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Young KA, Wojdyla K, Lai T, Mulholland KE, Aldaz Casanova S, Antrobus R, Andrews SR, Biggins L, Mahler-Araujo B, Barton PR, Anderson KR, Fearnley GW, Sharpe HJ. The receptor protein tyrosine phosphatase PTPRK promotes intestinal repair and catalysis-independent tumour suppression. J Cell Sci 2024; 137:jcs261914. [PMID: 38904097 DOI: 10.1242/jcs.261914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/28/2024] [Indexed: 06/22/2024] Open
Abstract
PTPRK is a receptor tyrosine phosphatase that is linked to the regulation of growth factor signalling and tumour suppression. It is stabilized at the plasma membrane by trans homophilic interactions upon cell-cell contact. PTPRK regulates cell-cell adhesion but is also reported to regulate numerous cancer-associated signalling pathways. However, the signalling mechanism of PTPRK remains to be determined. Here, we find that PTPRK regulates cell adhesion signalling, suppresses invasion and promotes collective, directed migration in colorectal cancer cells. In vivo, PTPRK supports recovery from inflammation-induced colitis. In addition, we confirm that PTPRK functions as a tumour suppressor in the mouse colon and in colorectal cancer xenografts. PTPRK regulates growth factor and adhesion signalling, and suppresses epithelial to mesenchymal transition (EMT). Contrary to the prevailing notion that PTPRK directly dephosphorylates EGFR, we find that PTPRK regulation of both EGFR and EMT is independent of its catalytic function. This suggests that additional adaptor and scaffold functions are important features of PTPRK signalling.
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Affiliation(s)
| | | | - Tiffany Lai
- Signalling programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | | | - Robin Antrobus
- Cambridge Institute for Medical Research, Hills Road, Cambridge CB2 0XY, UK
| | | | - Laura Biggins
- Bioinformatics, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Philippa R Barton
- Cambridge Institute for Medical Research, Hills Road, Cambridge CB2 0XY, UK
| | - Keith R Anderson
- Molecular biology department, Genentech, South San Francisco, CA 94080, USA
| | | | - Hayley J Sharpe
- Signalling programme, Babraham Institute, Cambridge CB22 3AT, UK
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2
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Risemberg EL, Smeekens JM, Cruz Cisneros MC, Hampton BK, Hock P, Linnertz CL, Miller DR, Orgel K, Shaw GD, de Villena FPM, Burks AW, Valdar W, Kulis MD, Ferris MT. A mutation in Themis contributes to anaphylaxis severity following oral peanut challenge in CC027 mice. J Allergy Clin Immunol 2024:S0091-6749(24)00411-1. [PMID: 38670234 DOI: 10.1016/j.jaci.2024.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND The development of peanut allergy is due to a combination of genetic and environmental factors, although specific genes have proven difficult to identify. Previously, we reported that peanut-sensitized Collaborative Cross strain CC027/GeniUnc (CC027) mice develop anaphylaxis upon oral challenge to peanut, in contrast to C3H/HeJ (C3H) mice. OBJECTIVE This study aimed to determine the genetic basis of orally induced anaphylaxis to peanut in CC027 mice. METHODS A genetic mapping population between CC027 and C3H mice was designed to identify the genetic factors that drive oral anaphylaxis. A total of 356 CC027xC3H backcrossed mice were generated, sensitized to peanut, then challenged to peanut by oral gavage. Anaphylaxis and peanut-specific IgE were quantified for all mice. T-cell phenotyping was conducted on CC027 mice and 5 additional Collaborative Cross strains. RESULTS Anaphylaxis to peanut was absent in 77% of backcrossed mice, with 19% showing moderate anaphylaxis and 4% having severe anaphylaxis. There were 8 genetic loci associated with variation in response to peanut challenge-6 associated with anaphylaxis (temperature decrease) and 2 associated with peanut-specific IgE levels. There were 2 major loci that impacted multiple aspects of the severity of acute anaphylaxis, at which the CC027 allele was associated with worse outcome. At one of these loci, CC027 has a private genetic variant in the Themis gene. Consistent with described functions of Themis, we found that CC027 mice have more immature T cells with fewer CD8+, CD4+, and CD4+CD25+CD127- regulatory T cells. CONCLUSIONS Our results demonstrate a key role for Themis in the orally reactive CC027 mouse model of peanut allergy.
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Affiliation(s)
- Ellen L Risemberg
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Johanna M Smeekens
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Marta C Cruz Cisneros
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kelly Orgel
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - A Wesley Burks
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.
| | - Michael D Kulis
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC.
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC.
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Skoracka K, Hryhorowicz S, Tovoli F, Raiteri A, Rychter AM, Słomski R, Dobrowolska A, Granito A, Krela-Kaźmierczak I. From an understanding of etiopathogenesis to novel therapies-what is new in the treatment of celiac disease? Front Pharmacol 2024; 15:1378172. [PMID: 38698821 PMCID: PMC11063403 DOI: 10.3389/fphar.2024.1378172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Celiac disease, a chronic autoimmune disorder caused by genetic factors and exposure to gluten, is increasingly being recognized and diagnosed in both children and adults. Scientists have been searching for a cure for this disease for many years, but despite the impressive development of knowledge in this field, a gluten-free diet remains the only recommended therapy for all patients. At the same time, the increasing diagnosis of celiac disease in adults, which was considered a childhood disease in the 20th century, has opened a discussion on the etiopathology of the disease, which is proven to be very complex and involves genetic, immunological, nutritional, environmental and gut microbiota-related factors. In this review, we extensively discuss these factors and summarize the knowledge of the proposed state-of-the-art treatments for celiac disease to address the question of whether a better understanding of the etiopathogenesis of celiac disease has opened new directions for therapy.
