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Das S, Chandra A, Das A, Senapati S, Chatterjee G, Chatterjee R. Identifying the genetic associations among the psoriasis patients in eastern India. J Hum Genet 2024; 69:205-213. [PMID: 38409498 DOI: 10.1038/s10038-024-01227-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/28/2024]
Abstract
Psoriasis is a multifactorial genetic disorder manifested by hyperproliferation and abnormal differentiation of epidermal keratinocytes, along with the infiltration of inflammatory cells into the skin. Although ~80 genetic susceptibility variants were reported in psoriasis, many loci showed population-specific associations, warranting the need for more population-specific association studies in psoriasis. We determined the association of forty single nucleotide polymorphisms (SNPs) among 2136 psoriasis patients and normal individuals from eastern India. We investigated the expression of corresponding genes and evaluated the protein structure stability for the genes with susceptible coding variants. We found fifteen SNPs significantly associated with psoriasis, while additional three SNPs showed significant association when we classified the patients based on the presence of HLA-Cw6 allele. Epistatic interaction between HLA-Cw6 and other associated loci showed significant association with the SNPs at PSORS1 region, along with other five SNPs outside PSORS1. Three genes showed significant differential expression in psoriatic tissues compared to the adjacent normal skin tissues but were not differential when classified the patients based on their genotypes. SNP rs495337 at SPATA2 (Spermatogenesis Associated 2) showed a 1.2-fold increased risk among the HLA-Cw6 patients compared to combined samples. We found significant downregulation of SPATA2 among the patients with risk genotypes and HLA-Cw6 allele compared to the non-risk genotypes. Protein structure stability analysis showed reduced structural stability for all the mutant residues caused by the associated coding variants. Our study evaluated the genetic associations of psoriasis-susceptible variants in India and evaluated the possible functional significance of these associated variants in psoriasis.
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Affiliation(s)
- Shantanab Das
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal, 700108, India
| | - Aditi Chandra
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal, 700108, India
| | - Anamika Das
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal, 700108, India
| | - Swapan Senapati
- Consultant Dermatologist, Uttarpara, Hooghly, West Bengal, 712258, India
| | - Gobinda Chatterjee
- Department of Dermatology, IPGMER/SSKM Hospital, Kolkata, West Bengal, India
| | - Raghunath Chatterjee
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal, 700108, India.
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Chandra A, Das S, Mazumder S, Senapati S, Chatterjee G, Chatterjee R. Functional Mapping of Genetic Interactions between HLA-Cw6 and LCE3A in Psoriasis. J Invest Dermatol 2021; 141:2630-2638.e7. [PMID: 34029573 DOI: 10.1016/j.jid.2021.04.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 12/31/2022]
Abstract
Functional studies to delineate the molecular mechanisms of causal genetic variants are the main focus in the post-GWAS era. Previous GWASs have identified >50 susceptibility loci associated with psoriasis. Functional understanding of the biology underlying the disease risk of most of these associated loci is unclear. In this study, we identified a regulatory SNP at the putative enhancer of the LCE3A gene within the epidermal differentiation complex that showed epistatic interaction with HLA-Cw6. The variant allele disrupted signal transducer and activator of transcription 3 binding to the region, thereby regulating the expression of the downstream LCE3A gene. Electrophoretic mobility shift and pulldown assay confirmed the preferential binding of signal transducer and activator of transcription 3 to the DNA with a wild-type allele compared with the DNA with a variant allele. The reporter assay further validated the IL-6‒stimulated phosphorylated signal transducer and activator of transcription 3‒mediated LCE3A activation in the presence of the wild-type allele. Interestingly, the presence of the HLA-Cw6 allele leads to IL-6‒mediated phosphorylation of signal transducer and activator of transcription 3, followed by its nuclear localization in the epidermal keratinocytes of psoriatic skin, suggesting indirect interaction of the HLA-Cw6 allele and a regulatory SNP upstream of the LCE3A gene. This study reflects an interesting approach to dissecting the molecular mechanism underlying the genetic interaction observed between HLA-Cw6 and LCE3A in psoriasis pathogenesis.
