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Casanova NG, Camp SM, Gonzalez-Garay ML, Batai K, Garman L, Montgomery CG, Ellis N, Kittles R, Bime C, Hsu AP, Holland S, Lussier YA, Karnes J, Sweiss N, Maier LA, Koth L, Moller DR, Kaminski N, Garcia JGN. Examination of eQTL Polymorphisms Associated with Increased Risk of Progressive Complicated Sarcoidosis in European and African Descent Subjects. EUROPEAN JOURNAL OF RESPIRATORY MEDICINE 2023; 5:359-371. [PMID: 38390497 PMCID: PMC10883688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Background A limited pool of SNPs are linked to the development and severity of sarcoidosis, a systemic granulomatous inflammatory disease. By integrating genome-wide association studies (GWAS) data and expression quantitative trait loci (eQTL) single nuclear polymorphisms (SNPs), we aimed to identify novel sarcoidosis SNPs potentially influencing the development of complicated sarcoidosis. Methods A GWAS (Affymetrix 6.0) involving 209 African-American (AA) and 193 European-American (EA, 75 and 51 complicated cases respectively) and publicly-available GWAS controls (GAIN) was utilized. Annotation of multi-tissue eQTL SNPs present on the GWAS created a pool of ~46,000 eQTL SNPs examined for association with sarcoidosis risk and severity (Logistic Model, Plink). The most significant EA/AA eQTL SNPs were genotyped in a sarcoidosis validation cohort (n=1034) and cross-validated in two independent GWAS cohorts. Results No single GWAS SNP achieved significance (p<1x10-8), however, analysis of the eQTL/GWAS SNP pool yielded 621 eQTL SNPs (p<10-4) associated with 730 genes that highlighted innate immunity, MHC Class II, and allograft rejection pathways with multiple SNPs validated in an independent sarcoidosis cohort (105 SNPs analyzed) (NOTCH4, IL27RA, BTNL2, ANXA11, HLA-DRB1). These studies confirm significant association of eQTL/GWAS SNPs in EAs and AAs with sarcoidosis risk and severity (complicated sarcoidosis) involving HLA region and innate immunity. Conclusion Despite the challenge of deciphering the genetic basis for sarcoidosis risk/severity, these results suggest that integrated eQTL/GWAS approaches may identify novel variants/genes and support the contribution of dysregulated innate immune responses to sarcoidosis severity.
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Affiliation(s)
- Nancy G Casanova
- Department of Molecular Medicine, Univeristy of Florida, Scripps, Jupiter FL, USA
| | - Sara M Camp
- Center for Inflammation Science and Systems Medicine, University of Florida, Wertheim Scripps Research Institute, Jupiter FL, USA
| | - Manuel L Gonzalez-Garay
- Division of Health Equities, Department of Population Sciences, City of Hope, Duarte, California, USA
| | - Ken Batai
- Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Lori Garman
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | | | - Nathan Ellis
- University of Arizona Cancer Center, Tucson, AZ, USA
| | - Rick Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope, Duarte, California, USA
| | - Christian Bime
- Department of Medicine University of Arizona, Tucson, AZ, USA
| | - Amy P Hsu
- National Institute of Allergy and Infectious Diseases. National Institutes of Health, USA
| | - Steven Holland
- National Institute of Allergy and Infectious Diseases. National Institutes of Health, USA
| | - Yves A Lussier
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | - Jason Karnes
- Department of Pharmacology, University of Arizona, College of Pharmacy, Tucson, AZ, USA
| | - Nadera Sweiss
- Department of Medicine University of Illinois, Chicago, IL, USA
| | - Lisa A Maier
- Department of Medicine National Jewish Health, University of Colorado, Denver, CO, USA
| | - Laura Koth
- Department of Medicine University of California San Francisco, San Francisco, CA, US, USA
| | - David R Moller
- Department of Medicine Johns Hopkins University School of Medicine, Baltimore Maryland, USA
| | - Naftali Kaminski
- Department of Medicine Yale University School of Medicine, New Haven, CT, USA
| | - Joe G N Garcia
- Center for Inflammation Science and Systems Medicine, University of Florida, Wertheim Scripps Research Institute, Jupiter FL, USA
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Dong PP, Wang RR, Abduriyim S. Diversity and evolution of the MHC class II DRB gene in the Capra sibirica experienced a demographic fluctuation in China. Sci Rep 2023; 13:19352. [PMID: 37935954 PMCID: PMC10630338 DOI: 10.1038/s41598-023-46717-5] [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: 08/17/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023] Open
Abstract
The major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates, and their proteins play a critical role in adaptive immunity for defense against a variety of pathogens. MHC diversity was lost in many species after experiencing a decline in size. To understand the variation and evolution of MHC genes in the Siberian ibex, Capra sibirica, which has undergone a population decline, we analyzed the variation of the second exon of MHC class II DRB genes in samples collected from five geographic localities in Xinjiang, China, that belong to three diverged mitochondrial clades. Consequently, we identified a total of 26 putative functional alleles (PFAs) with 260 bp in length from 43 individuals, and found one (for 27 individuals) to three (for 5 individuals) PFAs per individual, indicating the presence of one or two DRB loci per haploid genome. The Casi-DRB1*16 was the most frequently occurring PFA, Casi-DRB1*22 was found in only seven individuals, 14 PFAs occurred once, 7 PFAs twice, implying high frequency of rare PFAs. Interestingly, more than half (15) of the PFAs were specific to clade I, only two and three PFAs were specific to clades II and III, respectively. So, we assume that the polygamy and sexual segregation nature of this species likely contributed to the allelic diversity of DRB genes. Genetic diversity indices showed that PFAs of clade II were lower in nucleotide, amino acid, and supertype diversity compared to those of the other two clades. The pattern of allele sharing and FST values between the three clades was to some extent in agreement with the pattern observed in mitochondrial DNA divergence. In addition, recombination analyses revealed no evidence for significant signatures of recombination events. Alleles shared by clades III and the other two clades diverged 6 million years ago, and systematic neighbor grids showed Trans-species polymorphism. Together with the PAML and MEME analyses, the results indicated that the DRB gene in C. sibirica evolved under balancing and positive selection. However, by comparison, it can be clearly seen that different populations were under different selective pressures. Our results are valuable in understanding the diversity and evolution of the DRB gene in a mountain living C. sibirica and in making decisions on future long-term protection strategies.
