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Replacing the Burden of the Gluten Free Diet: Then, Now, and the Future. Int J Mol Sci 2022; 23:ijms232315108. [PMID: 36499446 PMCID: PMC9741045 DOI: 10.3390/ijms232315108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/26/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022] Open
Abstract
Without a doubt, a majority of diseases are food-pattern-related. However, one disease stands out as an increasingly more common autoimmune-mediated enteropathy triggered by the ingestion of gluten. Celiac disease (CD) is an old disease, with changing clinical patterns, affecting any age, including infancy and adolescence, and becoming more frequent among the elderly. The gluten-free diet (GFD) has been the sole provider of clinical, serological, and histological improvement for patients with CD for more than seven decades. Nowadays, complete avoidance of dietary gluten is rarely possible because of the wide availability of wheat and other processed foods that contain even more gluten, to the detriment of gluten-free products. Undeniably, there is a definite need for replacing the burdensome GFD. An add-on therapy that could control the dietary transgressions and inadvertent gluten consumption that can possibly lead to overt CD should be considered while on GFD. Nevertheless, future drugs should be able to provide patients some freedom to self-manage CD and increase food independence, while actively reducing exposure and mucosal damage and alleviating GI symptoms. Numerous clinical trials assessing different molecules have already been performed with favorable outcomes, and hopefully they will soon be available for patient use.
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Nazarova LS, Danilko KV, Malievsky VA, Karimov DO, Bakirov AB, Viktorova TV. Interaction Of Immune Response Mediator Genes In A Predisposition To Juvenile Idiopathic Arthritis. RUSSIAN OPEN MEDICAL JOURNAL 2022. [DOI: 10.15275/rusomj.2022.0311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Background/objective — The goal of our study was to investigate the role of interaction between the polymorphic loci of immune response mediator genes (TNFA rs1800629, LTA rs909253, IL1B rs16944, IL2-IL21 rs6822844, IL2RA rs2104286, IL6 rs1800795, IL10 rs1800872, MIF rs755622, CTLA4 rs3087243, NFKB1 rs28362491, PTPN22 rs2476601, and PADI4 rs2240336) in the formation of a genetic predisposition to juvenile idiopathic arthritis (JIA). Material and Methods — The study involved 330 JIA patients and 342 volunteers from the Republic of Bashkortostan. Genotyping was conducted via the real-time polymerase chain reaction. The gene-gene interactions were studied using the multifactor dimensionality reduction algorithm. Results — In general analysis, the best model of gene-gene interaction in JIA was a combination of IL1B rs16944 – IL10 rs1800872 – NFKB1 rs28362491 – PADI4 rs2240336 polymorphic loci. However, after gender-based stratification the best results were obtained when examining the combinations of IL6 rs1800795 – PADI4 rs2240336 loci in girls and of IL10 rs1800872 – IL6 rs1800795 – IL2RA rs2104286 loci in boys. Within all of these models, the genotype combinations associated with both augmented and reduced JIA risks were identified (taking into account gender-specific differences). Conclusion — The results of our study implied that an important role in the formation of a predisposition to JIA is played by gene-gene interactions of IL1B rs16944, IL2RA rs2104286, IL6 rs1800795, IL10 rs1800872, NFKB1 rs28362491, and PADI4 rs2240336 polymorphic loci (taking into account gender-specific differences).
