Lymphoid Tyrosine Phosphatase Gene Polymorphisms in Inflammatory Bowel Disease

This study aims:

1. To investigate the association between single nucleotide polymorphisms of PTPN22 gene (rs2476601, rs33996649 and rs2488457) and inflammatory bowel disease.
2. To correlate the relation between the studied SNPs and disease activity /response to therapy.

Study Overview

• Status: Unknown
• Conditions: Inflammatory Bowel Diseases
• Intervention / Treatment: Genetic: PCR-RFLP

Detailed Description

The inflammatory bowel diseases (IBD) are chronic inflammatory disorders of the gastrointestinal tract that manifests as Crohn's disease (CD) and Ulcerative colitis (UC), clinically characterized by periods of remission interrupted by episodes of clinical disease activity (Zallot et al., 2013). Patients with IBD display some common symptoms such as severe diarrhea, pain, fatigue and weight loss , but the localization is slightly different: whereas CD affects the whole gastrointestinal tract, UC primarily affects the distal intestine and ileum (De Lange et al., 2015).

Lennard-Jones et al. have defined macroscopic and microscopic criteria to establish the diagnosis of Crohn's disease. The macroscopic diagnostic tools include physical examination, endoscopy and radiology. Microscopic features can be assessed on mucosal biopsy and/or operative specimen. The diagnosis depends on the finding of discontinuous and often granulomatous intestinal inflammation (Lennard-Jones et al., 1997). Diagnosis of ulcerative colitis is based on history, endoscopic appearances, histopathology of multiple mucosal biopsies and appropriate radiology (Silverberg et al., 2005, Satsangi et al., 2006).

The incidence pattern of UC has changed over the last two decades, with incidence continuing to rise in the West and rising incidence in previously low incidence areas such as Asia and the Middle East (0.15- 6.5 per 100,000)(Ng et al., 2017). Marked increase in UC diagnoses was noted over a 15-year period (1995-2009). In Cairo University, 17 cases were recorded in 1995-1999 and 76 cases were recorded in 2005-2009 (Esmat et al., 2014).

Both CD and UC are complex diseases genetically, in which hundreds of independent genetic loci contribute to disease susceptibility (Norouzinia et al., 2015) . Nevertheless, the molecular mechanisms and functions of many IBD associated genes remain unknown. In addition to genetics, IBDs are powerfully influenced by microbiological and environmental aspect (Norouzinia et al., 2017).

Genome-wide association studies (GWAS) have allowed a better understanding of IBD thus, several genetic susceptibility loci have been identified for UC and CD (Yamamoto-Furusho et al., 2015). Among the genetic factors involved, there are several polymorphisms in molecules of the Immune system associated with either susceptibility or protective effects to IBD progression, but even with contradictory associations, mainly depending on the onset (adult or pediatric), sample size differences and on the ethnicity-dependent genetic background (Neuman et al., 2012, Ng et al., 2012, Peng et al., 2017, Girardelli et al., 2018).

PTPN22 protein contains three domains, including: an N-terminal PTP catalytic domain; an interdomain region; and a C-terminal domain with four proline-rich regions that function as motifs for interaction with other protein (Stanford et al., 2014).Tyrosine phosphatase is involved in maintaining intestinal epithelial barrier function, regulating autophagosome function and immune responses to invading bacteria in intestinal cells, limiting pro-inflammatory cytokine secretion in the intestine as well as controlling differentiation and function of CD4+ T-cells in vivo (Spalinger et al., 2015). The lymphoid tyrosine phosphatase (Lyp) encoded by PTPN22 plays a critical role as a negative regulator of T-cell activation by dephosphorylating T-cell receptor activation dependent kinases (Csk kinase) (Cloutier et al., 1999). PTPN22 is a critical regulator of the (Nod Like Receptor Family Pyrine Domain Containing 3 ) NLRP3 inflammasome by controlling NLRP3 tyrosine phosphorylation . Further, PTPN22 controls NLRP3-mediated IL-1beta secretion in an autophagy dependent manner (Yilmaz et al., 2018) .

PTPN22 gene is located on the short arm of Chromosome 1 (1p13.2). There are 24 exons in the gene (NCBI website).About 21 SNPs were found in PTPN22 gene (rs1310182, rs3789604, rs33996649, rs1217414, rs2476601, rs12760457, rs2488457,,,,etc).SNP rs2476601 (C1858>T) in exon 14 results in the substitution of arginine 620 with a tryptophan residue in the protein product (referred to as 620W variant) (Spalinger et al., 2016). SNP rs33996649 (G788>A) in exon 10 mediates substitution of arginine 263 with a glutamine residue (referred to as 263Q variant) and affects the ability of Lyp to interact with the Csk kinase, thus avoiding the formation of the complex and the resulting suppression of T-cell activation(Hedjoudje et al., 2017) . SNP rs2488457 (G -1123>C) is located in the promoter region (Chen et al., 2013).A transcription factor binding site for activator protein 4 (AP-4) at position -1123 is predicted in the presence of the G allele rather than the C allele (Jüliger et al., 2003).