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Affiliation(s)
- Pei-Pei Dong
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Rui-Rui Wang
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China
| | - Shamshidin Abduriyim
- College of Life Science, Shihezi University, Shihezi, 832003, Xinjiang, China.
- Xinjiang Production and Construction Corps Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Shihezi University, Shihezi, 832003, Xinjiang, China.
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3
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Papiris SA, Kolilekas L, Rivera N, Spanos M, Li G, Gokulnath P, Chatterjee E, Georgakopoulos A, Kallieri M, Papaioannou AI, Raptakis T, Apollonatou V, Antonogiannaki EM, Gialafos E, Chatziioannou S, Grunewald J, Manali ED. From Karl Wurm and Guy Scadding's staging to 18F-FDG PET/CT scan phenotyping and far beyond: perspective in the evading history of phenotyping in sarcoidosis. Front Med (Lausanne) 2023; 10:1174518. [PMID: 37234239 PMCID: PMC10206027 DOI: 10.3389/fmed.2023.1174518] [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: 02/26/2023] [Accepted: 04/05/2023] [Indexed: 05/27/2023] Open
Abstract
Sarcoidosis is an inflammatory granulomatous disease of unknown etiology involving any organ or tissue along with any combination of active sites, even the most silent ones clinically. The unpredictable nature of the sites involved in sarcoidosis dictates the highly variable natural history of the disease and the necessity to cluster cases at diagnosis based on clinical and/or imaging common characteristics in an attempt to classify patients based on their more homogeneous phenotypes, possibly with similar clinical behavior, prognosis, outcome, and therefore with therapeutic requirements. In the course of the disease's history, this attempt relates to the availability of a means of detection of the sites involved, from the Karl Wurm and Guy Scadding's chest x-ray staging through the ACCESS, the WASOG Sarcoidosis Organ Assessment Instruments, and the GenPhenReSa study to the 18F-FDG PET/CT scan phenotyping and far beyond to new technologies and/or the current "omics." The hybrid molecular imaging of the 18F-FDG PET/CT scan, by unveiling the glucose metabolism of inflammatory cells, can identify high sensitivity inflammatory active granulomas, the hallmark of sarcoidosis-even in clinically and physiologically silent sites-and, as recently shown, is successful in identifying an unexpected ordered stratification into four phenotypes: (I) hilar-mediastinal nodal, (II) lungs and hilar-mediastinal nodal, (III) an extended nodal supraclavicular, thoracic, abdominal, inguinal, and (IV) all the above in addition to systemic organs and tissues, which is therefore the ideal phenotyping instrument. During the "omics era," studies could provide significant, distinct, and exclusive insights into sarcoidosis phenotypes linking clinical, laboratory, imaging, and histologic characteristics with molecular signatures. In this context, the personalization of treatment for sarcoidosis patients might have reached its goal.
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Affiliation(s)
- Spyros A. Papiris
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital Attikon, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Natalia Rivera
- Respiratory Medicine Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Michail Spanos
- Cardiovascular Research Center, Simches 3 Massachusetts General Hospital, Boston, MA, United States
| | - Guoping Li
- Cardiovascular Research Center, Simches 3 Massachusetts General Hospital, Boston, MA, United States
| | - Priyanka Gokulnath
- Cardiovascular Research Center, Simches 3 Massachusetts General Hospital, Boston, MA, United States
| | - Emeli Chatterjee
- Cardiovascular Research Center, Simches 3 Massachusetts General Hospital, Boston, MA, United States
| | - Alexandros Georgakopoulos
- 2nd Department of Radiology, Nuclear Medicine Section, Medical School, General University Hospital “Attikon”, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Kallieri
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital Attikon, National and Kapodistrian University of Athens, Athens, Greece
| | - Andriana I. Papaioannou
- 1st Respiratory Medicine Department, Athens Medical School, Sotiria Chest Hospital of Athens, National and Kapodistrian University of Athens, Athens, Greece
| | - Thomas Raptakis
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital Attikon, National and Kapodistrian University of Athens, Athens, Greece
| | - Vasiliki Apollonatou
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital Attikon, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Elias Gialafos
- Department of Cardiology, Medical School, General University Hospital “Attikon”, National and Kapodistrian University of Athens, Athens, Greece
- First Department of Neurology, Medical School, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Sofia Chatziioannou
- 2nd Department of Radiology, Nuclear Medicine Section, Medical School, General University Hospital “Attikon”, National and Kapodistrian University of Athens, Athens, Greece
- Division of Nuclear Medicine, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Johan Grunewald
- Respiratory Medicine Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Effrosyni D. Manali
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital Attikon, National and Kapodistrian University of Athens, Athens, Greece
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Ezeh N, Caplan A, Rosenbach M, Imadojemu S. Cutaneous Sarcoidosis. Dermatol Clin 2023; 41:455-470. [DOI: 10.1016/j.det.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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Zhang Q, Xu Z, Huang H, Zhang M. Whole Exome Sequencing Identified Two Single Nucleotide Polymorphisms of Human Leukocyte Antigen-DRB5 in Familial Sarcoidosis in China. Curr Gene Ther 2023; 23:215-227. [PMID: 36658707 DOI: 10.2174/1566523223666230119143501] [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: 08/31/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND Sarcoidosis is a multisystem granulomatous disorder whose etiology is related to genetic and immunological factors. Familial aggregation and ethnic prevalence suggest a genetic predisposition and inherited susceptibility to sarcoidosis. OBJECTIVE This study aimed to identify suspected risk loci for familial sarcoidosis patients. METHODS We conducted whole exome sequencing on two sarcoidosis patients and five healthy family members in a Chinese family for a case-control study. The two sarcoidosis patients were siblings who showed chronic disease. RESULTS The Gene Ontology results showed single nucleotide polymorphisms in three genes, including human leukocyte antigen (HLA)-DRB1, HLA-DRB5, and KIR2DL4, associated with both 'antigen processing and presentation' and 'regulation of immune response.' Sanger sequencing verified two nonsynonymous mutations in HLA-DRB5 (rs696318 and rs115817940) located on 6p21.3 in the major histocompatibility complex (MHC) class II beta 1 region. The structural model simulated on Prot- Param protein analysis by the Expert Protein Analysis System predicted that the hydropathy index changed at two mutation sites (rs696318: p.F96L, -1.844 to -1.656 and rs115817940: p.T106N, -0.322 to -0.633), which indicated the probability of changes in peptide-binding selectivity. CONCLUSION Our results indicated that two nonsynonymous mutations of HLA-DRB5 have been identified in two sarcoidosis siblings, while their healthy family members do not have the mutations. The two HLA-DRB5 alleles may influence genetic susceptibility and chronic disease progression through peptide mutations on the MHC class II molecule among the two affected family members.