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Affiliation(s)
- Kinga Skoracka
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Francesco Tovoli
- Division of Internal Medicine, Hepatobiliary and Immunoallergic Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Alberto Raiteri
- Division of Internal Medicine, Hepatobiliary and Immunoallergic Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Anna Maria Rychter
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
- Laboratory of Nutrigenetics, Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Ryszard Słomski
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Agnieszka Dobrowolska
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Alessandro Granito
- Division of Internal Medicine, Hepatobiliary and Immunoallergic Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Iwona Krela-Kaźmierczak
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
- Laboratory of Nutrigenetics, Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
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Gautam N, Wojciech L, Yap J, Chua YL, Ding EM, Sim DC, Tan AS, Ahl PJ, Prasad M, Tung DW, Connolly JE, Adriani G, Brzostek J, Gascoigne NR. Themis controls T cell activation, effector functions, and metabolism of peripheral CD8 + T cells. Life Sci Alliance 2023; 6:e202302156. [PMID: 37739454 PMCID: PMC10517225 DOI: 10.26508/lsa.202302156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/24/2023] Open
Abstract
Themis is important in regulating positive selection of thymocytes during T cell development, but its role in peripheral T cells is less understood. Here, we investigated T cell activation and its sequelae using a tamoxifen-mediated, acute Themis deletion mouse model. We find that proliferation, effector functions including anti-tumor killing, and up-regulation of energy metabolism are severely compromised. This study reveals the phenomenon of peripheral adaptation to loss of Themis, by demonstrating direct TCR-induced defects after acute deletion of Themis that were not evident in peripheral T cells chronically deprived of Themis in dLck-Cre deletion model. Peripheral adaptation to long-term loss was compared using chronic versus acute tamoxifen-mediated deletion and with the (chronic) dLck-Cre deletion model. We found that upon chronic tamoxifen-mediated Themis deletion, there was modulation in the gene expression profile for both TCR and cytokine signaling pathways. This profile overlapped with (chronic) dLck-Cre deletion model. Hence, we found that peripheral adaptation induced changes to both TCR and cytokine signaling modules. Our data highlight the importance of Themis in the activation of CD8+ T cells.
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Affiliation(s)
- Namrata Gautam
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Lukasz Wojciech
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jiawei Yap
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yen Leong Chua
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Eyan Mw Ding
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Don Cn Sim
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Alrina Sm Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Patricia J Ahl
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mukul Prasad
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Desmond Wh Tung
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - John E Connolly
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Giulia Adriani
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore
| | - Joanna Brzostek
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nicholas Rj Gascoigne
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Translational Cancer Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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5
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Risemberg EL, Smeekens JM, Cisneros MCC, Hampton BK, Hock P, Linnertz CL, Miller DR, Orgel K, Shaw GD, de Villena FPM, Burks AW, Valdar W, Kulis MD, Ferris MT. A mutation in Themis contributes to peanut-induced oral anaphylaxis in CC027 mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557467. [PMID: 37745496 PMCID: PMC10515941 DOI: 10.1101/2023.09.13.557467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Background The development of peanut allergy is due to a combination of genetic and environmental factors, although specific genes have proven difficult to identify. Previously, we reported that peanut-sensitized CC027/GeniUnc (CC027) mice develop anaphylaxis upon oral challenge to peanut, unlike C3H/HeJ (C3H) mice. Objective To determine the genetic basis of orally-induced anaphylaxis to peanut in CC027 mice. Methods A genetic mapping population between CC027 and C3H mice was designed to identify the genetic factors that drive oral anaphylaxis. A total of 356 CC027xC3H backcrossed mice were generated, sensitized to peanut, then challenged to peanut by oral gavage. Anaphylaxis and peanut-specific IgE were quantified for all mice. T-cell phenotyping was conducted on CC027 and five additional CC strains. Results Anaphylaxis to peanut was absent in 77% of backcrossed mice, with 19% showing moderate anaphylaxis, and 4% having severe anaphylaxis. A total of eight genetic loci were associated with variation in response to peanut challenge, six associated with anaphylaxis (temperature decrease) and two associated with peanut-specific IgE levels. There were two major loci that impacted multiple aspects of the severity of acute anaphylaxis, at which the CC027 allele was associated with worse outcome. At one of these loci, CC027 has a private genetic variant in the Themis (thymocyte-expressed molecule involved in selection) gene. Consistent with Themis' described functions, we found that CC027 have more immature T cells with fewer CD8+, CD4+, and CD4+CD25+CD127- regulatory T cells. Conclusion Our results demonstrate a key role for Themis in the orally-reactive CC027 mouse model of peanut allergy.
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Affiliation(s)
- Ellen L. Risemberg
- Curriculum in Bioinformatics and Computational Biology, UNC Chapel Hill
- Department of Genetics, UNC Chapel Hill
| | - Johanna M. Smeekens
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - Marta C. Cruz Cisneros
- Department of Genetics, UNC Chapel Hill
- Curriculum in Genetics and Molecular Biology, UNC Chapel Hill
| | - Brea K. Hampton
- Department of Genetics, UNC Chapel Hill
- Curriculum in Genetics and Molecular Biology, UNC Chapel Hill
| | | | | | | | - Kelly Orgel
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - Ginger D. Shaw
- Department of Genetics, UNC Chapel Hill
- Lineberger Comprehensive Cancer Center, UNC Chapel Hill
| | | | - A. Wesley Burks
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - William Valdar
- Department of Genetics, UNC Chapel Hill
- Lineberger Comprehensive Cancer Center, UNC Chapel Hill
| | - Michael D. Kulis
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
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Kim M, Huda MN, Evans LW, Que E, Gertz ER, Maeda-Smithies N, Bennett BJ. Integrative analysis of hepatic transcriptional profiles reveals genetic regulation of atherosclerosis in hyperlipidemic Diversity Outbred-F1 mice. Sci Rep 2023; 13:9475. [PMID: 37301941 PMCID: PMC10257719 DOI: 10.1038/s41598-023-35917-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Atherogenesis is an insipidus but precipitating process leading to serious consequences of many cardiovascular diseases (CVD). Numerous genetic loci contributing to atherosclerosis have been identified in human genome-wide association studies, but these studies have limitations in the ability to control environmental factors and to decipher cause/effect relationships. To assess the power of hyperlipidemic Diversity Outbred (DO) mice in facilitating quantitative trait loci (QTL) analysis of complex traits, we generated a high-resolution genetic panel of atherosclerosis susceptible (DO-F1) mouse cohort by crossing 200 DO females with C57BL/6J males carrying two human genes: encoding apolipoprotein E3-Leiden and cholesterol ester transfer protein. We examined atherosclerotic traits including plasma lipids and glucose in the 235 female and 226 male progeny before and after 16 weeks of a high-fat/cholesterol diet, and aortic plaque size at 24 weeks. We also assessed the liver transcriptome using RNA-sequencing. Our QTL mapping for atherosclerotic traits identified one previously reported female-specific QTL on Chr10 with a narrower interval of 22.73 to 30.80 Mb, and one novel male-specific QTL at 31.89 to 40.25 Mb on Chr19. Liver transcription levels of several genes within each QTL were highly correlated with the atherogenic traits. A majority of these candidates have already known atherogenic potential in humans and/or mice, but integrative QTL, eQTL, and correlation analyses further pointed Ptprk as a major candidate of the Chr10 QTL, while Pten and Cyp2c67 of the Chr19 QTL in our DO-F1 cohort. Finally, through additional analyses of RNA-seq data we identified genetic regulation of hepatic transcription factors, including Nr1h3, contributes to atherogenesis in this cohort. Thus, an integrative approach using DO-F1 mice effectively validates the influence of genetic factors on atherosclerosis in DO mice and suggests an opportunity to discover therapeutics in the setting of hyperlipidemia.
