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Wang D, Chen W, Wang Y, Yu J, Bai Y, Luo S, Song C, Wang M, Yu Y, Li Z, Han Y, Zhen Q, Sun L. Genome-Wide Meta-Analysis Identifies 11 Susceptibility Variants of Vitiligo in the Chinese Han Population. J Invest Dermatol 2024; 144:1843-1849.e1. [PMID: 38286188 DOI: 10.1016/j.jid.2024.01.010] [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: 08/12/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2024]
Abstract
Vitiligo is an autoimmune disease involving loss of melanocytes. Although several genetic studies have confirmed that genetic factors play an important role, its pathogenesis remains incompletely characterized. In this study, a genome-wide meta-analysis was conducted to search for more susceptibility variants of vitiligo. Tang et al performed a GWAS for cohort I (1117 vitiligo cases and 1701 healthy controls) previously, and we conducted a GWAS for cohort II (3323 vitiligo cases and 7186 healthy controls) in this study, with the results subjected to a genome-wide meta-analysis and linkage disequilibrium analysis. We identify, to our knowledge, 11 previously unreported susceptibility variants, of which 6 variants are located in the intronic regions, and the remaining 5 variants are located within intergenic regions between genes. In addition, the results of polygenic risk score show that the best evaluated effect for target data is among significant SNVs of the base data. The susceptibility genes of vitiligo are mainly enriched in the immune-related functions and pathways. The susceptibility variants expand the role of genetic factors associated with vitiligo. The bioinformatics analysis for risk genes provides further insight into the pathogenesis of vitiligo.
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Affiliation(s)
- Daiyue Wang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Weiwei Chen
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Yirui Wang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Jing Yu
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Yuanming Bai
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Sihan Luo
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Can Song
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Minhao Wang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Yanxia Yu
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Zhuo Li
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China
| | - Yang Han
- Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China; School of Public Health, North China University of Science and Technology, Tangshan, China; Health Science Center, North China University of Science and Technology, Tangshan, China
| | - Qi Zhen
- Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China; School of Public Health, North China University of Science and Technology, Tangshan, China; Health Science Center, North China University of Science and Technology, Tangshan, China.
| | - Liangdan Sun
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China; Department of Dermatology, North China University of Science and Technology Affiliated Hospital, Tangshan, China; School of Public Health, North China University of Science and Technology, Tangshan, China; Health Science Center, North China University of Science and Technology, Tangshan, China; Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China; Inflammation and Immune Diseases Laboratory, North China University of Science and Technology, Tangshan, China.
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2
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Irving-Pease EK, Refoyo-Martínez A, Barrie W, Ingason A, Pearson A, Fischer A, Sjögren KG, Halgren AS, Macleod R, Demeter F, Henriksen RA, Vimala T, McColl H, Vaughn AH, Speidel L, Stern AJ, Scorrano G, Ramsøe A, Schork AJ, Rosengren A, Zhao L, Kristiansen K, Iversen AKN, Fugger L, Sudmant PH, Lawson DJ, Durbin R, Korneliussen T, Werge T, Allentoft ME, Sikora M, Nielsen R, Racimo F, Willerslev E. The selection landscape and genetic legacy of ancient Eurasians. Nature 2024; 625:312-320. [PMID: 38200293 PMCID: PMC10781624 DOI: 10.1038/s41586-023-06705-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/03/2023] [Indexed: 01/12/2024]
Abstract
The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer's disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.
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Affiliation(s)
- Evan K Irving-Pease
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Alba Refoyo-Martínez
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - William Barrie
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
| | - Alice Pearson
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Anders Fischer
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Sealand Archaeology, Kalundborg, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Alma S Halgren
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Ruairidh Macleod
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- UCL Genetics Institute, University College London, London, UK
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie, Muséum national d'Histoire naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | - Rasmus A Henriksen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Tharsika Vimala
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew H Vaughn
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Leo Speidel
- UCL Genetics Institute, University College London, London, UK
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Aaron J Stern
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Gabriele Scorrano
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Abigail Ramsøe
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew J Schork
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Anders Rosengren
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
| | - Lei Zhao
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Astrid K N Iversen
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
- MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Peter H Sudmant
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Daniel J Lawson
- Institute of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct Hans, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Science, Curtin University, Perth, Western Australia, Australia
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Departments of Integrative Biology and Statistics, UC Berkeley, Berkeley, CA, USA.
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany.
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Martín-Masot R, Herrador-López M, Navas-López VM, Carmona FD, Nestares T, Bossini-Castillo L. Celiac Disease Is a Risk Factor for Mature T and NK Cell Lymphoma: A Mendelian Randomization Study. Int J Mol Sci 2023; 24:ijms24087216. [PMID: 37108375 PMCID: PMC10139431 DOI: 10.3390/ijms24087216] [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: 03/03/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Celiac disease (CeD) is an immune-mediated disorder triggered by gluten ingestion that damages the small intestine. Although CeD has been associated with a higher risk for cancer, the role of CeD as a risk factor for specific malignancies, such as enteropathy-associated T-cell lymphoma (EATL), remains controversial. Using two-sample Mendelian randomization (2SMR) methods and the summarized results of large genome-wide association studies from public repositories, we addressed the causal relationship between CeD and eight different malignancies. Eleven non-HLA SNPs were selected as instrumental variables (IVs), and causality estimates were obtained using four 2SMR methods: random-effects inverse variance-weighted, weighted median estimation, MR-Egger regression, and MR pleiotropy residual sum and outlier (MR-PRESSO). We identified a significant causal relationship between CeD and mature T/NK cell lymphomas. Under a multivariate Mendelian randomization model, we observed that the causal effect of CeD was not dependent on other known lymphoma risk factors. We found that the most instrumental IV was located in the TAGAP locus, suggesting that aberrant T cell activation might be relevant in the T/NK cell malignization process. Our findings provide new insights into the connection between immune imbalance and the development of severe comorbidities, such as EATL, in patients with CeD.