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Affiliation(s)
- Liliia Sh. Nazarova
- Ufa Research Institute of Occupational Health and Human Ecology; Bashkir State Medical University, Ufa, Russia
| | | | | | - Denis O. Karimov
- Ufa Research Institute of Occupational Health and Human Ecology, Ufa, Russia
| | - Akhat B. Bakirov
- Ufa Research Institute of Occupational Health and Human Ecology; Bashkir State Medical University, Ufa, Russia
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3
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Jadidi N, Alesaeidi S, Arab F, Pakzad B, Siasi E, Esmaeilzadeh E. miRNA-binding site polymorphism in IL-15RA gene in rheumatoid arthritis and systemic lupus erythematosus: correlation with disease risk and clinical characteristics. Clin Rheumatol 2022; 41:3487-3494. [PMID: 35857215 DOI: 10.1007/s10067-022-06298-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 11/29/2022]
Abstract
INTRODUCTION/OBJECTIVES MiRSNPs may interfere with mRNA stability through effects on microRNAs (miRNAs)-mRNA interactions via direct changes in miRNA binding site or effect on the secondary structure of this region and changes in accessibility of this region to miRNAs. Studies have confirmed that an elevated level of interleukin-15 receptor alpha (IL-15RA) has an important role in the pathogenesis of systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). In the present study, for the first time, we aimed to evaluate the possible correlation between a miRSNP, rs2296135, in IL-15RA gene with the risk of SLE and RA. METHODS In this case-control study, 100 SLE patients, 100 RA patients, and 110 healthy participants were enrolled to assess rs2296135 genotypes with real-time PCR high-resolution melting method. RESULTS According to our findings, AA genotype and A allele of rs2296135 were considerably associated with enhanced risk of RA (for AA genotype, OR = 2.29; 95% CI [1.06-5.02]; for A allele, OR = 1.65; 95% CI [1.10-2.48]). However, this common variant was not significantly correlated with SLE risk in population under study. Stratification analysis in the RA group verified that patients with the A allele had considerably higher serum concentrations of C-reactive protein (CRP) (P < 0.001). In SLE subjects, the frequency of arthritis (P: 0.021) and renal involvement (P: 0.025) in patients with A allele was significantly higher than in other SLE individuals. CONCLUSION The current study proposes a substantial association between rs2296135 polymorphism in IL-15RA gene with augmented risk of RA and some clinical characteristics in RA and SLE patients.
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Affiliation(s)
- Nilofar Jadidi
- Department of Genetics, Faculty of Basic Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran.,Department of Biology, Faculty of Basic Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Samira Alesaeidi
- Rheumatology and Internal Medicine, Rheumatology Research Center, Amir-Alam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Arab
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahram Pakzad
- Division of Rheumatology, Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Elham Siasi
- Department of Genetics, Faculty of Basic Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Emran Esmaeilzadeh
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran. .,Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran.
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James J, Chen Y, Hernandez CM, Forster F, Dagnell M, Cheng Q, Saei AA, Gharibi H, Lahore GF, Åstrand A, Malhotra R, Malissen B, Zubarev RA, Arnér ESJ, Holmdahl R. Redox regulation of PTPN22 affects the severity of T-cell-dependent autoimmune inflammation. eLife 2022; 11:74549. [PMID: 35587260 PMCID: PMC9119677 DOI: 10.7554/elife.74549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/16/2022] [Indexed: 12/16/2022] Open
Abstract
Chronic autoimmune diseases are associated with mutations in PTPN22, a modifier of T cell receptor (TCR) signaling. As with all protein tyrosine phosphatases, the activity of PTPN22 is redox regulated, but if or how such regulation can modulate inflammatory pathways in vivo is not known. To determine this, we created a mouse with a cysteine-to-serine mutation at position 129 in PTPN22 (C129S), a residue proposed to alter the redox regulatory properties of PTPN22 by forming a disulfide with the catalytic C227 residue. The C129S mutant mouse showed a stronger T-cell-dependent inflammatory response and development of T-cell-dependent autoimmune arthritis due to enhanced TCR signaling and activation of T cells, an effect neutralized by a mutation in Ncf1, a component of the NOX2 complex. Activity assays with purified proteins suggest that the functional results can be explained by an increased sensitivity to oxidation of the C129S mutated PTPN22 protein. We also observed that the disulfide of native PTPN22 can be directly reduced by the thioredoxin system, while the C129S mutant lacking this disulfide was less amenable to reductive reactivation. In conclusion, we show that PTPN22 functionally interacts with Ncf1 and is regulated by oxidation via the noncatalytic C129 residue and oxidation-prone PTPN22 leads to increased severity in the development of T-cell-dependent autoimmunity.
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Affiliation(s)
- Jaime James
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yifei Chen
- Division of Biochemistry, Dept. of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.,Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Clara M Hernandez
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Florian Forster
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Markus Dagnell
- Division of Biochemistry, Dept. of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Qing Cheng
- Division of Biochemistry, Dept. of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Amir A Saei
- Division of Physiological Chemistry I, Dept. of Medical Biochemistry and Biophysics Karolinska Institute, Stockholm, Sweden.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Hassan Gharibi
- Division of Physiological Chemistry I, Dept. of Medical Biochemistry and Biophysics Karolinska Institute, Stockholm, Sweden
| | - Gonzalo Fernandez Lahore
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Annika Åstrand
- Project Leader Department, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Rajneesh Malhotra
- Translational Science and Experimental Medicine, Research and Early Development Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Bernard Malissen
- Centre d'Immunophénomique, Aix Marseille Université, INSERM, Marseille, France
| | - Roman A Zubarev
- Division of Physiological Chemistry I, Dept. of Medical Biochemistry and Biophysics Karolinska Institute, Stockholm, Sweden.,Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Elias S J Arnér
- Division of Biochemistry, Dept. of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.,Department of Selenoprotein Research, National Institute of Oncology, Budapest, Hungary
| | - Rikard Holmdahl
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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5
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Shumanska M, Bogeski I. Redoxing PTPN22 activity. eLife 2022; 11:79125. [PMID: 35588003 PMCID: PMC9119671 DOI: 10.7554/elife.79125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The oxidative state of a critical cysteine residue determines the enzymatic activity of a phosphatase involved in T-cell immune responses.