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Affiliation(s)
- Myungsuk Kim
- Department of Nutrition, University of California, Davis, CA, USA
- Korea Institute of Science and Technology (KIST), Gangneung, Gangwon-Do, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Seoul, 02792, Republic of Korea
| | - M Nazmul Huda
- Department of Nutrition, University of California, Davis, CA, USA
- Western Human Nutrition Research Center, Agricultural Research Service, US Department of Agriculture, Davis, CA, USA
| | - Levi W Evans
- Western Human Nutrition Research Center, Agricultural Research Service, US Department of Agriculture, Davis, CA, USA
| | - Excel Que
- Western Human Nutrition Research Center, Agricultural Research Service, US Department of Agriculture, Davis, CA, USA
| | - Erik R Gertz
- Western Human Nutrition Research Center, Agricultural Research Service, US Department of Agriculture, Davis, CA, USA
| | - Nobuyo Maeda-Smithies
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brian J Bennett
- Department of Nutrition, University of California, Davis, CA, USA.
- Western Human Nutrition Research Center, Agricultural Research Service, US Department of Agriculture, Davis, CA, USA.
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Romero-Garmendia I. Separation of epithelial and immune cells from biopsy samples. Methods Cell Biol 2023; 179:59-68. [PMID: 37625880 DOI: 10.1016/bs.mcb.2022.12.006] [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] [Indexed: 01/26/2023]
Abstract
Celiac disease (CD) is a chronic and autoimmune disease that develops in genetically predisposed individuals upon exposure to dietary gluten. The availability of the target tissue for research has made it possible to identify alterations in the transcriptome and methylome in the celiac gut. However, gene expression and methylation is highly variable among different cell types, and separation of cellular populations in target tissue must be considered for the understanding of the specific cellular and immune responses to gluten. In this context, a few studies have demonstrated that focusing on an isolated cell population, novel candidate genes involved in the pathogenesis of the disease can be identified. Here, we describe a method to separate epithelial and immune cells from biopsy samples for DNA and RNA isolation. With minor variations, the same technique can be applied to other tissues and cell types.
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Affiliation(s)
- Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.
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8
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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9
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Nanayakkara M, Bellomo C, Furone F, Maglio M, Marano A, Lania G, Porpora M, Nicoletti M, Auricchio S, Barone MV. PTPRK, an EGFR Phosphatase, Is Decreased in CeD Biopsies and Intestinal Organoids. Cells 2022; 12:cells12010115. [PMID: 36611909 PMCID: PMC9818839 DOI: 10.3390/cells12010115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/12/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND & AIMS Celiac disease (CeD) is an immune-mediated enteropathy triggered in genetically susceptible (HLA-DQ2/8) individuals by a group of wheat proteins and related prolamins from cereals. The celiac intestine is characterized by an inversion of the differentiation/proliferation program of the enterocytes, with an increase in the proliferative compartment and crypt hyperplasia, which are the mechanisms that regulate the increased proliferation in CeD that arenot completely understood.The aim of this study is to understand the role of Protein Tyrosine Phosphatase Receptor Type K (PTPRK), a nodal phosphatase that regulates EGFR activation in the proliferation of the enterocytes from CeD biopsies and organoids. METHODS The levels of PTPRK were evaluated by RT PCR, western blot (WB) and immunofluorescence techniques in intestinal biopsies and organoids from CeD patients and controls. Additionally, pEGFR and pERK were evaluated by WB and proliferation by BrdU incorporation. PTPRK si-RNA was silenced in CTR organoids and was overexpressed in CeD organoids. RESULTS PTPRK was reduced in Gluten Containing Diet-Celiac Disease (GCD-CeD) and Potential-Celiac Disease(Pot-CeD) biopsies (p < 0.01-p < 0.05) whereas pEGFR (p < 0.01 p < 0.01), pERK (p < 0.01 p < 0.01) and proliferation were increased. (p < 0.05 p < 0.05) respect to the controls.The CeD organoids reproduced these same alterations. Silencing of PTPRK in CTR organoids increased pEGFR, pERK and proliferation. The overexpression of PTPRK in CeD organoids reduced pEGFR, pERK and proliferation. CONCLUSIONS modulation of PTPRK levels can reduce or increase pEGFR, pERK and proliferation in CeD or CTR organoids, respectively. The CeD organoids can be a good model to study the mechanisms of the disease.
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Affiliation(s)
- Merlin Nanayakkara
- Department of Translational Medical Science, Section of Pediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Claudia Bellomo
- Department of Translational Medical Science, Section of Pediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Francesca Furone
- Department of Translational Medical Science, Section of Pediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Mariantonia Maglio
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Antonella Marano
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Giuliana Lania
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Monia Porpora
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Martina Nicoletti
- Department of Translational Medical Science, Section of Pediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Salvatore Auricchio
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), University Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Maria Vittoria Barone
- Department of Translational Medical Science, Section of Pediatrics, University Federico II, Via S. Pansini 5, 80131 Naples, Italy
- ELFID (European Laboratory for the Investigation of Food Induced Diseases), University Federico II, Via S. Pansini 5, 80131 Naples, Italy
- Correspondence: ; Tel.: +39-0817464568; Fax: +39-0817463116
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10
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Liu Y, Cong Y, Niu Y, Yuan Y, Tan F, Lai Q, Hu Y, Hou B, Li J, Lin C, Zheng H, Dong J, Tang J, Chen Q, Brzostek J, Zhang X, Chen XL, Wang HR, Gascoigne NRJ, Xu B, Lin SH, Fu G. Themis is indispensable for IL-2 and IL-15 signaling in T cells. Sci Signal 2022; 15:eabi9983. [PMID: 35167340 DOI: 10.1126/scisignal.abi9983] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
To perform their antiviral and antitumor functions, T cells must integrate signals both from the T cell receptor (TCR), which instruct the cell to remain quiescent or become activated, and from cytokines that guide cellular proliferation and differentiation. In mature CD8+ T cells, Themis has been implicated in integrating TCR and cytokine signals. We investigated whether Themis plays a direct role in cytokine signaling in mature T cells. Themis was required for IL-2- and IL-15-driven CD8+ T cell proliferation both in mice and in vitro. Mechanistically, we found that Themis promoted the activation of the transcription factor Stat and mechanistic target of rapamycin signaling downstream of cytokine receptors. Metabolomics and stable isotope tracing analyses revealed that Themis deficiency reduced glycolysis and serine and nucleotide biosynthesis, demonstrating a receptor-proximal requirement for Themis in triggering the metabolic changes that enable T cell proliferation. The cellular, metabolic, and biochemical defects caused by Themis deficiency were corrected in mice lacking both Themis and the phosphatase Shp1, suggesting that Themis mediates IL-2 and IL-15 receptor-proximal signaling by restraining the activity of Shp1. Together, these results not only shed light on the mechanisms of cytokine signaling but also provide new clues on manipulating T cells for clinical applications.
