0085] The human BCL2 gene (also known as BCL2 apoptosis regulator (Gene ID: 596, updated on June 20, 2021)) encodes an integral mitochondrial outer membrane protein that blocks apoptotic death in some cells (e.g., lymphocytes). The human BCL2 gene encodes two transcripts generated by alternative splicing: a 6881 bp BCL2 transcript variant α (NCBI Reference Sequence: NM_000633.3, updated on July 1, 2021) and a 1595 bp BCL2 transcript variant β (NCBI Reference Sequence: NM_000657.3, updated on July 1, 2021), which encode BCL2 isoform α protein (NCBI Reference Sequence: NP_000624.2, updated on July 1, 2021) and BCL2 isoform β protein (NCBI Reference Sequence: NP_000648.2, updated on July 1, 2021), respectively.

[0086] The human CISH gene (cytokine-induced SH2-containing protein, Gene ID: 1154, updated on June 20, 2021) encodes a protein containing an SH2 domain and a SOCS box domain, which belongs to the cytokine-induced STAT inhibitor (CIS), also known as suppressor of cytokine signaling (SOCS) or STAT-induced STAT inhibitor (SSI) protein family. The human CISH gene encodes two transcripts: 2176bp CISH transcript variant 1 (NCBI reference sequence: NM_013324.7, updated on July 1, 2021) and 2019bp CISH transcript variant 2 (NCBI reference sequence: NM_145071.4, updated on July 1, 2021), which encode CISH subtype 1 protein (NCBI reference sequence: NP_037456.5, updated on July 1, 2021) and CISH subtype 2 protein (NCBI reference sequence: NP_659508.1, updated on July 1, 2021), respectively.

[0087] The human PTGER2 gene (prostaglandin E receptor 2, Gene ID: 5732, updated on June 20, 2021) encodes a receptor for prostaglandin E2, a metabolite of arachidonic acid with different biological activities in various tissues. The human PTGER2 gene encodes a 2548 bp transcript (NCBI Reference Sequence: NM_000956.4, updated on June 24, 2021), which encodes the PTGER2 protein (NCBI Reference Sequence: NP_000947.2, updated on June 24, 2021).

[0088] The human DPP4 gene (Dipeptidyl peptidase 4, Gene ID: 1803, updated on June 28, 2021) (also known as: ADABP, ADCP2, CD26, DPPIV and TP103) encodes dipeptidyl peptidase 4, which is identical to adenosine deaminase complex protein 2 and T cell activation antigen CD26. The human DPP4 gene encodes 4 transcripts: 3573 bp DPP4 transcript variant 1 (NCBI Reference Sequence: NM_001935.4, updated on June 29, 2021), 3570 bp DPP4 transcript variant 2 (NCBI Reference Sequence: NM_001379604.1, updated on July 1, 2021), 3567 bp DPP4 transcript variant 3 (NCBI Reference Sequence: NM_001379605.1, updated on July 1, 2021). June 30), 3519bp DPP4 transcript variant 4 (NCBI reference sequence: NM_001379606.1, updated on July 1, 2021), the four transcripts encode four protein isoforms: DPP4 isoform 1 (NCBI reference sequence: NP_001926.2, updated on June 29, 2021), DPP4 isoform 2 (NCBI reference sequence: NP_001366533.1, updated on July 1, 2021), DPP 4 isoform 3 (NCBI reference sequence: NP_001366534.1, updated on June 30, 2021) and DPP 4 isoform 4 (NCBI reference sequence: NP_001366535.1, updated on July 1, 2021).

[0089] The human SOCS2 gene (Gene ID: 8835, updated on 11 June 2021) (also known as: CIS2, Cish2, SOCS-2, SSI-2, SSI2, STATI2) encodes a member of the suppressor of cytokine signaling (SOCS) family. The human SOCS2 gene encodes 5 transcripts: 2606 bp SOCS2 transcript variant 1 (NCBI Reference Sequence: NM_003877.5, updated on 27 June 2021), 2653 bp SOCS2 transcript variant 2 (NCBI Reference Sequence: NM_001270467.2, updated on 27 June 2021), 2581 bp SOCS2 transcript variant 3 (NCBI Reference Sequence: NM_001270468.2, updated on 27 June 2021). June 27, 2021), 2431bp SOCS2 transcript variant 4 (NCBI reference sequence: NM_001270469.2, updated on June 27, 2021), 2888bp SOCS2 transcript variant 5 (NCBI reference sequence: NM_001270470.1, updated on June 23, 2021), 2386bp SOCS2 transcript variant 6 (NCBI reference sequence: NM_001270471.2, updated on June 26, 2021). These transcripts encode a 198 amino acid SOCS2 protein (NCBI reference sequence: NP_003868.1, updated on June 27, 2021).

[0090] The human FLT3LG gene (fms-related receptor tyrosine kinase 3 ligand, Gene ID: 2323, updated on June 11, 2021) (also known as: FL, FLG3L, FLT3L) encodes a protein that controls the development of dendritic cells. The human FLT3LG gene encodes 5 transcripts: 1101bp FLT3LG transcript variant 1 (NCBI reference sequence: NM_001204502.2, updated on June 27, 2021), 1051bp FLT3LG transcript variant 2 (NCBI reference sequence: NM_001204503.2, updated on June 27, 2021), 1050bp FLT3LG transcript variant 3 (NCBI reference sequence: NM_001459.4, updated on June 26, 2021), 1078bp FLT3LG transcript variant 4 (NCBI reference sequence: NM_001278637.2, updated on May 3, 2021), 1067bp FLT3LG transcript variant 5 (NCBI reference sequence: NM 001278638.2, updated on May 3, 2021). These transcripts encode two protein isoforms, FLT3LG isoform 1 precursor protein (NCBI Reference Sequence: NP_001450.2, updated on June 26, 2021) and FLT3LG isoform 2 (NCBI Reference Sequence: NP_001265566.1, updated on May 3, 2021).

[0091] The gene expression profile of the gene can be determined by any suitable method known to those skilled in the art.

[0092] The term "gene expression profile" or "gene signature" refers to the expression pattern of at least one gene in the above-mentioned gene set in a cell that appears due to a biological process in the cell (herein, the action of an IL7R antagonist or agonist). According to the present disclosure, the gene expression profile of the biomarker can be determined by measuring the relative amount of the product gene expressed in cells treated with an ILR7 antagonist (e.g., an anti-IL7R antagonist antibody or an antigen-binding fragment thereof) or an IL7R agonist as described above, preferably by performing a single sample GSEA (ssGSEA) in the GSVA algorithm, by calculating the gene set enrichment score for each sample as the normalized difference of the empirical cumulative distribution function of the gene expression ranking inside and outside the gene set.

[0093] Typically, these methods include measuring the amount of mRNA or protein as described above. The method for measuring the amount of mRNA is well known in the art. For example, the mRNA contained in the sample is first extracted according to standard methods, for example, using a lyase or a chemical solution, or extracted by a nucleic acid binding resin according to the manufacturer's instructions. Then, as described in the disclosed embodiments, the extracted mRNA is detected by hybridization (e.g., Northern blot analysis) and / or amplification (e.g., RT-PCR) using specific primer pairs and probes for the gene. Quantitative or semi-quantitative RT-PCR is preferred. In another specific embodiment, the mRNA expression level is measured by RNA seq method.

[0094] In some embodiments, the expression levels of the genes measured by, for example, quantitative RT-PCR are normalized by subtracting the expression level of a housekeeping gene determined in the same experiment from each gene, and the gene expression profile may correspond to the normalized gene expression level of one gene or to the sum of the normalized gene expression levels of each of at least two, three, preferably four genes selected from the BCL2, CISH, PTGER2, and DPP4 genes, more preferably to the sum of the normalized gene expression levels of each of 4, 5, or 6 genes selected from the BCL2, CISH, PTGER2, DPP4, SOCS2, and FLT3LG genes.

[0095] In another embodiment, determining the gene expression profile comprises determining the expression level of the gene, in particular determining the expression level of the gene by RNA-seq or DNA microarray.

[0096] In vitro methods for assessing therapeutic response to IL7 receptor modulator therapy during treatment.

[0097] In a specific embodiment, the expression profile of at least one of these genes, preferably 2, 3, 4, 5, and more preferably a combination of all genes provides information for monitoring the antagonist or agonist effect of a compound (IL7R antagonist (e.g., anti-IL7R antagonist antibody or antigen-binding fragment thereof) or IL7R agonist) in a patient during treatment and thereby monitoring the efficacy of the treatment.

[0098] The biomarkers disclosed herein enable classification of patients as responders to the treatment by determining the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in a patient sample, and by determining whether the gene expression profile of the genes is high or low compared to a control value.

[0099] The present disclosure relates to an in vitro method for evaluating a human patient's therapeutic response to treatment with an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof) by determining the gene expression profile of 1, 2, 3 or 4 genes selected from human BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS and FLT3LG genes, in a patient sample that has received at least one dose of an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof), wherein a lower gene expression profile of the gene in the patient sample compared to a control value indicates that the patient may respond to the antagonist treatment.

