WO2018041989A1 - Methods for diagnosing and treating refractory celiac disease type 2 - Google Patents

Abstract

The present invention relates to methods diagnosing and treating refractory celiac disease type 2 (RCDII). The inventors demonstrated that in a subset of celiac disease patients, intraepithelial lymphocytes with intracellular expression of CD3 (iCD3+ innate IEL) and JAKl or STAT3 gain-of-function mutations display enhanced response to IL-15 and acquire a selective advantage that favors clonal expansion and transformation into lymphoma. In particular, the present invention thus relates to a method for diagnosing RCDII in a patient comprising the detected presence of at least one JAKl or STAT3 gain-of-function mutation in a sample obtained from the patient and concluding that the patient suffers from RCDII when the mutation is detected.

Description

METHODS FOR DIAGNOSING AND TREATING REFRACTORY CELIAC

DISEASE TYPE 2

FIELD OF THE INVENTION:

The present invention relates to methods diagnosing and treating refractory celiac disease type 2.

BACKGROUND OF THE INVENTION:

Celiac disease, also known as celiac sprue, is a quite common autoimmune disease having genetic, immunological and environmental components. At the basis of the celiac disease lies a permanent intolerance to gliadins and glutenins present in wheat, or to similar proteins (prolamines) soluble in alcohol contained in barley, rye, spelt, kamut and other minor cereals, collectively called gluten. In celiac disease, the mucosa of the small intestine becomes damaged upon exposure to dietary gluten. Subsequently, intestinal villi become flattened followed by compensative hyper-proliferation of the crypts; enterocytes take up a cubic rather than cylindrical shape and the number of lymphocytes in increases in the gut epithelium (intraepithelial lymphocytes= IEL). Refractory celiac disease (RCD) affects patients who have failed to heal after 6-12 months of strict gluten-free diet (GFD) and when other causes of symptoms (including overt lymphoma) have been ruled out. It may also occur in patients who had previously responded to GFD. RCD may be categorized as RCDI (when IEL remain polyclonal and display a normal T mainly CD8+ immunophenotype) and RCDII (characterized by an expansion of clonal innate- like IEL with intracellular but no surface CD3, often referred as aberrant immunophenotype). RCDI patients usually respond to therapeutic agents such as corticosteroids and immunosuppressive drugs. RCDII is now considered as an intraepithelial lymphoma and is associated with serious complications including severe malnutrition, dissemination and/or further transformation into high-grade enteropathy-associated T-cell lymphoma (EATL) with very severe prognosis in approximately 40% of cases. The diagnosis of RCD requires a combination of clinical and pathologic findings. In fact, the diagnosis is made on the basis of a strong evidence of CD, supplemented with systematic exclusion of other causes of non-responsive CD or villous atrophy and of overt EATL. Although RCD is a diagnosis of exclusion, it is supported by objective findings in laboratory and histological studies. The availability of novel tests for detection of abnormal (clonal) intraepithelial lymphocytes in the intestine is needed to facilitate the confirmation of RCDII.

SUMMARY OF THE INVENTION: The present invention relates to methods for diagnosis and treatment of refractory celiac disease type 2. In particular, the present invention is defined by the claims.

DETAILED DESCRIPTION OF THE INVENTION:

The inventors demonstrate that in a subset of celiac patients, intraepithelial lymphocytes with intracellular expression of CD3 (iCD3+ innate IEL) with gain-of-function JAKl or STAT3 mutations display enhanced response to IL-15 and acquire a selective advantage that favors clonal expansion and transformation into lymphoma. Accordingly, detecting such gain-of- function mutations offers a novel method for diagnosing refractory celiac disease type 2.

The first objet of the present invention thus relates to a method for diagnosing refractory celiac disease type 2 (RCDII) in a patient comprising detecting the presence of at least one gain- of-function JAKl or STAT3 mutation in sample obtained from the patient and concluding that the patient suffers from refractory celiac disease type 2 when the mutation is detected.

As used herein, the term "JAKl" has its general meaning in the art and refers to Janus kinase 1 which is encoded by JAKl gene (Gene ID: 3716). JAKl is also known as JTK3; JAKl A; or JAK1B. JAKl is a protein tyrosine kinase of the JAK (Janus protein tyrosine kinase) family highly expressed in immune cells where it is essential for signaling by members of the IL-2 receptor family (IL-2R, IL-4R, IL-7R, IL-9R, IL-15R and IL-21R), the IL-4 receptor family (IL-4R, IL-13R), the gpl30 receptor family and class II cytokine receptors. Exemplary human nucleic acid and amino acid sequences are represented by the NCBI reference sequences NM_001320923.1 and NP_001307852.1 respectively.

As used herein, the term "STAT3" has its general meaning in the art and refers to signal transducer and activator of transcription 3, which is encoded by STAT3 gene (Gene ID: 6774). STAT3 is also known as APRF; HIES; ADMIO; and ADMIOl . Exemplary human nucleic acid and amino acid sequences are represented by the NCBI reference sequences NM_139276.2 and NP_644805.1 respectively.

As used herein, the term "gain-of-function mutation" refers to a mutation that is associated with an increase of the gene or gene product activity. An increase of activity can be due to an increase in transcription and/or processing of the RNA, an increase in translation, stability, transport, or activity of the gene product, or any combination thereof. In some embodiments, normal activity of a gene or gene product is increased from 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 up to 100%.

In some embodiments, the gain-of-function JAKl mutation is G1097D/C/V/A, which indicates the substitution of the glycine (G) residue at position 1097 by an aspartic acid (D), a cysteine (C), a valine (V) or an alanine (A) residue. In some embodiments, the gain-of function STAT3 mutation is D661V/Y/H, which indicates the substitution of the aspartic acid (D) residue at position 661 by a valine (V), a tyrosine (Y) or a histidine (H) residue.

In some embodiments, the sample is a biopsy sample. In some embodiments, the sample is a mucosal tissue sample. As used herein, the term "mucosal tissue sample" means any sample derived from the intestine of the patient, which comprises mucosal and lymphoid cells. The mucosal tissue sample is obtained for the purpose of diagnosis of in vitro evaluation. In some embodiments, the mucosal tissue sample results from an endoscopic biopsy performed in the intestine of the subject. Said endoscopic biopsies may be taken from various areas of the intestine. In some embodiments, the mucosal tissue sample is isolated from an inflamed mucosa of the patient's intestine.

The presence of the mutation is determined by detection assays known those skilled in the art, such as protein or peptide detection methods and/or molecular biological detection, including but not limited to targeted next generation sequencing, Sanger sequencing, RNA- sequencing, PCR, qRT-PCR, Northern, Southern or Western blots, chip arrays and antibody assays. In a preferred embodiment, the presence of the mutation is determined by targeted next generation sequencing.

