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Song W, Bian WJ, Li H, Guo QH, Wang J, Tang B, Zhang JY, Wei W, Liu XR, Liao WP, Li B, He N. IFIH1 variants are associated with generalised epilepsy preceded by febrile seizures. J Med Genet 2024; 61:895-903. [PMID: 38964834 PMCID: PMC11420756 DOI: 10.1136/jmg-2024-109950] [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: 02/27/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024]
Abstract
BACKGROUND IFIH1 variants have been reported to be associated with immune-related disorders with/without seizures. It is unknown whether IFIH1 variants are associated with common epilepsy without acquired causes and the mechanism underlying phenotypic variation remains elusive. METHODS Trio-based whole-exome sequencing was performed on patients with febrile seizures or epilepsy with antecedent febrile seizures. Previously reported variants were systematically reviewed to investigate genotype-phenotype associations. RESULTS Two de novo heterozygous and three biallelic missense variants were identified in five patients with generalised epilepsy with antecedent febrile seizures. The variants were predicted to be damaging by in silico tools and were associated with hydrogen bonding changes to neighbouring amino acids or decreased protein stability. Patients exhibited an early onset age and became seizure-free with favourable outcome. Further analysis revealed that de novo missense variants located in the Hel region resulted in seizures with multiple neurological abnormalities, while those in the pincer domain or C-terminal domain led to seizures with normal neurodevelopment, suggesting a sub-molecular effect. Biallelic missense variants, which were inherited from unaffected parents and presented low allele frequencies in general populations, were associated with seizures without neurological abnormalities. Truncation variants were related to refractory epilepsy and severe developmental delay, suggesting a genotype-phenotype correlation. IFIH1 is predominantly expressed in the neonatal stage and decreases dramatically in the adulthood, which is consistent with the early onset age and favourable outcome of the patients. CONCLUSIONS IFIH1 variants are potentially associated with generalised epilepsy with antecedent febrile seizures. The sub-molecular implication and genotype-phenotype association help explain phenotype variations of IFIH1 variants.
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Affiliation(s)
- Wang Song
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wen-Jun Bian
- Department of Neurology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Hua Li
- Department of Neurology, The Guangdong 999 Brain Hospital, Guangzhou, Guangdong, China
| | - Qing-Hui Guo
- Department of Pediatrics, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Jie Wang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Bin Tang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jia-Yuan Zhang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wei Wei
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiao-Rong Liu
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wei-Ping Liao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Bin Li
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Na He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
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Maiti AK. Bioinformatic analysis predicts the regulatory function of noncoding SNPs associated with Long COVID-19 syndrome. Immunogenetics 2024:10.1007/s00251-024-01348-6. [PMID: 39042286 DOI: 10.1007/s00251-024-01348-6] [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: 04/30/2024] [Accepted: 07/09/2024] [Indexed: 07/24/2024]
Abstract
Long or Post COVID-19 is a condition of collected symptoms persisted after recovery from COVID-19. Host genetic factors play a crucial role in developing Long COVID-19, and GWAS studies identified several SNPs/genes in various ethnic populations. In African-American population two SNPS, rs10999901 (C>T, p = 3.6E-08, OR = 1.39, MAF-0,27, GRCH38, chr10:71584799 bp) and rs1868001 (G>A, p = 6.7E-09, OR = 1.40, MAF-0.46, GRCH38, chr10:71587815 bp) and in Hispanic population, rs3759084 (A>C, p = 9.7E-09, OR = 1.56, MAF-0.17, chr12: 81,110,156 bp) are strongly associated with Long COVID-19. All these three SNPs reside in noncoding regions implying their regulatory function in the genome. In silico dissection suggests that rs10999901 and rs1868001 physically interact with the CDH23 and C10orf105 genes. Both SNPs act as distant enhancers and bind with several transcription factors (TFs). Further, rs10999901 SNP is a CpG that is methylated in CD4++ T cells and monocytes and loses its methylation due to transition from C>T. rs3759084 is located in the promoter (- 687 bp) of MYF5, acts as a distant enhancer, and physically interacts with PTPRQ. These results offer plausible explanations for their association and provide the basis for experiments to dissect the development of symptoms of Long COVID-19.