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Affiliation(s)
- Rafael Martín-Masot
- Sección de Gastroenterología y Nutrición Infantil, Hospital Regional Universitario de Málaga, 29011 Málaga, Spain
- Instituto de Nutrición y Tecnología de los Alimentos "José Mataix Verdú" (INYTA), Centro de Investigación Biomédica (CIBM), Universidad de Granada, 18016 Granada, Spain
| | - Marta Herrador-López
- Sección de Gastroenterología y Nutrición Infantil, Hospital Regional Universitario de Málaga, 29011 Málaga, Spain
| | - Víctor Manuel Navas-López
- Sección de Gastroenterología y Nutrición Infantil, Hospital Regional Universitario de Málaga, 29011 Málaga, Spain
| | - Francisco David Carmona
- Departamento de Genética e Instituto de Biotecnología, Centro de Investigación Biomédica (CIBM), Universidad de Granada, 18016 Granada, Spain
- Reproducción Humana y Enfermedades Hereditarias y Complejas (IBS-TEC14), Terapias Avanzadas y Tecnologías Biomédicas, Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - Teresa Nestares
- Instituto de Nutrición y Tecnología de los Alimentos "José Mataix Verdú" (INYTA), Centro de Investigación Biomédica (CIBM), Universidad de Granada, 18016 Granada, Spain
- Departamento de Fisiología, Facultad de Farmacia, Universidad de Granada, 18071 Granada, Spain
| | - Lara Bossini-Castillo
- Departamento de Genética e Instituto de Biotecnología, Centro de Investigación Biomédica (CIBM), Universidad de Granada, 18016 Granada, Spain
- Reproducción Humana y Enfermedades Hereditarias y Complejas (IBS-TEC14), Terapias Avanzadas y Tecnologías Biomédicas, Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
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4
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rs2013278 in the multiple immunological-trait susceptibility locus CD28 regulates the production of non-functional splicing isoforms. Hum Genomics 2022; 16:46. [PMID: 36271469 PMCID: PMC9585755 DOI: 10.1186/s40246-022-00419-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/30/2022] [Indexed: 11/22/2022] Open
Abstract
Background Ligation of CD28 with ligands such as CD80 or CD86 provides a critical second signal alongside antigen presentation by class II major histocompatibility complex expressed on antigen-presenting cells through the T cell antigen receptor for naïve T cell activation. A number of studies suggested that CD28 plays an important role in the pathogenesis of various human diseases. Recent genome-wide association studies (GWASs) identified CD28 as a susceptibility locus for lymphocyte and eosinophil counts, multiple sclerosis, ulcerative colitis, celiac disease, rheumatoid arthritis, asthma, and primary biliary cholangitis. However, the primary functional variant and molecular mechanisms of disease susceptibility in this locus remain to be elucidated. This study aimed to identify the primary functional variant from thousands of genetic variants in the CD28 locus and elucidate its functional effect on the CD28 molecule. Results Among the genetic variants exhibiting stronger linkage disequilibrium (LD) with all GWAS-lead variants in the CD28 locus, rs2013278, located in the Rbfox binding motif related to splicing regulation, was identified as a primary functional variant related to multiple immunological traits. Relative endogenous expression levels of CD28 splicing isoforms (CD28i and CD28Δex2) compared with full-length CD28 in allele knock-in cell lines generated using CRISPR/Cas9 were directly regulated by rs2013278 (P < 0.05). Although full-length CD28 protein expressed on Jurkat T cells showed higher binding affinity for CD80/CD86, both CD28i and CD28Δex2 encoded loss-of-function isoforms. Conclusion The present study demonstrated for the first time that CD28 has a shared disease-related primary functional variant (i.e., rs2013278) that regulates the CD28 alternative splicing that generates loss-of-function isoforms. They reduce disease risk by inducing anergy of effector T cells that over-react to autoantigens and allergens. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00419-7.
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5
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Non-coding RNA network associated with obesity and rheumatoid arthritis. Immunobiology 2022; 227:152281. [DOI: 10.1016/j.imbio.2022.152281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022]
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6
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Azarova IE, Klyosova EY, Kolomoets II, Polonikov AV. Polymorphic Variants of the Neutrophil Cytosolic Factor 2 Gene: Associations with Susceptibility to Type 2 Diabetes Mellitus and Cardiovascular Autonomic Neuropathy. RUSS J GENET+ 2022; 58:593-602. [DOI: 10.1134/s1022795422050039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 07/28/2024]
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7
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Talotta R, Bahrami S, Laska MJ. Sequence complementarity between human noncoding RNAs and SARS-CoV-2 genes: What are the implications for human health? Biochim Biophys Acta Mol Basis Dis 2022; 1868:166291. [PMID: 34662705 PMCID: PMC8518135 DOI: 10.1016/j.bbadis.2021.166291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/17/2021] [Accepted: 10/09/2021] [Indexed: 12/12/2022]
Abstract
Objectives To investigate in silico the presence of nucleotide sequence complementarity between the RNA genome of Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2) and human non-coding (nc)RNA genes. Methods The FASTA sequence (NC_045512.2) of each of the 11 SARS-CoV-2 isolate Wuhan-Hu-1 genes was retrieved from NCBI.nlm.nih.gov/gene and the Ensembl.org library interrogated for any base-pair match with human ncRNA genes. SARS-CoV-2 gene-matched human ncRNAs were screened for functional activity using bioinformatic analysis. Finally, associations between identified ncRNAs and human diseases were searched in GWAS databases. Results A total of 252 matches were found between the nucleotide sequence of SARS-CoV-2 genes and human ncRNAs. With the exception of two small nuclear RNAs, all of them were long non-coding (lnc)RNAs expressed mainly in testis and central nervous system under physiological conditions. The percentage of alignment ranged from 91.30% to 100% with a mean nucleotide alignment length of 17.5 ± 2.4. Thirty-three (13.09%) of them contained predicted R-loop forming sequences, but none of these intersected the complementary sequences of SARS-CoV-2. However, in 31 cases matches fell on ncRNA regulatory sites, whose adjacent coding genes are mostly involved in cancer, immunological and neurological pathways. Similarly, several polymorphic variants of detected non-coding genes have been associated with neuropsychiatric and proliferative disorders. Conclusion This pivotal in silico study shows that SARS-CoV-2 genes have Watson-Crick nucleotide complementarity to human ncRNA sequences, potentially disrupting ncRNA epigenetic control of target genes. It remains to be elucidated whether this could result in the development of human disease in the long term.
