The invention relates to the identification of biomarkers of the response status of a patient for a treatment with anti-TNFalpha agents,for treatment with anti-α4β7 agents or with both anti-TNFalpha agent and anti-α4β7agents and to their use in assessing such status, in particular for assessing nonresponsive status for a treatment with anti-TNFalpha agents or respectively with anti-α4β7 agent in human patients suffering from inflammatory condition or disease, in particular Inflammatory Bowel Disease (IBD), in particular Ulcerative Colitis or Crohn's disease. The invention describes a method of in vitro assessing whether a treatment with anti- TNFalpha agent or with anti-α4β7 agent may be useful in a human patient suffering from inflammatory condition or disease, in particular when said condition or disease is a chronic and/or relapsing one, particularly a gastrointestinal, more particularly intestinal, inflammatory condition or disease which is eligible for treatment with anti-TNFalpha agent or respectively with anti-α4β7 agent. In a specific embodiment the method is suitable to assess whether such patient would be non- responsive to treatment with such anti-TNFalpha agent or respectively with anti-α4β7 agent and comprising determining a molecular signature in a biological sample previously obtained from said human patient.

The present invention provides a method of assessing whether an individual is at high risk or low risk of inflammatory bowel disease (IBD) progression by determining the expression level of two or more genes in a whole blood sample. Also provided are methods for treating IBD in an individual who is determined to be at high risk or low risk for IBD progression, and kits for assessing whether an individual is at high risk or low risk for IBD progression. Arrays, and methods of providing arrays, of patient-identified selected gene expression products from a whole blood sample of a patient are also provided.

The present disclosure relates to methods of diagnosing a dysbiosis in a subject, methods of determining a suitable treatment, and methods of treating a dysbiosis. In some aspects, the present disclosure relates to diagnosing or determining a subtype of irritable bowel syndrome (IBS).

An apparatus and method are provided for use in studying a patient's bowel which combines recording and analysis of physiologic parameters and patient sensory perception. A pain input detector, a pain transducer, and a processor are provided. A gas pressure transducer and flow meter may also be provided. Output data may be generated to reflect perceived patient pain, volume of gas delivered to the patient's bowel, and bowel pressure. An indication of perceived patient pain is processed by the processor to generate data that may used to validate a scan of a patient or may be used as a diagnostic tool.

The present invention relates to compositions and methods for identifying and treating metastatic small bowel neuroendocrine tumors.

The present invention provides for a human cell atlas of the colon from healthy and diseased subjects. The atlas was obtained by single sequencing of about 117,000 cells. The present invention discloses novel markers for cell types. Moreover, genes associated with disease are identified in the colon and colon specific cell types. The invention provides for diagnostic assays based on gene markers and cell composition, as well as target cell types that express genes associated with disease. Finally, disclosed are novel cell types and methods of quantitating, detecting and isolating the cell types.

Among the various aspects of the present disclosure is the provision of methods of diagnosing and treating inflammatory bowel disease (IBD) including ulcerative colitis (UC) or Crohn's disease (CD). In particular, the present disclosure provides in part a panel of IBD biomarkers useful in diagnosing and making treatment decisions. In addition, the present disclosure provides methods of treating IBD with a plasminogen activator inhibitor-1(PAI-1) inhibitor or tissue plasminogen activator (tPA).

The invention relates to the use of human Gelsolin as a diagnostic and prognostic marker of inflammatory bowel diseases by ex vivo detection of the protein level in faecal samples.

The invention relates to the use of Rho GDP dissociation inhibitory 2 protein as a diagnostic and prognostic marker of inflammatory bowel diseases by means of the ex vivo detection of the protein level in faecal samples of patients.

The invention relates to an in vitro method for diagnosis, prognosis, risk assessment, monitoring, therapy guidance and/or therapy control of an autoimmune disorder of the digestive system, such as inflammatory bowel disease and autoimmune liver disease, in which autoantibodies that bind Chitinase-3-Like Protein 1 (CHI3L1) protein are detected as a marker of such disease. The invention therefore relate to the use of CHI3L1 as an autoantigen in autoimmune diagnostics if diseases of the digestive system. A kit and system for conducting the method are encompassed by the invention.

The present disclosure relates to methods of diagnosing a dysbiosis in a subject, methods of determining a suitable treatment, and methods of treating a dysbiosis. In some aspects, the present disclosure relates to diagnosing or determining a subtype of irritable bowel syndrome (IBS).

The present invention describes methods of diagnosing inflammatory bowel disease, including but not limited to Crohn's Disease (CD), Ulcerative Colitis (UC), and/or Medically Refractive Ulcerative Colitis (MR-UC), using RNASET2, TL1A and/or IFN-ϒ. The invention further provides a process for patient identification and/or stratification.

The present invention relates to genomic regions which are useful markers for determining whether a subject suffers from an inflammatory bowel disease, such as ulcerative colitis or Crohn's disease, or is healthy. Also disclosed are useful primers for measuring expression levels of said markers, as well as computer-implemented methods.

Pharmacological compositions of single-stranded antisense miR-214 oligonucleotides that are chemically modified to increase their efficacy for intracolonic (enema) administration to treat Ulcerative Colitis (UC) or proctitis provide a an improved method of inhibiting miR-214. These miR-214 inhibitors have a combination of chemical modifications such as phosphorothioate (PS) linkages between the nucleotides, 5-methyl groups in cytidines (mC), and locked nucleic acids (LNA). The sequences have been constructed computationally to avoid off-target effects, especially for genes expressed in the human and mouse colon. The oligonucleotides are highly efficient in penetrating colonic tissue and do not induce liver toxicity.