In some embodiments, mutations are detected from RNA or DNA isolated from the sample, preferably after amplification. For instance, the isolated RNA may be subjected to coupled reverse transcription and amplification, such as reverse transcription and amplification by polymerase chain reaction (RT-PCR) using oligonucleotide primers that are specific for a mutated site or that enable amplification of a region containing the mutated site. According to the first alternative, conditions for primer annealing may be chosen to ensure specific reverse transcription (where appropriate) and amplification so that the appearance of an amplification product be a diagnostic of the presence of a particular mutation. Otherwise, RNA may be reversely transcribed and amplified, or DNA may be amplified, after which a mutated site may be detected in the amplified sequence by hybridization with a suitable probe or by direct sequencing, or any other appropriate method known in the art. For instance, a cDNA obtained from RNA may be cloned and sequenced to identify a mutation. Actually numerous strategies for genotype analysis are available (Antonarakis et al, 1989; Cooper et al, 1991 ; Grompe, 1993). Briefly, the nucleic acid molecule may be tested for the presence or absence of a restriction site. When a base substitution mutation creates or abolishes the recognition site of a restriction enzyme, this allows a simple direct PCR test for the mutation. Further strategies include, but are not limited to, direct sequencing, restriction fragment length polymorphism (RFLP) analysis, hybridization with allele-specific oligonucleotides (ASO) that are short synthetic probes which hybridize only to a perfectly matched sequence under suitably stringent hybridization conditions, allele-specific PCR, PCR using mutagenic primers, ligase-PCR, HOT cleavage, denaturing gradient gel electrophoresis (DGGE), temperature denaturing gradient gel electrophoresis (TGGE), single-stranded conformational polymorphism (SSCP) and denaturing high performance liquid chromatography (Kuklin et al, 1997). Direct sequencing may be accomplished by any method, including without limitation chemical sequencing using the Maxam-Gilbert method, enzymatic sequencing, using the Sanger method, mass spectrometry sequencing, sequencing using a chip-based technology and real-time quantitative PCR. Preferably, DNA will initially be subjected to amplification by PCR using a specific set of primers. However several other methods are available, allowing DNA to be studied independently of PCR, such as the rolling circle amplification (RCA), the InvaderTMassay, or oligonucleotide ligation assay (OLA). OLA may be used for revealing base substitution mutations. According to this method, two oligonucleotides are constructed that hybridize to adjacent sequences in the target nucleic acid, with the join sited at the position of the mutation. DNA ligase will covalently join the two oligonucleotides only if they are perfectly hybridized. Therefore, useful nucleic acid molecules, in particular oligonucleotide probes or primers, according to the present invention include those, which specifically hybridize at regions where the mutations are located. Oligonucleotide probes or primers may contain at least 10, 15, 20 or 30 nucleotides. Their length may be shorter than 400, 300, 200 or 100 nucleotides.

In some embodiments, the mutation is detected by direct RNA sequencing. Direct RNA sequencing technology (Helicos Biosciences Corporation, Cambridge, MA) and transcriptome profiling using single-molecule direct RNA sequencing are described by Ozsolak et al. (Nature 461(7265 :814-818 (2009)) and Ozsolak and Milos (Methods Mol Biol 733:51-61 (2011)). True Single Molecule and Direct RNA Sequencing technologies are further described in U.S. Patent Publication Nos. 2008/0081330, 2009/0163366, 2008/0213770, 2010/0184045, 2010/0173363, 2010/0227321, 2008/0213770, and 2008/0103058 as well as U.S. Patent Nos. 7,666,593; 7,767,400; 7,501,245; and 7,593,109, each of which are hereby incorporated by reference in its entirety. In some embodiments, the mutation is detected by RNA-seq. The methods for performing RNA-seq are known and complete descriptions of the general methods can be found in Wang, Z., M. Gerstein, and M. Snyder, RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet, 2009. 10(1): p. 57-63, and Mortazavi, A., et al, Mapping and quantifying mammalian transcriptomes by RNA-Seq (Nature Methods, 2008. 5(7): p. 621-628). The mutation may be also detected at a protein level (e.g. for loss-of-function mutations) according to any appropriate method known in the art. In particular, a biological sample such as a tissue biopsy may be exposed to antibodies specific for a mutated form of the protein of interest (JAK1 or STAT3) i.e. antibodies that are capable of distinguishing between the mutated form of and the wild-type protein, to determine the presence or absence of the mutation. The antibodies may be monoclonal or polyclonal antibodies, single chain or double chain, or portions of an immunoglobulin molecule, including those portions known in the art as antigen binding fragments Fab, Fab', F(ab')2 and F(v). They can also be immunoconjugated, e.g. with a toxin, or labelled antibodies. Whereas polyclonal antibodies may be used, monoclonal antibodies are preferred for they are more reproducible in the long run. Procedures for raising "polyclonal antibodies" are also well known. Alternatively, binding agents other than antibodies may be used for the purpose of the invention. These may be for instance aptamers, which are a class of molecules that represent an alternative to antibodies in terms of molecular recognition. Aptamers are oligonucleotide or oligopeptide sequences with the capacity to recognize virtually any class of target molecules with high affinity and specificity. Such ligands may be isolated through Systematic Evolution of Ligands by Exponential enrichment (SELEX) of a random sequence library. Flow cytometry and immunohistochemistry are preferred methods for detecting the presence of the mutation.

The diagnostic method of the present invention is thus particularly suitable for determining whether the patient suffering from refractory celiac disease type 2 (RCDII) has or is at risk of having an enteropathy-associated T-cell lymphoma (EATL), since the detection of the gain-of- function mutation indicates that the patient has or is at risk of having an enteropathy- associated T-cell lymphoma.

More, the diagnostic method of the present invention is also particularly suitable for the detection of JAK1 or STAT3 gain-of-function mutations in RCDII patients, which will confirm diagnosis and indicate the risk of already suffering from or potentially developing an EATL.

The second object of the present invention relates to a method of treating refractory celiac disease type 2 in a patient in need thereof comprising administering to the patient a therapeutically effective amount of an IL-15 antagonist. In particular, the method of the present invention comprises detecting at least one gain-of-function of the present invention and administering to the patient the therapeutically effective amount of an IL-15 antagonist.

The third object of the present invention relates to a method of treating refractory celiac disease type 2 in a patient in need thereof comprising administering to the patient a therapeutically effective amount of a JAK/STAT inhibitor. In particular, the method of the present invention comprises detecting at least one gain-of-function of the present invention and administering to the patient the therapeutically effective amount of a JAK/STAT inhibitor.