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Affiliation(s)
- Yongchao Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yu Cong
- Department of Hematology, First Affiliated Hospital and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China.,Cancer Research Center of Xiamen University, Xiamen, China
| | - Yujia Niu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yin Yuan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Fancheng Tan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qian Lai
- Department of Hematology, First Affiliated Hospital and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
| | - Yanyan Hu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Bowen Hou
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jian Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Chunjie Lin
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Haiping Zheng
- Department of Hematology, First Affiliated Hospital and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
| | - Junchen Dong
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jian Tang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qinwei Chen
- Department of Hematology, First Affiliated Hospital and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
| | - Joanna Brzostek
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xueqin Zhang
- Department of Obstetrics and Gynecology, Affiliated Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Xiao Lei Chen
- Department of Hematology, First Affiliated Hospital and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
| | - Hong-Rui Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Obstetrics and Gynecology, Affiliated Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Nicholas R J Gascoigne
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Bing Xu
- Department of Hematology, First Affiliated Hospital and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China.,Key Laboratory of Xiamen for Diagnosis and Treatment of Hematological Malignancy, Xiamen, China
| | - Shu-Hai Lin
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Guo Fu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Hematology, First Affiliated Hospital and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China.,Cancer Research Center of Xiamen University, Xiamen, China.,Department of Obstetrics and Gynecology, Affiliated Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
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11
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García-Santisteban I, Romero-Garmendia I, Cilleros-Portet A, Bilbao JR, Fernandez-Jimenez N. Celiac disease susceptibility: The genome and beyond. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 358:1-45. [PMID: 33707051 DOI: 10.1016/bs.ircmb.2020.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Celiac Disease (CeD) is an immune-mediated complex disease that is triggered by the ingestion of gluten and develops in genetically susceptible individuals. It has been known for a long time that the Human Leucocyte Antigen (HLA) molecules DQ2 and DQ8 are necessary, although not sufficient, for the disease development, and therefore other susceptibility genes and (epi)genetic events must participate in CeD pathogenesis. The advances in Genomics during the last 15 years have made CeD one of the immune-related disorders with the best-characterized genetic component. In the present work, we will first review the main Genome-Wide Association Studies (GWAS) carried out in the disorder, and emphasize post-GWAS discoveries, including diverse integrative strategies, SNP prioritization approaches, and insights into the Microbiome through the host Genomics. Second, we will explore CeD-related Epigenetics and Epigenomics, mostly focusing on the emerging knowledge of the celiac methylome, and the vast but yet under-explored non-coding RNA (ncRNA) landscape. We conclude that much has been done in the field although there are still completely unvisited areas in the post-Genomics of CeD. Chromatin conformation and accessibility, and Epitranscriptomics are promising domains that need to be unveiled to complete the big picture of the celiac Genome.
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Affiliation(s)
- Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain; Spanish Biomedical Research Center in Diabetes and associated Metabolic Disorders, CIBERDEM, Madrid, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain.
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12
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Jauregi-Miguel A, Santin I, Garcia-Etxebarria K, Olazagoitia-Garmendia A, Romero-Garmendia I, Sebastian-delaCruz M, Irastorza I, Castellanos-Rubio A, Bilbao JR. MAGI2 Gene Region and Celiac Disease. Front Nutr 2019; 6:187. [PMID: 31921880 PMCID: PMC6930898 DOI: 10.3389/fnut.2019.00187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/03/2019] [Indexed: 12/13/2022] Open
Abstract
Celiac disease (CD) patients present a loss of intestinal barrier function due to structural alterations in the tight junction (TJ) network, the most apical unions between epithelial cells. The association of TJ-related gene variants points to an implication of this network in disease susceptibility. This work aims to characterize the functional implication of TJ-related, disease-associated loci in CD pathogenesis. We performed an association study of 8 TJ-related gene variants in a cohort of 270 CD and 91 non-CD controls. The expression level of transcripts located in the associated SNP region was analyzed by RT-PCR in several human tissues and in duodenal biopsies of celiac patients and non-CD controls. (si)RNA-driven silencing combined with gliadin in the Caco2 intestinal cell line was used to analyze the implication of transcripts from the associated region in the regulation of TJ genes. We replicated the association of rs6962966*A variant [p = 0.0029; OR = 1.88 (95%1.24–2.87)], located in an intron of TJ-related MAGI2 coding gene and upstream of RP4-587D13.2 transcript, bioinformatically classified as a long non-coding RNA (lncRNA). The expression of both genes is correlated and constitutively downregulated in CD intestine. Silencing of lncRNA decreases the levels of MAGI2 protein. At the same time, silencing of MAGI2 affects the expression of several TJ-related genes. The associated region is functionally altered in disease, probably affecting CD-related TJ genes.