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Affiliation(s)
- Rossella Talotta
- Department of Clinical and Experimental Medicine, Rheumatology Unit, AOU "Gaetano Martino", University of Messina, Messina, Italy.
| | - Shervin Bahrami
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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8
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Gnodi E, Meneveri R, Barisani D. Celiac disease: From genetics to epigenetics. World J Gastroenterol 2022; 28:449-463. [PMID: 35125829 PMCID: PMC8790554 DOI: 10.3748/wjg.v28.i4.449] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/16/2021] [Accepted: 01/11/2022] [Indexed: 02/06/2023] Open
Abstract
Celiac disease (CeD) is a multifactorial autoimmune disorder spread worldwide. The exposure to gluten, a protein found in cereals like wheat, barley and rye, is the main environmental factor involved in its pathogenesis. Even if the genetic predisposition represented by HLA-DQ2 or HLA-DQ8 haplotypes is widely recognised as mandatory for CeD development, it is not enough to explain the total predisposition for the disease. Furthermore, the onset of CeD comprehend a wide spectrum of symptoms, that often leads to a delay in CeD diagnosis. To overcome this deficiency and help detecting people with increased risk for CeD, also clarifying CeD traits linked to disease familiarity, different studies have tried to make light on other predisposing elements. These were in many cases genetic variants shared with other autoimmune diseases. Since inherited traits can be regulated by epigenetic modifications, also induced by environmental factors, the most recent studies focused on the potential involvement of epigenetics in CeD. Epigenetic factors can in fact modulate gene expression with many mechanisms, generating more or less stable changes in gene expression without affecting the DNA sequence. Here we analyze the different epigenetic modifications in CeD, in particular DNA methylation, histone modifications, non-coding RNAs and RNA methylation. Special attention is dedicated to the additional predispositions to CeD, the involvement of epigenetics in developing CeD complications, the pathogenic pathways modulated by epigenetic factors such as microRNAs and the potential use of epigenetic profiling as biomarker to discriminate different classes of patients.
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Affiliation(s)
- Elisa Gnodi
- School of Medicine and Surgery, University of Milano-Bicocca, Monza 20900, Italy
| | - Raffaella Meneveri
- School of Medicine and Surgery, University of Milano-Bicocca, Monza 20900, Italy
| | - Donatella Barisani
- School of Medicine and Surgery, University of Milano-Bicocca, Monza 20900, Italy
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9
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Ghozzi M, Melayah S, Adaily N, Ghedira I. Frequency of serological markers of rheumatoid arthritis in adult patients with active celiac disease. J Clin Lab Anal 2022; 36:e24249. [PMID: 35060192 DOI: 10.1002/jcla.24249] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Celiac disease (CD) and rheumatoid arthritis (RA) are multisystem autoimmune diseases affecting 1% of general populationa. Both diseases share genetic and immunological features. AIM In this retrospective study, we aim to determine the frequency of auto-antibodies of RA in adult patients with CD. MATERIALS AND METHODS Seventy seven adult patients with active CD were included in the present study. Ninety healthy blood donors (HBD) served as control group. Anti-cyclic citrullinated peptides antibodies (CCP-Ab) and rheumatoid factors (RF; IgA, IgG and IgM) were determined by enzyme linked immunosorbent assay (ELISA) for patients and control group. For statistical analysis, we used Chi-square or Fisher's exact test. RESULTS Our study included 77 adult patients with active celiac disease (57 female, 20 male). Twenty-four (31.2%) active celiac patients and 7 (7.8%) blood donors had CCP-Ab or RF (31.2% vs 7.8%, p < 10-4). Only two patients (2.6%) had both CCP-Ab and RF. IgA was the predominant isotype of RF in celiac patients (n = 18; 23.4%) while none of healthy blood donors had RF-IgA (23.4% vs 0.0%, p < 10-4). CONCLUSION The current study has shown that CD is associated with a high frequency of RF-IgA suggesting that celiac patients could be at a higher risk of developing RA.