[0100] In another specific embodiment, the present disclosure relates to an in vitro method for evaluating a human patient's therapeutic response to treatment with an IL7R agonist (e.g., IL7) by determining the gene expression profile of 1, 2, 3 or 4 genes selected from human BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS and FLT3LG genes, in a patient sample that has received at least one dose of an IL7R agonist, wherein a higher gene expression profile of the gene in the patient sample compared to a control value indicates that the patient may respond to the agonist treatment.

[0101] As used herein, the term "assessing a therapeutic response to a treatment" refers to being able to assess whether a treatment given to a patient is likely to be effective for the patient (e.g., providing a measurable benefit or positive medical response to the patient) after a period of time following administration of the treatment. In other words, according to the present disclosure, assessing a response to a treatment refers to being able to assess the effect of an IL7R antagonist (e.g., an anti-IL7R antagonist antibody or antigen-binding fragment thereof) or an IL7R agonist in a patient's cells, which can be correlated with the patient's likely response to the treatment.

[0102] In particular, the antagonist or agonist effect of the compound in the patient and the possible response of the patient to treatment with the antagonist or agonist are assessed by comparing the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in the patient who received at least one dose of the antagonist with the control value.

[0103] According to the method for evaluating treatment response of the present disclosure, a sample is previously collected from a patient who has received at least one dose of an IL7R antagonist (eg, an anti-IL7R antagonist antibody or antigen-binding fragment thereof) or an IL7R agonist.

[0104] The term "patient sample" refers to any biological sample from a patient. Examples of such samples include tissues, cell samples, organs, biopsy samples, tumor samples, etc.

[0105] Preferred biological samples are peripheral blood mononuclear cells, tissues containing infiltrating immune cells, or tumors.

[0106] In a specific embodiment, the sample comprises immune cells. Immune cells include lymphocytes, such as B cells and T cells and natural killer cells. The immune cells can be obtained from many non-limiting sources, including peripheral blood mononuclear cells, bone marrow, lymph node tissue, umbilical cord blood, thymus tissue, tissue from the site of infection, ascites, pleural effusion, spleen tissue and tumor, and a unit of blood collected from a subject using any technique known to the technician. Immune cells can be extracted from blood or derived from stem cells. In a preferred embodiment, the sample is a tissue sample, preferably a tumor tissue containing infiltrating immune cells from a cancer patient or a blood patient sample, more preferably isolated human peripheral blood mononuclear cells.

[0107] According to the present disclosure, a patient who has received treatment with an IL7R antagonist or agonist refers to a patient who has received at least one dose of an IL7R antagonist (e.g., an anti-IL7R antagonist antibody or antigen-binding fragment thereof) or an IL7R agonist. The therapeutic response can be assessed after each dose of an IL7R antagonist or IL7R agonist is administered throughout the treatment process according to the present method to monitor the therapeutic response over time.

[0108] As used herein, the term "control value" may refer to a gene signature (i.e., at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2, and DPP4 genes, preferably at least 1 selected from BCL2, CISH, PTGER2, DPP4, SOCS2, and FLT3LG genes) in a biological sample obtained from the patient at different times (preferably before administration of a dose of an IL7R antagonist (e.g., an anti-IL7R antagonist antibody or antigen-binding fragment thereof), or before administration of any dose of the antagonist, or before any treatment for the condition or disease). , 2, 3, 4, 5 or 6 genes), or refers to a gene signature in a biological sample obtained from patient cells cultured in vitro without the antagonist or agonist or with a compound (e.g., an antibody) known to have no effect on the IL7 / IL7R pathway (i.e., a gene expression profile of at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, and DPP4 genes, preferably a gene expression profile of at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2, and FLT3LG genes). Alternatively, the control value can be a predetermined value, such as a threshold value, a standard value, or a range obtained from a source other than patient data. The control predetermined value can be determined based on comparative measurements between patients prior to administration of a dose of the antagonist (e.g., an anti-IL7R antagonist antibody or antigen-binding fragment thereof) and patients who have received administration of a dose of the antagonist, or comparative measurements between patient cells cultured in vitro with or without the antagonist or agonist or with a compound (e.g., an antibody) known to have no effect on the IL7 / IL7R signaling pathway.

[0109] In a specific embodiment, according to the method of evaluating the therapeutic response of IL7 receptor modulator treatment during the treatment process disclosed herein, the control value refers to the gene signature (i.e., the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably the gene expression profile of at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes) in the biological sample obtained from the patient at different times (preferably before the administration of a dose of IL7R antagonist (e.g., anti-IL7R antagonist antibody or antigen-binding fragment thereof), or before the administration of any antagonist dose, or before any treatment for the condition or disease), or the control value refers to a control predetermined value determined based on the following: comparative measurements between patients before the administration of a dose of antagonist (e.g., anti-IL7R antagonist antibody or antigen-binding fragment thereof) and patients who have received the antagonist dose.

[0110] In a preferred embodiment, the gene expression profile of biomarkers in a sample collected from the patient is assessed at least 1, 2, 3 or 7 days after administration of the antibody dose, preferably 10, 14, 21, 28 days, and more particularly at least 30, 35, 40, 45, 50, 55, 60, 70, 80, 90, 100, 120 days after administration of the antibody dose.

[0111] A lower gene expression profile of the biomarker in a sample from a patient who has received at least one dose of an IL7R antagonist (e.g., an anti-IL7R antagonist antibody or antigen-binding fragment thereof) compared to a control value is associated with antagonism of the antagonist (e.g., an anti-IL7R antagonist antibody or antigen-binding fragment thereof) in the patient, and therefore with the patient's therapeutic response to treatment with the IL7R antagonist (e.g., an anti-IL7R antagonist antibody or antigen-binding fragment thereof).

[0112] Typically, the gene expression profile of the biomarkers in the patient sample is considered to be lower than the control value if the log2 fold change of the gene expression profile of at least 1, 2, 3 or 4 genes selected from the BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in the patient relative to the control value gene expression profile is lower than at least 0.1, preferably 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, more preferably 1, 2, 3, 4, and further preferably 5.

[0113] In particular, when the gene expression levels are determined by quantitative RT-PCR, the gene expression profile of the biomarker in the patient sample is considered to be lower than the control value if the log2 fold change of the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in the patient relative to the control value gene expression profile is lower than at least 0.4.

[0114] In another specific embodiment, when gene expression levels are determined by RNA-seq, the gene expression profile of the biomarker in the patient sample is considered to be lower than the control value if the log2 fold change of the gene expression profile of at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2, and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2, and FLT3LG genes in the patient relative to the control value gene expression profile is less than at least 0.1.

[0115] If, after treatment with an IL7R antagonist (e.g., an anti-IL7R antagonist antibody or antigen-binding fragment thereof), the gene expression profile of the biomarker in a sample of a patient who has received at least one dose of the antagonist is not below a control value, then treatment should be interrupted or modified, for example by changing the IL7R antagonist compound or by changing the concentration of the IL7R antagonist. The methods of assessing treatment response disclosed herein can indicate the success or failure of treating a patient with an IL7R antagonist (e.g., an anti-IL7R antagonist antibody or antigen-binding fragment).

[0116] In another specific embodiment, a higher gene expression profile of a biomarker in a sample of a patient receiving at least one dose of an IL7R agonist compared to a control value is associated with an agonist effect of the agonist in the patient, and thus with a therapeutic response of the patient to treatment with the IL7R agonist.

[0117] Typically, if the log2 fold change of at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in the patient relative to the control value gene expression profile is higher than at least 0.1, preferably 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, more preferably 1, 2, 3, even more preferably 4, and even more preferably 5, the gene expression profile of the biomarker in the patient sample is considered to be higher than the control value.

[0118] In particular, when the gene expression levels are determined by quantitative RT-PCR, if the log2 fold change of the gene expression profile of at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in the patient relative to the control value gene expression profile is higher than at least 0.4, then the gene expression profile of the biomarker in the patient sample is considered to be higher than the control value.

[0119] In another specific embodiment, when gene expression levels are determined by RNA-seq, the gene expression profile of the biomarker in the patient sample is considered to be higher than the control value if the log2 fold change of the gene expression profile of at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2, and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2, and FLT3LG genes in the patient relative to the control value gene expression profile is higher than at least 0.1.

[0120] If, after treatment with an IL7R agonist, the gene expression profile of the biomarker in a sample of a patient who has received at least one dose of the agonist is not above the control value, then treatment should be interrupted or modified, for example by changing the IL7R antagonist compound or by changing the concentration of the IL7R antagonist. The disclosed methods for assessing treatment response can indicate the success or failure of treating a patient with an IL7R agonist.

[0121] According to the present disclosure, a patient treated with an IL7R antagonist (eg, an anti-IL7R antagonist antibody or antigen-binding fragment) suffers from a condition or disease associated with enhanced IL7-induced IL7R signaling pathway (IL7 / IL7R pathway).

[0122] Various pathological conditions are associated with abnormally high levels of IL-7 and / or IL-7R. The disease associated with the enhanced IL7 signaling pathway induced by IL7 can be selected from autoimmune diseases, inflammatory diseases, allergic diseases, cancer diseases, infectious diseases, respiratory diseases and transplantation-related diseases involving activation or proliferation of CD127-positive pathological cells, particularly autoimmune diseases or inflammatory diseases involving activation or proliferation of CD127-positive cells, more preferably chronic inflammatory diseases (e.g., Sjögren's syndrome) or inflammatory bowel diseases (e.g., ulcerative colitis).

