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Li B, Hu P, Liang H, Zhao X, Zhang A, Xu Y, Zhang B, Zhang J. Evaluating the causal effect of circulating proteome on the risk of inflammatory bowel disease-related traits using Mendelian randomization. Front Immunol 2024; 15:1434369. [PMID: 39144148 PMCID: PMC11321985 DOI: 10.3389/fimmu.2024.1434369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 07/17/2024] [Indexed: 08/16/2024] Open
Abstract
Objective This study sought to identify circulating proteins causally linked to Inflammatory Bowel Disease (IBD) traits through a Mendelian Randomization (MR) analytical framework. Methods Using a large-scale, two-sample MR approach, we estimated the genetic links of numerous plasma proteins with IBD and its subtypes, leveraging information from the Inflammatory Bowel Disease Genetics Consortium. To assess the robustness of MR findings, methods like Bayesian colocalization, and Steiger filtering analysis, evaluation of protein-altering variants. Further insights into IBD's underlying mechanisms and therapeutic targets were gleaned from single-cell sequencing analyses, protein-protein interaction assessments, pathway enrichment analyses, and evaluation of drug targets. Results By cis-only MR analysis, we identified 83 protein-phenotype associations involving 27 different proteins associated with at least one IBD subtype. Among these proteins, DAG1, IL10, IL12B, IL23R, MST1, STAT3 and TNFRSF6B showed overlapping positive or negative associations in all IBD phenotypes. Extending to cis + trans MR analysis, we further identified 117 protein-feature associations, including 44 unique proteins, most of which were not detected in the cis-only analysis. In addition, by performing co-localization analysis and Steiger filtering analysis on the prioritized associations, we further confirmed the causal relationship between these proteins and the IBD phenotype and verified the exact causal direction from the protein to the IBD-related feature. Conclusion MR analysis facilitated the identification of numerous circulating proteins associated with IBD traits, unveiling protein-mediated mechanisms and promising therapeutic targets.
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Affiliation(s)
- Beining Li
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
- The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Ping Hu
- Department of Orthopedic, Tianjin Medical University General Hospital, Tianjin, China
| | - Hongyan Liang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xingliang Zhao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Aiting Zhang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yingchong Xu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Bin Zhang
- Department of Orthopedic, Tianjin Medical University General Hospital, Tianjin, China
| | - Jie Zhang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
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Fougiaxis V, He B, Khan T, Vatinel R, Koutroumpa NM, Afantitis A, Lesire L, Sierocki P, Deprez B, Deprez-Poulain R. ERAP Inhibitors in Autoimmunity and Immuno-Oncology: Medicinal Chemistry Insights. J Med Chem 2024; 67:11597-11621. [PMID: 39011823 DOI: 10.1021/acs.jmedchem.4c00840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Endoplasmic reticulum aminopeptidases ERAP1 and 2 are intracellular aminopeptidases that trim antigenic precursors and generate antigens presented by major histocompatibility complex class I (MHC-I) molecules. They thus modulate the antigenic repertoire and drive the adaptive immune response. ERAPs are considered as emerging targets for precision immuno-oncology or for the treatment of autoimmune diseases, in particular MHC-I-opathies. This perspective covers the structural and biological characterization of ERAP, their relevance to these diseases and the ongoing research on small-molecule inhibitors. We describe the chemical and pharmacological space explored by medicinal chemists to exploit the potential of these targets given their localization, biological functions, and family depth. Specific emphasis is put on the binding mode, potency, selectivity, and physchem properties of inhibitors featuring diverse scaffolds. The discussion provides valuable insights for the future development of ERAP inhibitors and analysis of persisting challenges for the translation for clinical applications.