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Affiliation(s)
- Mariam Ghozzi
- Laboratory of Immunology, Farhat Hached University Hospital, Sousse, Tunisia.,Faculty of Pharmacy, Department of Immunology, University of Monastir, Monastir, Tunisia.,Research Laboratory for "Epidemiology and Immunogenetics of Viral Infections" (LR14SP02), Sahloul University Hospital, University of Sousse, Sousse, Tunisia
| | - Sarra Melayah
- Laboratory of Immunology, Farhat Hached University Hospital, Sousse, Tunisia.,Faculty of Pharmacy, Department of Immunology, University of Monastir, Monastir, Tunisia
| | - Najeh Adaily
- Laboratory of Immunology, Farhat Hached University Hospital, Sousse, Tunisia
| | - Ibtissem Ghedira
- Laboratory of Immunology, Farhat Hached University Hospital, Sousse, Tunisia.,Faculty of Pharmacy, Department of Immunology, University of Monastir, Monastir, Tunisia
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10
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Bakutenko IY, Haurylchyk ID, Nikitchenko NV, Sechko E, Kozyro IA, Tchitchko AM, Batyan GM, Sukalo AV, Ryabokon NI. Neutrophil cytosolic factor 2 (NCF2) gene polymorphism is associated with juvenile-onset systemic lupus erythematosus, but probably not with other autoimmune rheumatic diseases in children. Mol Genet Genomic Med 2022; 10:e1859. [PMID: 34971477 PMCID: PMC8801135 DOI: 10.1002/mgg3.1859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 11/08/2021] [Accepted: 12/17/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Genetic variations of neutrophil cytosolic factor 2 (NCF2), a subunit of NADPH oxidase, are usually associated with chronic granulomatous disease, and their relationship with autoimmune disorders through the defective NADPH oxidase function during phagocytosis is suggested. Our study aimed to explore whether there is an association between the non-synonymous single nucleotide polymorphism in the NCF2 gene (rs17849502, NC_000001.11:g.183563445G>T) and the development of juvenile autoimmune rheumatic diseases. METHODS In order to test this hypothesis, we conducted a pilot case-control study. In total, 709 children and adolescents, all Belarusians, were involved in the study including patients with juvenile-onset systemic lupus erythematosus (JSLE), juvenile idiopathic arthritis (JIA), Kawasaki disease (KD), and subjects without autoimmune and inflammatory diseases as the clinical control, as well as health newborns as the population control. Real-time polymerase chain reaction was used for genotyping. RESULTS The minor T allele of NCF2 occurred most frequently in patients with JSLE (OR = 2.60, 95% CI = 1.18-5.73, p = 0.023 as compared to the clinical control). In groups with JIA and KD, its frequency did not differ from the control. The TT genotype was only observed in 5.7% of patients with JSLE (p = 0.007), but not in other groups. CONCLUSION Therefore, our study suggested that NCF2 rs17849502 polymorphism is a potential genetic risk factor for JSLE, while it is probably not for such autoimmune rheumatic diseases as JIA or KD.
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Affiliation(s)
- Ivan Y. Bakutenko
- Laboratory of Molecular Basis of Genome StabilityInstitute of Genetics and CytologyNational Academy of Sciences of BelarusMinskBelarus
| | - Irena D. Haurylchyk
- Laboratory of Molecular Basis of Genome StabilityInstitute of Genetics and CytologyNational Academy of Sciences of BelarusMinskBelarus
| | - Natalia V. Nikitchenko
- Laboratory of Molecular Basis of Genome StabilityInstitute of Genetics and CytologyNational Academy of Sciences of BelarusMinskBelarus
| | - Elena V. Sechko
- 1st Department of Childhood DiseasesBelarusian State Medical UniversityMinskBelarus
| | - Inna A. Kozyro
- 1st Department of Childhood DiseasesBelarusian State Medical UniversityMinskBelarus
| | - Alexei M. Tchitchko
- 1st Department of Childhood DiseasesBelarusian State Medical UniversityMinskBelarus
| | - Galina M. Batyan
- 1st Department of Childhood DiseasesBelarusian State Medical UniversityMinskBelarus
| | - Alexander V. Sukalo
- 1st Department of Childhood DiseasesBelarusian State Medical UniversityMinskBelarus
| | - Nadezhda I. Ryabokon
- Laboratory of Molecular Basis of Genome StabilityInstitute of Genetics and CytologyNational Academy of Sciences of BelarusMinskBelarus
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11
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Ho D, Nyaga DM, Schierding W, Saffery R, Perry JK, Taylor JA, Vickers MH, Kempa-Liehr AW, O'Sullivan JM. Identifying the lungs as a susceptible site for allele-specific regulatory changes associated with type 1 diabetes risk. Commun Biol 2021; 4:1072. [PMID: 34521982 PMCID: PMC8440780 DOI: 10.1038/s42003-021-02594-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/20/2021] [Indexed: 02/08/2023] Open
Abstract
Type 1 diabetes (T1D) etiology is complex. We developed a machine learning approach that ranked the tissue-specific transcription regulatory effects for T1D SNPs and estimated their relative contributions to conversion to T1D by integrating case and control genotypes (Wellcome Trust Case Control Consortium and UK Biobank) with tissue-specific expression quantitative trait loci (eQTL) data. Here we show an eQTL (rs6679677) associated with changes to AP4B1-AS1 transcript levels in lung tissue makes the largest gene regulatory contribution to the risk of T1D development. Luciferase reporter assays confirmed allele-specific enhancer activity for the rs6679677 tagged locus in lung epithelial cells (i.e. A549 cells; C > A reduces expression, p = 0.005). Our results identify tissue-specific eQTLs for SNPs associated with T1D. The strongest tissue-specific eQTL effects were in the lung and may help explain associations between respiratory infections and risk of islet autoantibody seroconversion in young children.
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Affiliation(s)
- Daniel Ho
- Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Denis M Nyaga
- Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Richard Saffery
- Murdoch Children Research Institute, The University of Melbourne, Melbourne, Australia
| | - Jo K Perry
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - John A Taylor
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Mark H Vickers
- Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Andreas W Kempa-Liehr
- Department of Engineering Science, The University of Auckland, Auckland, New Zealand
| | - Justin M O'Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.
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12
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Baglaenko Y, Macfarlane D, Marson A, Nigrovic PA, Raychaudhuri S. Genome editing to define the function of risk loci and variants in rheumatic disease. Nat Rev Rheumatol 2021; 17:462-474. [PMID: 34188205 PMCID: PMC10782829 DOI: 10.1038/s41584-021-00637-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2021] [Indexed: 02/06/2023]
Abstract
Discoveries in human genetic studies have revolutionized our understanding of complex rheumatic and autoimmune diseases, including the identification of hundreds of genetic loci and single nucleotide polymorphisms that potentially predispose individuals to disease. However, in most cases, the exact disease-causing variants and their mechanisms of action remain unresolved. Functional follow-up of these findings is most challenging for genomic variants that are in non-coding genomic regions, where the large majority of common disease-associated variants are located, and/or that probably affect disease progression via cell type-specific gene regulation. To deliver on the therapeutic promise of human genetic studies, defining the mechanisms of action of these alleles is essential. Genome editing technology, such as CRISPR-Cas, has created a vast toolbox for targeted genetic and epigenetic modifications that presents unprecedented opportunities to decipher disease-causing loci, genes and variants in autoimmunity. In this Review, we discuss the past 5-10 years of progress in resolving the mechanisms underlying rheumatic disease-associated alleles, with an emphasis on how genomic editing techniques can enable targeted dissection and mechanistic studies of causal autoimmune risk variants.