[0123] Sjögren's syndrome is an autoimmune disease that primarily affects the exocrine glands, resulting in impaired function. Sjögren's syndrome is an autoimmune disease that is characterized by inflammatory manifestations and can be classified as an inflammatory disease. Symptoms of Sjögren's syndrome include, for example, dry eyes and dry mouth. Sjögren's syndrome is often associated with other immune system diseases such as rheumatoid arthritis, lupus erythematosus or progressive systemic sclerosis.

[0124] In a specific embodiment, the disease associated with enhanced IL7R signaling pathway induced by IL7 is an infectious disease, preferably selected from chronic infectious diseases, primary and secondary infectious diseases.

[0125] In a specific embodiment, the disease associated with enhanced IL7R signaling pathway induced by IL7 is an autoimmune disease, preferably selected from diabetes, multiple sclerosis, Sjögren's syndrome, lupus, psoriasis and atopic dermatitis.

[0126] In another specific embodiment, the disease associated with increased IL7R signaling pathway induced by IL7 is a chronic inflammatory disease, preferably selected from rheumatoid arthritis, ankylosing spondylitis and inflammatory bowel disease.

[0127] In another specific embodiment, the disease associated with enhanced IL7-induced IL7R signaling pathway is an allergic disease.

[0128] The disease associated with enhanced IL7R signaling pathway induced by IL7 may also be cancer, such as blood cancer, preferably selected from T-cell acute lymphoblastic leukemia, B-cell acute lymphoblastic leukemia, chronic lymphocytic leukemia, T-cell prolymphocytic leukemia and Hodgkin's lymphoma.

[0129] In a preferred embodiment, the disease associated with enhanced IL7R signaling pathway induced by IL7 is Sjögren's syndrome or inflammatory bowel disease, such as ulcerative colitis or Crohn's disease.

[0130] According to the present disclosure, patients treated with IL7R agonists suffer from a condition or disease associated with impaired healthy T cell activity, preferably a condition or disease associated with impaired healthy T cell activity that can be rescued by the IL7R signaling pathway induced by IL7, preferably a cancer disease or infectious disease that develops independently of the IL7R signaling pathway. In a specific embodiment, the patient treated with an IL7R agonist suffers from a condition or disease that requires an enhanced immune response (e.g., immunotherapy in a cancer disease or infectious disease).

[0131] In another specific embodiment, the present invention relates to the therapeutic use of an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof) or agonist in a human patient in need thereof, wherein the antagonist (particularly the antibody) or agonist is administered to the patient after the patient has been administered at least one dose of an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof) or an IL7R agonist, and when the patient is assessed as likely to respond to treatment with the antagonist or agonist by the method described above.

[0132] The present invention also relates to a method for treating a disease associated with enhanced IL7R signaling pathway induced by IL7 or a disease associated with impaired healthy T cell activity as described above in a human patient in need thereof, comprising:

[0133] (a) providing a sample previously collected from a patient who has received at least one dose of an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof) or an IL7R agonist;

[0134] (b) determining whether the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably the gene expression profile of at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, FLT3LG and SOCS2 genes is lower or higher compared to a control value, wherein a lower or higher gene expression profile of the gene indicates that the patient may respond to the IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof) or IL7R agonist treatment, respectively;

[0135] (c) re-administering a therapeutically effective amount of an IL7R antagonist (eg, an anti-IL7 receptor antagonist antibody or antigen-binding fragment thereof) or an IL7R agonist to the patient who is assessed to be likely to respond to treatment with the antagonist or agonist.

[0136] In other words, the present disclosure relates to a method for evaluating a therapeutic response to an IL7R antagonist treatment in a human patient in need thereof, the patient suffering from a disease associated with an enhanced IL7R signaling pathway induced by IL7 as described above, comprising:

[0137] (a) providing a sample collected from the patient at a first time point or an earlier time point;

[0138] (b) providing a sample collected from the patient at a second or subsequent time point;

[0139] (b) determining whether the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, FLT3LG and SOCS2 genes, in a patient sample collected at a second or subsequent time point is lower compared to the patient sample collected at the first or earlier time point, wherein a lower gene expression profile indicates that the patient is likely to respond to the treatment;

[0140] (c) re-administering a therapeutically effective amount of an IL7R antagonist (eg, an anti-IL7 receptor antagonist antibody or antigen-binding fragment thereof) to the patient who is assessed to be likely to respond to treatment with the antagonist.

[0141] The present disclosure also relates to a method for evaluating a therapeutic response to an IL7R agonist treatment in a human patient in need thereof, the patient suffering from a condition or disease associated with impaired healthy T cell activity, preferably, the condition or disease can be rescued by an IL7R signaling pathway induced by IL7, the method comprising:

[0142] (a) providing a sample collected from the patient at a first time point or an earlier time point,

[0143] (b) providing a sample collected from the patient at a second or subsequent time point,

[0144] (b) determining whether the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably the gene expression profile of at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, FLT3LG and SOCS2 genes, is higher in the patient sample collected at the second time point or a subsequent time point compared to the patient sample collected at the first time point or an earlier time point, wherein a higher gene expression profile indicates that the patient is likely to respond to the treatment;

[0145] (c) re-administering a therapeutically effective amount of an IL7R agonist to said patient who is assessed to be likely to respond to treatment with said agonist.

[0146] The present disclosure relates to the use of an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof as described above) or an IL7R agonist in the preparation of a medicament for treating a disease associated with an IL7-induced IL7R signaling pathway or a disease associated with impaired activity of healthy T cells in a human patient in need thereof, wherein the antagonist or agonist is administered to the patient after the patient has been administered at least one dose of the IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof as described above) or IL7R agonist, and when the patient is assessed as likely to respond to treatment with the antagonist or agonist by the method described above.

[0147] In a specific embodiment, the disorder or disease associated with IL7-induced enhancement of the IL7 signaling pathway treated with an IL7R antagonist is selected from autoimmune diseases, inflammatory diseases, allergic diseases, cancer diseases, infectious diseases, respiratory diseases and transplantation-related diseases involving activation or proliferation of CD127-positive pathological cells, in particular autoimmune diseases or inflammatory diseases involving activation or proliferation of CD127-positive cells, more preferably chronic inflammatory diseases (such as Sjögren's syndrome) or inflammatory bowel disease (such as ulcerative colitis), preferably diabetes, sarcoidosis, cancer, autoimmune diseases (preferably selected from multiple sclerosis, Sjögren's syndrome, lupus, psoriasis and atopic dermatitis) or chronic inflammatory diseases (preferably selected from rheumatoid arthritis, ankylosing spondylitis and inflammatory bowel disease (preferably ulcerative colitis or Crohn's disease)).

[0148] In a specific embodiment, the IL7R antagonist is an anti-IL7R antagonist antibody or an antigen-binding fragment thereof according to the present disclosure, which comprises: (a) a variable heavy chain comprising three CDRs, wherein VHCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 1, VHCDR2 comprises or consists of the amino acid sequence of SEQ ID NO: 2, and VHCDR3 comprises or consists of the amino acid sequence of SEQ ID NO: 3 or 11; (b) a variable light chain comprising three CDRs, wherein VLCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 4 or 12, VLCDR2 comprises or consists of the amino acid sequence of SEQ ID NO: 5 or 13, and VLCDR3 comprises or consists of the amino acid sequence of SEQ ID NO: 6.

[0149] In a preferred embodiment, the anti-IL7 receptor antagonist antibody or its antigen-binding fragment comprises: (a) a variable heavy chain comprising three CDRs, wherein VHCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 1, VHCDR2 comprises or consists of the amino acid sequence of SEQ ID NO: 2, and VHCDR3 comprises or consists of the amino acid sequence of SEQ ID NO: 3; (b) a variable light chain comprising three CDRs, wherein VLCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 4, VLCDR2 comprises or consists of the amino acid sequence of SEQ ID NO: 5, and VLCDR3 comprises or consists of the amino acid sequence of SEQ ID NO: 6.

[0150] In a specific embodiment, the anti-IL7R antagonist antibody or antigen-binding fragment thereof comprises a heavy chain variable domain and a light chain variable domain, the heavy chain variable domain comprising or consisting of an amino acid sequence selected from SEQ ID NOs: 14-17, and the light chain variable domain comprising or consisting of an amino acid sequence selected from SEQ ID NOs: 18-21. Preferably, the anti-IL7R antagonist is the N13B2h3 antibody or antigen-binding fragment thereof as described in WO2015 / 189302 and comprises a heavy chain variable domain and a light chain variable domain, the heavy chain variable domain comprising or consisting of an amino acid sequence selected from SEQ ID NOs: 17, and the light chain variable domain comprising or consisting of an amino acid sequence selected from SEQ ID NOs: 21. More preferably, the antibody or antigen-binding fragment thereof comprises a complete heavy chain and a complete light chain, the complete heavy chain comprising or consisting of SEQ ID NO: 22, and the complete light chain comprising SEQ ID NO: NO: 23 or composed thereof.