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Affiliation(s)
- Magdalena Shumanska
- Molecular Physiology Division, Institute of Cardiovascular Physiology, University Medical Center, Georg-August University, Göttingen, Germany
| | - Ivan Bogeski
- Molecular Physiology Division, Institute of Cardiovascular Physiology, University Medical Center, Georg-August University, Göttingen, Germany
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Zeinalzadeh S, Kheradmand N, Rasouli G, Esmaeilzadeh E, Pakzad B, Behroozi J, Chamanara M, Zoshk MY, Ehtesham N, Sabet MN. Association of a miRNA-binding site polymorphism in IL-16 gene with disease risk and clinical characteristics of rheumatoid arthritis and systemic lupus erythematosus. Clin Rheumatol 2022; 41:2189-2196. [PMID: 35332405 DOI: 10.1007/s10067-022-06131-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/16/2022] [Accepted: 03/13/2022] [Indexed: 11/29/2022]
Abstract
INTRODUCTION /objectives. Single nucleotide polymorphisms (SNPs) located at the 3'-UTR region of the target genes of microRNAs (miRNAs) can dysregulate their expression via disrupting the binding site of miRNAs. Interleukin-16 (IL-16) is involved in the pathogenesis of rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). In the current study, we assessed the possible association between rs1131445 polymorphism in IL-16 gene with risk and clinical characteristics of RA and SLE in the Iranian population. METHODS In this case-control study, 120 patients with RA, 120 patients with SLE, and 120 unrelated healthy subjects were collected to estimate rs1131445 (T > C) polymorphism in IL-16 gene using real-time PCR high-resolution melting (HRM) method. RESULTS Our results demonstrated considerable associations between TC genotype and C allele of rs1131445 with enhanced risk of RA (ORfor TC genotype = 3.01; 95%CI [1.667-5.526], P < 0.001; ORfor C allele = 1.96; 95%CI [1.314-2.941], P < 0.001). Besides, there was a marginal association between CC genotype and increased risk of RA (P: 0.031). However, there was an insignificant correlation between genotypes and allele frequencies of rs1131445 with incidence risk of SLE (P > 0.05). Moreover, stratification analysis indicated that the C allele in rs1131445 was linked with disease activity-associated laboratory parameters such as CRP and ESR in both RA and SLE patients, as well as the higher incidence of neurological symptoms in SLE subjects (P < 0.05). CONCLUSION These results proposed a significant association between IL-16 polymorphism and augmented risk of RA and clinical characteristics of RA and SLE.
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Affiliation(s)
| | - Nahid Kheradmand
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ghazal Rasouli
- Faculty of Basic Sciences, Central Tehran Branch, Islamic Azad University, Isfahan, Iran
| | | | - Bahram Pakzad
- Division of Rheumatology, Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Javad Behroozi
- Research Center for Cancer Screening and Epidemiology, AJA University of Medical Sciences, Tehran, Iran.,Department of Genetics and Advanced Medical Technology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Mohsen Chamanara
- Toxicology Research Center, Aja University of Medical Sciences, Tehran, Iran.,Department of Pharmacology, School of Medicine, Aja University of Medical Sciences, Tehran, Iran
| | | | - Naeim Ehtesham
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran
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Laghmouchi A, Graça NAG, Voorberg J. Emerging Concepts in Immune Thrombotic Thrombocytopenic Purpura. Front Immunol 2021; 12:757192. [PMID: 34858410 PMCID: PMC8631936 DOI: 10.3389/fimmu.2021.757192] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/27/2021] [Indexed: 12/23/2022] Open
Abstract
Immune thrombotic thrombocytopenic purpura (iTTP) is an autoimmune disorder of which the etiology is not fully understood. Autoantibodies targeting ADAMTS13 in iTTP patients have extensively been studied, the immunological mechanisms leading to the breach of tolerance remain to be uncovered. This review addresses the current knowledge on genetic factors associated with the development of iTTP and the interplay between the patient's immune system and environmental factors in the induction of autoimmunity against ADAMTS13. HLA-DRB1*11 has been identified as a risk factor for iTTP in the Caucasian population. Interestingly, HLA-DRB1*08:03 was recently identified as a risk factor in the Japanese population. Combined in vitro and in silico MHC class II peptide presentation approaches suggest that an ADAMTS13-derived peptide may bind to both HLA-DRB1*11 and HLA-DRB1*08:03 through different anchor-residues. It is apparent that iTTP is associated with the presence of infectious microorganisms, viruses being the most widely associated with development of iTTP. Infections may potentially lead to loss of tolerance resulting in the shift from immune homeostasis to autoimmunity. In the model we propose in this review, infections disrupt the epithelial barriers in the gut or lung, promoting exposure of antigen presenting cells in the mucosa-associated lymphoid tissue to the microorganisms. This may result in breach of tolerance through the presentation of microorganism-derived peptides that are homologous to ADAMTS13 on risk alleles for iTTP.