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Affiliation(s)
- Qian Zhang
- Department of Respiratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan-100730, Beijing
| | - Zuojun Xu
- Department of Respiratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan-100730, Beijing
| | - Hui Huang
- Department of Respiratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan-100730, Beijing
| | - Meijun Zhang
- ANNOROAD CO., Building B1, Yizhuang Biological Medicine Park, Kechuang 6th Street, Beijing Economic Development Zone, Beijing, China
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HLA-DRA Gene Polymorphisms Are Associated with Graves’ Disease as an Autoimmune Thyroid Disease. BIOMED RESEARCH INTERNATIONAL 2022; 2022:6839634. [PMID: 36132072 PMCID: PMC9484895 DOI: 10.1155/2022/6839634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022]
Abstract
Background Autoimmune thyroid disease (AITD), one of the most prevalent organ-specific autoimmune diseases, mainly includes Graves' disease (GD) and Hashimoto's thyroiditis (HT). This study was aimed at researching the association between AITD and single nucleotide polymorphisms (SNPs) of the HLA-DRA gene. Methods Using Hi-SNP high-throughput sequencing technology, we detected the distribution of three SNPs (rs3177928, rs7197, and rs3129878) of HLA-DRA genotypes in 1033 AITD patients (634 GD and 399 HT ones) and 791 healthy volunteers in Chinese Han Population. Chi-square test, multivariate logistic regression, and haplotype analysis were performed by SPSS and Haploview software to analyze the relationship between HLA-DRA gene polymorphisms and AITD. Results The results show that allele frequency and genotype distribution of rs3177928 and rs7197 were correlated with AITD and GD compared with the healthy control group, but not with HT. Rs3177928 and rs7197 were correlated with AITD and HT in the allele model, dominant model, and overdominant model before and after gender and age adjustment, but not with HT. In addition, we found that two loci (rs3177928 and rs7197) constituted a linkage disequilibrium (LD) region, and haplotype AA was associated with AITD and GD. However, we found no association between rs3129878 and AITD. Conclusion Our study is the first to find that rs3177928 and rs7197 of HLA-DRA are significantly correlated with AITD and GD in the Chinese Han population. This will help further reveal the pathogenesis of AITD and provide new candidate genes for the prediction or treatment of AITD.
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Zhang Q, Huang H, Zhang M, Fang C, Wang N, Jing X, Guo J, Sun W, Yang X, Xu Z. Exome Sequencing Reveals Genetic Variability and Identifies Chronic Prognostic Loci in Chinese Sarcoidosis Patients. Front Oncol 2022; 12:910227. [PMID: 35860586 PMCID: PMC9289133 DOI: 10.3389/fonc.2022.910227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Background Sarcoidosis is an inflammatory disease characterized by non-caseating granuloma formation in various organs, with several recognized genetic and environmental risk factors. Despite substantial progress, the genetic determinants associated with its prognosis remain largely unknown. Objectives This study aimed to identify the genetic changes involved in sarcoidosis and evaluate their clinical relevance. Methods We performed whole-exome sequencing (WES) in 116 sporadic sarcoidosis patients (acute sarcoidosis patients, n=58; chronic sarcoidosis patients, n=58). In addition, 208 healthy controls were selected from 1000 G East Asian population data. To identify genes enriched in sarcoidosis, Fisher exact tests were performed. The identified genes were included for further pathway analysis using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Additionally, we used the STRING database to construct a protein network of rare variants and Cytoscape to identify hub genes of signaling pathways. Results WES and Fisher’s exact test identified 1,311 variants in 439 protein-coding genes. A total of 135 single nucleotide polymorphisms (SNPs) on 30 protein-coding genes involved in the immunological process based on the GO and KEGG enrichment analysis. Pathway enrichment analysis showed osteoclast differentiation and cytokine–cytokine receptor interactions. Three missense mutations (rs76740888, rs149664918, and rs78251590) in two genes (PRSS3 and CNN2) of immune-related genes showed significantly different mutation frequencies between the disease group and healthy controls. The correlation of genetic abnormalities with clinical outcomes using multivariate analysis of the clinical features and mutation loci showed that the missense variant (rs76740888, Chr9:33796673 G>A) of PRSS3 [p=0.04, odds ratio (OR) = 2.49] was significantly associated with chronic disease prognosis. Additionally, the top two hub genes were CCL4 and CXCR4 based on protein–protein interaction (PPI) network analysis. Conclusion Our study provides new insights into the molecular pathogenesis of sarcoidosis and identifies novel genetic alterations in this disease, especially PRSS3, which may be promising targets for future therapeutic strategies for chronic sarcoidosis.
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Affiliation(s)
- Qian Zhang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hui Huang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | | | - Chuling Fang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Na Wang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaoyan Jing
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jian Guo
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wei Sun
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaoyu Yang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zuojun Xu
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- *Correspondence: Zuojun Xu,
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Wu JH, Imadojemu S, Caplan AS. The Evolving Landscape of Cutaneous Sarcoidosis: Pathogenic Insight, Clinical Challenges, and New Frontiers in Therapy. Am J Clin Dermatol 2022; 23:499-514. [PMID: 35583850 DOI: 10.1007/s40257-022-00693-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2022] [Indexed: 12/13/2022]
Abstract
Sarcoidosis is a multisystem disorder of unknown etiology characterized by accumulation of granulomas in affected tissue. Cutaneous manifestations are among the most common extrapulmonary manifestations in sarcoidosis and can lead to disfiguring disease requiring chronic therapy. In many patients, skin disease may be the first recognized manifestation of sarcoidosis, necessitating a thorough evaluation for systemic involvement. Although the precise etiology of sarcoidosis and the pathogenic mechanisms leading to granuloma formation, persistence, or resolution remain unclear, recent research has led to significant advances in our understanding of this disease. This article reviews recent advances in epidemiology, sarcoidosis clinical assessment with a focus on the dermatologist's role, disease pathogenesis, and new therapies in use and under investigation for cutaneous and systemic sarcoidosis.