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Affiliation(s)
- Amaia Jauregi-Miguel
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain
| | - Izortze Santin
- Department of Biochemistry and Molecular Biology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain.,CIBER in Diabetes and Associated Metabolic Diseases, Madrid, Spain
| | - Koldo Garcia-Etxebarria
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain
| | - Ane Olazagoitia-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain
| | - Maialen Sebastian-delaCruz
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain
| | - Iñaki Irastorza
- Department of Pediatrics, Biocruces-Bizkaia Health Research Institute, Cruces University Hospital, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Barakaldo, Spain
| | | | - Ainara Castellanos-Rubio
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Jose Ramón Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Leioa, Spain.,CIBER in Diabetes and Associated Metabolic Diseases, Madrid, Spain
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13
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Celiac Diasease-associated lncRNA Named HCG14 Regulates NOD1 Expression in Intestinal Cells. J Pediatr Gastroenterol Nutr 2018; 67:225-231. [PMID: 29601440 DOI: 10.1097/mpg.0000000000001970] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVE The aim of the study is to identify additional celiac disease associated loci in the major histocompatibility complex (MHC) independent from classical HLA risk alleles (HLA-DR3-DQ2) and to characterize their potential functional impact in celiac disease pathogenesis at the intestinal level. METHODS We performed a high-resolution single-nucleotide polymorphism (SNP) genotyping of the MHC region, comparing HLA-DR3 homozygous celiac patients and non-celiac controls carrying a single copy of the B8-DR3-DQ2 conserved extended haplotype. Expression level of potential novel risk genes was determined by RT-PCR in intestinal biopsies and in intestinal and immune cells isolated from control and celiac individuals. Small interfering RNA-driven silencing of selected genes was performed in the intestinal cell line T84. RESULTS MHC genotyping revealed 2 associated SNPs, one located in TRIM27 gene and another in the non-coding gene HCG14. After stratification analysis, only HCG14 showed significant association independent from HLA-DR-DQ loci. Expression of HCG14 was slightly downregulated in epithelial cells isolated from duodenal biopsies of celiac patients, and eQTL analysis revealed that polymorphisms in HCG14 region were associated with decreased NOD1 expression in duodenal intestinal cells. CONCLUSIONS We have successfully employed a conserved extended haplotype-matching strategy and identified a novel additional celiac disease risk variant in the lncRNA HCG14. This lncRNA seems to regulate the expression of NOD1 in an allele-specific manner. Further functional studies are needed to clarify the role of HCG14 in the regulation of gene expression and to determine the molecular mechanisms by which the risk variant in HCG14 contributes to celiac disease pathogenesis.
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14
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Romero-Garmendia I, Garcia-Etxebarria K, Hernandez-Vargas H, Santin I, Jauregi-Miguel A, Plaza-Izurieta L, Cros MP, Legarda M, Irastorza I, Herceg Z, Fernandez-Jimenez N, Bilbao JR. Transcription Factor Binding Site Enrichment Analysis in Co-Expression Modules in Celiac Disease. Genes (Basel) 2018; 9:E245. [PMID: 29748492 PMCID: PMC5977185 DOI: 10.3390/genes9050245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to construct celiac co-expression patterns at a whole genome level and to identify transcription factors (TFs) that could drive the gliadin-related changes in coordination of gene expression observed in celiac disease (CD). Differential co-expression modules were identified in the acute and chronic responses to gliadin using expression data from a previous microarray study in duodenal biopsies. Transcription factor binding site (TFBS) and Gene Ontology (GO) annotation enrichment analyses were performed in differentially co-expressed genes (DCGs) and selection of candidate regulators was performed. Expression of candidates was measured in clinical samples and the activation of the TFs was further characterized in C2BBe1 cells upon gliadin challenge. Enrichment analyses of the DCGs identified 10 TFs and five were selected for further investigation. Expression changes related to active CD were detected in four TFs, as well as in several of their in silico predicted targets. The activation of TFs was further characterized in C2BBe1 cells upon gliadin challenge, and an increase in nuclear translocation of CAMP Responsive Element Binding Protein 1 (CREB1) and IFN regulatory factor-1 (IRF1) in response to gliadin was observed. Using transcriptome-wide co-expression analyses we are able to propose novel genes involved in CD pathogenesis that respond upon gliadin stimulation, also in non-celiac models.
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Affiliation(s)
- Irati Romero-Garmendia
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Koldo Garcia-Etxebarria
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Hector Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Izortze Santin
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain.
| | - Amaia Jauregi-Miguel
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Leticia Plaza-Izurieta
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
| | - Marie-Pierre Cros
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Maria Legarda
- Pediatric Gastroenterology Unit, Cruces University Hospital, University of the Basque Country-(UPV/EHU) and Biocruces Health Research Institute, 48903 Barakaldo, Spain.
| | - Iñaki Irastorza
- Pediatric Gastroenterology Unit, Cruces University Hospital, University of the Basque Country-(UPV/EHU) and Biocruces Health Research Institute, 48903 Barakaldo, Spain.
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Nora Fernandez-Jimenez
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69372 Lyon CEDEX 08, France.
| | - Jose Ramon Bilbao
- University of the Basque Country (UPV-EHU) and Biocruces Health Research Institute, 48940 Leioa, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain.
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15
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Profiling Celiac Disease-Related Transcriptional Changes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 336:149-174. [DOI: 10.1016/bs.ircmb.2017.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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16
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Duguet F, Locard-Paulet M, Marcellin M, Chaoui K, Bernard I, Andreoletti O, Lesourne R, Burlet-Schiltz O, Gonzalez de Peredo A, Saoudi A. Proteomic Analysis of Regulatory T Cells Reveals the Importance of Themis1 in the Control of Their Suppressive Function. Mol Cell Proteomics 2017; 16:1416-1432. [PMID: 28373295 DOI: 10.1074/mcp.m116.062745] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 03/13/2017] [Indexed: 01/25/2023] Open
Abstract
Regulatory T cells (Treg) represent a minor subpopulation of T lymphocytes that is crucial for the maintenance of immune homeostasis. Here, we present a large-scale quantitative mass spectrometry study that defines a specific proteomic "signature" of Treg. Treg and conventional T lymphocyte (Tconv) subpopulations were sorted by flow cytometry and subjected to global proteomic analysis by single-run nanoLC-MS/MS on a fast-sequencing Q-Exactive mass spectrometer. Besides "historical" proteins that characterize Treg, our study identified numerous new proteins that are up- or downregulated in Treg versus Tconv. We focused on Themis1, a protein particularly under-represented in Treg, and recently described as being involved in the pathogenesis of immune diseases. Using a transgenic mouse model overexpressing Themis1, we provided in vivo and in vitro evidence of its importance for Treg suppressive functions, in an animal model of inflammatory bowel disease and in coculture assays. We showed that this enhanced suppressive activity in vitro is associated with an accumulation of Tregs. Thus, our study highlights the usefulness of label free quantitative methods to better characterize the Treg cell lineage and demonstrates the potential role of Themis1 in the suppressive functions of these cells.