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Affiliation(s)
- Vasileios Fougiaxis
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ben He
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
| | - Tuhina Khan
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
| | - Rodolphe Vatinel
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
| | | | | | - Laetitia Lesire
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
| | - Pierre Sierocki
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
| | - Benoit Deprez
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
| | - Rebecca Deprez-Poulain
- U1177 - Drugs and Molecules for Living Systems, Univ. Lille, Inserm, Institut Pasteur de Lille, F-59000 Lille, France
- European Genomic Institute for Diabetes, EGID, University of Lille, F-59000 Lille, France
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Abbas MA, Masry MAA, ALQusi SM, Hadhoud MM, Fouda EAM. The association between endoplasmic reticulum aminopeptidase 2 gene single nucleotide polymorphisms and the risk of psoriasis and psoriatic arthritis in Egyptians. Mol Biol Rep 2024; 51:847. [PMID: 39046539 DOI: 10.1007/s11033-024-09733-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/17/2024] [Indexed: 07/25/2024]
Abstract
BACKGROUND Psoriasis (Ps) is a disorder attributed to the immune system that involves inflammation of the skin and joints. Psoriasis is a multifactorial disorder in which genetic factors represent about 70% of the disease risk. This study aims to establish the correlation between the ERAP2 gene's single nucleotide polymorphisms (SNPs) rs2910686 and rs2248374 with the susceptibility to Ps and/or psoriatic arthritis (PsA) among the Egyptian population. METHODS AND RESULTS Genotyping of ERAP2 gene SNPs (rs2910686 and rs2248374) in 120 psoriatic patients with and without arthritis and 100 controls was done using real-time PCR. The genotype frequency and distribution of the ERAP2 SNP (rs2910686 and rs2248374) were in Hardy-Weinberg equilibrium (HWE). For rs2910686, the TC and CC genotypes and C allele frequency were significant risk factors for PsA compared to the controls (OR = 5.708, OR = 10.165, and OR = 4.282, respectively). They also were significant risk factors for Ps compared to the controls (OR = 5.165, OR = 5.040, and OR = 3.258, respectively). For rs2248374, the AG genotype significantly increased the risk of PsA (OR = 2.605) and Ps (OR = 3.768) compared to controls. The AG genotype was significantly related to the risk of Ps (OR = 3.369) G allele with PsA (OR = 1.608) and Ps (OR = 1.965) compared to controls. CONCLUSION In Egyptian individuals, the ERAP2 gene polymorphisms (rs2248374 and rs2910686) may contribute genetically to the pathophysiology of psoriasis and PsA.
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Affiliation(s)
- Mona A Abbas
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Menoufia University, Yassen Abd Al Ghafar Street, Shebin El-Kom City, Menoufia governorate, 32511, Egypt.
| | | | - Salah M ALQusi
- Department of Organic Chemistry, Faculty of Science, Menoufia University, Menoufia, Egypt
| | - Mahmoud M Hadhoud
- Department of Orthopedic Surgery, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Eman A M Fouda
- Department of Biochemistry, Faculty of Science, Menoufia University, Menoufia, Egypt
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Venema WJ, Hiddingh S, van Loosdregt J, Bowes J, Balliu B, de Boer JH, Ossewaarde-van Norel J, Thompson SD, Langefeld CD, de Ligt A, van der Veken LT, Krijger PHL, de Laat W, Kuiper JJW. A cis-regulatory element regulates ERAP2 expression through autoimmune disease risk SNPs. CELL GENOMICS 2024; 4:100460. [PMID: 38190099 PMCID: PMC10794781 DOI: 10.1016/j.xgen.2023.100460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/04/2023] [Accepted: 11/09/2023] [Indexed: 01/09/2024]
Abstract
Single-nucleotide polymorphisms (SNPs) near the ERAP2 gene are associated with various autoimmune conditions, as well as protection against lethal infections. Due to high linkage disequilibrium, numerous trait-associated SNPs are correlated with ERAP2 expression; however, their functional mechanisms remain unidentified. We show by reciprocal allelic replacement that ERAP2 expression is directly controlled by the splice region variant rs2248374. However, disease-associated variants in the downstream LNPEP gene promoter are independently associated with ERAP2 expression. Allele-specific conformation capture assays revealed long-range chromatin contacts between the gene promoters of LNPEP and ERAP2 and showed that interactions were stronger in patients carrying the alleles that increase susceptibility to autoimmune diseases. Replacing the SNPs in the LNPEP promoter by reference sequences lowered ERAP2 expression. These findings show that multiple SNPs act in concert to regulate ERAP2 expression and that disease-associated variants can convert a gene promoter region into a potent enhancer of a distal gene.
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Affiliation(s)
- Wouter J Venema
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Sanne Hiddingh
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jorg van Loosdregt
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Brunilda Balliu
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joke H de Boer
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | | | - Susan D Thompson
- Department of Pediatrics, University of Cincinnati College of Medicine, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Aafke de Ligt
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Lars T van der Veken
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
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