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Affiliation(s)
- Julie H Wu
- Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, 240 East 38th Street, 11th Floor, New York, NY, 10016, USA
| | - Sotonye Imadojemu
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Avrom S Caplan
- Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, 240 East 38th Street, 11th Floor, New York, NY, 10016, USA.
- New York University Sarcoidosis Program, New York University Grossman School of Medicine, New York, NY, USA.
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Abstract
PURPOSE OF REVIEW Epidemiological and clinical observations as well as familial clustering support the existence of a genetic predisposition to sarcoidosis. In this article, we review the most recent findings in genetics of sarcoidosis and discuss how the identification of risk alleles may help advancing our understanding of disease etiology and development. RECENT FINDINGS Genetic studies of sarcoidosis phenotypes have identified novel and ancestry-specific associations. Gene-environment interaction studies highlighted the importance of integrating genetic information when assessing the relationship between sarcoidosis and environmental exposures. A case-control-family study revealed that the heritability of sarcoidosis is only 49%, suggesting the existence of additional important contributors to disease risk. The application of whole-exome sequencing has identified associations with disease activity and prognosis. Finally, gene expression studies of circulating immune cells have identified shared and unique pathways between sarcoidosis and other granulomatous diseases. SUMMARY Sarcoidosis genetic research has led to the identification of a number of associations with both sarcoidoses per se and disease phenotypes. Newer sequencing technologies are likely to increase the number of genetic variants associated with sarcoidosis. However, studying phenotypically and ethnically homogeneous patient subsets remains critically important regardless of the genetic approach used.
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Garman L, Montgomery CG, Rivera NV. Recent advances in sarcoidosis genomics: epigenetics, gene expression, and gene by environment (G × E) interaction studies. Curr Opin Pulm Med 2020; 26:544-553. [PMID: 32701681 PMCID: PMC7735660 DOI: 10.1097/mcp.0000000000000719] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW We aim to review the most recent findings in genomics of sarcoidosis and highlight the gaps in the field. RECENT FINDINGS Original explorations of sarcoidosis subphenotypes, including cases associated with the World Trade Center and ocular sarcoidosis, have identified novel risk loci. Innovative gene--environment interaction studies utilizing modern analytical techniques have discovered risk loci associated with smoking and insecticide exposure. The application of whole-exome sequencing has identified genetic variants associated with persistent sarcoidosis and rare functional variations. A single epigenomics study has provided background knowledge of DNA methylation mechanisms in comparison with gene expression data. The application of machine-learning techniques has suggested new drug repositioning for the treatment of sarcoidosis. Several gene expression studies have identified prominent inflammatory pathways enriched in the affected tissue. SUMMARY Certainly, sarcoidosis research has recently advanced in the exploration of disease subphenotypes, utilizing novel analytical techniques, and including measures of clinical variation. Nevertheless, large-scale and diverse cohorts investigated with advanced sequencing methods, such as whole-genome and single-cell RNA sequencing, epigenomics, and meta-analysis coupled with cutting-edge analytic approaches, when employed, will broaden and translate genomics findings into clinical applications, and ultimately open venues for personalized medicine.
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Affiliation(s)
- Lori Garman
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Courtney G. Montgomery
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Natalia V. Rivera
- Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Rheumatology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center of Molecular Medicine (CMM), Karolinska Institutet, Stockholm, Sweden
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Calender A, Weichhart T, Valeyre D, Pacheco Y. Current Insights in Genetics of Sarcoidosis: Functional and Clinical Impacts. J Clin Med 2020; 9:E2633. [PMID: 32823753 PMCID: PMC7465171 DOI: 10.3390/jcm9082633] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Sarcoidosis is a complex disease that belongs to the vast group of autoinflammatory disorders, but the etiological mechanisms of which are not known. At the crosstalk of environmental, infectious, and genetic factors, sarcoidosis is a multifactorial disease that requires a multidisciplinary approach for which genetic research, in particular, next generation sequencing (NGS) tools, has made it possible to identify new pathways and propose mechanistic hypotheses. Codified treatments for the disease cannot always respond to the most progressive forms and the identification of new genetic and metabolic tracks is a challenge for the future management of the most severe patients. Here, we review the current knowledge regarding the genes identified by both genome wide association studies (GWAS) and whole exome sequencing (WES), as well the connection of these pathways with the current research on sarcoidosis immune-related disorders.
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Affiliation(s)
- Alain Calender
- Department of Molecular and Medical genetics, Hospices Civils de Lyon, University Hospital, 69500 Bron, France;
- CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory, University Claude Bernard Lyon 1, 69007 Lyon, France
| | - Thomas Weichhart
- Center for Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, 1090 Vienna, Austria;
| | - Dominique Valeyre
- INSERM UMR 1272, Department of Pulmonology, Avicenne Hospital, University Sorbonne Paris Nord, Saint Joseph Hospital, AP-HP, 75014 Paris, France;
| | - Yves Pacheco
- Department of Molecular and Medical genetics, Hospices Civils de Lyon, University Hospital, 69500 Bron, France;
- CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory, University Claude Bernard Lyon 1, 69007 Lyon, France
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Asouri M, Alinejad Rokni H, Sahraian MA, Fattahi S, Motamed N, Doosti R, Rahimi H, Lotfi M, Moslemi A, Karimpoor M, Mahboudi F, Akhavan-Niaki H. Analysis of Single Nucleotide Polymorphisms in HLA-DRA, IL2RA , and HMGB1 Genes in Multiple Sclerosis. Rep Biochem Mol Biol 2020; 9:198-208. [PMID: 33178870 PMCID: PMC7603253 DOI: 10.29252/rbmb.9.2.199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/23/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND Multiple sclerosis (MS) is a common demyelinating neurodegenerative disorder with significant heritability. Previous studies have associated genetic variants in human leukocyte antigen (HLA) complex, IL2RA , and HMGB1 genes with the pathophysiology of MS. METHODS In order to investigate the gene association in the Iranian population, we performed a genotyping study of 36 variants in the mentioned genes using Sanger sequencing in 102 MS patients and 113 healthy controls. RESULTS Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms including rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05). Moreover, the strong linkage disequilibrium of two common haplotypes was estimated from the HLA-DRA gene. CONCLUSION This association study may suggest the role of these polymorphisms in the genetic susceptibility of MS in the Iranian population and would facilitate the recognition of causative variants in this disease.