[0151] In another specific embodiment, the anti-IL7R antagonist antibody or its antigen-binding fragment comprises a heavy chain variable domain and a light chain variable domain, the heavy chain variable domain comprises or consists of the amino acid sequence SEQ ID NO: 7, and the light chain variable domain comprises or consists of an amino acid sequence selected from SEQ ID NO: 8, 24-26.

[0152] In a more preferred embodiment, the anti-IL7R antagonist antibody or its antigen-binding fragment comprises a heavy chain variable domain and a light chain variable domain, the heavy chain variable domain comprises or consists of the amino acid sequence SEQ ID NO: 7, and the light chain variable domain comprises or consists of the amino acid sequence SEQ ID NO: 8; preferably, the antibody or its antigen-binding fragment comprises a complete heavy chain and a complete light chain, the complete heavy chain comprises or consists of SEQ ID NO: 9, and the complete light chain comprises or consists of SEQ ID NO: 10.

[0153] In the context of the present disclosure, the terms "treat" or "treatment" as used herein refers to reversing, alleviating, inhibiting the development of, or preventing the disease or condition to which the term applies, or reversing, alleviating, inhibiting the development of, or preventing one or more symptoms of the disease or condition to which the term applies.

[0154] As used herein, "therapeutically effective amount" or "effective amount" refers to the amount of the composition sufficient to achieve treatment when the composition is administered to a subject to treat a condition, disease or condition. The therapeutically effective amount will vary depending on the compound, formulation or composition, the disease and its severity, and the age, weight, physical condition and responsiveness of the subject to be treated.

[0155] The IL7R antagonists described herein (e.g., anti-IL7R antagonist antibodies or antigen-binding fragments thereof) or IL7R agonists can be administered by any means known to those skilled in the art, including but not limited to intravenous, oral, intratumoral, intralesional, intradermal, topical, intraperitoneal, intramuscular, parenteral, subcutaneous, and local administration. Thus, the composition can be formulated as an injectable, topical, or ingestible formulation. Administration of a compound or therapeutic agent to a subject according to the present disclosure can exhibit beneficial effects in a dose-dependent manner. Thus, within a broad range, it is expected that administration of a larger amount of the composition will result in an increased beneficial biological effect than administration of a smaller amount of the composition. In addition, it is expected to be effective at doses below the level at which toxicity occurs.

[0156] It will be understood that the specific dose of IL7R antagonist or agonist administered in any given case will be adjusted depending on the composition administered, the volume of the composition that can be effectively delivered to the site of administration, the disease to be treated or inhibited, the condition of the subject, and other relevant medical factors that may alter the activity of the composition or the response of the subject, as is well known to those skilled in the art.

[0157] For example, the specific dosage of an IL7R antagonist or agonist for a particular subject depends on age, weight, general health, diet, time and mode of administration, excretion rate, co-administered drugs, and the severity of the particular disease for which the therapy is applied. The dosage for a given patient can be determined using conventional considerations, such as by routine comparison of the different activities of the compositions described herein and known drugs, such as by appropriate conventional pharmacological protocols. The composition can be administered in a single dose regimen or a multiple dose regimen.

[0158] Suitable dosage ranges for IL7R antagonists (e.g., anti-IL7R antagonist antibodies or antigen-binding fragments thereof) or IL7R agonists can be on the order of several hundred micrograms of agent, ranging from about 0.001 to 100 mg / kg, preferably about 0.1 to 20 mg / kg, more preferably about 1 to 12 mg / kg, and even more preferably 8-12 mg / kg. For example, a fixed dose of 400, 450, 500, 600, 700, 850, 900 mg can be used.

[0159] A method for assessing the likelihood of a human patient's therapeutic response to treatment with an IL7R modulator prior to treatment.

[0160] The combined expression profile of biomarkers can also provide information on the patient's status, classifying the patient as likely to respond before any treatment and recommending treatment of the patient with an antagonist (e.g., an anti-IL7 receptor antagonist antibody or antigen-binding fragment thereof) or IL7R agonist described herein.

[0161] For example, the assay may involve culturing a sample from the patient in the presence of an IL7R antagonist or agonist prior to treatment to assess the biological response.

[0162] Thus, in another specific embodiment, the present disclosure relates to a method for assessing the likelihood of a human patient's response to treatment with an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or antigen-binding fragment thereof) or agonist prior to treatment with the antagonist or agonist, comprising the steps of:

[0163] a) culturing a sample previously collected from the patient prior to treatment with the antagonist or agonist in the presence of an IL7 receptor antagonist and / or an IL7R agonist;

[0164] b) determining the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably the gene expression profile of at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes, wherein a lower or higher gene expression profile of the genes in the cultured sample compared to the control value indicates that the patient may respond to antagonist or agonist treatment, respectively.

[0165] As used herein, the term "assessing the likelihood of a treatment response" refers to the ability to assess whether a patient is responsive to an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or antigen-binding fragment thereof) or an IL7R agonist treatment, in other words, assessing whether an antagonist or agonist treatment is effective for the patient before treatment (e.g., providing a measurable benefit or positive medical response to the patient). Such an ability to assess whether a patient is responsive to the antagonist or agonist treatment is typically performed before the patient begins antagonist or agonist treatment.

[0166] According to the method for evaluating the possibility of treatment response, a sample is collected from the patient before the antagonist or agonist treatment begins. The sample is preferably an immune cell, more preferably a peripheral blood mononuclear cell, collected from the patient before the antagonist or agonist treatment.

[0167] In a specific embodiment, the cell is an immune cell. Immune cells include lymphocytes, such as B cells and T cells, and natural killer cells. The immune cells can be obtained from many non-limiting sources, including peripheral blood mononuclear cells, bone marrow, lymph node tissue, umbilical cord blood, thymus tissue, tissue from the site of infection, ascites, pleural effusion, spleen tissue and tumor, and a unit of blood collected from a subject using any technique known to the technician. Immune cells can be extracted from blood or derived from stem cells. In a preferred embodiment, the sample is a tissue sample, preferably a tumor tissue containing infiltrating immune cells from a cancer patient or a blood patient sample, more preferably isolated human peripheral blood mononuclear cells.

[0168] Subsequently, the sample is cultured in vitro in the presence of an IL7R antagonist (eg, an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof) and / or an IL7R agonist.

[0169] The sample can be cultured in a culture medium under culture conditions known in the art to amplify, and then harvested for analysis of gene expression levels. In a preferred embodiment, the sample is cultured at 37° C. for at least 3 hours, preferably 2, 4, 5 or 6 hours, and then harvested for further analysis.

[0170] Many culture media are commercially available and are well known to those skilled in the art. The culture medium may be a minimal medium, which particularly comprises the mineral salts, amino acids, vitamins and carbon sources necessary for the cells and a buffer system for adjusting the pH value. Minimal culture media that can be used in the method of the present invention include, but are not limited to, for example, DMEM / F12 culture medium, DMEM culture medium, RPMI culture medium, Ham's F12 culture medium, IMDM culture medium and KnockOut TM DMEM medium (Life Technologies). The medium may contain interleukin-7, preferably human recombinant interleukin-7.

[0171] In a specific embodiment, in the method for evaluating the possibility of a human patient's response to treatment with an IL7R antagonist, in step a), a sample collected from the patient prior to treatment with the antagonist is cultured in the presence of an IL7 receptor antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof) and an IL7 cytokine (preferably human recombinant interleukin-7) to allow the cells to expand.

[0172] The culture medium contains an IL7R antagonist, preferably an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof, more preferably an IL7R antagonist at a concentration of 1-10000 ng / mL (preferably 500-10000 ng / mL, more preferably 1000-10000 ng / mL).

[0173] The culture medium comprises an IL7R agonist, preferably at a concentration of 1 to 10000 ng / mL (preferably 500 to 10000 ng / mL, more preferably 1000 to 10000 ng / mL).

[0174] After a cell culture step with an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof) and / or an IL7R agonist, the cells are harvested and the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably the gene expression profile of at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes, is determined in the cultured cells as described above.

[0175] The method also includes determining whether the gene expression profile of the gene is high or low compared to a control value. For example, a gene expression profile of at least one of the genes that is lower or higher than a control value may indicate that the patient may respond to antagonist or agonist treatment, respectively.

[0176] In a specific embodiment, according to the method of assessing the likelihood of a treatment response in a human patient disclosed herein, the control value can be the gene expression profile of the gene in patient cells cultured in vitro without the antagonist or agonist or with a compound (e.g., an antibody) known to have no effect on the IL7 / IL7R pathway, or a control predetermined value established based on comparative measurements between patient cells cultured in vitro with or without the antagonist or agonist or with a compound (e.g., an antibody) known to have no effect on the IL7 / IL7R pathway.

[0177] A lower gene expression profile of at least one biomarker in patient cells cultured in vitro with an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or antigen-binding fragment thereof) compared to a control value indicates an IL7R antagonist effect in the patient cells and is therefore associated with the likelihood of a therapeutic response of the patient to IL7R antagonist treatment.

[0178] Generally, if the log2 fold change of the gene expression profile of a gene in a patient sample cultured in vitro with an IL7R antagonist (e.g., an anti-IL7R antagonist antibody or an antigen-binding fragment thereof) relative to the control value gene expression profile is less than at least 0.1, preferably 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, more preferably 1, 2, 3, 4, and even more preferably 5, the gene expression profile of the gene in the patient is considered to be lower than the control value.