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Affiliation(s)
| | | | - Jan Voorberg
- Department of Molecular Hematology, Sanquin-Academic Medical Center Landsteiner Laboratory, Amsterdam, Netherlands
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8
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Correlation between an intronic SNP genotype and ARL15 level in rheumatoid arthritis. J Genet 2021. [DOI: 10.1007/s12041-021-01286-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Fernandez Lahore G, Förster M, Johannesson M, Sabatier P, Lönnblom E, Aoun M, He Y, Nandakumar KS, Zubarev RA, Holmdahl R. Polymorphic estrogen receptor binding site causes Cd2-dependent sex bias in the susceptibility to autoimmune diseases. Nat Commun 2021; 12:5565. [PMID: 34552089 PMCID: PMC8458462 DOI: 10.1038/s41467-021-25828-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/20/2021] [Indexed: 01/22/2023] Open
Abstract
Complex autoimmune diseases are sexually dimorphic. An interplay between predisposing genetics and sex-related factors probably controls the sex discrepancy in the immune response, but the underlying mechanisms are unclear. Here we positionally identify a polymorphic estrogen receptor binding site that regulates Cd2 expression, leading to female-specific differences in T cell-dependent mouse models of autoimmunity. Female mice with reduced Cd2 expression have impaired autoreactive T cell responses. T cells lacking Cd2 costimulation upregulate inhibitory Lag-3. These findings help explain sexual dimorphism in human autoimmunity, as we find that CD2 polymorphisms are associated with rheumatoid arthritis and 17-β-estradiol-regulation of CD2 is conserved in human T cells. Hormonal regulation of CD2 might have implications for CD2-targeted therapy, as anti-Cd2 treatment more potently affects T cells in female mice. These results demonstrate the relevance of sex-genotype interactions, providing strong evidence for CD2 as a sex-sensitive predisposing factor in autoimmunity.
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Affiliation(s)
- Gonzalo Fernandez Lahore
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Michael Förster
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Martina Johannesson
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Pierre Sabatier
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Erik Lönnblom
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Mike Aoun
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Yibo He
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Kutty Selva Nandakumar
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
- SMU-KI United Medical Inflammation Centre, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Roman A Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, 119146, Russia
| | - Rikard Holmdahl
- Division Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden.
- The Second Affiliated Hospital of Xi'an Jiaotong University (Xibei Hospital), 710004, Xi'an, China.