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Affiliation(s)
- Mohsen Asouri
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
- North Research Center, Pasteur Institute of Iran, Amol, Iran.
| | - Hamid Alinejad Rokni
- Systems Biology and Health Data Analytics Lab, the Graduate School of Biomedical Engineering, UNSW Sydney, 2052, NSW, AU.
| | - Mohammad Ali Sahraian
- Multiple Sclerosis Research Center; Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Sadegh Fattahi
- North Research Center, Pasteur Institute of Iran, Amol, Iran.
| | - Nima Motamed
- Department of Social Medicine, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Rozita Doosti
- Multiple Sclerosis Research Center; Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Hamzeh Rahimi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Maryam Lotfi
- North Research Center, Pasteur Institute of Iran, Amol, Iran.
| | - Azam Moslemi
- Department of Biostatistics, Faculty of Medical Sciences, Arak University of Medical Sciences, Arak, Iran.
| | - Morteza Karimpoor
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Fereidoun Mahboudi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Haleh Akhavan-Niaki
- Zoonoses Research Center, North Research Center, Pasteur Institute of Iran, Amol, Iran.
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
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Arbustini E, Narula N, Giuliani L, Di Toro A. Genetic Basis of Myocarditis: Myth or Reality? MYOCARDITIS 2020. [PMCID: PMC7122345 DOI: 10.1007/978-3-030-35276-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The genetic basis of myocarditis remains an intriguing concept, at least as long as the definition of myocarditis constitutes the definitive presence of myocardial inflammation sufficient to cause the observed ventricular dysfunction in the setting of cardiotropic infections. Autoimmune or immune-mediated myocardial inflammation constitutes a complex area of clinical interest, wherein numerous and not yet fully understood role of hereditary auto-inflammatory diseases can result in inflammation of the pericardium and myocardium. Finally, myocardial involvement in hereditary immunodeficiency diseases, cellular and humoral, is a possible trigger for infections which may complicate the diseases themselves. Whether the role of constitutional genetics can make the patient susceptible to myocardial inflammation remains yet to be explored.
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Inaoka PT, Shono M, Kamada M, Espinoza JL. Host-microbe interactions in the pathogenesis and clinical course of sarcoidosis. J Biomed Sci 2019; 26:45. [PMID: 31182092 PMCID: PMC6558716 DOI: 10.1186/s12929-019-0537-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/22/2019] [Indexed: 12/27/2022] Open
Abstract
Sarcoidosis is a rare inflammatory disease characterized by the development of granulomas in various organs, especially in the lungs and lymph nodes. Clinics of the disease largely depends on the organ involved and may range from mild symptoms to life threatening manifestations. Over the last two decades, significant advances in the diagnosis, clinical assessment and treatment of sarcoidosis have been achieved, however, the precise etiology of this disease remains unknown. Current evidence suggests that, in genetically predisposed individuals, an excessive immune response to unknown antigen/s is crucial for the development of sarcoidosis. Epidemiological and microbiological studies suggest that, at least in a fraction of patients, microbes or their products may trigger the immune response leading to sarcoid granuloma formation. In this article, we discuss the scientific evidence on the interaction of microbes with immune cells that may be implicated in the immunopathogenesis of sarcoidosis, and highlight recent studies exploring potential implications of human microbiota in the pathogenesis and the clinical course of sarcoidosis.
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Affiliation(s)
- Pleiades T Inaoka
- Department of Physical Therapy, School of Health Sciences, Kanazawa University, Kodatsuno, Kanazawa, 577-8502, Japan
| | - Masato Shono
- Faculty of Medicine, Kindai University, 377-2, Ohno-Higashi, Osaka-Sayama, Osaka, 577-8502, Japan
| | - Mishio Kamada
- Faculty of Medicine, Kindai University, 377-2, Ohno-Higashi, Osaka-Sayama, Osaka, 577-8502, Japan
| | - J Luis Espinoza
- Department of Hematology and Rheumatology, Kindai University Faculty of Medicine, 377-2, Ohno-Higashi, Osaka-Sayama, Osaka, 577-8502, Japan.
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15
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Hippich M, Beyerlein A, Hagopian WA, Krischer JP, Vehik K, Knoop J, Winker C, Toppari J, Lernmark Å, Rewers MJ, Steck AK, She JX, Akolkar B, Robertson CC, Onengut-Gumuscu S, Rich SS, Bonifacio E, Ziegler AG. Genetic Contribution to the Divergence in Type 1 Diabetes Risk Between Children From the General Population and Children From Affected Families. Diabetes 2019; 68:847-857. [PMID: 30655385 PMCID: PMC6425872 DOI: 10.2337/db18-0882] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/04/2019] [Indexed: 12/20/2022]
Abstract
The risk for autoimmunity and subsequently type 1 diabetes is 10-fold higher in children with a first-degree family history of type 1 diabetes (FDR children) than in children in the general population (GP children). We analyzed children with high-risk HLA genotypes (n = 4,573) in the longitudinal TEDDY birth cohort to determine how much of the divergent risk is attributable to genetic enrichment in affected families. Enrichment for susceptible genotypes of multiple type 1 diabetes-associated genes and a novel risk gene, BTNL2, was identified in FDR children compared with GP children. After correction for genetic enrichment, the risks in the FDR and GP children converged but were not identical for multiple islet autoantibodies (hazard ratio [HR] 2.26 [95% CI 1.6-3.02]) and for diabetes (HR 2.92 [95% CI 2.05-4.16]). Convergence varied depending upon the degree of genetic susceptibility. Risks were similar in the highest genetic susceptibility group for multiple islet autoantibodies (14.3% vs .12.7%) and diabetes (4.8% vs. 4.1%) and were up to 5.8-fold divergent for children in the lowest genetic susceptibility group, decreasing incrementally in GP children but not in FDR children. These findings suggest that additional factors enriched within affected families preferentially increase the risk of autoimmunity and type 1 diabetes in lower genetic susceptibility strata.