As used herein, the term "treatment" or "treat" refer to both prophylactic or preventive treatment as well as curative or disease modifying treatment, including the treatment of patients at risk of contracting the disease or suspected to have contracted the disease as well as patients who are already sick or have been diagnosed as suffering from a disease or medical condition, and includes suppression of clinical relapse. The treatment may be administered to a subject having a medical disorder or who ultimately may acquire the disorder, in order to prevent, cure, delay the onset, reduce the severity or ameliorate one or more symptoms of a disorder or recurring disorder, or in order to prolong the survival of a subject beyond a point to be expected in the absence of such treatment. The term "therapeutic regimen" addresses the pattern of treatment of a disease, e.g., the pattern of dosing used during therapy. A therapeutic regimen may include an induction regimen and a maintenance regimen. The term "induction regimen" or "induction period" refers to a therapeutic regimen (or the portion of a therapeutic regimen) that is used for the initial treatment of a disease. The general goal of an induction regimen is to provide a high level of drug to a patient during the initial period of a treatment regimen. An induction regimen may employ (in part or in whole) a "loading regimen", which may include administering a greater dose of the drug than a physician would employ during a maintenance regimen, administering a drug more frequently than a physician would during a maintenance- regimen, or both. The term "maintenance regimen" or "maintenance period" refers to a therapeutic regimen (or the portion of a therapeutic regimen) that is used for the maintenance of a patient during disease treatment, e.g. to keep the patient in remission for long periods of time (months or years). A maintenance regimen may employ continuous therapy (e.g. administering a drug at a regular intervals, e.g. weekly, monthly, yearly, etc.) or intermittent therapy (e.g. interrupted treatment, intermittent treatment, treatment at relapse, or treatment upon achievement of a particular predetermined criteria (e.g. pain, disease manifestation, etc.)).

In some embodiments, the therapeutic method of the present invention is particularly suitable for preventing enteropathy-associated T-cell lymphoma in a patient diagnosed with refractory celiac disease type 2 (RCDII), by the method of the present invention.

As used herein, the term "IL-15" has its general meaning in the art and refers to interleukin 15, which is encoded by IL15 gene (Gene ID: 3600). IL-15 is a cytokine that regulates T and natural killer cell activation and proliferation. IL-15 and IL-2 share many biological activities. IL-15 induces the activation of kinases of the JAK family and followed by subsequent phosphorylation and activation of transcription factors such as STAT3, STAT5 and STAT6. Exemplary human nucleic acid and amino acid sequences are represented by the NCBI reference sequences NM_000585.4 and NP 000576.1 respectively.

As used herein, the term "IL-15 antagonist" refers to any compound or composition that specifically antagonizes the biological activity of IL-15, i.e.by preventing IL-15 from signal- transduction through the IL-15 receptor complex. The term IL-15 -specific antagonist thus includes, inter alia, compounds and compositions that block or downregulate the production, modification, transport, or secretion of IL-15 or IL-15 receptor subunits, compounds and compositions that interfere with the interaction between IL-15 and subunits of the IL-15 receptor complex, and compounds and compositions that interfere with IL-15 signaling events.

Several antagonists of IL-15, including IL-15 muteins, IL-15 conjugates and IL-15 antibodies are described in U.S. Patent No. 5,795,966, WO2005085282 and WO2015181394. Antagonists according to the invention include muteins of mature or native IL-15 wherein the IL-15 has been substituted at one or more amino acid residues or regions that play a role in binding to the β or γ subunits of the IL- 15 receptor complex. Typically, such muteins are created by additions, deletions or substitutions at or near key positions. Antagonists include those muteins wherein at least one of the critical amino acids E64, 168 and N65 have been replaced by a charged group (D, E or K) or by an oppositely charged group (K). In some embodiments, the IL-15 antagonist is an IL-15 mutant polypeptide having the amino acid sequence as indicated in SEQ ID NO: l wherein the leucine residue at position 45 is substituted by an aspartic acid residue, the asparagine residue at position 65 is substituted by a lysine residue and the leucine residue at position 69 is substituted by an arginine residue. In some embodiments, the IL-15 antagonist is an immunoadhesin. As used herein, the term "immunoadhesin" designates antibody-like molecules, which combine the binding specificity of the IL-15 mutant polypeptide of the invention with the effector functions of immunoglobulin constant domains. In some embodiments, the immunoglobulin constant domain sequence in the immunoadhesin may be obtained from any immunoglobulin, such as IgGl, IgG2, IgG3 or IgG4 subtypes, IgA (including IgAl and IgA2), IgE, IgD or IgM. In some embodiments, the immunoglobulin sequence typically, but not necessarily, is an immunoglobulin constant domain (Fc region). Immunoadhesins can possess many of the valuable chemical and biological properties of human antibodies. Since immunoadhesins can be constructed from a human protein sequence with a desired specificity linked to an appropriate human immunoglobulin hinge and constant domain (Fc) sequence, the binding specificity of interest can be achieved using entirely human components. Such immunoadhesins are minimally immunogenic to the patient and are safe for chronic or repeated use. The artisan skilled in the art can easily select the most appropriate Fc domain (Chan AC, Carter PJ. Therapeutic antibodies for autoimmunity and inflammation. Nat Rev Immunol. 2010 May;10(5):301-16. doi: 10.1038/nri2761. Review.). In a particular embodiment, the Fc region includes or not a mutation that inhibits complement fixation and/or Fc receptor binding (Zheng et al, Transplantation. 2006 Jan 15;81(1): 109-16).

SEQ ID NO : 1 : IL- 15 (Homo sapiens)

NWVNVISDLK KIEDLIQSMH IDATLYTESD VHPSCKVTAM KCFLLELQVI SLESGDASIH DTVENLIILA NNSLSSNGNV TESGCKECEE LEEKNIKEFL QSFVHIVQMF INTS

In some embodiments, the IL-15 antagonist is selected from monoclonal antibodies that immunoreact with mature IL-15 and prevents signal transduction through the IL-15 receptor complex.