[0179] In particular, when the gene expression levels are determined by quantitative RT-PCR, the gene expression profile of the biomarker in the patient sample is considered to be lower than the control value if the log2 fold change of the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in the patient relative to the control value gene expression profile is lower than at least 0.4.

[0180] In another specific embodiment, when gene expression levels are determined by RNA-seq, the gene expression profile of the biomarker in the patient sample is considered to be lower than the control value if the log2 fold change of the gene expression profile of at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2, and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2, and FLT3LG genes in the patient relative to the control value gene expression profile is less than at least 0.1.

[0181] In another specific embodiment, an increased gene expression profile of at least one biomarker in patient cells cultured in vitro with an IL7R agonist compared to a control value indicates an IL7R agonist effect in said patient cells and is therefore associated with the likelihood of a therapeutic response of the patient to IL7R agonist treatment.

[0182] Generally, if the log2 fold change of the gene expression profile of a gene in a patient sample cultured in vitro with an IL7R agonist relative to the gene expression profile of the control value is greater than at least 0.1, preferably 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, more preferably 1, 2, 3, 4, and even more preferably 5, the gene expression profile of the gene in the patient is considered to be higher than the control value.

[0183] In particular, when the gene expression levels are determined by quantitative RT-PCR, if the log2 fold change of the gene expression profile of at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in the patient relative to the control value gene expression profile is higher than at least 0.4, then the gene expression profile of the biomarker in the patient sample is considered to be higher than the control value.

[0184] In another specific embodiment, when gene expression levels are determined by RNA-seq, the gene expression profile of the biomarker in the patient sample is considered to be higher than the control value if the log2 fold change of the gene expression profile of at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2, and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in the patient relative to the control value gene expression profile is higher than at least 0.1.

[0185] According to the present disclosure, patients treated with an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof) suffer from a condition or disease associated with enhanced IL7R signaling induced by IL7, wherein the condition or disease is preferably selected from the above-mentioned autoimmune diseases, inflammatory diseases, allergic diseases, cancer diseases, infectious diseases, respiratory diseases and transplantation-related diseases involving activation or proliferation of CD127-positive pathological cells, in particular, autoimmune diseases or inflammatory diseases involving activation or proliferation of CD127-positive cells, more preferably chronic inflammatory diseases (e.g., Sjögren's syndrome) or inflammatory bowel diseases (e.g., ulcerative colitis).

[0186] According to the present disclosure, a patient treated with an IL7R agonist suffers from a condition or disease associated with impaired healthy T cell activity, preferably a cancer disease or an infectious disease that is independent of the IL7R pathway for its own development.

[0187] The present disclosure also relates to the therapeutic use of an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof) or an IL7R agonist in human patients, wherein the patient is previously assessed as likely to respond to treatment with the antagonist or agonist by the methods described above prior to the treatment.

[0188] The present invention also relates to a method of treating a disease associated with IL7-induced IL7R pathway enhancement in a human patient in need thereof with an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof), comprising:

[0189] (a) culturing a sample collected from a patient prior to the treatment in the presence of an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof);

[0190] (b) determining whether the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, FLT3LG and SOCS2 genes in the sample is lower compared to a control value, wherein a lower gene expression profile in the patient sample compared to the control value indicates that the patient is likely to respond to the treatment; and

[0191] (c) administering a therapeutically effective amount of an IL7R antagonist (eg, an anti-IL7 receptor antagonist antibody or antigen-binding fragment thereof) to said patient assessed as likely to respond to said treatment.

[0192] The present disclosure also relates to methods of treating the above-mentioned diseases associated with impaired healthy T cell activity in a human patient in need thereof with an IL7R agonist, comprising:

[0193] (a) culturing a sample previously collected from a patient prior to said treatment with an IL7R agonist;

[0194] (b) determining whether the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, FLT3LG and SOCS2 genes in the sample is higher compared to a control value, wherein a higher gene expression profile in the patient sample compared to the control value indicates that the patient is likely to respond to the treatment; and

[0195] (c) administering to said patient assessed as likely to respond to said treatment a therapeutically effective amount of an IL7R agonist.

[0196] The present disclosure also relates to the use of an IL7R antagonist (e.g., an anti-IL7 receptor antagonist antibody or an antigen-binding fragment thereof) or an IL7R agonist in the preparation of a medicament for treating the above-mentioned diseases associated with the IL7 / IL7R pathway or diseases associated with impaired healthy T cell activity in human patients in need thereof, wherein the patient is pre-assessed as being likely to respond to treatment with the antagonist or agonist by the method described above.

[0197] In a specific embodiment, the anti-IL7R antagonist is an N13B2h1, N13B2h2 or N13B2h3 antibody or an antigen-binding fragment thereof as described in WO2015 / 189302, or an N13B2-hVL3, N13B2-hVL4, N13B2-hVL5 or N13B2-hVL6 antibody or an antigen-binding fragment thereof as described in WO2018 / 104483, and comprises: (a) a variable heavy chain comprising three CDRs, wherein VHCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 1, VHCDR2 comprises or consists of the amino acid sequence of SEQ ID NO: 2, and VHCDR3 comprises or consists of the amino acid sequence of SEQ ID NO: 3 or 11; (b) a variable light chain comprising three CDRs, wherein VLCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 4 or 12, VLCDR2 comprises NO: 5 or 13 or consist thereof, and VLCDR3 comprises or consists of the amino acid sequence of SEQ ID NO: 6.

[0198] In a preferred embodiment, the anti-IL7 receptor antagonist antibody or its antigen-binding fragment is the N13B2h3 antibody or its antigen-binding fragment as described in WO2015 / 189302, or the N13B2-hVL3, N13B2-hVL4, N13B2-hVL5 or N13B2-hVL6 antibody or its antigen-binding fragment (preferably the N13B2-hVL6 antibody or its antigen-binding fragment) as described in WO2018 / 104483, and comprises: (a) a variable heavy chain comprising three CDRs, wherein VHCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 1, VHCDR2 comprises or consists of the amino acid sequence of SEQ ID NO: 2, and VHCDR3 comprises or consists of the amino acid sequence of SEQ ID NO: 3; (b) a variable light chain comprising three CDRs, wherein VLCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 4, VLCDR2 comprises NO:5 or consist of the amino acid sequence, and VLCDR3 comprises or consists of the amino acid sequence of SEQ ID NO:6.

[0199] In a specific embodiment, the anti-IL7R antagonist antibody or antigen-binding fragment thereof comprises a heavy chain variable domain and a light chain variable domain, the heavy chain variable domain comprising or consisting of an amino acid sequence selected from SEQ ID NOs: 14-17, and the light chain variable domain comprising or consisting of an amino acid sequence selected from SEQ ID NOs: 18-21; preferably, the anti-IL7R antagonist is the N13B2h3 antibody or antigen-binding fragment thereof as described in WO2015 / 189302, and comprises a heavy chain variable domain and a light chain variable domain, the heavy chain variable domain comprising or consisting of an amino acid sequence of SEQ ID NO: 17, and the light chain variable domain comprising or consisting of an amino acid sequence of SEQ ID NO: 21; more preferably, the antibody or antigen-binding fragment thereof comprises a complete heavy chain and a complete light chain, the complete heavy chain comprising or consisting of SEQ ID NO: 22, and the complete light chain comprising SEQ ID NO: NO: 23 or composed thereof.

[0200] In another specific embodiment, the anti-IL7R antagonist is an N13B2-hVL3, N13B2-hVL4, N13B2-hVL5 or N13B2-hVL6 antibody or an antigen-binding fragment thereof as described in WO2018 / 104483, and comprises a heavy chain variable domain and a light chain variable domain, wherein the heavy chain variable domain comprises or consists of the amino acid sequence SEQ ID NO: 7, and the light chain variable domain comprises or consists of an amino acid sequence selected from SEQ ID NO: 8, 24-26.

[0201] In a more preferred embodiment, the anti-IL7R antagonist antibody or its antigen-binding fragment comprises a heavy chain variable domain and a light chain variable domain, the heavy chain variable domain comprises or consists of the amino acid sequence SEQ ID NO: 7, and the light chain variable domain comprises or consists of the amino acid sequence SEQ ID NO: 8; preferably, the antibody or its antigen-binding fragment comprises a complete heavy chain and a complete light chain, the complete heavy chain comprises or consists of SEQ ID NO: 9, and the complete light chain comprises or consists of SEQ ID NO: 10.

[0202] As noted above, the antagonists (preferably antibodies or antigen-binding fragments thereof) or agonists described herein can be administered by any means known to those of skill in the art.

[0203] Suitable dosage ranges for IL7R antagonists (preferably anti-IL7R antagonist antibodies or antigen-binding fragments thereof) or IL7R agonists may be of the order of several hundred micrograms of agent, ranging from about 0.001 to 100 mg / kg, preferably about 0.1 to 20 mg / kg, more preferably about 1 to 12 mg / kg, and even more preferably 8 to 12 mg / kg. For example, a fixed dose of 400, 450, 500, 600, 700, 850, 900 mg may be used.