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Strong association of common variants in the miRNA-binding site of NOD2 gene with clinicopathological characteristics and disease activity of systemic lupus erythematosus. Clin Rheumatol 2021; 40:4559-4567. [PMID: 34173079 DOI: 10.1007/s10067-021-05812-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 02/07/2023]
Abstract
INTRODUCTION/OBJECTIVES Systemic lupus erythematosus (SLE) is a multifactorial systemic autoimmune disease, in which genetic susceptibility plays a pivotal role. The nucleotide oligomerization domain 2 (NOD2) gene is one of the main regulators of chronic inflammatory conditions and could be involved in SLE pathogenesis. Single nucleotide polymorphisms (SNPs) in miRNA binding sites which are located in 3'UTR of the NOD2 gene could be associated with SLE risk by dysregulation of NOD2 expression. In the present study, we assessed the possible association between SNPs rs3135500 and rs3135499 in the NOD2 gene with SLE risk in the Iranian population. METHODS A case-control study using 110 SLE patients and 120 control subjects was undertaken to estimate rs3135500 (G > A) and rs3135499 (A > C) genotypes via real-time PCR high-resolution melting method (HRM). RESULTS No significant association was observed between allele and genotype frequencies of rs3135500 and rs3135499 polymorphisms and SLE risk in this population (P > 0.05). However, there was an obvious association between rs3135500 (A allele) with laboratory factors that are associated with disease activity (P < 0.05) and some clinical manifestations that are associated with disease severity such as neurological symptoms, skin manifestations, renal involvements, and higher serum concentration of creatinine (P < 0.05). Besides, rs3135499 (C allele) was correlated with renal involvement and also the concentration of creatinine (P < 0.05). Moreover, in the patients group, the risk alleles in these polymorphisms were associated with lower age of onset (P < 0.05). CONCLUSIONS Our results suggest a substantial association between NOD2 polymorphisms with clinicopathological characteristics and SLE disease activity. Key Points • Single nucleotide polymorphisms (SNPs) in miRNA binding sites which are located in 3'UTR of the NOD2 gene could be associated with SLE risk by dysregulation of NOD2 expression. • Our results suggested that two miRSNPs (rs3135500 and rs3135499) in the NOD2 gene were meaningfully correlated with clinicopathological characteristics and disease activity of SLE.
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Ehtesham N, Zare Rafie M, Esmaeilzadeh E, Dehani M, Davar S, Mosallaei M, Pakzad B, Ghorashi T, Darvish H, Soosanabadi M. Three functional variants in the NLRP3 gene are associated with susceptibility and clinical characteristics of systemic lupus erythematosus. Lupus 2021; 30:1273-1282. [PMID: 33951966 DOI: 10.1177/09612033211014273] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Nod-like receptor pyrin domain containing 3 (NLRP3) gene encodes an intracellular receptor whose dysregulation in systemic lupus erythematosus (SLE) has been reported in multiple studies. Activation of NLRP3 inflammasome leads to the induction of inflammatory response via cleaving and producing of specific cytokines. In the present study, we assessed the possible association between three functional polymorphisms in this gene and SLE risk in the Iranian population. These variants include two gain of function (rs4612666 and rs10754558) and one loss of function (rs6672995) which are correlated with modulation of expression of NLRP3. METHODS A case-control study involving 110 SLE patients and 116 control subjects was undertaken to estimate the frequency of rs4612666, rs10754558, and rs6672995 genotypes using real-time PCR high resolution melting method (HRM). RESULTS Our findings revealed significant associations between GG genotype and G allele of rs10754558 with increased risk of SLE (OR for GG genotype= 2.82; 95%CI [1.45-5.46]/OR for G allele= 1.97; 95%CI [1.36-2.87]). Although, no significant associations were recognized between allele and genotype frequencies of rs4612666 and rs6672995 polymorphisms with SLE risk (P > 0.05). Also, our analysis revealed that the C allele in rs4612666 and G allele in rs10754558 was correlated with the severity of disease activity (P < 0.001). Moreover, these common variants were associated with lower age of onset and some clinical symptoms in the patient group, such as skin manifestation, neurological symptom and, renal involvement (P < 0.05). CONCLUSION This study demonstrates a substantial association between NLRP3 polymorphisms with increased risk, clinical symptoms, and the severity of disease activity of SLE.
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Affiliation(s)
- Naeim Ehtesham
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable disease, Isfahan University of Medical Sciences, Isfahan, Iran.,Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Zare Rafie
- School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | | | - Mohammad Dehani
- School of Medicine, Aja University of Medical Science, Tehran, Iran
| | - Saeideh Davar
- Department of Epidemiology and Biostatistics, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Meysam Mosallaei
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable disease, Isfahan University of Medical Sciences, Isfahan, Iran.,Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bahram Pakzad
- Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Tahereh Ghorashi
- Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Hossein Darvish
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Mohsen Soosanabadi
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
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12
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Mehra P, Wells AD. Variant to Gene Mapping to Discover New Targets for Immune Tolerance. Front Immunol 2021; 12:633219. [PMID: 33936046 PMCID: PMC8082446 DOI: 10.3389/fimmu.2021.633219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/16/2021] [Indexed: 01/04/2023] Open
Abstract
The breakdown of immunological tolerance leads to autoimmune disease, and the mechanisms that maintain self-tolerance, especially in humans, are not fully understood. Genome-wide association studies (GWAS) have identified hundreds of human genetic loci statistically linked to autoimmune disease risk, and epigenetic modifications of DNA and chromatin at these loci have been associated with autoimmune disease risk. Because the vast majority of these signals are located far from genes, identifying causal variants, and their functional consequences on the correct effector genes, has been challenging. These limitations have hampered the translation of GWAS findings into novel drug targets and clinical interventions, but recent advances in understanding the spatial organization of the genome in the nucleus have offered mechanistic insights into gene regulation and answers to questions left open by GWAS. Here we discuss the potential for 'variant-to-gene mapping' approaches that integrate GWAS with 3D functional genomic data to identify human genes involved in the maintenance of tolerance.