Antagonists according to the invention also include IL-15 antisense nucleic acids, IL- 15 ribozymes, small molecules targeting IL-15, IL-15 receptor antibodies, IL-15 receptor antisense nucleic acids, IL-15 receptor ribozymes and small molecules targeting the IL-15 receptor. As used herein, the term "antibody" thus refers to any antibody- like molecule that has an antigen binding region, and this term includes antibody fragments that comprise an antigen binding domain such as Fab', Fab, F(ab')2, single domain antibodies (DABs), TandAbs dimer, Fv, scFv (single chain Fv), dsFv, ds-scFv, Fd, linear antibodies, minibodies, diabodies, bispecific antibody fragments, bibody, tribody (scFv-Fab fusions, bispecific or trispecific, respectively), sc-diabody, kappa(lamda) bodies (scFv-CL fusions), BiTE (Bispecific T-cell Engager, scFv-scFv tandems to attract T cells), DVD-Ig (dual variable domain antibody; bispecific format), SIP (small immunoprotein; a kind of minibody), SMIP ("small modular immunopharmaceutical"), scFv-Fc dimer, DART ("Dual Affinity ReTargeting"; ds-stabilized diabody), small antibody mimetics comprising one or more CDRs, and the like. The techniques for preparing and using various antibody-based constructs and fragments are well known in the art (see Kabat et al., 1991, specifically incorporated herein by reference). Diabodies, in particular, are further described in EP 404, 097 and WO 93/1 1 161, whereas linear antibodies are further described in Zapata et al. (1995). Antibodies can be fragmented using conventional techniques. For example, F(ab')2 fragments can be generated by treating the antibody with pepsin. The resulting F(ab')2 fragment can be treated to reduce disulfide bridges to produce Fab' fragments. Papain digestion can lead to the formation of Fab fragments. Fab, Fab' and F(ab')2, scFv, Fv, dsFv, Fd, dAbs, TandAbs, ds-scFv, dimers, minibodies, diabodies, bispecific antibody fragments and other fragments can also be synthesized by recombinant techniques or can be chemically synthesized. Techniques for producing antibody fragments are well known and described in the art. For example, Beckman et al. (2006), Holliger & Hudson (2005), Le Gall et al. (2004), Reff & Heard (2001), Reiter et al. (1996) and Young et al. (1995) further describe and enable the production of effective antibody fragments. In some embodiments, the antibody of the present invention is a single chain antibody. As used herein the term "single domain antibody" has its general meaning in the art and refers to the single heavy chain variable domain of antibodies of the type that can be found in Camelid mammals, which are naturally devoid of light chains. Such single domain antibodies are also called "nanobodies®". For a general description of (single) domain antibodies, reference is also made to the prior art cited above as well as to EP 0 368 684, Ward et al. (Nature 1989 Oct 12; 341 (6242): 544-6), Holt et al. (Trends BiotechnoL, 2003, 21(11)_:484-490), WO 06/030220 and WO 06/003388. In some embodiments, the antibody is a humanized antibody. In some embodiments, the antibody is a fully human antibody. In some embodiments, the antibody comprises human heavy chain constant region sequences but will induce antibody dependent cellular cytotoxicity (ADCC). In some embodiments, the antibody of the present invention does not comprise an Fc domain capable of substantially binding to a FcgRIIIA (CD 16) polypeptide. In some embodiments, the antibody of the present invention lacks an Fc domain (e.g. lacks a CH2 and/or CH3 domain) or comprises an Fc domain of IgG2 or IgG4 isotype. In some embodiments, the antibody of the present invention consists of or comprises a Fab, Fab', Fab'-SH, F (ab') 2, Fv, a diabody, single- chain antibody fragment or a multispecific antibody with multiple different antibody fragments. In some embodiments, the antibody of the present invention is not linked to a toxic moiety. In some embodiments, one or more amino acids selected from amino acid residues can be replaced with different amino acid residues such that an antibody with altered C2q binding and/or reduced or abolished complement dependent cytotoxicity (CDC). This approach is described in further detail in U.S. Patent Nos. 6,194,551 by ldusogie et al.

Other examples of IL-15 antagonists include IL-15 antisense nucleic acids, IL-15 ribozymes, small molecules targeting IL-15, IL-15 receptor antibodies, IL-15 receptor antisense nucleic acids, IL-15 receptor ribozymes as well as small molecules targeting the IL-15 receptor.

As used herein the term "JAK inhibitor" is intended to describe compounds inhibiting the activity or expression of at least JAKl and/or JAK2. JAK inhibitors down-regulate the quantity or activity of JAK molecules. In some embodiments, the JAK inhibitor is a JAK2 inhibitor. In some embodiments, the JAK inhibitor is a JAKl inhibitor. In some embodiments, the JAK inhibitor can also inhibit other members of the JAK family (i.e., JAK3 or TYK2). In some embodiments, the JAK inhibitor is selective. By "selective" is meant that the compound binds to or inhibits a JAKl and/or JAK2 with greater affinity or potency compared to at least one other JAK (e.g., JAK2, JAK3 and/or TYK2). In some embodiments, the JAK inhibitor is selective for JAKl and JAK2 over JAK3 and TYK2. In some embodiments, the compounds of the invention are selective inhibitors of JAKl over JAK2, JAK3 and TYK2. Selectivity can be at least about 5-fold, at least about 10-fold, at least about 20-fold, at least about 50-fold, at least about 100-fold, at least about 200-fold, at least about 500-fold or at least about 1000-fold. Selectivity can be measured by routine methods in the art. In some embodiments, selectivity can be measured by the Km of each enzyme. In some embodiments, selectivity of compounds for JAKl and/or JAK2 can be determined by the cellular ATP concentration.

JAK inhibitors are well known in the art. For example, JAK inhibitors include phenylaminopyrimidine compounds (WO2009/029998), substituted tricyclic heteroaryl compounds (WO2008/079965), cyclopentyl-propanenitrile compounds (WO2008/157208 and WO2008/157207), indazole derivative compounds (WO2008/114812), substituted ammo- thiophene carboxylic acid amide compounds (WO2008/156726), naphthyridine derivative compounds (WO2008/112217), quinoxaline derivative compounds (WO2008/148867), pyrrolopyrimidine derivative compounds (WO2008/119792), purinone and imidazopyridinone derivative compounds (WO2008/060301 ), 2,4-pyrimidinediamine derivative compounds (WO2008/118823), deazapurine compounds (WO2007/117494) and tricyclic heteroaryl compounds (WO2008/079521). Examples of JAK inhibitors include compounds disclosed in the following publications: US2004/176601, US2004/038992, US2007/135466, US2004/ 102455, WO2009/054941, US2007/134259, US2004/265963, US2008/194603, US2007/207995, US2008/260754, US2006/063756, US2008/261973, US2007/142402, US2005/159385, US2006/293361, US2004/205835, WO2008/148867, US2008/207613, US2008/279867, US2004/09799, US2002/055514, US2003/236244, US2004/097504, US2004/147507, US2004/ 176271, US2006/217379, US2008/092199, US2007/043063, US2008/021013, US2004/ 152625, WO2008/079521, US2009/186815, US2007/203142, WO2008/144011, US2006/270694 and US2001/044442. JAK inhibitors further include compounds disclosed in the following publications: WO2003/011285, WO2007/145957, WO2008/156726, WO2009/035575, WO2009/054941, and WO2009/075830. JAK inhibitors further include compounds disclosed in the following patent applications: US Serial Nos. 61/137475 and 61/134338.