[0204] Methods for Selecting IL7R Modulator Compounds

[0205] In another specific embodiment, the present disclosure relates to an in vitro method for selecting an IL7R antagonist compound (preferably an IL7Rα antagonist compound) that may be effective in treating the above-mentioned diseases associated with enhanced IL7R signaling pathway induced by IL7, the method comprising the following steps:

[0206] a) culturing human cells with the compound;

[0207] b) determining the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in said cell, and

[0208] c) selecting a compound which induces a lower gene expression profile of said gene in said cell compared to a control value.

[0209] In another specific embodiment, the present disclosure relates to an in vitro method for selecting an IL7R agonist compound that may be effective in treating the above-mentioned diseases associated with impaired healthy T cell activity, the method comprising the steps of:

[0210] a) culturing human cells with said agonist compound,

[0211] b) determining the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in the cell, and

[0212] c) selecting compounds which induce a higher gene expression profile of said gene, respectively, in said cells compared to a control value.

[0213] According to the method of selecting an IL7R antagonist or agonist compound of the present disclosure, the control value may be the gene expression profile of the gene in cells cultured without the use of a compound or a compound known to have no effect on the IL7 / IL7R signaling pathway.

[0214] In a preferred embodiment, the compound is an anti-IL7R antagonist antibody or an antigen-binding fragment thereof.

[0215] The cells that can be used to select the compound can be immortalized cell lines expressing CD127, such as T cell lines (eg, Jurkat cells), or cells collected from a donor (preferably a healthy human donor).

[0216] In a specific embodiment, the cell is an immune cell, which includes lymphocytes (particularly T cells, natural killer cells). The immune cell can be obtained from many non-limiting sources, including peripheral blood mononuclear cells, bone marrow, lymph node tissue, umbilical cord blood, thymus tissue, tissue from the site of infection, ascites, pleural effusion, spleen tissue and tumor, and a unit of blood collected from a subject using any technique known to the technician. Immune cells can be extracted from blood or derived from stem cells. In a preferred embodiment, the cell is a peripheral blood mononuclear cell.

[0217] When compared to the control value, the antagonist induces a lower gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in cells cultured with the compound (preferably, at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in cells cultured with the compound). When the log2 fold change of the gene expression profile of at least 1, 2, 3, 4, 5 or 6 genes among the ER2, DPP4, SOCS2 and FLT3LG genes relative to the control value gene expression profile is less than at least 0.1, preferably 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, more preferably 1, 2, 3, 4, and even more preferably 5), the antagonist can be considered to be a suitable IL7-R antagonist (preferably an anti-IL7R antagonist antibody or an antigen-binding fragment thereof) and the antagonist may be effective in treating diseases associated with IL7-induced enhancement of the IL7R signaling pathway.

[0218] In particular, when the gene expression levels are determined by quantitative RT-PCR, the gene expression profile of the biomarker in the patient sample is considered to be lower than the control value if the log2 fold change of the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in the patient relative to the control value gene expression profile is lower than at least 0.4.

[0219] In another specific embodiment, when gene expression levels are determined by RNA-seq, the gene expression profile of the biomarker in the patient sample is considered to be lower than the control value if the log2 fold change of the gene expression profile of at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2, and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2, and FLT3LG genes in the patient relative to the control value gene expression profile is less than at least 0.1.

[0220] In addition, when compared to the control value, the agonist induces a higher gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in cells cultured with the compound (preferably, at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in cells cultured with the compound). When the log2 fold change of the gene expression profile of at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes relative to the control value gene expression profile is higher than at least 0.1, preferably 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, more preferably 1, 2, 3, 4, and even more preferably 5), the agonist can be considered to be a suitable IL7R agonist and the agonist may be effective in treating the above-mentioned diseases associated with impaired healthy T cell activity.

[0221] In particular, when the gene expression levels are determined by quantitative RT-PCR, if the log2 fold change of the gene expression profile of at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in the patient relative to the control value gene expression profile is higher than at least 0.4, then the gene expression profile of the biomarker in the patient sample is considered to be higher than the control value.

[0222] In another specific embodiment, when gene expression levels are determined by RNA-seq, the gene expression profile of the biomarker in the patient sample is considered to be higher than the control value if the log2 fold change of the gene expression profile of at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2, and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes in the patient relative to the control value gene expression profile is higher than at least 0.1.

[0223] Reagent test kit

[0224] On the other hand, the present disclosure relates to a kit, preferably a kit for an in vitro method for evaluating a therapeutic response to an IL7R antagonist or an IL7R agonist, or a kit for an in vitro method for evaluating the likelihood of a human patient's therapeutic response to an IL7R antagonist or agonist, the kit comprising or consisting of a set of reagents that specifically detect the gene expression profile of at least 1, 2, 3 or 4 genes selected from the group consisting of BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from the group consisting of BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes.

[0225] Preferably, the kit comprises containers, each of which contains more than one compound, and the concentration or amount of the compound is conducive to the reconstitution and / or use of a set of reagents and the implementation of the method of the present disclosure, wherein the set of reagents specifically detects the gene expression profile of at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes.

[0226] In particular, the kit comprises primer pairs and / or probes specifically targeting at least 1, 2, 3 or 4 genes selected from BCL2, CISH, PTGER2 and DPP4 genes, preferably at least 1, 2, 3, 4, 5 or 6 genes selected from BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes.

[0227] The kit may also include instructions for preparing and / or using the reagents to determine the expression level of the gene according to the methods of the present disclosure.

[0228] The present invention also relates to the use of the kit in the method disclosed herein.

[0229] The invention will now be illustrated by the following non-limiting examples with reference to the accompanying drawings. BRIEF DESCRIPTION OF THE DRAWINGS

[0230] Figure 1: Box plot representation of ssGSEA signatures of six genes (BCL2, CISH, PTGER2, DPP4, FLT3LG and SOCS2) using RNAseq methods on A) paired samples at D1 and D15 of N13B2-hVL6 or placebo and B) paired samples at D1, D15 and D57 from N13B2-hVL6 treated samples. For N13B2-hVL6, a significant and large decrease in the signature of these six genes related to the IL7 / IL7R pathway was observed.

[0231] Figure 2: Box plot representation of a novel 4-gene (BCL2, CISH, PTGER2, DPP4) ssGSEA signature using RNAseq method on A) D1 and D15 paired samples of N13B2-hVL6 or placebo and B) D1, D15 and D57 paired samples from N13B2-hVL6 treated samples. For N13B2-hVL6, a significant and large decrease in the signature of these 4 genes related to the IL7 / IL7R pathway was observed.

[0232] Figure 3 : Box plot representation of a new 4-gene (BCL2, CISH, PTGER2, DPP4) signature on D1 and D15 paired samples of N13B2-hVL6 or placebo using RT-qPCR. For N13B2-hVL6, a significant and substantial decrease in the signature of these 4 genes associated with the IL7 / IL7R pathway was observed.

[0233] Figure 4 : Box plot representation of 4 gene ssGSEA signatures, where BCL2, CISH, PTGER2, DPP4 gene expression was calculated using GSVA R package based on RNAseq sequencing of human PBMCs pre-incubated with 3 anti-human IL7Ra monoclonal antibodies (monoclonal antibody 1: N13B2-hVL6 (disclosed in WO2018 / 104483), monoclonal antibody 2: MD707-13 (anti-site 1 antibody disclosed in WO2013 / 056984), monoclonal antibody 3: GSK WO2011 (1A11 disclosed in GSK patent WO2011 / 094259)) and stimulated with recombinant IL7 for 3 hours. For the 3 antibodies, a significant and large decrease in the ssGSEA signature of these 4 genes related to the IL7 / IL7R pathway was observed.

[0234] Figure 5: Box plot representation of 6-gene ssGSEA signature, where BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG gene expression was calculated using GSVA R package based on RNAseq sequencing of human PBMCs pre-incubated with 3 anti-human IL7Ra monoclonal antibodies (monoclonal antibody 1: N13B2-hVL6 (disclosed in WO2018 / 104483), monoclonal antibody 2: MD707-13 (anti-site 1 antibody disclosed in WO2013 / 056984), monoclonal antibody 3: GSK WO2011 (1A11 disclosed in GSK patent WO2011 / 094259)) and stimulated with recombinant IL7 for 3 hours. For the 3 antibodies, a significant and large decrease in the ssGSEA signature of these 6 genes related to the IL7 / IL7R pathway was observed.

[0235] Figure 6 : Box plot representation of 4-gene ssGSEA signatures, where BCL2, CISH, PTGER2, DPP4 gene expression was calculated using the GSVA R package based on RNAseq sequencing of human PBMCs stimulated with recombinant IL7. A significant and substantial increase in the ssGSEA signature associated with the IL7 / IL7R pathway was observed.

[0236] Figure 7 : Box plot representation of 6-gene ssGSEA signature, where BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG gene expression was calculated using the GSVA R package based on RNAseq sequencing of human PBMCs stimulated with recombinant IL7. A significant and substantial increase in the ssGSEA signature associated with the IL7 / IL7R pathway was observed.