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Affiliation(s)
- Parul Mehra
- Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Andrew D Wells
- Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Sayaman RW, Saad M, Thorsson V, Hu D, Hendrickx W, Roelands J, Porta-Pardo E, Mokrab Y, Farshidfar F, Kirchhoff T, Sweis RF, Bathe OF, Heimann C, Campbell MJ, Stretch C, Huntsman S, Graff RE, Syed N, Radvanyi L, Shelley S, Wolf D, Marincola FM, Ceccarelli M, Galon J, Ziv E, Bedognetti D. Germline genetic contribution to the immune landscape of cancer. Immunity 2021; 54:367-386.e8. [PMID: 33567262 DOI: 10.1016/j.immuni.2021.01.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 10/14/2020] [Accepted: 01/13/2021] [Indexed: 02/07/2023]
Abstract
Understanding the contribution of the host's genetic background to cancer immunity may lead to improved stratification for immunotherapy and to the identification of novel therapeutic targets. We investigated the effect of common and rare germline variants on 139 well-defined immune traits in ∼9000 cancer patients enrolled in TCGA. High heritability was observed for estimates of NK cell and T cell subset infiltration and for interferon signaling. Common variants of IFIH1, TMEM173 (STING1), and TMEM108 were associated with differential interferon signaling and variants mapping to RBL1 correlated with T cell subset abundance. Pathogenic or likely pathogenic variants in BRCA1 and in genes involved in telomere stabilization and Wnt-β-catenin also acted as immune modulators. Our findings provide evidence for the impact of germline genetics on the composition and functional orientation of the tumor immune microenvironment. The curated datasets, variants, and genes identified provide a resource toward further understanding of tumor-immune interactions.
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Affiliation(s)
- Rosalyn W Sayaman
- Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Biological Sciences and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Mohamad Saad
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar; Neuroscience Research Center, Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon
| | | | - Donglei Hu
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wouter Hendrickx
- Research Branch, Sidra Medicine, PO Box 26999 Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Jessica Roelands
- Research Branch, Sidra Medicine, PO Box 26999 Doha, Qatar; Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Eduard Porta-Pardo
- Barcelona Supercomputing Center (BSC); Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08034 Barcelona, Catalonia, Spain
| | - Younes Mokrab
- Research Branch, Sidra Medicine, PO Box 26999 Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar; Weill Cornell Medicine, Doha, Qatar
| | - Farshad Farshidfar
- Department of Oncology, University of Calgary, Alberta AB T2N 4N1, Canada; Arnie Charbonneau Cancer Institute, Calgary, Alberta AB T2N 4N1, Canada; Department of Biomedical Data Science and Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; Tenaya Therapeutics, South San Francisco, CA 94080, USA
| | - Tomas Kirchhoff
- Perlmutter Cancer Center, New York University School of Medicine, New York University Langone Health, New York, NY 10016, USA
| | - Randy F Sweis
- Department of Medicine, Section of Hematology/Oncology, Committee on Clinical Pharmacology and Pharmacogenomics, Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Oliver F Bathe
- Department of Oncology, University of Calgary, Alberta AB T2N 4N1, Canada; Arnie Charbonneau Cancer Institute, Calgary, Alberta AB T2N 4N1, Canada; Department of Surgery, University of Calgary, Calgary, Alberta AB T2N 4N1, Canada
| | | | - Michael J Campbell
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cynthia Stretch
- Department of Oncology, University of Calgary, Alberta AB T2N 4N1, Canada; Arnie Charbonneau Cancer Institute, Calgary, Alberta AB T2N 4N1, Canada
| | - Scott Huntsman
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Najeeb Syed
- Research Branch, Sidra Medicine, PO Box 26999 Doha, Qatar; Department of Science and Technology, University of Sannio, 82100 Benevento, Italy
| | - Laszlo Radvanyi
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Simon Shelley
- Department of Research and Development, Leukemia Therapeutics, LLC, Hull, MA 02045, USA
| | - Denise Wolf
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology, University of Naples "Federico II," 80128 Naples, Italy; Istituto di Ricerche Genetiche "G. Salvatore," Biogem s.c.ar.l., 83031 Ariano Irpino, Italy
| | - Jérôme Galon
- INSERM, Laboratory of Integrative Cancer Immunology, Equipe Labellisée Ligue Contre Le Cancer, Centre de Recherche de Cordeliers, Université de Paris, Sorbonne Université, Paris, France
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Davide Bedognetti
- Research Branch, Sidra Medicine, PO Box 26999 Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar; Department of Internal Medicine and Medical Specialties (Di.M.I.), University of Genoa, 16132 Genoa, Italy.