Specific JAK inhibitors include AG490, AUB-6-96, AZ960, AZD1480, baricitinib (LY3009104, INCB28050), BMS-911543, CEP-701, CMP6, CP352,664, CP690,550, CYT- 387, INCB20, Jak2-IA, lestaurtinib (CEP-701), LS104, LY2784544, NS018, pacritinib (SB1518), Pyridone 6, ruxolitinib (INCB018424), SB1518, TG101209, TG101348 (SAR302503), TG101348, tofacitinib (CP-690,550), WHI-PI 54, WP1066, XL019, and XLOI 9. Ruxolitinib (Jakafi™, INCBO 18424; (3R)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin- 4-yl)pyrazol-l-yl]propanenitrile) is a potent, orally available, selective inhibitor of both JAK1 and JAK2 of the JAK-STAT signaling pathway. CYT387 is an inhibitor of Janus kinases JAK1 and JAK2, acting as an ATP competitor with IC50 values of 11 and 18 nM, respectively. TG101348 (SAR302503) is an orally available inhibitor of JAK2. TG101348 acts as a competitive inhibitor of JAK2 with IC50=6 nM. Related kinases such as FLT3 and RET are also sensitive to TG101348, with IC50=25 nM and IC50=17 nM, respectively. AZD1480 is an orally bioavailable inhibitor of JAK2 with potential antineoplastic activity. JAK2 inhibitor AZD 1480 inhibits JAK2 activation, leading to the inhibition of the JAK/STAT signaling including activation of STAT3. Lestaurtinib (CEP-701) is a tyrosine kinase inhibitor structurally related to staurosporine. Tofacitinib (Xeljanz®, tasocitinib or CP-690,550) is a known inhibitor of JAK1 and JAK3. Tofacitinib is used to inhibit JAK/STAT signaling and is used for treatment of rheumatoid arthritis. Pacritinib (SB 1815) is an orally bioavailable inhibitor of JAK2 and the JAK2 mutant JAK2V617F . Pacritinib competes with JAK2 for ATP binding, which may result in inhibition of JAK2 activation, inhibition of the JAK/STAT signaling pathway, and therefore caspase-dependent apoptosis. Baricitinib (LY3009104, INCB28050) is an orally bioavailable inhibitor of JAK1 and JAK2 with IC50=5.9 nm and IC50=5.7 nm, respectively. Baricitinib preferentially inhibits JAK1 and JAK2, with a selectivity of 10-fold over Tyk2 and 100-fold over JAK3. XLOI 9 is an orally bioavailable inhibitor of JAK2. XLOI 9 inhibits the activation of JAK2 as well as the mutated form JAK2V617F. NS018 is a potent JAK2 inhibitor with some inhibition of Src-family kinases. NS018 has been shown to be highly active against JAK2 with a 50% inhibition (IC50) of <1 nM, and had 30- to 50-fold greater selectivity for JAK2 over other JAK-family kinases.

In some embodiments, the JAK inhibitor is an inhibitor of expression of at least one

JAK gene (e.g. antisense nucleic acids, ribozymes, siRNA...).

The term "therapeutically effective amount" describes the amount of the active agent (e.g. IL-15 antagonist or JAK inhibitor) sufficient for treating or reducing the symptoms at reasonable benefit/risk-ratio applicable to any medical treatment. It will be understood that the total daily usage of the compounds and compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular subject will depend upon a variety of factors including the nature of the disorder being treated and its severity, the activity of the specific compound employed, the specific composition employed, the age, body weight, general health status, sex and diet of the subject, the time and route of administration, the compounds rate of clearance, the duration of the treatment, drugs used in combination with the active ingredients and other factors well known in the medical arts. For example, it is well within the skill of the art to start doses of the compound at levels lower than those required to achieve the desired therapeutic effect and to gradually increase the dosage until the desired effect is achieved. However, the daily dosage of the products may be varied over a wide range from 0.01 to 1,000 mg per adult per day. Typically, the compositions contain 0.01, 0.05, 0.1, 0.5, 1.0, 2.5, 5.0, 10.0, 15.0, 25.0, 50.0, 100, 250 and 500 mg of the active ingredient for the symptomatic adjustment of the dosage to the subject being treated. A medicament typically contains from about 0.01 mg to about 500 mg of the active ingredient, typically from 1 mg to about 100 mg of the active ingredient. An effective amount of the drug is usually supplied at a dosage level from 0.0002 mg/kg to about 20 mg/kg of body weight per day, especially from about 0.001 mg/kg to 7 mg/kg of body weight per day.

Typically, the active agent (e.g. IL-15 antagonist or JAK inhibitor) is combined with pharmaceutically acceptable excipients, and optionally sustained-release matrices, such as biodegradable polymers, to form pharmaceutical compositions. The term "pharmaceutically" or "pharmaceutically acceptable" refers to molecular entities and compositions that do not produce an adverse, allergic or other untoward reaction when administered to a mammal, especially a human, as appropriate. A pharmaceutically acceptable carrier or excipient refers to a non-toxic solid, semi-solid or liquid filler, diluent, encapsulating material or formulation auxiliary of any type. The carrier can also be a solvent or dispersion medium containing for example water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof as well as vegetables oils. The proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminium monostearate and gelatin. In the pharmaceutical compositions of the present invention, the active ingredients of the invention can be administered in a unit administration form, as a mixture with conventional pharmaceutical supports. Suitable unit administration forms comprise oral-route forms such as tablets, gel capsules, powders, granules and oral suspensions or solutions, sublingual and buccal administration forms, aerosols, implants, subcutaneous, transdermal, topical, intraperitoneal, intramuscular, intravenous, subdermal, transdermal, intrathecal and intranasal administration forms and rectal administration forms.

The invention will be further illustrated by the following figures and examples. However, these examples and figures should not be interpreted in any way as limiting the scope of the present invention.

EXAMPLE:

Methods:

Patients and controls

Endoscopic biopsies from 28 RCDII patients described in (Malamut et al, 2010) were obtained according to a protocol approved by the Ile-de-France Ethics committee II (Paris, France). Surgical samples of control small intestine (n=33), control adult blood (n=4) and umbilical cord blood (CB) (n=12) were obtained in accordance with National guidelines.

Analysis of Y -(D)- J gene rearrangements.

TCRD, TCRG and TCRB rearrangements were assessed on 100 ng DNA from duodenal biopsies by multiplex polymerase chain reaction (PCR) as described in BIOMED-2 Concerted Action protocols (van Dongen et al, 2003). See also supplemental experimental procedures.

Next generation sequencing

NGS targeted sequencing of a custom-made panel of 80 oncogenes was performed on exonic fragments enriched from genomic DNA and analyzed using in-house Poly Web software, as described in supplementary methods.

Statistical analysis

Statistical analyses were performed using Mann- Whitney tests with Prism 6 software (GraphPad Software Inc.).