[0237] Example

[0238] 150-base paired-end sequencing was performed on an Illumina HiSeq from Genewiz on rRNA and globin-depleted RNA from paxgen blood samples from a cohort of healthy volunteers treated with anti-IL7R antagonist antibodies.

[0239] The sequencing quality of the raw fastq file was evaluated by the fastQC bioinformatics tool. The reads were pseudo-aligned with CRGh38 / hg38 using the bioinformatics tool salmon and the index preparation option genecode, and the raw count table of the number of reads per gene and the normalized TPM table were generated using the bioinformatics tool salmon and the option geneMap. The pseudo-mapped quality reads were evaluated using the fastQC bioinformatics tool, where the average read length of all samples was 20-30M, and more than 90% of the bases were ≥30.

[0240] The healthy volunteer cohort included 22 PBMC samples before injection of anti-human IL7R antagonist antibody (N13B2-hVL6) (10 mg / kg) or placebo, paired PBMC samples collected on day 15 after injection, and 4 of them collected on day 57 after injection, for a total of 48 samples. Only one sample did not pass the different quality controls and was moved to the study.

[0241] The inventors identified six genes that are truly related to the IL7 / IL7R signaling pathway: BCL2, CISH, SOCS2, FLT3LG, PTGER2 and DPP4.

[0242] To evaluate the validity of the gene signatures for these genes, single-sample GSEA signatures (ssGSEA) were calculated.

[0243] A significant and large decrease in the ssGSEA signature of 6 genes was observed during treatment at D15 for samples from healthy volunteers treated with N13B2-hVL6, but not for samples from healthy volunteers treated with placebo ( Figure 1A This decrease was observed even at D57 after N13B2-hVL6 injection, which is consistent with the long-term detection (more than 3 months) of antibodies in the sera of healthy volunteers treated with N13B2-hVL6 ( Figure 1B ).

[0244] For samples from healthy volunteers treated with N13B2-hVL6, a significant and large decrease in the ssGSEA signature of only four genes was observed during treatment at D15, but this was not observed for samples from healthy volunteers treated with placebo ( Figure 2A As in the case of the 6-gene signature, this decrease was observed even at D57 after N13B2-hVL6 injection ( Figure 2B ).

[0245] Compared with the ssGSEA analysis of only one gene, higher sensitivity was observed for the ssGSEA signatures of four and six genes after both short-term and long-term treatment, as shown in Table 1 below:

[0246]

[0247]

[0248] Table 1: ssGSEA analysis of 4 and 6 genes in samples from subjects treated with 10 mg:kg N13B2-hVL6

[0249] This new signature is strongly correlated with the biological effects of anti-IL7R antagonist antibodies and can be used as a tool to track the biological effects of anti-IL7R antagonist antibodies in different new experiments.

[0250] RNA seq technology is very sensitive, but an expensive technology. The gene signature was also validated by another less expensive technology (RT-qPCR), but RT-qPCR has a lower sensitivity. FLT3G and SOCS2 genes were not analyzed in RT-qPCR.

[0251] The inventors performed RT-qPCR validation of these 4 genes as a concomitant test for anti-IL7R antagonist antibodies.

[0252] Real-time quantitative analysis (RT-qPCR) of these four genes was performed on 5 pairs of samples D1 and D15 from volunteers treated with placebo in vivo and 5 pairs of samples D1 and D15 from volunteers treated with N13B2-hVL6 (10 mg / kg) in vivo that had been analyzed in Genewiz's RNAseq sequencing.

[0253] To this end, reverse transcription (RT) was performed using Thermo's SuperScript IV VILO Master Mix with EzDNASE #11766050 to obtain complementary DNA (cDNA), and genomic DNA was removed by DNase treatment. Fast Advanced Master Mix #4444557 (5 mL) and TaqMan probes were used to quantify each gene and housekeeping gene (Table 2).

[0254] Product ID Gene ID Analysis ID 4448892 BCL2 Hs01048932_g1 4448892 CISH Hs00367082_g1 4453320 PTGER2 Hs00168754_m1 4448892 DPP4 Hs00897405_m1 4331182 TBP Hs00427620_m1 4331182 HPRT Hs02800695_m1 4331182 ACTB Hs03023943_g1

[0255] Table 2: List of TaqMan probes used for RT-qPCR

[0256] The sum of -ΔCt of the four genes (BCL2, CISH, PTGER2, DPP4) detected by RT-qPCR normalized to the TBP housekeeping gene was calculated and used as a signature.

[0257] The box plot representation of the signature ( Figure 3 ) showed that the decrease observed in RNA sequencing for D15 samples from healthy volunteers treated with N13B2-hVL6 could also be observed in RT-qPCR analysis.

[0258] To validate the RT-qPCR signature of these four genes, RT-qPCR analysis of these four genes was performed on samples from subjects treated with 1 mg / kg, 4 mg / kg, and 6 mg / kg N13B2-hVL6 ( Table 3 ) using TBP as a housekeeping gene, and the log2 fold change (log2FC) between paired samples D15 and D1 was calculated.

[0259]

[0260] Table 3: RT-qPCR analysis of four genes was performed on samples from subjects treated with 1 mg / kg, 4 mg / kg, 6 mg / kg and 10 mg / kg N13B2-hVL6 using TBP as a housekeeping gene, and the p value and log2FC between D15 and D1 were calculated.

[0261] Significant decreases in the 4-gene RT-qPCR signature were observed at all doses of N13B2-hVL6 treatment.

[0262] This signature was validated using additional antibodies. To this end, RNAseq was performed on human PBMCs pre-incubated with three anti-human IL7Rα monoclonal antibodies (mAb 1: N13B2-hVL6, mAb 2: MD707-13, and mAb 13: GSKWO2011) and stimulated with recombinant IL7 for 3 h.

[0263] Significant and substantial decreases in the ssGSEA signatures of 4 and 6 genes associated with the IL7 / IL7R pathway were observed for all three antibodies ( Figure 4 and Figure 5 ).

[0264] To verify that this new signature could also be associated with IL7R agonist effects and could be used as a tool to track the biological effects of IL7R agonists, RNA sequencing was performed on PBMCs treated with IL7 cytokines. Freshly isolated human PBMCs from healthy donors (provided by Establissement du Sang) were incubated with 5 ng / ml recombinant human IL-7 (AbDSerotec) for 3 hours at 37° C. The reaction was terminated on ice and the cell pellet was resuspended in RLT buffer (in RNase / DNase-free water) (Qiagen) containing 1% β-mercaptoethanol and stored at -80° C.

[0265] RNA was extracted using an RNA mini kit according to the manufacturer's instructions (Qiagen). RNA quality and quantity were assessed by infrared spectroscopy (Nanodrop) and Agilent Bioanalyzer (Agilent RNA 6000 Pico Kit).

[0266] Smart-Seq2 libraries were prepared by Broad Technology Labs and sequenced by Broad Genomics Platform according to the SmartSeq2 protocol (with some modifications) (Trombetta, JJ et al., Curr. Protoc. Mol. Biol. 107, 4.22.1–4.22.17 (2014)). In brief, total RNA was purified using RNA-SPRI beads, polyA+ mRNA was reverse transcribed into cDNA, and amplified cDNA was subjected to transposon-based fragmentation, which used a barcode combination specific to each sample and barcoded each fragment of each converted transcript using dual indexing.

[0267] Sequencing was performed with double-end 2x 25bp and 8 additional cycles per index. Data were separated by barcodes and aligned using tophat version 2.0.10 and default settings. Transcripts were quantified using the BroadTechnology Labs computational pipeline using Cuffquant version 2.2.167. In short, if 50% of the reads were aligned and at least 100,000 pairs were aligned for each sample, the data was processed by CuffNorm. Normalization used default settings, including "geometric" normalization, and expression level information was used as log2-transformed FPKM values ​​(number of fragments per kilobase of transcript per million mapped fragments) for subsequent analysis. RNA-seq results can be accessed in the GEO database with accession number GSE103643 (Belarif et al., Nature communications, (2018) 9:4483).

[0268] A single-sample GSEA (ssGSEA) signature was calculated based on the target genes BCL2, CISH, SOCS2, FLT3LG, PTGER2, and DPP4.

[0269] like Figure 6 and 7 As shown, for samples stimulated with IL7, a significant and large increase in the ssGSEA signature of 4 and 6 genes related to the IL7 / IL7R pathway was observed.

[0270] It was observed that the sensitivity of the ssGSEA signatures of 4 and 6 genes was higher compared to the ssGSEA analysis of only one gene, as shown in Table 4.

[0271]

[0272] Table 4: 4 and 6 gene ssGSEA analysis of PBMC samples stimulated with IL7 cytokine.

[0273] in conclusion

[0274] This study led to the discovery of six genes (four in particular) whose gene expression profiles reflect IL7 / IL7R pathway activity. The gene expression profile of at least one of these four genes can be easily quantified by RT-qPCR, which can be used to assess the activity of IL7R antagonists or agonists and can serve as a companion test to monitor the biological effects of IL7R antagonists or agonists.