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Vitamin D3 receptor polymorphisms regulate T cells and T cell-dependent inflammatory diseases. Proc Natl Acad Sci U S A 2020; 117:24986-24997. [PMID: 32958661 DOI: 10.1073/pnas.2001966117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
It has proven difficult to identify the underlying genes in complex autoimmune diseases. Here, we use forward genetics to identify polymorphisms in the vitamin D receptor gene (Vdr) promoter, controlling Vdr expression and T cell activation. We isolated these polymorphisms in a congenic mouse line, allowing us to study the immunomodulatory properties of VDR in a physiological context. Congenic mice overexpressed VDR selectively in T cells, and thus did not suffer from calcemic effects. VDR overexpression resulted in an enhanced antigen-specific T cell response and more severe autoimmune phenotypes. In contrast, vitamin D3-deficiency inhibited T cell responses and protected mice from developing autoimmune arthritis. Our observations are likely translatable to humans, as Vdr is overexpressed in rheumatic joints. Genetic control of VDR availability codetermines the proinflammatory behavior of T cells, suggesting that increased presence of VDR at the site of inflammation might limit the antiinflammatory properties of its ligand.
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Oftedal BE, Wolff ASB. New era of therapy for endocrine autoimmune disorders. Scand J Immunol 2020; 92:e12961. [PMID: 32853446 DOI: 10.1111/sji.12961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 12/24/2022]
Abstract
The new era of immune and reconstitution therapy of autoimmune disorders is ongoing. However, endocrine autoimmune diseases comprise a group of elaborating pathologies where the development of new treatment strategies remains slow. Substitution of the missing hormones is still standard practice, taking care of the devastating symptoms but not the cause of disease. As our knowledge of the genetic contribution to the aetiology of endocrine disorders increases and early diagnostic tools are available, it is now possible to identify persons at risk before they acquire full-blown disease. This review summarizes current knowledge and treatment of endocrine autoimmune disorders, focusing on type 1 diabetes, Addison's disease, autoimmune thyroid diseases and primary ovarian insufficiency. We explore which new therapies might be used in the different stages of the disease, focus on legalized therapy and elaborate on the ongoing clinical studies for these diseases and the research front, before hypothesizing on the way ahead.
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Affiliation(s)
- Bergithe E Oftedal
- Department of Clinical Science, University of Bergen, Bergen, Norway.,KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway
| | - Anette S B Wolff
- Department of Clinical Science, University of Bergen, Bergen, Norway.,KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
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Field MA. Detecting pathogenic variants in autoimmune diseases using high-throughput sequencing. Immunol Cell Biol 2020; 99:146-156. [PMID: 32623783 PMCID: PMC7891608 DOI: 10.1111/imcb.12372] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/22/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022]
Abstract
Sequencing the first human genome in 2003 took 15 years and cost $2.7 billion. Advances in sequencing technologies have since decreased costs to the point where it is now feasible to resequence a whole human genome for $1000 in a single day. These advances have allowed the generation of huge volumes of high‐quality human sequence data used to construct increasingly large catalogs of both population‐level and disease‐causing variation. The existence of such databases, coupled with a high‐quality human reference genome, means we are able to interrogate and annotate all types of genetic variation and identify pathogenic variants for many diseases. Increasingly, sequencing‐based approaches are being used to elucidate the underlying genetic cause of autoimmune diseases, a group of roughly 80 polygenic diseases characterized by abnormal immune responses where healthy tissue is attacked. Although sequence data generation has become routine and affordable, significant challenges remain with no gold‐standard methodology to identify pathogenic variants currently available. This review examines the latest methodologies used to identify pathogenic variants in autoimmune diseases and considers available sequencing options and subsequent bioinformatic methodologies and strategies. The development of reliable and robust sequencing and analytic workflows to detect pathogenic variants is critical to realize the potential of precision medicine programs where patient variant information is used to inform clinical practice.