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Affiliation(s)
- Yuriy Baglaenko
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Dana Macfarlane
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Alexander Marson
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter A Nigrovic
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Immunology, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK.
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13
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Abstract
BACKGROUND It is not known if genetic background, characteristics at diagnosis, physical and psychological well-being, and adherence to a gluten-free diet are comparable between patients with familial or sporadic celiac disease. These issues were investigated in a follow-up study. METHODS Altogether 1064 patients were analyzed for celiac disease-associated serology, predisposing HLA-DQ, and non-HLA genotypes. Medical data were collected from patient records and supplementary interviews. Current symptoms and quality of life were further evaluated with the Gastrointestinal Symptom Rating Scale (GSRS), the Psychological General Well-Being questionnaire (PGWB), and Short Form 36 (SF-36) questionnaires. RESULTS Familial and sporadic groups differed (P < 0.001) in the reason for diagnosis and clinical presentation at diagnosis, familial patients being more often screen-detected (26% vs. 2%, P < 0.001) and having less often gastrointestinal (49% vs. 69%) and severe symptoms (47% vs. 65%). The groups were comparable in terms of histological damage, frequency of malabsorption, comorbidities, childhood diagnoses, and short-term treatment response. At the time of the study, familial cases reported fewer symptoms (21% vs. 30%, P = 0.004) and lower prevalence of all (78% vs. 86%, P = 0.007), neurological (10% vs. 15%, P = 0.013), and dermatological (9% vs. 17%, P = 0.001) comorbidities. Dietary adherence and GSRS scores were comparable, but familial cases had better quality of life according to PGWB and SF-36. High-risk genotype HLA-DQ2.5/DQ2.5 was more frequent among familial cases, and four non-HLA SNPs were associated with familial celiac disease. CONCLUSIONS Despite the greater proportion of high-risk genotypes, familial cases had milder symptoms at presentation than did sporadic cases. Worse experience of symptoms and poorer quality of life in sporadic disease indicate a need for intensified support.
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14
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Ha E, Bae SC, Kim K. Large-scale meta-analysis across East Asian and European populations updated genetic architecture and variant-driven biology of rheumatoid arthritis, identifying 11 novel susceptibility loci. Ann Rheum Dis 2020; 80:558-565. [PMID: 33310728 PMCID: PMC8053349 DOI: 10.1136/annrheumdis-2020-219065] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/23/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023]
Abstract
Objectives Nearly 110 susceptibility loci for rheumatoid arthritis (RA) with modest effect sizes have been identified by population-based genetic association studies, suggesting a large number of undiscovered variants behind a highly polygenic genetic architecture of RA. Here, we performed the largest-ever trans-ancestral meta-analysis with the aim to identify new RA loci and to better understand RA biology underlying genetic associations. Methods Genome-wide RA association summary statistics in three large case–control collections consisting of 311 292 individuals of Korean, Japanese and European populations were used in an inverse-variance-weighted fixed-effects meta-analysis. Several computational analyses using public omics resources were conducted to prioritise causal variants and genes, RA variant-implicating features (tissues, pathways and transcription factors) and potentially repurposable drugs for RA treatment. Results We identified 11 new RA susceptibility loci that explained 6.9% and 1.8% of the single-nucleotide polymorphism-based heritability in East Asians and Europeans, respectively, and confirmed 71 known non-human leukocyte antigens (HLA) susceptibility loci, identifying 90 independent association signals. The RA variants were preferentially located in binding sites of various transcription factors and in cell type-specific transcription–activation histone marks that simultaneously highlighted the importance of CD4+ T-cell activation and the potential role of non-immune organs in RA pathogenesis. A total of 615 plausible effector genes, based on gene-based associations, expression-associated variants and chromatin interaction, included targets of drugs approved for RA treatments and potentially repurposable drugs approved for other indications. Conclusion Our findings provide useful insights regarding RA genetic aetiology and variant-driven RA pathogenesis.
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Affiliation(s)
- Eunji Ha
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Republic of Korea .,Hanyang University Institute for Rheumatology Research, Seoul, Republic of Korea
| | - Kwangwoo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
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15
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Sallese M, Lopetuso LR, Efthymakis K, Neri M. Beyond the HLA Genes in Gluten-Related Disorders. Front Nutr 2020; 7:575844. [PMID: 33262997 PMCID: PMC7688450 DOI: 10.3389/fnut.2020.575844] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
Most common food grains contain gluten proteins and can cause adverse medical conditions generally known as gluten-related disorders. Celiac disease is an immune-mediated enteropathy triggered by gluten in individuals carrying a specific genetic make-up. The presence of the human leukocyte antigens (HLA)-DQ2 and HLA-DQ8 haplotypes together with gluten intake is a necessary, although not sufficient, condition, to develop celiac disease. Fine mapping of the human genome has revealed numerous genetic variants important in the development of this disease. Most of the genetic variants are small nucleotide polymorphisms located within promoters and transcriptional enhancer sequences. Their importance is underlined by an increased risk in DQ2/DQ8 carriers who also have these non-HLA alleles. In addition, several immune-mediated diseases share susceptibility loci with celiac disease, shedding light on the reasons for co-occurrence between these diseases. Finally, most of the genes potentially involved in celiac disease by fine genetic mapping of non-HLA loci were confirmed in gene expression studies. In contrast to celiac disease, very little is known about the genetic make-up of non-celiac wheat sensitivity (NCWS), a clinically defined pathology that shares symptoms and gluten dependence with the celiac disease. We recently identified differentially expressed genes and miRNAs in the intestinal mucosa of these patients. Remarkably, the differentially expressed genes were long non-coding RNAs possibly involved in the regulation of cell functions. Thus, we can speculate that important aspects of these diseases depend on alteration of regulatory genetic circuits. Furthermore, our finding suggests that innate immune response is involved in the pathogenic mechanism of NCWS. This review is intended to convey the idea that in order to fully understand celiac disease and its relationship with other gluten-related disorders, it is worth learning more about non-HLA variants.