Claims

1. An in vitro method for evaluating a human patient's therapeutic response to treatment with an IL7R antagonist or IL7R agonist, comprising the steps of: Determining the gene expression profile of each of the following genes in a patient sample: BCL2, CISH, PTGER2 and DPP4 genes, preferably in addition to FLT3LG or SOCS2 genes, more preferably BCL2, CISH, PTGER2, DPP4, FLT3LG and SOCS2 genes, wherein the patient has received at least one dose of an IL7R antagonist or an IL7R agonist, wherein A lower or higher gene expression profile of the gene in the patient sample compared to the control value indicates that the patient is likely to respond to treatment with an IL7R antagonist or an IL7R agonist, respectively.

2. The method according to claim 1, wherein: The sample is collected from the patient at least 15 days in advance after the patient has been administered at least one dose of the IL7R antagonist or IL7R agonist.

3. An in vitro method for assessing the likelihood of a human patient to respond to treatment with an IL7R antagonist or agonist prior to treatment, comprising the steps of: a) culturing a sample previously collected from a patient prior to the treatment in the presence of the IL7R antagonist or IL7R agonist; b) determining the gene expression profile of each of the following genes in the cultured sample: BCL2, CISH, PTGER2 and DPP4 genes, preferably in addition to FLT3LG or SOCS2 genes, more preferably BCL2, CISH, PTGER2, DPP4, FLT3LG and SOCS2 genes, wherein A gene expression profile of the gene in the cultured sample that is lower or higher than the control value indicates that the patient is likely to respond to treatment with the IL7R antagonist or IL7R agonist, respectively.

4. The method according to any one of claims 1 to 3, wherein: The IL7R antagonist is an anti-IL7R antibody or an antigen-binding fragment thereof; preferably, the anti-IL7R antibody or an antigen-binding fragment thereof comprises: a) a variable heavy chain comprising three CDRs, wherein: - VHCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 1, - VHCDR2 comprises or consists of the amino acid sequence of SEQ ID NO: 2, and - VHCDR3 comprises or consists of the amino acid sequence of SEQ ID NO: 3 or 11, preferably SEQ ID NO: 3; b) a variable light chain comprising three CDRs, wherein: - VLCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 4 or 12, preferably SEQ ID NO: 4, - VLCDR2 comprises or consists of the amino acid sequence of SEQ ID NO: 5 or 13, preferably SEQ ID NO: 5, and - VLCDR3 comprises or consists of the amino acid sequence of SEQ ID NO: 6, More preferably, the anti-IL7R antagonist antibody or antigen-binding fragment thereof comprises a heavy chain variable domain and a light chain variable domain, the heavy chain variable domain comprises or consists of the amino acid sequence of SEQ ID NO: 7, and the light chain variable domain comprises or consists of the amino acid sequence of SEQ ID NO: 8; Still more preferably, the antibody or antigen-binding fragment thereof comprises a complete heavy chain comprising or consisting of SEQ ID NO:9 and a complete light chain comprising or consisting of SEQ ID NO:

10.

5. The method for assessing a therapeutic response to an IL7R antagonist according to any one of claims 1, 2 or 4 or the method for assessing the likelihood of a human patient responding to a therapeutic response to an IL7R antagonist according to any one of claims 3 or 4, wherein When the patient suffers from a disease associated with enhanced IL7R signaling pathway induced by IL7, the disease is preferably selected from autoimmune diseases, inflammatory diseases, allergic diseases, cancer diseases, infectious diseases, respiratory diseases and transplantation-related diseases involving activation or proliferation of CD127-positive pathological cells, in particular autoimmune diseases or inflammatory diseases involving activation or proliferation of CD127-positive cells, more preferably chronic inflammatory diseases such as Sjögren's syndrome or inflammatory bowel diseases such as ulcerative colitis.

6. The method for assessing a therapeutic response to an IL7R agonist according to any one of claims 1, 2 or 4 or the method for assessing the likelihood of a human patient responding to a therapeutic response to an IL7R agonist according to any one of claims 3 or 4, wherein: The patient suffers from a disease associated with impaired healthy T cell activity, preferably a cancer disease or an infectious disease that develops independently of the IL7R pathway.

7. The method according to any one of claims 1 to 6, wherein: The patient sample is a tissue sample, preferably a tumor tissue containing infiltrating immune cells from a cancer patient or a blood patient sample, preferably isolated human peripheral blood mononuclear cells.

8. The method according to any one of claims 1 to 7, wherein: The gene expression profile is determined by detecting the mRNA expression of the gene, preferably by detecting the mRNA expression of the gene by RT-qPCR.

9. An IL7R antagonist for use in treating a disease associated with the IL7R signaling pathway induced by IL7 in a human patient in need thereof, wherein the disease is preferably selected from autoimmune diseases, inflammatory diseases, allergic diseases, cancer diseases, infectious diseases, respiratory diseases and transplantation-related diseases involving activation or proliferation of CD127-positive diseased cells, in particular autoimmune diseases or inflammatory diseases involving activation or proliferation of CD127-positive cells, more preferably chronic inflammatory diseases such as Sjögren's syndrome or inflammatory bowel diseases such as ulcerative colitis; wherein, The IL7R antagonist is administered to the patient after the patient has been administered at least one dose of the IL7R antagonist and when the patient is assessed as likely to respond to the treatment by the method of any one of claims 1 to 2 and 4 to 8.

10. An IL7R antagonist for use in treating a disease associated with the IL7R signaling pathway induced by IL7 in a human patient in need thereof, wherein the disease is preferably selected from autoimmune diseases, inflammatory diseases, allergic diseases, cancer diseases, infectious diseases, respiratory diseases and transplantation-related diseases involving activation or proliferation of CD127-positive diseased cells, in particular autoimmune diseases or inflammatory diseases involving activation or proliferation of CD127-positive cells, more preferably chronic inflammatory diseases such as Sjögren's syndrome or inflammatory bowel diseases such as ulcerative colitis; wherein, The patient is pre-assessed as likely to respond to treatment with the IL7R antagonist by the method of any one of claims 3 to 8.

11. The IL7R antagonist according to claim 9 or 10, for use according to claim 9 or 10, wherein: The IL7R antagonist is an anti-IL7R antagonist antibody or an antigen-binding fragment thereof, and the anti-IL7R antagonist antibody or an antigen-binding fragment thereof comprises: a) a variable heavy chain comprising three CDRs, wherein: - VHCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 1, - VHCDR2 comprises or consists of the amino acid sequence of SEQ ID NO: 2, and - VHCDR3 comprises or consists of the amino acid sequence of SEQ ID NO: 3 or 11, preferably SEQ ID NO: 3; b) a variable light chain comprising three CDRs, wherein: - VLCDR1 comprises or consists of the amino acid sequence of SEQ ID NO: 4 or 12, preferably SEQ ID NO: 4, - VLCDR2 comprises or consists of the amino acid sequence of SEQ ID NO: 5 or 13, preferably SEQ ID NO: 5, and VLCDR3 comprises or consists of the amino acid sequence of SEQ ID NO: 6; Preferably, the antibody or antigen-binding fragment thereof comprises a heavy chain variable domain and a light chain variable domain, the heavy chain variable domain comprises or consists of the amino acid sequence of SEQ ID NO: 7, and the light chain variable domain comprises or consists of the amino acid sequence of SEQ ID NO: 8; Still more preferably, the antibody or antigen-binding fragment thereof comprises a complete heavy chain comprising or consisting of SEQ ID NO:9 and a complete light chain comprising or consisting of SEQ ID NO:

10.

12. An IL7R agonist for use in treating a disease associated with impaired healthy T cell activity in a human patient in need thereof, wherein the disease is preferably a cancer disease or an infectious disease whose development is independent of the IL7R pathway; wherein The IL7R agonist is administered to the patient after the patient has been administered at least one dose of the IL7R agonist and when the patient is assessed by the method of any one of claims 1 to 2 and 4 to 8 as likely to respond to the treatment.

13. An IL7R agonist for use in treating a disease associated with impaired healthy T cell activity in a human patient in need thereof, wherein the disease is preferably a cancer disease or an infectious disease whose development is independent of the IL7R pathway; wherein The patient is pre-assessed as likely to respond to treatment with the IL7R antagonist by the method of any one of claims 3 to 8.

14. An in vitro method for selecting a compound that may be effective in treating a disease associated with IL7-induced IL7R signaling pathway or a disease associated with impaired healthy T cell activity, comprising the steps of: a) culturing human cells, preferably immune cells, more preferably peripheral blood mononuclear cells, in the presence of the compound; b) determining the gene expression profile of each of the following genes in the cell: BCL2, CISH, PTGER2 and DPP4 genes, preferably in addition to FLT3LG or SOCS2 genes, more preferably BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes, and c) selecting a compound that induces a lower or higher gene expression profile of a gene in the cell compared to a control value; Preferably, the gene expression profile is determined by detecting the mRNA expression of the gene, preferably by detecting the mRNA expression of the gene by RT-qPCR.

15. A kit for use in the method according to any one of claims 1 to 14, the kit consisting of a set of reagents that specifically detect the gene expression profile of each of the following genes: BCL2, CISH, PTGER2 and DPP4 genes, preferably in addition to FLT3LG or SOCS2 genes, more preferably BCL2, CISH, PTGER2, DPP4, SOCS2 and FLT3LG genes; even more preferably, the reagents are primer pairs and / or probes specific to each gene.

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