Results:

We have shown that one rare but severe complication of celiac disease (CD) is the onset of CD103⁺ lymphomas, which develop within the gut epithelium as a massive expansion of clonal surface(s)CD3^" intracellular(i)CD3⁺ intra epithelial lymphocytes (IEL) that selectively respond to IL-15 and develop NK-like cytotoxicity against epithelial cells (Cellier et al, 1998; Malamut et al, 2010; Mention et al, 2003). As a consequence, patients develop severe villous atrophy resistant to a gluten-free-diet. This condition is now defined as clonal or type II refractory CD (RCDII) (reviewed in: (Malamut et al., 2012). Confirming and extending previous results (Cellier et al, 1998; Mention et al, 2003; Schmitz et al, 2013), we observed that RCDII IEL displayed many overlapping features with iCD3⁺ innate IEL: they expressed CD122 but not CD127, NK receptors, notably NKp46, GzmB and T-bet but not Eomes. They also displayed a T cell signature characterized by intracellular expression of CD3s and CD3y and clonal TCR rearrangements. Taking advantage of the clonality of RCDII IEL, TCR rearrangements were characterized in intestinal biopsies from 28 patients and in IL-15- dependent sCD3^" iCD3⁺ IEL lines derived from 14 of these 28 biopsies to ascertain that clonal TCR rearrangements were present in sCD3^" iCD3⁺ IEL. In the majority of patients (68% - 19/28), multiplex PCR and CDR3 sequencing demonstrated incomplete or non- functional TCRG, D and B rearrangements. In-frame rearrangements of both TCRG and TCRD genes were detected in 8/28 cases (28.5%), of which one (#20) also had an in-frame TCRB but no TCRA rearrangement. In only one case TCRB and TCRA rearrangements were detected, but the latter was non-productive. These data indicate that, in most cases, RCDII IEL derive from cells that have initiated but have not completed T cell differentiation. Altogether, these findings demonstrated that malignant RCDII IEL arise from the subset of iCD3⁺ innate IEL.

As mentioned above, RCDII IEL depend for their survival and growth on IL-15, a cytokine which is up-regulated in the gut epithelium in CD (Mention et al, 2003). Despite this, iCD3⁺ innate IEL remain a minor subset of IEL in most patients with active CD, calling into question the mechanism(s) that drive(s) the selective expansion of clonal iCD3⁺ innate IEL in RCDII. One possible hypothesis was that clonal RCDII IEL have acquired somatic mutation(s) which selectively increase(s) their responsiveness to IL-15. In keeping with this, next generation sequencing targeting a panel of 80 oncogenes mutated in human lymphoid malignancies showed G1097D/C/V/A mutations in JAK1 kinase domain and D661V/Y mutations in STAT3 SH2 domain in duodenal biopsies and RCDII IEL lines from 7 and 2 out of 12 RCDII patients respectively. Mutations were absent in polyclonal autologous T-IEL lines, indicating their somatic acquisition by malignant cells. G1097D/S/N JAK1 and D661V/Y STAT3 mutations able to enhance STAT3 activation in response to IL-6 were reported in a few cases of anaplastic large cell lymphoma (Crescenzo et al., 2015) and in large granular lymphocytic leukemia (Koskela et al., 2012). IL-15 induced much more robust phosphorylation of STAT3 in RCDII lines harboring JAK1 G1097D/C mutations than in normal non mutated T-IEL lines. We have previously shown that activation of STAT5 but not STAT3 is necessary for IL-15-induced survival of RCDII IEL (Malamut et al., 2010). Interestingly low concentrations of the JAK1 inhibitor Ruxotinilib, which abolished phosphorylation of STAT3 but only mildly decreased STAT5 phosphorylation did not induce apoptosis but reduced IL-15 driven-proliferation of RCDII IEL carrying G1097D/C JAK1 mutations. Altogether these results support the hypothesis that somatic mutations can confer RCDII IEL with a selective advantage that allows their clonal expansion from iCD3⁺ innate IEL in an IL-15 rich environment.

EXAMPLE 2:

Methods:

Patients:

The study has been extended to 69 patients with celiac disease (CD) responsive or not to gluten-free diet and complicated or not with enteropathy-associated T cell lymphoma (EATL). All included patients have been recruited since 2000 at Hopital Europeen Georges Pompidou by C. Cellier, PUPH and G. Malamut PUPH or in the frame of the National network INCA called CELAC (coordinators C. Cellier PUPH, O. Hermine PUPH and G. Malamut PUPH). Patients data were collected and analyzed by G. Malamut.

Patients diagnosis was established by combining histology and immunohistochemistry, flow cytometry and analysis of T cell receptor clonality.

Histological and immunohistochemical data were obtained and/or reviewed in the Department of Pathology of Hopital Necker by N. Brousse (PUPH retired in 2016) and J. Bruneau (MCU-PH). A count of over 50% of intraepithelial lymphocytes (IEL) positive of CD3 but negative for CD8 and CD4 is considered as indicative of RCDII. False positive can be observed in cases with high frequency of TCRgamma delta IEL (generally CD8 and CD4-). False negative are possible in few RCDII cases where innate-like IEL express CD8.

Flow cytometry analysis of lymphocytes isolated from duodenal biopsies was performed in the laboratory of Intestinal Immunity (Dir N. Cerf-Bensussan) by B. Meresse (CR1 INSERM, who moved to in Lille in September 2016) and N Guegan (AI University Paris Descartes). Flow cytometry allows a much more precise assessment of IEL phenotype than immunohistochemistry. A count of 20-25%% CD103+CD45+ IEL lacking surface CD3 but containing intracellular CD3 is considered as indicative of RCDII.

Analysis of clonality based on the rearrangements of the gamma chain of the T cell receptor was performed in DNA extracted from frozen biopsies in the laboratory of Biological Hematology of Hopital Necker as part of routine diagnostic for detection of T cell malignancies. Given the oligoclonality of IEL, very precise calibration of the threshold is necessary to define if a clone can be considered as significant.

CD defines patients with proven CD (HLA-DQ27anti-TG2⁺). Out of the 7 patients indicated as CD, 3 had uncomplicated CD responsive to gluten free diet while 4 had developed EATL at time of diagnosis of CD but had no evidence of RCDII in duodenal biopsies. RCD defines patients with CD refractory to gluten free diet for over 6 months. 6 CD patients were classified as type I RCD (RCDI) based on normal IEL phenotype by immunohistochemistry and flow cytometry and lack of detectable clonality in biopsies. 53 patients were classified as type II RCD (RCDII) based on detection in duodenal biopsies of: i) an excess of IEL with an innate-like phenotype and ii) clonal rearrangements of TCR gamma.

EATL (enteropathy-associated lymphomas) is defined as overt lymphoma and characterized by medium to large-sized cells with evidence of abnormal cytological features and expression of CD30 and of the proliferation marker KI67. Diagnosis can be obvious in case of massive infiltration but more difficult in some cases limited to small number of CD30⁺ KI67⁺ large cells. In the table below, EATL is used to indicate biopsies containing evidence of overt lymphoma. EATL was diagnosed in 9 patients classified as CD (see above) and in 17 patients classified as RCDII. In 3 CD and in 14 RCDII, detection of mutations was performed in biopsies containing EATL and on duodenal biopsies without evidence of EATL. In 6 patients with CD and in 3 patients with RCDII, mutations were only studied in EATL-containing biopsies.

Next generation targeted sequencing:

Targeted sequencing of exon-enriched fragments was performed on genomic DNA extracted from frozen biopsies using a custom-made panel designed by the laboratory of Biological Hematology to sequence exons from 112 oncogenes. This panel includes most of the 80 oncogenes analyzed in the initial study. Exon capture, library building and MI sequencing were performed in the laboratory of Biological Hematology.