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Affiliation(s)
- Michele Sallese
- Department of Medical, Oral and Biotechnological Sciences, 'G. D'Annunzio' University of Chieti-Pescara, Chieti, Italy.,Center for Advanced Studies and Technology (CAST), 'G. D'Annunzio' University of Chieti-Pescara, Chieti, Italy
| | - Loris Riccardo Lopetuso
- Center for Advanced Studies and Technology (CAST), 'G. D'Annunzio' University of Chieti-Pescara, Chieti, Italy.,Department of Medicine and Aging Sciences, 'G. D'Annunzio' University of Chieti-Pescara, Chieti, Italy
| | - Konstantinos Efthymakis
- Department of Medicine and Aging Sciences, 'G. D'Annunzio' University of Chieti-Pescara, Chieti, Italy
| | - Matteo Neri
- Center for Advanced Studies and Technology (CAST), 'G. D'Annunzio' University of Chieti-Pescara, Chieti, Italy.,Department of Medicine and Aging Sciences, 'G. D'Annunzio' University of Chieti-Pescara, Chieti, Italy
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16
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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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17
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Ricaño-Ponce I, Gutierrez-Achury J, Costa AF, Deelen P, Kurilshikov A, Zorro MM, Platteel M, van der Graaf A, Sanna S, Daffra O, Zhernakova A, Fu J, Trynka G, Smecuol E, Niveloni SI, Bai JC, Kumar V, Wijmenga C. Immunochip meta-analysis in European and Argentinian populations identifies two novel genetic loci associated with celiac disease. Eur J Hum Genet 2020; 28:313-323. [PMID: 31591516 PMCID: PMC7028987 DOI: 10.1038/s41431-019-0520-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 12/30/2022] Open
Abstract
Celiac disease (CeD) is a common immune-mediated disease of the small intestine that is triggered by exposure to dietary gluten. While the HLA locus plays a major role in disease susceptibility, 39 non-HLA loci were also identified in a study of 24,269 individuals. We now build on this earlier study by adding 4125 additional Caucasian samples including an Argentinian cohort. In doing so, we not only confirm the previous associations, we also identify two novel independent genome-wide significant associations at loci: 12p13.31 and 22q13.1. By applying a genomics approach and differential expression analysis in CeD intestinal biopsies, we prioritize potential causal genes at these novel loci, including LTBR, CYTH4, and RAC2. Nineteen prioritized causal genes are overlapping known drug targets. Pathway enrichment analysis and expression of these genes in CeD biopsies suggest that they have roles in regulating multiple pathways such as the tumor necrosis factor (TNF) mediated signaling pathway and positive regulation of I-κB kinase/NF-κB signaling.
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Affiliation(s)
- Isis Ricaño-Ponce
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Javier Gutierrez-Achury
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Ana Florencia Costa
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Maria Magdalena Zorro
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Mathieu Platteel
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Serena Sanna
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Oscar Daffra
- Gastroenterology Service, OSEP Mendoza, Mendoza, Argentina
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Gosia Trynka
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Edgardo Smecuol
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Sonia Isabel Niveloni
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Julio Cesar Bai
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525GA, Nijmegen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands.
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.
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Abstract
PURPOSE OF REVIEW Aberrant epigenetic changes in DNA methylation, histone marks, and noncoding RNA expression regulate the pathogenesis of many rheumatic diseases. The present article will review the recent advances in the epigenetic profile of inflammatory arthritis and discuss diagnostic biomarkers and potential therapeutic targets. RECENT FINDINGS Methylation signatures of fibroblast-like synoviocytes not only distinguish rheumatoid arthritis (RA) and osteoarthritis (OA), but also early RA from late RA or juvenile idiopathic arthritis. Methylation patterns are also specific to individual joint locations, which might explain the distribution of joint involvement in some rheumatic diseases. Hypomethylation in systemic lupus erythematosus (SLE) T cells is, in part, because of active demethylation and 5-hydroxymethylation. The methylation status of some genes in SLE is associated with disease severity and has potential as a diagnostic marker. An integrative analysis of OA methylome, transcriptome, and proteome in chondrocytes has identified multiple-evidence genes that might be evaluated for therapeutic potential. Class-specific histone deacetylase inhibitors are being evaluated for therapy in inflammatory arthritis. SUMMARY Disease pathogenesis is regulated by the interplay of genetics, environment, and epigenetics. Understanding how these mechanisms regulate cell function in health and disease has implications for individualized therapy.
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Márquez A, Kerick M, Zhernakova A, Gutierrez-Achury J, Chen WM, Onengut-Gumuscu S, González-Álvaro I, Rodriguez-Rodriguez L, Rios-Fernández R, González-Gay MA, Mayes MD, Raychaudhuri S, Rich SS, Wijmenga C, Martín J. Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single-disease and cross-phenotype associations. Genome Med 2018; 10:97. [PMID: 30572963 PMCID: PMC6302306 DOI: 10.1186/s13073-018-0604-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/22/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In recent years, research has consistently proven the occurrence of genetic overlap across autoimmune diseases, which supports the existence of common pathogenic mechanisms in autoimmunity. The objective of this study was to further investigate this shared genetic component. METHODS For this purpose, we performed a cross-disease meta-analysis of Immunochip data from 37,159 patients diagnosed with a seropositive autoimmune disease (11,489 celiac disease (CeD), 15,523 rheumatoid arthritis (RA), 3477 systemic sclerosis (SSc), and 6670 type 1 diabetes (T1D)) and 22,308 healthy controls of European origin using the R package ASSET. RESULTS We identified 38 risk variants shared by at least two of the conditions analyzed, five of which represent new pleiotropic loci in autoimmunity. We also identified six novel genome-wide associations for the diseases studied. Cell-specific functional annotations and biological pathway enrichment analyses suggested that pleiotropic variants may act by deregulating gene expression in different subsets of T cells, especially Th17 and regulatory T cells. Finally, drug repositioning analysis evidenced several drugs that could represent promising candidates for CeD, RA, SSc, and T1D treatment. CONCLUSIONS In this study, we have been able to advance in the knowledge of the genetic overlap existing in autoimmunity, thus shedding light on common molecular mechanisms of disease and suggesting novel drug targets that could be explored for the treatment of the autoimmune diseases studied.