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Affiliation(s)
- Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.,John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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McCombe PA, Lee JD, Woodruff TM, Henderson RD. The Peripheral Immune System and Amyotrophic Lateral Sclerosis. Front Neurol 2020; 11:279. [PMID: 32373052 PMCID: PMC7186478 DOI: 10.3389/fneur.2020.00279] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 03/25/2020] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative disease that is defined by loss of upper and lower motor neurons, associated with accumulation of protein aggregates in cells. There is also pathology in extra-motor areas of the brain, Possible causes of cell death include failure to deal with the aggregated proteins, glutamate toxicity and mitochondrial failure. ALS also involves abnormalities of metabolism and the immune system, including neuroinflammation in the brain and spinal cord. Strikingly, there are also abnormalities of the peripheral immune system, with alterations of T lymphocytes, monocytes, complement and cytokines in the peripheral blood of patients with ALS. The precise contribution of the peripheral immune system in ALS pathogenesis is an active area of research. Although some trials of immunomodulatory agents have been negative, there is strong preclinical evidence of benefit from immune modulation and further trials are currently underway. Here, we review the emerging evidence implicating peripheral immune alterations contributing to ALS, and their potential as future therapeutic targets for clinical intervention.
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Affiliation(s)
- Pamela A. McCombe
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
- Wesley Medical Research, The Wesley Hospital, Brisbane, QLD, Australia
| | - John D. Lee
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Trent M. Woodruff
- Wesley Medical Research, The Wesley Hospital, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
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Salloom DF. Interleukin-2 serum level, genetic polymorphism (rs2069763), anti-rubella antibody and risk of multiple sclerosis among Iraqi patients. Meta Gene 2020. [DOI: 10.1016/j.mgene.2019.100642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Gorlov I, Xiao X, Mayes M, Gorlova O, Amos C. SNP eQTL status and eQTL density in the adjacent region of the SNP are associated with its statistical significance in GWA studies. BMC Genet 2019; 20:85. [PMID: 31718536 PMCID: PMC6852916 DOI: 10.1186/s12863-019-0786-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 10/18/2019] [Indexed: 01/05/2023] Open
Abstract
Background Over the relatively short history of Genome Wide Association Studies (GWASs), hundreds of GWASs have been published and thousands of disease risk-associated SNPs have been identified. Summary statistics from the conducted GWASs are often available and can be used to identify SNP features associated with the level of GWAS statistical significance. Those features could be used to select SNPs from gray zones (SNPs that are nominally significant but do not reach the genome-wide level of significance) for targeted analyses. Methods We used summary statistics from recently published breast and lung cancer and scleroderma GWASs to explore the association between the level of the GWAS statistical significance and the expression quantitative trait loci (eQTL) status of the SNP. Data from the Genotype-Tissue Expression Project (GTEx) were used to identify eQTL SNPs. Results We found that SNPs reported as eQTLs were more significant in GWAS (higher -log10p) regardless of the tissue specificity of the eQTL. Pan-tissue eQTLs (those reported as eQTLs in multiple tissues) tended to be more significant in the GWAS compared to those reported as eQTL in only one tissue type. eQTL density in the ±5 kb adjacent region of a given SNP was also positively associated with the level of GWAS statistical significance regardless of the eQTL status of the SNP. We found that SNPs located in the regions of high eQTL density were more likely to be located in regulatory elements (transcription factor or miRNA binding sites). When SNPs were stratified by the level of statistical significance, the proportion of eQTLs was positively associated with the mean level of statistical significance in the group. The association curve reaches a plateau around -log10p ≈ 5. The observed associations suggest that quasi-significant SNPs (10− 5 < p < 5 × 10− 8) and SNPs at the genome wide level of statistical significance (p < 5 × 10− 8) may have a similar proportions of risk associated SNPs. Conclusions The results of this study indicate that the SNP’s eQTL status, as well as eQTL density in the adjacent region are positively associated with the level of statistical significance of the SNP in GWAS.
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Affiliation(s)
- Ivan Gorlov
- The Geisel School of Medicine, Department of Biomedical Data Science, Dartmouth College, HB7936, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA.
| | - Xiangjun Xiao
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Maureen Mayes
- Department of Internal Medicine, Division of Rheumatology, University of Texas McGovern Medical School, Houston, TX, USA
| | - Olga Gorlova
- The Geisel School of Medicine, Department of Biomedical Data Science, Dartmouth College, HB7936, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Christopher Amos
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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