The first part of data sequence analysis was performed by Paris Descartes University / Institut IMAGINE's Bioinformatics core facilities). Paired-end sequences were mapped on the human genome reference (NCBI build37/hgl9 version) using the Burrows- Wheeler Aligner. Downstream processing was carried out with the Genome Analysis Toolkit (GATK), SAMtools, and Picard, according documented best practices

(http://www.broadinstitute.org/gatk/guide/topic?name=best-practices). Variant calls were made with the GATK Unified Genotyper based on the 72 version of ENSEMBL database. Genome variations were next defined and analyzed by S. Cording, post-doctoral researcher in the laboratory of Intestinal Immunity in collaboration with L. Lhermitte MCU and Amelie Trinquand, AHU (Department of Bilogical Hematology) using the in-house Polyweb interface and the Cosmic as well as dbSNP and EXAC data bases in order notably to exclude irrelevant and common polymorphisms present in public databases and to identify known oncogenic mutations. Data analysis according to clinical diagnoses was performed by S. Cording in collaboration wih G. Malamut and N. Cerf-Bensussan. Depending on the infiltration of the biopsies and whether mutations were mono or biallelic, the frequency of reads containing mutations varied between 1 and 20%. Mean read/sequence was around 600. Minimum threshold to conclude to a mutation was > 50 reads for the sequence of interest with > 10 alternative reads.

Results:

RCDII:

At least one JAK1 mutation was detected in 24 out of 50 (48%) duodenal biopsies classified as RCDII without EATL. 22 were in position 1097 (92%), with the G residue replaced by diverse aminoacids. One patient displayed a distinct SI 0431 GOF mutation located in the activating loop of the tyrosine kinase domain of JAK1. This mutation does not seem to be described in human cancer but was in vitro selected in BaF3 cells as conferring cytokine independent growth. It was associated with constitutive STAT5 activation. In 1/23 patients, the JAK1 mutation was a large deletion difficult to interpret. Three patients with the JAK1 1097 mutation had additional mutations. In two of them, the additional mutation(s) suggest(s) that the second allele of JAK1 is not functional (Table 1 and data not shown). Of note, loss of the second allele of JAK2 is frequently observed in patients with myeloproliferative disorder with the canonic GOF mutation JAK2 V617F (Percy & McMullin Hemato. Oncol 2005 23:91-93) and may perhaps promote oncogenesis.

Interestingly, the 1097 JAK1 mutation was detected in 4% of the reads in the duodenal biopsy of a patient who had developed a jejunal EATL and was initially classified as CD+ EATL. Flow cytometry had revealed 17% IEL with an innate-like phenotype in the duodenal biopsies. This % is just below the threshold of 20% admitted for flow cytometry and is too low to be detected by immunohistochemistry. By combining TNGS and flow cytometry, we have requalified this patient as RCDII+ EATL.

At least 1 STAT3 mutation was detected in 13/50 patients (26%). The most frequent was in position D661 (4 cases: 31%) but 8 other mutations were observed, 5 of which have been previously reported as oncogenic in Cosmic.

Overall 66% of patients displayed at least a JAK1 or a Stat3 mutation. Two patients had both JAK1 1097 and STAT3 mutations. One had massive systemic diffusion of clonal innate- like IEL and both patients ultimately developed EATL.

RCDII+EATL

Among the 16 cases of EATL complicating RCDII, 9 displayed at least 1 JAK1 mutation (56%) and 8 at least 1 STAT3 mutation (50%). 5 patients had both JAK1 and STAT3 mutations (30%), while 4 patients had neither JAK1 nor STAT3 mutation (Table 1 and data not shown). Out of the 9 JAKl mutations, 8 were in position 1097. The remaining patient displayed the same GOF SI 0431 discussed above, which was observed in the duodenal RCDII biopsy without histological evidence of EATL (Table 1 and data not shown).

Among the 5 patients with both JAKl and STAT3 mutations, 2 had the same mutations in RCDII duodenal biopsies without EATL as indicated above. In the 2 other patients, only the JAKl mutation was present in duodenal RCDII biopsies.

CD and RCDI

No mutation was detected in duodenal biopsies obtained from 3 uncomplicated CD and from 6 RCD1. Mutations were also absent in the duodenal biopsies from 4 patients who developed an EATL diagnosed at the same time as CD. The lack of detectable mutation is coherent with the lack of evidence of RCDII IEL and of clonality in the duodenal biopsies.

CD+ EATL

A least 1 JAKl mutation was detected in 6/10 patients (60%), which was in 5/6 cases in position 1097. Two patients had several JAKl mutations as well as several STAT3 mutations and one had several JAKl mutations without STAT3 mutations. In 3 patients, no mutation in STAT3 or JAKl was detected. Overall 7 out of 10 patients had at least one mutation in JAKl or STAT3.

Discussion & conclusion:

Detection of JAKl and or STAT3 mutations in biopsies from patients with CD is observed in RCDII and EATL but not in CD or RCDI. In patients, in whom EATL develops without prior step of RCDII, mutations are not detected in intestinal sites distal from EATL.

Overall one JAKl and/or one STAT3 mutations is observed in 66% of RCDII and approximately 70% of EATL developing either in RCDII or CD. The concomitant presence of JAKl and STAT3 mutations is observed in 30% of EATL and was associated with the subsequent development of EATL in the 2 RCDII patients in whom it was detected prior EATL development. It is not excluded that some samples from RCDII patients negative for both mutations are false negative, due the limited infiltration of the tissue. This is not excluded notably for two patients in whom the frequency of abnormal IEL was around 30%. Yet other mutations may be involved. Thus in two other patients with RCDII and EATL negative for JAKl and STAT3 mutations, stop gain of function mutations in SOCS1 were observed, indicating that alternative mutations may dysregulate the JAK-STAT pathway in CD-associated lymphomagenesis. STAT3 mutations found in RCDII and EATL are diverse. They are mostly located in the SH2 domain and have been described in other neoplasms and lymphoid malignancies, notably in the 661 and 740 positions.

JAKl mutations in position 1097 are observed in 44% of RCDII and 50 % of EATL complicating RCDII or arising in CD patients without evidence of RCDII. Other JAKl mutations can occur but are in most cases associated with JAKl 097 mutations

Importantly the JAKl 097 mutation is not one of the hot spot mutation reported for JAKl in Cosmic. Thus Cosmic only reports this mutation in one case of HTLVl + leukemia out of 426 cases studied. Analysis of the literature indicates that JAKl mutations are present in lymphoid neoplasms with a frequency between 2% and 6% (up to 18% in report in adult T leukemias) but reported mutations were never in 1097 (except in the article reported in Cosmic). Up to now, JAKl mutations in position 1097 seem only recurrent in anaplastic T cell lymphomas. In one study (Crescenzo et al Cancer Cell 2015) JAKl mutations were noted in 8% of cases with 10/13 cases with 1097 mutations). It is not excluded that anaplastic T cell lymphomas which arise in tissues, share mechanisms of oncogenesis with lymphomas complicating CD. A recent article emphasizes their dependency on cytokines signalling. In addition, the cellular origin of anaplastic T lymphoma is unclear. We do not exclude that some of them derive from innate-like lymphocytes and we intend to test this hypothesis by using appropriate markers.