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Affiliation(s)
- Fanny Duguet
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 31077 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, 31077 Toulouse, France.,§Centre de Physiopathologie de Toulouse Purpan, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, UPS, 31024, Toulouse, France
| | - Marie Locard-Paulet
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 31077 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, 31077 Toulouse, France
| | - Marlène Marcellin
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 31077 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, 31077 Toulouse, France
| | - Karima Chaoui
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 31077 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, 31077 Toulouse, France
| | - Isabelle Bernard
- §Centre de Physiopathologie de Toulouse Purpan, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, UPS, 31024, Toulouse, France
| | - Olivier Andreoletti
- ¶UMR INRA ENVT 1225, Interactions Hôtes Agents Pathogènes, Ecole Nationale Vétérinaire de Toulouse, 31000 Toulouse, France
| | - Renaud Lesourne
- §Centre de Physiopathologie de Toulouse Purpan, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, UPS, 31024, Toulouse, France
| | - Odile Burlet-Schiltz
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 31077 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, 31077 Toulouse, France
| | - Anne Gonzalez de Peredo
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 31077 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Institut de Pharmacologie et de Biologie Structurale, 31077 Toulouse, France;
| | - Abdelhadi Saoudi
- §Centre de Physiopathologie de Toulouse Purpan, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, UPS, 31024, Toulouse, France
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17
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Garcia-Etxebarria K, Jauregi-Miguel A, Romero-Garmendia I, Plaza-Izurieta L, Legarda M, Irastorza I, Bilbao JR. Ancestry-based stratified analysis of Immunochip data identifies novel associations with celiac disease. Eur J Hum Genet 2016; 24:1831-1834. [PMID: 27650971 DOI: 10.1038/ejhg.2016.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 07/24/2016] [Accepted: 08/05/2016] [Indexed: 12/15/2022] Open
Abstract
To identify candidate genes in celiac disease (CD), we reanalyzed the whole Immunochip CD cohort using a different approach that clusters individuals based on immunoancestry prior to disease association analysis, rather than by geographical origin. We detected 636 new associated SNPs (P<7.02 × 10-07) and identified 5 novel genomic regions, extended 8 others previously identified and also detected 18 isolated signals defined by one or very few significant SNPs. To test whether we could identify putative candidate genes, we performed expression analyses of several genes from the top novel region (chr2:134533564-136169524), from a previously identified locus that is now extended, and a gene marked by an isolated SNP, in duodenum biopsies of active and treated CD patients, and non-celiac controls. In the largest novel region, CCNT2 and R3HDM1 were constitutively underexpressed in disease, even after gluten removal. Moreover, several genes within this region were coexpressed in patients, but not in controls. Other novel genes like KIF21B, REL and SORD also showed altered expression in active disease. Apart from the identification of novel CD loci, these results suggest that ancestry-based stratified analysis is an efficient strategy for association studies in complex diseases.
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Affiliation(s)
- Koldo Garcia-Etxebarria
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain
| | - Amaia Jauregi-Miguel
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain
| | - Leticia Plaza-Izurieta
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain
| | - Maria Legarda
- Department of Pediatrics, Pediatric Gastroenterology Unit, Cruces University Hospital, University of the Basque Country (UPV-EHU), Barakaldo, Spain
| | - Iñaki Irastorza
- Department of Pediatrics, Pediatric Gastroenterology Unit, Cruces University Hospital, University of the Basque Country (UPV-EHU), Barakaldo, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV-EHU), BioCruces Health Research Institute, Leioa, Spain
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18
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Agarwal S, Kovilam O, Zach TL, Agrawal DK. Immunopathogenesis and therapeutic approaches in pediatric celiac disease. Expert Rev Clin Immunol 2016; 12:857-69. [PMID: 26999328 PMCID: PMC4975578 DOI: 10.1586/1744666x.2016.1168294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/16/2016] [Indexed: 01/06/2023]
Abstract
Celiac Disease is an autoimmune enteropathy with increasing incidence worldwide in both adults and children. It occurs as an inflammatory condition with destruction of the normal architecture of villi on consumption of gluten and related protein products found in wheat, barley and rye. However, the exact pathogenesis is not yet fully understood. A gluten-free diet remains the main modality of therapy to date. While some patients continue to have symptoms even on a gluten-free diet, adherence to this diet is also difficult, especially for the children. Hence, there is continued interest in novel methods of therapy and the current research focus is on the promising novel non-dietary modalities of treatment. Here, we critically reviewed the existing literature regarding the pathogenesis of celiac disease in children including the role of in-utero exposure leading to neonatal and infant sensitization and its application for the development of new therapeutic approaches for these patients.
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Affiliation(s)
- Shreya Agarwal
- Department of Clinical & Translational Science, Creighton University School of Medicine, Omaha, NE, USA
| | - Oormila Kovilam
- Department of Obstetrics and Gynecology, Creighton University School of Medicine, Omaha, NE, USA
| | - Terence L. Zach
- Department of Pediatrics, Creighton University School of Medicine, Omaha, NE, USA
| | - Devendra K. Agrawal
- Department of Clinical & Translational Science, Creighton University School of Medicine, Omaha, NE, USA
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Increased THEMIS First Exon Usage in CD4+ T-Cells Is Associated with a Genotype that Is Protective against Multiple Sclerosis. PLoS One 2016; 11:e0158327. [PMID: 27438997 PMCID: PMC4954697 DOI: 10.1371/journal.pone.0158327] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/14/2016] [Indexed: 01/21/2023] Open
Abstract
Multiple sclerosis is an autoimmune disease of the central nervous system. Genome wide association studies have identified over 100 common variants associated with multiple sclerosis, the majority of which implicate immunologically relevant genes, particularly those involved in T-cell development. SNP rs13204742 at the THEMIS/PTPRK locus is one such variant. Here, we have demonstrated mutually exclusive use of exon 1 and 2 amongst 16 novel THEMIS isoforms. We also show inverse correlation between THEMIS expression in human CD4+ T-cells and dosage of the multiple sclerosis risk allele at rs13204742, driven by reduced expression of exon 1- containing isoforms. In silico analysis suggests that this may be due to cell-specific, allele-dependent binding of the transcription factors FoxP3 and/or E47. Research exploring the functional implications of GWAS variants is important for gaining an understanding of disease pathogenesis, with the ultimate aim of identifying new therapeutic targets.
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Pedros C, Gaud G, Bernard I, Kassem S, Chabod M, Lagrange D, Andréoletti O, Dejean AS, Lesourne R, Fournié GJ, Saoudi A. An Epistatic Interaction between Themis1 and Vav1 Modulates Regulatory T Cell Function and Inflammatory Bowel Disease Development. THE JOURNAL OF IMMUNOLOGY 2015; 195:1608-16. [PMID: 26163585 DOI: 10.4049/jimmunol.1402562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 06/17/2015] [Indexed: 12/13/2022]
Abstract
The development of inflammatory diseases depends on complex interactions between several genes and various environmental factors. Discovering new genetic risk factors and understanding the mechanisms whereby they influence disease development is of paramount importance. We previously reported that deficiency in Themis1, a new actor of TCR signaling, impairs regulatory T cell (Treg) function and predisposes Brown-Norway (BN) rats to spontaneous inflammatory bowel disease (IBD). In this study, we reveal that the epistasis between Themis1 and Vav1 controls the occurrence of these phenotypes. Indeed, by contrast with BN rats, Themis1 deficiency in Lewis rats neither impairs Treg suppressive functions nor induces pathological manifestations. By using congenic lines on the BN genomic background, we show that the impact of Themis1 deficiency on Treg suppressive functions depends on a 117-kb interval coding for a R63W polymorphism that impacts Vav1 expression and functions. Indeed, the introduction of a 117-kb interval containing the Lewis Vav1-R63 variant restores Treg function and protects Themis1-deficient BN rats from spontaneous IBD development. We further show that Themis1 binds more efficiently to the BN Vav1-W63 variant and is required to stabilize its recruitment to the transmembrane adaptor LAT and to fully promote the activation of Erk kinases. Together, these results highlight the importance of the signaling pathway involving epistasis between Themis1 and Vav1 in the control of Treg suppressive function and susceptibility to IBD development.