Contradictory results have been published regarding the association of PTPN22 gene SNPs with IBD (Bank et al., 2014, Sfar et al., 2010, Chen et al., 2013, Latiano et al., 2007, Diaz-Gallo et al., 2011, Wagenleiter et al., 2005, Zaid et al., 2018, Sadr et al., 2019).

In Egypt studies were done regarding the association of PTPN22 gene SNPs with{ Type1 DM (El-Kafoury et al., 2014), ITP (Anis et al., 2011) ,SLE (Elghzaly et al., 2015) , Alopecia Areata (El-Zawahry et al., 2013) and RA (Salama et al., 2014) }.

Uptodate , no studies were published regarding the association of PTPN22 gene SNPs with IBD in egyptians.

• Study Type: Observational
• Enrollment (Anticipated): 200

Contacts and Locations

• Study Contact: Name: menna refaat, Ass lecturer; Phone Number: 01011490613; Email: mennarefaat924@gmail.com
• Study Contact Backup: Name: eman reda, lecturer; Phone Number: 01001838796

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 18 years to 60 years (ADULT)
• Accepts Healthy Volunteers: N/A
• Genders Eligible for Study: All

• Sampling Method: Non-Probability Sample

Study Population

IBD Patients will Diagnosed according to established guidelines for UC/CD . Phenotype characteristics of UC and CD were defined according to the Montreal classification . The clinical disease activity will be assessed using the Montreal classification of UC disease activity and Crohn's Disease Activity Index (CDAI) for CD

Description

Inclusion Criteria:

• patients with inflammatory bowel disease

Exclusion Criteria:

• Patients with systemic autoimmune diseases (RA,SLE) will be excluded from the study .

Study Plan

How is the study designed?

Number of groups / cohorts

2

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
A; patients with inflammatory bowel disease	Genetic: PCR-RFLP; PCR-Restriction fragment length polymorphism
B; healthy subjects	Genetic: PCR-RFLP; PCR-Restriction fragment length polymorphism

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Association between single nucleotide polymorphisms of Lymphoid Tyrosine Phosphatase gene (rs2476601, rs33996649 and rs2488457) and inflammatory bowel disease	Three single nucleotide polymorphisms in the lymphoid tyrosine phosphatase gene(SNP (G788>A) in exon10, SNP (C1858>T) in exon 14 and SNP (G -1123>C) in the promoter region ) will be assessed in 100 patients diagnosed as inflammatory bowel disease and 100 healthy subjects by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) to detect association between these polymorphisms and inflammatory bowel disease	baseline

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
To correlate the relation between the studied SNPs and disease activity /response to therapy.	Serum Erythrocyte Sedimentation Rate ,C-Reactive Protien ,Anti Nuclear Antibody ,Antineutrophil Cytoplasmic Antibody (ANCA) and Anti Saccharomyces Cerevisiae (ASCA) and fecal calprotectin will be done to all patients.The three investigated polymorphisms in LYP will be correlated with the markers of disease activity and IBD patients response to therapy.	baseline

Collaborators and Investigators

• Sponsor: Assiut University

Publications and helpful links

General Publications

• Norouzinia M, Chaleshi V, Alizadeh AHM, Zali MR. Biomarkers in inflammatory bowel diseases: insight into diagnosis, prognosis and treatment. Gastroenterol Hepatol Bed Bench. 2017 Summer;10(3):155-167.

Study record dates

Study Major Dates

• Study Start (ANTICIPATED): May 1, 2020
• Primary Completion (ANTICIPATED): May 1, 2021
• Study Completion (ANTICIPATED): September 1, 2021

Study Registration Dates

• First Submitted: February 23, 2020
• First Submitted That Met QC Criteria: February 25, 2020
• First Posted (ACTUAL): February 26, 2020

Study Record Updates

• Last Update Posted (ACTUAL): February 26, 2020
• Last Update Submitted That Met QC Criteria: February 25, 2020
• Last Verified: February 1, 2020

More Information

Terms related to this study

• Additional Relevant MeSH Terms: Digestive System Diseases; Gastrointestinal Diseases; Gastroenteritis; Inflammatory Bowel Diseases; Intestinal Diseases
• Other Study ID Numbers: LYP polymorphisms in IBD

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: NO

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No