The present invention relates to methods of prognosing responsiveness to anti-TNFα therapy by determining the presence or absence of risk factors in the individual. In one embodiment, the risk factors are genetic markers, serological markers and/or clinical phenotypes associated with non-responsiveness to treatment with anti-TNFα therapy in an individual diagnosed with IBD.

A targeted DEFA5 antibody is disclosed herein. The targeted DEFA5 antibody has a high degree of specificity with DEFA5 protein, particularly with peptide sequences of the P, B, and/or M binding sites of the DEFA5 protein. The targeted DEFA5 antibody may be incorporated into an assay for diagnosing and treating ulcerative colitis and Crohns disease in a subject suffering from inflammatory bowel disease. The assay may be provided in a kit. The targeted DEFA5 antibody may be used in a method for measuring the level of DEFA5 or DEFA5 expression in a sample collected from a subject, and determining, based on the level of DEFA5 or DEFA5 expression, whether the subject is suffering from ulcerative colitis or Crohns disease. A treatment may be based on the determination of whether the subject has ulcerative colitis or Crohns disease.

In certain aspects, described herein are methods, bacteria, and compositions for the reduction of the amount, activity and/or proliferation of colonic group 3 innate lymphoid cells (ILC3s) and for the treatment and/or prevention of diseases associated with pathological immune responses, such as inflammatory bowel diseases.

Compositions and methods for the therapy and diagnosis of Inflammatory Bowel Disease (IBD), including Crohn's Disease and Ulcerative Colitis, are disclosed. Illustrative compositions comprise one or more bacterial polypeptides, immunogenic portions thereof, polynucleotides that encode such polypeptides, antigen presenting cell that expresses such polypeptides, and T cells that are specific for cells expressing such polypeptides. The disclosed compositions are useful, for example, in the diagnosis, prevention and/or treatment of IBD.

A method for determining a presence of inflammatory bowel disease in a subject. The method involves providing a gut sample obtained from a subject; measuring a level in said gut sample of one or more proteins, wherein said one or more proteins comprises at least one of: leukotriene A-4 hydrolase, catalase, transketolase, thioredoxin domain containing protein 17, vasodilator-stimulated phosphoprotein and thymosin beta-10; and comparing said measured level of each of said one or more proteins to a corresponding protein level for a normal subject. A method for determining a presence of pancolitis in a subject with ulcerative colitis is also provided.

This document relates to materials and methods involved in assessing inflammatory bowel disease patients at risk for developing cancer. For example, materials and methods for monitoring colorectal cancer risk in ulcerative colitis patients are provided.

In some embodiments, the invention provides a method for identifying an agent beneficial to treat a patient with inflammatory bowel disease comprising: a) determining a status of an intestinal barrier in the patient; and b) categorizing the status as severe dysfunction or moderate dysfunction, wherein a patient categorized as having severe dysfunction is identified as a patient who will benefit from treatment with an agent selected from the group consisting of an anti-TNF agent and/or an anti-IL-12/23 agent, and a patient categorized as having moderate dysfunction is identified as a patient who will benefit from treatment with an anti-integrin agent, an anti-janus kinase agent, and/or and a sphingosine-1- phosphate receptor agonist agent.

Biomarkers predictive of responsiveness to integrin beta7 antagonists, including anti-beta7 integrin subunit antibodies, and methods of using such biomarkers are provided. In addition, methods of treating gastrointestinal inflammatory disorders such as inflammatory bowel diseases including ulcerative colitis and Crohn's disease are provided. Also provided are methods of using such predictive biomarkers for the treatment of inflammatory bowel diseases including ulcerative colitis and Crohn's disease.

본 발명에 따른 차세대서열분석을 통해 선별한 유전자좌위의 단일염기다형성을 확인하여 염증성 장질환의 예측 또는 진단에 관한 정보를 제공하는 방법은 단일염기다형성을 확인하여 한국인 환자 중 염증성 장질환의 발생을 예측 또는 진단할 수 있는 방법으로 한국인 특이적으로 염증성 장질환 고위험군을 예측할 수 있기 때문에 임상적으로 큰 의미를 가지며, 이를 이용하여 개개인의 치료, 시술, 수술 등 다양한 처치 과정에서의 위험성을 감소시켜 염증성 장질환으로 인한 위험성을 감소시키는데 효과적으로 사용될 수 있을 것으로 기대된다.

본 발명에 따른 차세대서열분석을 통해 선별한 유전자좌위의 단일염기다형성을 확인하여 염증성 장질환의 예측 또는 진단에 관한 정보를 제공하는 방법은 단일염기다형성을 확인하여 한국인 환자 중 염증성 장질환의 발생을 예측 또는 진단할 수 있는 방법으로 한국인 특이적으로 염증성 장질환 고위험군을 예측할 수 있기 때문에 임상적으로 큰 의미를 가지며, 이를 이용하여 개개인의 치료, 시술, 수술 등 다양한 처치 과정에서의 위험성을 감소시켜 염증성 장질환으로 인한 위험성을 감소시키는데 효과적으로 사용될 수 있을 것으로 기대된다.

Resumen de: WO2018209318A2

Embodiments of the disclosure include systems, methods, and compositions for detection of imminent onset of a symptom of a gut inflammation medical condition. The disclosure also concerns microbial biosensors that detect a marker in the gut that is predictive of onset of at least one symptom of inflammatory bowel disease (IBD), for example, and such a sensor may include a promoter sensitive to the marker that is linked to expression of a detectable readout, such as in the feces of the individual with IBD.