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Affiliation(s)
- Markus Hippich
- Institute of Diabetes Research, Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
| | - Andreas Beyerlein
- Institute of Diabetes Research, Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | | | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Kendra Vehik
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Jan Knoop
- Institute of Diabetes Research, Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
| | - Christiane Winker
- Institute of Diabetes Research, Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
- Forschergruppe Diabetes e.V., Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, and Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital SUS, Malmo, Sweden
| | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO
| | - Andrea K Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD
| | | | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Ezio Bonifacio
- Forschergruppe Diabetes e.V., Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
- DFG Center for Regenerative Therapies Dresden, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
- Forschergruppe Diabetes e.V., Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
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Pathological Implications of Receptor for Advanced Glycation End-Product ( AGER) Gene Polymorphism. DISEASE MARKERS 2019; 2019:2067353. [PMID: 30863465 PMCID: PMC6378764 DOI: 10.1155/2019/2067353] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 01/01/2019] [Accepted: 01/15/2019] [Indexed: 12/12/2022]
Abstract
The receptor for advanced glycation end-products (RAGE) is a cell surface transmembrane multiligand receptor, encoded by the AGER gene. RAGE presents many transcripts, is expressed mainly in the lung, and involves multiple pathways (such as NFκB, Akt, p38, and MAP kinases) that initiate and perpetuate an unfavorable proinflammatory state. Due to these numerous functional activities, RAGE is implicated in multiple diseases. AGER is a highly polymorphic gene, with polymorphisms or SNP (single-nucleotide polymorphism) that could be responsible or co-responsible for disease development. This review was designed to shed light on the pathological implications of AGER polymorphisms. Five polymorphisms are described: rs2070600, rs1800624, rs1800625, rs184003, and a 63 bp deletion. The rs2070600 SNP may be associated with the development of human autoimmune disease, diabetes complications, cancer, and lung diseases such as chronic obstructive pulmonary disease and acute respiratory distress syndrome. The rs1800624 SNP involves AGER gene regulation and may be related to reduced risk of heart disease, cancer, Crohn's disease, and type 1 diabetes complications. The rs1800625 SNP may be associated with the development of diabetic retinopathy, cancer, and lupus but may be protective against cardiovascular risk. The rs184003 SNP seems related to coronary artery disease, breast cancer, and diabetes. The 63 bp deletion may be associated with reduced survival from heart diseases during diabetic nephropathy. Here, these potential associations between AGER polymorphisms and the development of diseases are discussed, as there have been conflicting findings on the pathological impact of AGER SNPs in the literature. These contradictory results might be explained by distinct AGER SNP frequencies depending on ethnicity.
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Drent M, Veltkamp M, Bast A. The mystery of Black Pete make-up: a sarcoid-like foreign-body reaction. SARCOIDOSIS VASCULITIS AND DIFFUSE LUNG DISEASES 2019; 36:172-173. [PMID: 32476951 DOI: 10.36141/svdld.v36i2.8329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 04/17/2019] [Indexed: 11/02/2022]
Affiliation(s)
- Marjolein Drent
- ILD Center of Excellence, St. Antonius Hospital, Nieuwegein, the Netherlands.,Dept of Pharmacology and Toxicology, Faculty of Health, Medicine and Life Science, Maastricht University, Maastricht, the Netherlands.,ild care foundation research team, Ede, the Netherlands
| | - Marcel Veltkamp
- ILD Center of Excellence, St. Antonius Hospital, Nieuwegein, the Netherlands.,ild care foundation research team, Ede, the Netherlands.,Division of Heart and Lungs, University Medical Center, Utrecht, the Netherlands
| | - Aalt Bast
- Dept of Pharmacology and Toxicology, Faculty of Health, Medicine and Life Science, Maastricht University, Maastricht, the Netherlands.,ild care foundation research team, Ede, the Netherlands.,Venlo Campus, Maastricht University, Venlo, the Netherlands
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18
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Saad MN, Mabrouk MS, Eldeib AM, Shaker OG. Comparative study for haplotype block partitioning methods - Evidence from chromosome 6 of the North American Rheumatoid Arthritis Consortium (NARAC) dataset. PLoS One 2019; 13:e0209603. [PMID: 30596705 PMCID: PMC6312333 DOI: 10.1371/journal.pone.0209603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/07/2018] [Indexed: 11/19/2022] Open
Abstract
Haplotype-based methods compete with “one-SNP-at-a-time” approaches on being preferred for association studies. Chromosome 6 contains most of the known genetic biomarkers for rheumatoid arthritis (RA) disease. Therefore, chromosome 6 serves as a benchmark for the haplotype methods testing. The aim of this study is to test the North American Rheumatoid Arthritis Consortium (NARAC) dataset to find out if haplotype block methods or single-locus approaches alone can sufficiently provide the significant single nucleotide polymorphisms (SNPs) associated with RA. In addition, could we be satisfied with only one method of the haplotype block methods for partitioning chromosome 6 of the NARAC dataset? In the NARAC dataset, chromosome 6 comprises 35,574 SNPs for 2,062 individuals (868 cases, 1,194 controls). Individual SNP approach and three haplotype block methods were applied to the NARAC dataset to identify the RA biomarkers. We employed three haplotype partitioning methods which are confidence interval test (CIT), four gamete test (FGT), and solid spine of linkage disequilibrium (SSLD). P-values after stringent Bonferroni correction for multiple testing were measured to assess the strength of association between the genetic variants and RA susceptibility. Moreover, the block size (in base pairs (bp) and number of SNPs included), number of blocks, percentage of uncovered SNPs by the block method, percentage of significant blocks from the total number of blocks, number of significant haplotypes and SNPs were used to compare among the three haplotype block methods. Individual SNP, CIT, FGT, and SSLD methods detected 432, 1,086, 1,099, and 1,322 associated SNPs, respectively. Each method identified significant SNPs that were not detected by any other method (Individual SNP: 12, FGT: 37, CIT: 55, and SSLD: 189 SNPs). 916 SNPs were discovered by all the three haplotype block methods. 367 SNPs were discovered by the haplotype block methods and the individual SNP approach. The P-values of these 367 SNPs were lower than those of the SNPs uniquely detected by only one method. The 367 SNPs detected by all the methods represent promising candidates for RA susceptibility. They should be further investigated for the European population. A hybrid technique including the four methods should be applied to detect the significant SNPs associated with RA for chromosome 6 of the NARAC dataset. Moreover, SSLD method may be preferred for its favored benefits in case of selecting only one method.