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Affiliation(s)
- Christophe Pedros
- Unité Mixte de Recherche, INSERM, U1043, 31300 Toulouse, France; Unité Mixte de Recherche, Centre National de la Recherche Scientifique, U5282, 31300 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, 31300 Toulouse, France; and
| | - Guillaume Gaud
- Unité Mixte de Recherche, INSERM, U1043, 31300 Toulouse, France; Unité Mixte de Recherche, Centre National de la Recherche Scientifique, U5282, 31300 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, 31300 Toulouse, France; and
| | - Isabelle Bernard
- Unité Mixte de Recherche, INSERM, U1043, 31300 Toulouse, France; Unité Mixte de Recherche, Centre National de la Recherche Scientifique, U5282, 31300 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, 31300 Toulouse, France; and
| | - Sahar Kassem
- Unité Mixte de Recherche, INSERM, U1043, 31300 Toulouse, France; Unité Mixte de Recherche, Centre National de la Recherche Scientifique, U5282, 31300 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, 31300 Toulouse, France; and
| | - Marianne Chabod
- Unité Mixte de Recherche, INSERM, U1043, 31300 Toulouse, France; Unité Mixte de Recherche, Centre National de la Recherche Scientifique, U5282, 31300 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, 31300 Toulouse, France; and
| | - Dominique Lagrange
- Unité Mixte de Recherche, INSERM, U1043, 31300 Toulouse, France; Unité Mixte de Recherche, Centre National de la Recherche Scientifique, U5282, 31300 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, 31300 Toulouse, France; and
| | - Olivier Andréoletti
- Unité Mixte de Recherche, Institut National de la Recherche Agronomique, Ecole Nationale Vétérinaire de Toulouse 1225, Interactions Hôtes Agents Pathogènes, Ecole Nationale Vétérinaire de Toulouse, 31000 Toulouse, France
| | - Anne S Dejean
- Unité Mixte de Recherche, INSERM, U1043, 31300 Toulouse, France; Unité Mixte de Recherche, Centre National de la Recherche Scientifique, U5282, 31300 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, 31300 Toulouse, France; and
| | - Renaud Lesourne
- Unité Mixte de Recherche, INSERM, U1043, 31300 Toulouse, France; Unité Mixte de Recherche, Centre National de la Recherche Scientifique, U5282, 31300 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, 31300 Toulouse, France; and
| | - Gilbert J Fournié
- Unité Mixte de Recherche, INSERM, U1043, 31300 Toulouse, France; Unité Mixte de Recherche, Centre National de la Recherche Scientifique, U5282, 31300 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, 31300 Toulouse, France; and
| | - Abdelhadi Saoudi
- Unité Mixte de Recherche, INSERM, U1043, 31300 Toulouse, France; Unité Mixte de Recherche, Centre National de la Recherche Scientifique, U5282, 31300 Toulouse, France; Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, 31300 Toulouse, France; and
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Plugis NM, Khosla C. Therapeutic approaches for celiac disease. Best Pract Res Clin Gastroenterol 2015; 29:503-21. [PMID: 26060114 PMCID: PMC4465084 DOI: 10.1016/j.bpg.2015.04.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/23/2015] [Accepted: 04/26/2015] [Indexed: 02/06/2023]
Abstract
Celiac disease is a common, lifelong autoimmune disorder for which dietary control is the only accepted form of therapy. A strict gluten-free diet is burdensome to patients and can be limited in efficacy, indicating there is an unmet need for novel therapeutic approaches to supplement or supplant dietary therapy. Many molecular events required for disease pathogenesis have been recently characterized and inspire most current and emerging drug-discovery efforts. Genome-wide association studies (GWAS) confirm the importance of human leukocyte antigen genes in our pathogenic model and identify a number of new risk loci in this complex disease. Here, we review the status of both emerging and potential therapeutic strategies in the context of disease pathophysiology. We conclude with a discussion of how genes identified during GWAS and follow-up studies that enhance susceptibility may offer insight into developing novel therapies.
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Paneque M, Mendes Á, Saraiva J, Sequeiros J. Genetic Counseling in Portugal: Education, Practice and a Developing Profession. J Genet Couns 2015; 24:548-52. [DOI: 10.1007/s10897-015-9827-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 02/18/2015] [Indexed: 01/30/2023]
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THEMIS is required for pathogenesis of cerebral malaria and protection against pulmonary tuberculosis. Infect Immun 2014; 83:759-68. [PMID: 25452553 DOI: 10.1128/iai.02586-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We identify an N-ethyl-N-nitrosourea (ENU)-induced I23N mutation in the THEMIS protein that causes protection against experimental cerebral malaria (ECM) caused by infection with Plasmodium berghei ANKA. Themis(I23N) homozygous mice show reduced CD4(+) and CD8(+) T lymphocyte numbers. ECM resistance in P. berghei ANKA-infected Themis(I23N) mice is associated with decreased cerebral cellular infiltration, retention of blood-brain barrier integrity, and reduced proinflammatory cytokine production. THEMIS(I23N) protein expression is absent from mutant mice, concurrent with the decreased THEMIS(I23N) stability observed in vitro. Biochemical studies in vitro and functional complementation in vivo in Themis(I23N/+):Lck(-/+) doubly heterozygous mice demonstrate that functional coupling of THEMIS to LCK tyrosine kinase is required for ECM pathogenesis. Damping of proinflammatory responses in Themis(I23N) mice causes susceptibility to pulmonary tuberculosis. Thus, THEMIS is required for the development and ultimately the function of proinflammatory T cells. Themis(I23N) mice can be used to study the newly discovered association of THEMIS (6p22.33) with inflammatory bowel disease and multiple sclerosis.