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Affiliation(s)
- Aditi Chandra
- Human Genetics Unit, Biological Sciences Division, Indian Statistical Institute, Kolkata, India
| | - Shantanab Das
- Human Genetics Unit, Biological Sciences Division, Indian Statistical Institute, Kolkata, India
| | - Sayani Mazumder
- Human Genetics Unit, Biological Sciences Division, Indian Statistical Institute, Kolkata, India
| | - Swapan Senapati
- Human Genetics Unit, Biological Sciences Division, Indian Statistical Institute, Kolkata, India
| | - Gobinda Chatterjee
- Department of Dermatology, Institute of Post Graduate Medical Education & Research and Seth Sukhlal Karnani Memorial Hospital, Kolkata, India
| | - Raghunath Chatterjee
- Human Genetics Unit, Biological Sciences Division, Indian Statistical Institute, Kolkata, India.
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Mei Q, Liu C, Zhang X, Li Q, Jia X, Wu J, Sun W, Qiao Y, Wu J, Li Y, Yu J, Fu S, Xu L. Associations between PTPN2 gene polymorphisms and psoriasis in Northeastern China. Gene 2019; 681:73-79. [PMID: 30266502 DOI: 10.1016/j.gene.2018.09.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 09/25/2018] [Indexed: 02/06/2023]
Abstract
Psoriasis is a chronic immune-mediated disease with a complex etiology involving various genetic and immunological factors as well as environmental factors. Psoriasis is thought to be mediated by T-cells polarized to a Th17 fate. PTPN2 encodes the T-cell protein tyrosine phosphatase, which acts as a negative regulator of the JAK/STAT signaling pathways downstream of cytokines and plays a prominent role in T-cell activation, signaling and/or effector function. To evaluate the association between PTPN2 gene polymorphisms and psoriasis in the Northeastern Chinese population. A case-control study was conducted, and 398 patients with psoriasis and 397 healthy controls were genotyped for thirteen genetic polymorphisms in PTPN2. Allele analysis revealed that rs2847297, rs657555 and rs482160 polymorphisms were significantly associated with psoriasis (p = 0.0018, p = 0.0017 and p = 0.0086, respectively). Genotype analysis also revealed that these polymorphisms were significantly associated with psoriasis under different models (codominant, dominant and recessive models) (p < 0.05). In this study, three haplotypes (H1, H7 and H11) were also found to be associated with psoriasis (p = 0.0015, p = 0.0094, and p = 0.0124, respectively). These results indicate that PTPN2 genetic polymorphisms are associated with psoriasis in the Northeastern Chinese population.
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Affiliation(s)
- Qingbu Mei
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China; Department of Genetics, Qiqihar Medical University, Qiqihar 161000, China
| | - Chang Liu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Xuelong Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Qiuyan Li
- Editorial Department of International Journal of Genetics, Harbin Medical University, Harbin 150081, China
| | - Xueyuan Jia
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Jie Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Yuandong Qiao
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Jiawei Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Yuzhen Li
- Department of dermatology, the Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Jingcui Yu
- Scientific Research Centre, the Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China; Key Laboratory of Medical Genetics, (Harbin Medical University), Heilongjiang Higher Education Institutions, Harbin 150081, China.
| | - Lidan Xu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.