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Affiliation(s)
- Mohamed N. Saad
- Biomedical Engineering Department, Faculty of Engineering, Minia University, Minia, Egypt
- * E-mail: ,
| | - Mai S. Mabrouk
- Biomedical Engineering Department, Faculty of Engineering, Misr University for Science and Technology (MUST), 6th of October City, Egypt
| | - Ayman M. Eldeib
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Giza, Egypt
| | - Olfat G. Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
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19
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Kishore A, Petrek M. Next-Generation Sequencing Based HLA Typing: Deciphering Immunogenetic Aspects of Sarcoidosis. Front Genet 2018; 9:503. [PMID: 30410504 PMCID: PMC6210504 DOI: 10.3389/fgene.2018.00503] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/05/2018] [Indexed: 12/31/2022] Open
Abstract
Unraveling of the HLA-related immunogenetic basis of several immune disorders is complex due to the extensive HLA polymorphism and strong linkage-disequilibrium between HLA loci. A lack of in phase sequence information, a relative deficiency of high resolution genotyping including non-coding regions and ambiguous haplotype assignment make it difficult to compare findings across association studies and to attribute a causal role to specific HLA alleles/haplotypes in disease susceptibility and modification of disease phenotypes. Earlier, historical antibody and DNA-based methods of HLA typing, primarily of low resolution at antigen/alellic group levels, yielded "indicative" findings which were partially improved by high-resolution DNA-based typing. Only recently, next-generation sequencing (NGS) approaches based on deep-sequencing of the complete HLA genes combined with bioinformatics tools began to provide the access to complete information at an allelic level. Analyzing HLA with NGS approaches, therefore, promises to provide further insight in the etiopathogenesis of several immune disorders in which HLA associations have been implicated. These range from coeliac disease and rheumatological conditions to even more complex disorders, such as type-1 diabetes, systemic lupus erythematosus and sarcoidosis. A systemic disease of unknown etiology, sarcoidosis has previously been associated with numerous HLA variants and also other gene polymorphisms, often in linkage with the HLA region. To date, the biological significance of these associations has only partially been defined. Therefore, more precise assignments of HLA alleles/haplotypes using NGS approaches could help to elucidate the exact role of HLA variation in the multifaceted etiopathogenesis of sarcoidosis, including epigenetic mechanisms. NGS-based HLA analyses may be also relevant for defining variable clinical phenotypes and for predicting the disease course or the response to current/plausible novel therapies.
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Affiliation(s)
- Amit Kishore
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czechia
| | - Martin Petrek
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czechia
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20
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Debiec H, Dossier C, Letouzé E, Gillies CE, Vivarelli M, Putler RK, Ars E, Jacqz-Aigrain E, Elie V, Colucci M, Debette S, Amouyel P, Elalaoui SC, Sefiani A, Dubois V, Simon T, Kretzler M, Ballarin J, Emma F, Sampson MG, Deschênes G, Ronco P. Transethnic, Genome-Wide Analysis Reveals Immune-Related Risk Alleles and Phenotypic Correlates in Pediatric Steroid-Sensitive Nephrotic Syndrome. J Am Soc Nephrol 2018; 29:2000-2013. [PMID: 29903748 PMCID: PMC6050942 DOI: 10.1681/asn.2017111185] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 04/09/2018] [Indexed: 12/20/2022] Open
Abstract
Background Steroid-sensitive nephrotic syndrome (SSNS) is a childhood disease with unclear pathophysiology and genetic architecture. We investigated the genomic basis of SSNS in children recruited in Europe and the biopsy-based North American NEPTUNE cohort.Methods We performed three ancestry-matched, genome-wide association studies (GWAS) in 273 children with NS (Children Cohort Nephrosis and Virus [NEPHROVIR] cohort: 132 European, 56 African, and 85 Maghrebian) followed by independent replication in 112 European children, transethnic meta-analysis, and conditional analysis. GWAS alleles were used to perform glomerular cis-expression quantitative trait loci studies in 39 children in the NEPTUNE cohort and epidemiologic studies in GWAS and NEPTUNE (97 children) cohorts.Results Transethnic meta-analysis identified one SSNS-associated single-nucleotide polymorphism (SNP) rs1063348 in the 3' untranslated region of HLA-DQB1 (P=9.3×10-23). Conditional analysis identified two additional independent risk alleles upstream of HLA-DRB1 (rs28366266, P=3.7×10-11) and in the 3' untranslated region of BTNL2 (rs9348883, P=9.4×10-7) within introns of HCG23 and LOC101929163 These three risk alleles were independent of the risk haplotype DRB1*07:01-DQA1*02:01-DQB1*02:02 identified in European patients. Increased burden of risk alleles across independent loci was associated with higher odds of SSNS. Increased burden of risk alleles across independent loci was associated with higher odds of SSNS, with younger age of onset across all cohorts, and with increased odds of complete remission across histologies in NEPTUNE children. rs1063348 associated with decreased glomerular expression of HLA-DRB1, HLA-DRB5, and HLA-DQB1.Conclusions Transethnic GWAS empowered discovery of three independent risk SNPs for pediatric SSNS. Characterization of these SNPs provide an entry for understanding immune dysregulation in NS and introducing a genomically defined classification.