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Affiliation(s)
- Ana Márquez
- Instituto de Parasitología y Biomedicina “López-Neyra”, CSIC, PTS Granada, Granada, Spain
- Systemic Autoimmune Disease Unit, Instituto de Investigación Biosanitaria de Granada, Granada, Spain
| | - Martin Kerick
- Instituto de Parasitología y Biomedicina “López-Neyra”, CSIC, PTS Granada, Granada, Spain
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | | | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | | | | | - Raquel Rios-Fernández
- Systemic Autoimmune Diseases Unit, Complejo Hospitalario de Granada, Hospital Campus de la Salud, Granada, Spain
| | - Miguel A. González-Gay
- Epidemiology, Genetics and Atherosclerosis Research Group on Systemic Inflammatory Diseases, IDIVAL, Santander, Spain
| | - Maureen D. Mayes
- Division of Rheumatology and Clinical Immunogenetics, The University of Texas Health Science Center-Houston, Houston, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Javier Martín
- Instituto de Parasitología y Biomedicina “López-Neyra”, CSIC, PTS Granada, Granada, Spain
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20
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Genetic variants at the 16p13 locus confer risk for eosinophilic esophagitis. Genes Immun 2018; 20:281-292. [PMID: 29904099 PMCID: PMC6286696 DOI: 10.1038/s41435-018-0034-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/06/2018] [Accepted: 04/11/2018] [Indexed: 02/08/2023]
Abstract
Eosinophilic esophagitis (EoE) is a chronic inflammatory disease of the esophagus triggered by immune hypersensitivity to food. Herein, we tested whether genetic risk factors for known, non-allergic, immune-mediated diseases, particularly those involving autoimmunity, were associated with EoE risk. We used the high-density Immunochip platform, encoding 200,000 genetic variants for major auto-immune disease. Accordingly, 1214 subjects with EoE of European ancestry and 3734 population controls were genotyped and assessed using data directly generated or imputed from the previously published GWAS. We found lack of association of EoE with the genetic variants in the major histocompatibility complex (MHC) class I, II, and III genes and nearly all other loci using a highly powered study design with dense genotyping throughout the locus. Importantly, we identified an EoE risk locus at 16p13 with genome-wide significance (Pcombined=2.05 × 10−9, odds ratio = 0.76−0.81). This region is known to encode for the genes CLEC16A, DEXI, and CIITI, which are expressed in immune cells and esophageal epithelial cells. Suggestive EoE risk were also seen 5q23 (intergenic) and 7p15 (JAZF1). Overall, we have identified an additional EoE risk locus at 16p13 and highlight a shared and unique genetic etiology of EoE with a spectrum of immune-associated diseases.
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Unalp-Arida A, Ruhl CE, Choung RS, Brantner TL, Murray JA. Lower Prevalence of Celiac Disease and Gluten-Related Disorders in Persons Living in Southern vs Northern Latitudes of the United States. Gastroenterology 2017; 152:1922-1932.e2. [PMID: 28238771 PMCID: PMC7002016 DOI: 10.1053/j.gastro.2017.02.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/26/2017] [Accepted: 02/14/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS The association between prevalence of celiac disease and geographic region is incompletely understood, but the occurrence of several autoimmune disorders has been found to vary along a North-South gradient. We examined geographic, demographic, and clinical factors associated with prevalence of celiac disease and gluten-free diet in the United States. METHODS In a population-based study, we analyzed data on gluten-related conditions from the National Health and Nutrition Examination Survey, from 2009 through 2014, on 22,277 participants 6 years and older. We identified persons with celiac disease based on results of serum tests for IgA against tissue transglutaminase and endomysium or on both a health care provider diagnosis and adherence to a gluten-free diet. Gluten avoidance without celiac disease was defined as adherence to a gluten-free diet without a diagnosis of celiac disease. We compared mean serum levels of biochemical and nutritional markers based on status of gluten-related conditions. RESULTS We found 0.7% of participants to have celiac disease and 1.1% of participants to avoid gluten without celiac disease. Celiac disease was more common among individuals who lived at latitudes of 35°-39° North (odds ratio, 3.2; 95% confidence interval, 1.4-7.1) or at latitudes of 40° North or more (odds ratio, 5.4; 95% CI, 2.6-11.3) than individuals who lived at latitudes below 35° North, independent of race or ethnicity, socioeconomic status, and body mass index. Gluten avoidance without celiac disease was more common among individuals who lived at latitudes of 40° North or more, independent of demographic factors and body mass index. Participants with undiagnosed celiac disease (identified by positive results from serologic tests) had lower mean levels of vitamin B-12 and folate (data collected from 2009 through 2012) than persons without celiac disease. Participants with a health care provider diagnosis of celiac disease had a lower mean level of hemoglobin than persons without celiac disease. Mean levels of albumin, calcium, iron, ferritin, cholesterol, vitamin B-6, and vitamin D (data collected from 2009 through 2010) did not differ between participants with gluten-related conditions and those without. CONCLUSIONS In the US population, a higher proportion of persons living at latitudes of 35° North or greater have celiac disease or avoid gluten than persons living south of this latitude, independent of race or ethnicity, socioeconomic status, or body mass index. Mean levels of vitamin B-12 and folate are lower in individuals with undiagnosed celiac disease, and levels of hemoglobin are lower in participants with a diagnosis of celiac disease, compared with individuals without celiac disease.