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Chandra A, Senapati S, Roy S, Chatterjee G, Chatterjee R. Epigenome-wide DNA methylation regulates cardinal pathological features of psoriasis. Clin Epigenetics 2018; 10:108. [PMID: 30092825 PMCID: PMC6085681 DOI: 10.1186/s13148-018-0541-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/29/2018] [Indexed: 02/05/2023] Open
Abstract
Background Psoriasis is a chronic inflammatory autoimmune skin disorder. Several studies suggested psoriasis to be a complex multifactorial disease, but the exact triggering factor is yet to be determined. Evidences suggest that in addition to genetic factors, epigenetic reprogramming is also involved in psoriasis development. Major histopathological features, like increased proliferation and abnormal differentiation of keratinocytes, and immune cell infiltrations are characteristic marks of psoriatic skin lesions. Following therapy, histopathological features as well as aberrant DNA methylation reversed to normal levels. To understand the role of DNA methylation in regulating these crucial histopathologic features, we investigated the genome-wide DNA methylation profile of psoriasis patients with different histopathological features. Results Genome-wide DNA methylation profiling of psoriatic and adjacent normal skin tissues identified several novel differentially methylated regions associated with psoriasis. Differentially methylated CpGs were significantly enriched in several psoriasis susceptibility (PSORS) regions and epigenetically regulated the expression of key pathogenic genes, even with low-CpG promoters. Top differentially methylated genes overlapped with PSORS regions including S100A9, SELENBP1, CARD14, KAZN and PTPN22 showed inverse correlation between methylation and gene expression. We identified differentially methylated genes associated with characteristic histopathological features in psoriasis. Psoriatic skin with Munro’s microabscess, a distinctive feature in psoriasis including parakeratosis and neutrophil accumulation at the stratum corneum, was enriched with differentially methylated genes involved in neutrophil chemotaxis. Rete peg elongation and focal hypergranulosis were also associated with epigenetically regulated genes, supporting the reversible nature of these characteristic features during remission and relapse of the lesions. Conclusion Our study, for the first time, indicated the possible involvement of DNA methylation in regulating the cardinal pathophysiological features in psoriasis. Common genes involved in regulation of these pathologies may be used to develop drugs for better clinical management of psoriasis. Electronic supplementary material The online version of this article (10.1186/s13148-018-0541-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aditi Chandra
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal, 700108, India
| | | | - Sudipta Roy
- MDDC, Lansdowne Place, Kolkata, West Bengal, India
| | - Gobinda Chatterjee
- Department of Dermatology, IPGMER/SSKM Hospital, Kolkata, West Bengal, India
| | - Raghunath Chatterjee
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal, 700108, India.
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Associations of ERAP1 coding variants and domain specific interaction with HLA-C∗06 in the early onset psoriasis patients of India. Hum Immunol 2017; 78:724-730. [PMID: 28867178 DOI: 10.1016/j.humimm.2017.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 08/20/2017] [Accepted: 08/29/2017] [Indexed: 11/23/2022]
Abstract
Interferon-γ-induced aminopeptidase ERAP1 trims peptides within the endoplasmic reticulum so that they can be loaded onto MHC class I and presented to the CD8+ T-cells. ERAP1 association and its interaction with HLA-C∗06 is controversial across different populations. We have investigated the association and possible functional role of non-synonymous SNPs at different exons of ERAP1 (rs26653: Arg127Pro, rs30187: Lys528Arg and rs27044: Gln730Glu) and their interactions with HLA-C∗06 in psoriasis. Significant associations of HLA-C∗06 (OR=5.47, P<2.2×10-16), rs30187 (OR 1.35, P=7.4×10-4) and rs27044 (OR=1.24, P=5.8×10-3) were observed. All three ERAP1 SNPs showed significant association only for HLA-C∗06 positive patients, while rs30187 and rs27044 showed significant association only for early onset patients (rs30187: OR=1.47, P=9.6×10-5; rs27044: OR=1.36, P=3.3×10-4). No differential expression of ERAP1 was observed either between paired uninvolved and involved skin tissues of psoriasis patients or between non-risk and risk variants in the involved skin. Significant epistatic interaction was observed between HLA-C∗06 and the SNP (rs27044) located at the peptide-binding cavity of ERAP1. Evolutionary conservation analysis among mammals showed confinement of Lys528 and Gln730 within highly conserved regions of ERAP1 and suggested the possible detrimental effect of this allele in ERAP1 regulation.
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