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Affiliation(s)
- Hanna Debiec
- Sorbonne Université, UPMC Paris 06, Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche S 1155, Paris, France
| | | | - Eric Letouzé
- Pediatric Pharmacology and Pharmacogenetics, CIC1426, Hôpital Robert Debré, Paris, France
- Université Paris Diderot, Institut Universitaire d'Hématologie, Paris, France
| | - Christopher E Gillies
- Pediatric Nephrology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Marina Vivarelli
- Nephrology and Dialysis Department, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Rosemary K Putler
- Pediatric Nephrology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Elisabet Ars
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Evelyne Jacqz-Aigrain
- Pediatric Pharmacology and Pharmacogenetics, CIC1426, Hôpital Robert Debré, Paris, France
| | - Valery Elie
- Pediatric Pharmacology and Pharmacogenetics, CIC1426, Hôpital Robert Debré, Paris, France
| | - Manuela Colucci
- Nephrology and Dialysis Department, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Stéphanie Debette
- University of Bordeaux, Institut National de la Santé et de la Recherche Médicale, Bordeaux Population Health Research Center, Unité Mixte de Recherche 1219, CHU Bordeaux, Bordeaux, France
| | - Philippe Amouyel
- University of Lille, Institut National de la Santé et de la Recherche Médicale, CHU Lille, Institut Pasteur de Lille, U1167 RID-AGE, Lille, France
| | - Siham C Elalaoui
- Department of Medical Genetics, Institut National d'Hygiène, Rabat, Morocco
| | - Abdelaziz Sefiani
- Human Genomic Center, Faculté de Médecine et de Pharmacie Rabat, Université Mohamed V. Rabat, Rabat, Morocco
| | - Valérie Dubois
- Etablissement Français du Sang Rhone-Alpes, Lyon, Rhone-Alpes, France
| | - Tabassome Simon
- Assistance Publique-Hôpitaux de Paris, Hôpital Saint Antoine, Department of Clinical Pharmacology, Unité de Recherche Clinique, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche S1148, Paris, France
| | - Matthias Kretzler
- Department of Internal Medicine and Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan;
| | - Jose Ballarin
- Department of Nephrology, Fundación Puigvert, Barcelona, Spain
| | - Francesco Emma
- Pediatric Nephrology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Matthew G Sampson
- Pediatric Nephrology, University of Michigan School of Medicine, Ann Arbor, Michigan;
| | - Georges Deschênes
- Department of Paediatric Nephrology and
- Institut National de la Santé et de la Recherche Médicale U1149, Unité de Formation et de Recherche de Médecine Xavier Bichat, Université Sorbonne Paris Cité, Paris, France; and
| | - Pierre Ronco
- Sorbonne Université, UPMC Paris 06, Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche S 1155, Paris, France;
- Assistance Publique-Hôpitaux de Paris, Nephrology and Dialysis Department, Tenon Hospital, Paris, France
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Rossides M, Grunewald J, Eklund A, Kullberg S, Di Giuseppe D, Askling J, Arkema E. Familial aggregation and heritability of sarcoidosis: a Swedish nested case−control study. Eur Respir J 2018; 52:13993003.00385-2018. [DOI: 10.1183/13993003.00385-2018] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/12/2018] [Indexed: 12/24/2022]
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22
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Partida-Zavala N, Ponce-Gallegos MA, Buendía-Roldán I, Falfán-Valencia R. Type 2 macrophages and Th2 CD4+ cells in interstitial lung diseases (ILDs): an overview. SARCOIDOSIS, VASCULITIS, AND DIFFUSE LUNG DISEASES : OFFICIAL JOURNAL OF WASOG 2018; 35:98-108. [PMID: 32476888 PMCID: PMC7170082 DOI: 10.36141/svdld.v35i2.6691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 02/06/2018] [Indexed: 12/23/2022]
Abstract
Interstitial lung diseases (ILDs) are a heterogeneous group characterized mainly by damage to pulmonary parenchyma, through histopathological processes such as granulomatous pneumopathy, inflammation and fibrosis. Factors that generate susceptibility to ILDs include age, exposure to occupational and environmental compounds, genetic, family history, radiation and chemotherapy/immunomodulatory and cigarette smoke. IFN-γ, IL-1β, and LPS are necessary to induce a classical activation of macrophages, whereas cytokines as IL-4 and IL-13 can induce an alternative activation in macrophages, through the JAK-STAT mediated signal transduction. M2 macrophages are identified based on the gene transcription or protein expression of a set of M2 markers. These markers include transmembrane glycoproteins, scavenger receptors, enzymes, growth factors, hormones, cytokines, and cytokine receptors with diverse and often yet unexplored functions. Fibrotic lung disorders may have a M2 polarization background. The Th2 pathway with an elevated CCL-18 (marker of M2) concentration in the bronchoalveolar lavage fluid (BALF) is linked to fibrosis in ILDs. Besides the role of M2 in tissue repair and ECM remodeling, activated fibroblasts summon and stimulate macrophages by producing MCP-1, M-CSF and other chemokines, as well as activated macrophages secrete cytokines that attract and stimulate proliferation, survival and migration of fibroblast mediated by platelet-derived growth factor (PDGF). (Sarcoidosis Vasc Diffuse Lung Dis 2018; 35: 98-108).
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Affiliation(s)
- Neftali Partida-Zavala
- Universidad Autónoma de Nayarit, Unidad Académica de Medicina. Tepic, Nayarit. México. Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas. Ciudad de México, Mexico
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas City, Mexico
| | - Marco Antonio Ponce-Gallegos
- Universidad Autónoma de Nayarit, Unidad Académica de Medicina. Tepic, Nayarit. México. Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas. Ciudad de México, Mexico
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas City, Mexico
| | - Ivette Buendía-Roldán
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas City, Mexico
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas City, Mexico
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Th17-lineage cells in pulmonary sarcoidosis and Löfgren's syndrome: Friend or foe? J Autoimmun 2018; 87:82-96. [DOI: 10.1016/j.jaut.2017.12.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 12/12/2017] [Indexed: 01/17/2023]
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