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Affiliation(s)
- Aynur Unalp-Arida
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | | | - Rok Seon Choung
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Tricia L Brantner
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Joseph A Murray
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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Conigliaro P, Chimenti M, Triggianese P, Sunzini F, Novelli L, Perricone C, Perricone R. Autoantibodies in inflammatory arthritis. Autoimmun Rev 2016; 15:673-83. [DOI: 10.1016/j.autrev.2016.03.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 02/28/2016] [Indexed: 02/07/2023]
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Márquez A, Vidal-Bralo L, Rodríguez-Rodríguez L, González-Gay MA, Balsa A, González-Álvaro I, Carreira P, Ortego-Centeno N, Ayala-Gutiérrez MM, García-Hernández FJ, González-Escribano MF, Sabio JM, Tolosa C, Suárez A, González A, Padyukov L, Worthington J, Vyse T, Alarcón-Riquelme ME, Martín J. A combined large-scale meta-analysis identifies COG6 as a novel shared risk locus for rheumatoid arthritis and systemic lupus erythematosus. Ann Rheum Dis 2016; 76:286-294. [PMID: 27193031 DOI: 10.1136/annrheumdis-2016-209436] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/14/2016] [Accepted: 04/29/2016] [Indexed: 02/06/2023]
Abstract
OBJECTIVES During the last years, genome-wide association studies (GWASs) have identified a number of common genetic risk factors for rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). However, the genetic overlap between these two immune-mediated diseases has not been thoroughly examined so far. The aim of the present study was to identify additional risk loci shared between RA and SLE. METHODS We performed a large-scale meta-analysis of GWAS data from RA (3911 cases and 4083 controls) and SLE (2237 cases and 6315 controls). The top-associated polymorphisms in the discovery phase were selected for replication in additional datasets comprising 13 641 RA cases and 31 921 controls and 1957 patients with SLE and 4588 controls. RESULTS The rs9603612 genetic variant, located nearby the COG6 gene, an established susceptibility locus for RA, reached genome-wide significance in the combined analysis including both discovery and replication sets (p value=2.95E-13). In silico expression quantitative trait locus analysis revealed that the associated polymorphism acts as a regulatory variant influencing COG6 expression. Moreover, protein-protein interaction and gene ontology enrichment analyses suggested the existence of overlap with specific biological processes, specially the type I interferon signalling pathway. Finally, genetic correlation and polygenic risk score analyses showed cross-phenotype associations between RA and SLE. CONCLUSIONS In conclusion, we have identified a new risk locus shared between RA and SLE through a meta-analysis including GWAS datasets of both diseases. This study represents the first comprehensive large-scale analysis on the genetic overlap between these two complex disorders.
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Affiliation(s)
- Ana Márquez
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC, PTS Granada, Granada, Spain.,Systemic Autoimmune Diseases Unit, Hospital Clínico San Cecilio, Granada, Spain
| | - Laura Vidal-Bralo
- Laboratorio de Investigación 10 and Rheumatology Unit, Instituto de Investigación Sanitaria-Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - Luis Rodríguez-Rodríguez
- Rheumatology Department and Heath Research Institute (IdISSC), Hospital Clinico San Carlos, Madrid, Spain
| | - Miguel A González-Gay
- Department of Rheumatology, Hospital Universitario Marqués de Valdecilla, IDIVAL, Santander, Spain
| | - Alejandro Balsa
- Department of Rheumatology and Institute for Health Research (IdiPAZ), University Hospital La Paz, Madrid, Spain
| | - Isidoro González-Álvaro
- Rheumatology Service and Health Research Institute (IP), Hospital Universitario de La Princesa, Madrid, Spain
| | | | | | | | | | | | - José Mario Sabio
- Department of Internal Medicine, Hospital Virgen de las Nieves, Granada, Spain
| | - Carles Tolosa
- Department of Internal Medicine, Hospital Parc Taulí, Sabadell, Spain
| | - Ana Suárez
- Department of Functional Biology, Immunology Area, Faculty of Medicine, University of Oviedo, Oviedo, Spain
| | - Antonio González
- Laboratorio de Investigación 10 and Rheumatology Unit, Instituto de Investigación Sanitaria-Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jane Worthington
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Institute of Inflammation and Repair, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Timothy Vyse
- Division of Genetics and Molecular Medicine, King's College London, London, UK.,Division of Immunology, Infection and Inflammatory Disease, King's College London, London, UK
| | - Marta E Alarcón-Riquelme
- Centro de Genómica e Investigación Oncológica (GENYO), Pfizer-Universidad de Granada-Junta de Andalucía, Granada, Spain.,Institute for Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Javier Martín
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC, PTS Granada, Granada, Spain
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Withoff S, Li Y, Jonkers I, Wijmenga C. Understanding Celiac Disease by Genomics. Trends Genet 2016; 32:295-308. [PMID: 26972670 DOI: 10.1016/j.tig.2016.02.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/15/2016] [Accepted: 02/16/2016] [Indexed: 02/06/2023]
Abstract
Celiac disease (CeD) is a complex immune-mediated disease. Genetic studies have implicated 43 predisposing loci that collectively explain some 50% of the genetic variance in CeD. More than ∼90% of CeD-associated single nucleotide polymorphisms (SNPs) localize to the non-coding genome, which we need to better understand to translate genetic knowledge into clinical practice. New genomic technologies and resources are permitting a systematic analysis of the functional elements in the non-coding part of the genome. Here we explain how investigating the regulatory and epigenomic landscape will help to pinpoint the cell types involved in CeD, and the driver genes and gene regulatory networks that are affected by CeD-associated SNPs.
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Affiliation(s)
- Sebo Withoff
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
| | - Yang Li
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Iris Jonkers
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
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