In addition to the cases reported in Table 1 , TNGS was performed in 4 cases considered as typical RCDII. Patients only differed from "classical "RCDII" by the T phenotype of IEL. In 3 patients, clonal IEL were gamma delta T cells with one case containing 2 STAT3 mutations and 1 case containing the 1097 JAKl mutation. In the 4^th patient, IEL were TCRalpha beta T cells lacking CD4 and CD8, all Vbeta20+. They contained the 1097 JAKl mutation.

Finally TNGS was performed in 12 cases of small intestinal T cell lymphoma, including

10 cases made of CD4+ T cells and 2 cases of CD8+. T cells Mutations in JAKl or STAT3 were observed in 4 CD4+ cases, including one case complicating CD, which displayed a STAT3 mutation. JAKl mutation in 1097 was observed in only one patient who also had STAT3 Y640F. JAKl misense mutations observed in the two other cases were not previously reported as oncogenic.

Overall this work confirms the interest to search for JAKl and STAT3 mutations to improve the diagnosis of RCDII and delineate the risk of overt lymphoma. The JAKl 1097 mutation is an interesting marker. Table 1 : Prevalence of JAK1/STAT3 mutations in biopsies from patients with celiac disase (CD) or refractory celiac disase type I (RCDI) or type II (RCDII) complicated or not with enteropathy associagted T cell lymphoma (EATL)

Mutations indicated in bold characters are known as oncogenic

1 RCDII+EATL : biopsies containing EATL and arising in RCDII. In only 3/17 patients, samples of RCDII away from EATL were not available in the 9 RCDII with EATL and mutations in JAKland/ or STAT3, at least one of the mutation was present in RCDII biopsies away from EATL

2 CD: duodenal biopsies from 3 uncomplicated CD and CD complicated with EATL but without evidence of RCDII

2 out of the 3 of he latter patients display JAK1 (1) or JAK and STAT3 (1) mutations in EATL arising in distal intestine

3 CD+EATL: biopsies containing EATL and arising in CD patients

REFERENCES: Throughout this application, various references describe the state of the art to which this invention pertains. The disclosures of these references are hereby incorporated by reference into the present disclosure.

Cellier, C, Patey, N., Mauvieux, L., Jabri, B., Delabesse, E., Cervoni, J.P., Burtin, M.L., Guy-Grand, D., Bouhnik, Y., Modigliani, R., et al. (1998). Abnormal intestinal intraepithelial lymphocytes in refractory sprue. Gastroenterology 114, 471-481.

Crescenzo, R., Abate, F., Lasorsa, E., Tabbo, F., Gaudiano, M., Chiesa, N., Di Giacomo, F., Spaccarotella, E., Barbarossa, L., Ercole, E., et al. (2015). Convergent mutations and kinase fusions lead to oncogenic STAT3 activation in anaplastic large cell lymphoma. Cancer cell 27, 516-532.

Koskela, H.L., Eldfors, S., Ellonen, P., van Adrichem, A.J., Kuusanmaki, H., Andersson, E.I., Lagstrom, S., Clemente, M.J., Olson, T., Jalkanen, S.E., et al. (2012). Somatic STAT3 mutations in large granular lymphocytic leukemia. N Engl J Med 366, 1905-1913.

Malamut, G., El Machhour, R., Montcuquet, N., Martin-Lanneree, S., Dusanter-Fourt, I., Verkarre, V., Mention, J.J., Rahmi, G., Kiyono, H., Butz, E.A., et al. (2010). IL-15 triggers an antiapoptotic pathway in human intraepithelial lymphocytes that is a potential new target in celiac disease-associated inflammation and lymphomagenesis. J Clin Invest 120, 2131-2143.

Malamut, G., Meresse, B., Cellier, C, and Cerf-Bensussan, N. (2012). Refractory celiac disease: from bench to bedside. Seminars in immunopathology 34, 601-613.

Mention, J. J., Ben Ahmed, M., Begue, B., Barbe, U., Verkarre, V., Asnafi, V., Colombel,

J.F., Cugnenc, P.H., Ruemmele, F.M., Mclntyre, E., et al. (2003). Interleukin 15: a key to disrupted intraepithelial lymphocyte homeostasis and lymphomagenesis in celiac disease. Gastroenterology 125, 730-745.

Schmitz, F., Tjon, J.M., Lai, Y., Thompson, A., Kooy-Winkelaar, Y., Lemmers, R.J., Verspaget, H.W., Mearin, M.L., Staal, F.J., Schreurs, M.W., et al. (2013). Identification of a potential physiological precursor of aberrant cells in refractory coeliac disease type II. Gut 62, 509-519.

Claims

CLAIMS:

1. A method for diagnosing refractory celiac disease type 2 (RCDII) in a patient comprising detecting the presence of at least one gain-of-function JAK1 or STAT3 mutation in a sample obtained from the patient and concluding that the patient suffers from refractory celiac disease type 2 when the mutation is detected.

2. The method of claim 1 wherein the gain-of-function JAK1 mutation is G1097D/C/V/A, which indicates that the glycine residue at position 1097 is substituted by an aspartic acid residue (D), a cysteine residue (C), a valine residue (V) or an alanine residue (A).

3. The method of claim 1 wherein the gain-of-function STAT3 mutation is D661V/Y/H which indicates that the aspartic acid residue at position 661 is substituted by a valine residue (V), a tyrosine residue (Y) or a histidine residue (H).

4. The method of claim 1 wherein the sample is a biopsy sample.

5. The method of claim 1 wherein the sample is a mucosal tissue sample.

6. A method of treating refractory celiac disease type 2 in a patient in need thereof comprising administering to the patient a therapeutically effective amount of an IL-15 antagonist.

7. A method of treating refractory celiac disease type 2 in a patient in need thereof comprising administering to the patient a therapeutically effective amount of a JAK inhibitor.

8. The method of claim 6 or 7 which comprises detecting at least one gain-of-function JAK1 or STAT3 mutation in a sample obtained from the patient and administering to the patient the therapeutically effective amount of an IL-15 antagonist or a JAK inhibitor.

9. The method of claim 6 wherein the IL-15 antagonists are selected from the group consisting of IL-15 muteins, IL-15 conjugates and IL-15 antibodies.

10. The method of claim 6 wherein the IL-15 antagonist is an IL-15 mutant polypeptide having the amino acid sequence as set forth in SEQ ID NO: 1 wherein the leucine residue at position 45 is substituted by an aspartic acid residue, the asparagine residue at position 65 is substituted by a lysine residue and the leucine residue at position 69 is substituted by an arginine residue.

11. The method of claim 6 wherein the IL-15 antagonist is selected from monoclonal antibodies that immunoreact with mature IL-15 and prevent signal transduction through the IL-15 receptor complex.