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Expression analysis in intestinal mucosa reveals complex relations among genes under the association peaks in celiac disease. Eur J Hum Genet 2014; 23:1100-5. [PMID: 25388004 PMCID: PMC4795102 DOI: 10.1038/ejhg.2014.244] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/30/2014] [Accepted: 10/04/2014] [Indexed: 12/17/2022] Open
Abstract
Celiac disease is a chronic immune-mediated disorder with an important genetic component. To date, there are 57 independent association signals from 39 non-HLA loci, and a total of 66 candidate genes have been proposed. We aimed to scrutinize the functional implication of 45 of those genes by analyzing their expression in the disease tissue of celiac patients (at diagnosis/treatment) compared with non-celiac controls. Moreover, we investigated the SNP genotype effect in gene expression and performed coexpression analyses. Several genes showed differential expression among disease groups, most of them related to immune response. Multiple trans-eQTLs but only four cis-eQTLs were found, and surprisingly the genotype effect seems to be stimulus dependent as it differs among groups. Coexpression levels vary from higher to lower levels in active patients at diagnosis, treated patients and non-celiac controls respectively. A subset of 18 genes tightly correlated in both groups of patients but not in controls was identified. Interestingly, this subset of genes was influenced by the genotype of three SNPs. One of the SNPs, rs1018326 on chromosome two is on top of a known lincRNA whose function is not yet described, and whose expression seems to be upregulated in active disease when comparing biopsy pairs from the same individuals. Our results strongly suggest that the effects of disease-associated SNPs go far beyond the oversimplistic idea of transcriptional control at a nearby locus. Further investigations are needed to determine how each variant disrupts fine-tuning mechanisms in the genome that eventually lead to disease.
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Senapati S, Gutierrez-Achury J, Sood A, Midha V, Szperl A, Romanos J, Zhernakova A, Franke L, Alonso S, Thelma BK, Wijmenga C, Trynka G. Evaluation of European coeliac disease risk variants in a north Indian population. Eur J Hum Genet 2014; 23:530-5. [PMID: 25052311 PMCID: PMC4666579 DOI: 10.1038/ejhg.2014.137] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 06/10/2014] [Accepted: 06/18/2014] [Indexed: 01/06/2023] Open
Abstract
Studies in European populations have contributed to a better understanding of the genetics of complex diseases, for example, in coeliac disease (CeD), studies of over 23 000 European samples have reported association to the HLA locus and another 39 loci. However, these associations have not been evaluated in detail in other ethnicities. We sought to better understand how disease-associated loci that have been mapped in Europeans translate to a disease risk for a population with a different ethnic background. We therefore performed a validation of European risk loci for CeD in 497 cases and 736 controls of north Indian origin. Using a dense-genotyping platform (Immunochip), we confirmed the strong association to the HLA region (rs2854275, P=8.2 × 10−49). Three loci showed suggestive association (rs4948256, P=9.3 × 10−7, rs4758538, P=8.6 × 10−5 and rs17080877, P=2.7 × 10−5). We directly replicated five previously reported European variants (P<0.05; mapping to loci harbouring FASLG/TNFSF18, SCHIP1/IL12A, PFKFB3/PRKCQ, ZMIZ1 and ICOSLG). Using a transferability test, we further confirmed association at PFKFB3/PRKCQ (rs2387397, P=2.8 × 10−4) and PTPRK/THEMIS (rs55743914, P=3.4 × 10−4). The north Indian population has a higher degree of consanguinity than Europeans and we therefore explored the role of recessively acting variants, which replicated the HLA locus (rs9271850, P=3.7 × 10−23) and suggested a role of additional four loci. To our knowledge, this is the first replication study of CeD variants in a non-European population.
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Affiliation(s)
| | - Javier Gutierrez-Achury
- Department of Genetics, University of Groningen, University Medical Hospital Groningen, Groningen, The Netherlands
| | - Ajit Sood
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, India
| | - Vandana Midha
- Department of Medicine, Dayanand Medical College and Hospital, Ludhiana, India
| | - Agata Szperl
- Department of Genetics, University of Groningen, University Medical Hospital Groningen, Groningen, The Netherlands
| | - Jihane Romanos
- Department of Genetics, University of Groningen, University Medical Hospital Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Hospital Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Hospital Groningen, Groningen, The Netherlands
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Leioa, Spain
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Hospital Groningen, Groningen, The Netherlands
| | - Gosia Trynka
- Department of Genetics, University of Groningen, University Medical Hospital Groningen, Groningen, The Netherlands
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Fernandez-Jimenez N, Castellanos-Rubio A, Plaza-Izurieta L, Irastorza I, Elcoroaristizabal X, Jauregi-Miguel A, Lopez-Euba T, Tutau C, de Pancorbo MM, Vitoria JC, Bilbao JR. Coregulation and modulation of NFκB-related genes in celiac disease: uncovered aspects of gut mucosal inflammation. Hum Mol Genet 2013; 23:1298-310. [PMID: 24163129 PMCID: PMC3919015 DOI: 10.1093/hmg/ddt520] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
It is known that the NFκB route is constitutively upregulated in celiac disease (CD), an immune-mediated disorder of the gut caused by intolerance to ingested gluten. Our aim was to scrutinize the expression patterns of several of the most biologically relevant components of the NFκB route in intestinal biopsies from active and treated patients and after in vitro gliadin challenge, and to assess normalization of the expression using an inhibitor of the MALT1 paracaspase. The expression of 93 NFκB genes was measured by RT-PCR in a set of uncultured active and treated CD and control biopsies, and in cultured biopsy series challenged with gliadin, the NFκB modulator, both compounds and none. Methylation of eight genes involved in NFκB signaling was analyzed by conventional pyrosequencing. Groups were compared and Pearson's correlation matrixes were constructed to check for coexpression and co-methylation. Our results confirm the upregulation of the NFκB pathway and show that constitutively altered genes usually belong to the core of the pathway and have central roles, whereas genes overexpressed only in active CD are more peripheral. Additionally, this is the first work to detect methylation level changes in celiac intestinal mucosa. Coexpression is very common in controls, whereas gliadin challenge and especially chronic inflammation present in untreated CD result in the disruption of the regulatory equilibrium. In contrast, co-methylation occurs more often in active CD. Importantly, NFκB modulation partially restores coregulation, opening the door to future therapeutic possibilities and targets.
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Affiliation(s)
- Nora Fernandez-Jimenez
- Immunogenetics Research Laboratory, Department of Genetics, Physical Anthropology and Animal Physiology, BioCruces Health Research Institute, University of the Basque Country-UPV/EHU, Leioa, Basque Country, Spain
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