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Affiliation(s)
- Amit K Maiti
- Department of Genetics and Genomics, Mydnavar, 28475 Greenfield Rd, Southfield, USA.
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Fazel-Najafabadi M, Looger LL, Rallabandi HR, Nath SK. A Multilayered Post-Genome-Wide Association Study Analysis Pipeline Defines Functional Variants and Target Genes for Systemic Lupus Erythematosus. Arthritis Rheumatol 2024; 76:1071-1084. [PMID: 38369936 PMCID: PMC11213670 DOI: 10.1002/art.42829] [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: 09/14/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE), an autoimmune disease with incompletely understood etiology, has a strong genetic component. Although genome-wide association studies (GWASs) have revealed multiple SLE susceptibility loci and associated single-nucleotide polymorphisms (SNPs), the precise causal variants, target genes, cell types, tissues, and mechanisms of action remain largely unknown. METHODS Here, we report a comprehensive post-GWAS analysis using extensive bioinformatics, molecular modeling, and integrative functional genomic and epigenomic analyses to optimize fine-mapping. We compile and cross-reference immune cell-specific expression quantitative trait loci (cis- and trans-expression quantitative trait loci) with promoter capture high-throughput capture chromatin conformation (PCHi-C), allele-specific chromatin accessibility, and massively parallel reporter assay data to define predisposing variants and target genes. We experimentally validate a predicted locus using CRISPR/Cas9 genome editing, quantitative polymerase chain reaction, and Western blot. RESULTS Anchoring on 452 index SNPs, we selected 9,931 high linkage disequilibrium (r2 > 0.8) SNPs and defined 182 independent non-human leukocyte antigen (HLA) SLE loci. The 3,746 SNPs from 143 loci were identified as regulating 564 unique genes. Target genes are enriched in lupus-related tissues and associated with other autoimmune diseases. Of these, 329 SNPs (106 loci) showed significant allele-specific chromatin accessibility and/or enhancer activity, indicating regulatory potential. Using CRISPR/Cas9, we validated reference SNP identifier 57668933 (rs57668933) as a functional variant regulating multiple targets, including SLE-risk gene ELF1 in B cells. CONCLUSION We demonstrate and validate post-GWAS strategies for using multidimensional data to prioritize likely causal variants with cognate gene targets underlying SLE pathogenesis. Our results provide a catalog of significantly SLE-associated SNPs and loci, target genes, and likely biochemical mechanisms to guide experimental characterization.
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Affiliation(s)
- Mehdi Fazel-Najafabadi
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Loren L. Looger
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92121, USA
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92121, USA
| | - Harikrishna Reddy Rallabandi
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
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Solomon O, Lanata CM, Adams C, Nititham J, Taylor KE, Chung SA, Yazdany J, Dall’Era M, Pons-Estel BA, Tusié-Luna T, Tsao B, Morand E, Alarcón-Riquelme ME, Barcellos LF, Criswell LA. Local Ancestry at the Major Histocompatibility Complex Region is Not a Major Contributor to Disease Heterogeneity in a Multiethnic Lupus Cohort. Arthritis Rheumatol 2024; 76:614-619. [PMID: 38073021 PMCID: PMC10965360 DOI: 10.1002/art.42766] [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: 11/17/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 01/31/2024]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is an autoimmune disease resulting in debilitating clinical manifestations that vary in severity by race and ethnicity with a disproportionate burden in African American, Mestizo, and Asian populations compared with populations of European descent. Differences in global and local genetic ancestry may shed light on the underlying mechanisms contributing to these disparities, including increased prevalence of lupus nephritis, younger age of symptom onset, and presence of autoantibodies. METHODS A total of 1,139 European, African American, and Mestizos patients with SLE were genotyped using the Affymetrix LAT1 World array. Global ancestry proportions were estimated using ADMIXTURE, and local ancestry was estimated using RFMIXv2.0. We investigated associations between lupus nephritis, age at onset, and autoantibody status with both global and local ancestry proportions within the Major Histocompatibility Complex region. RESULTS Our results showed small effect sizes that did not meet the threshold for statistical significance for global or local ancestry proportions in either African American or Mestizo patients with SLE who presented with the clinical manifestations of interest compared with those who did not. CONCLUSION These findings suggest that local genetic ancestry within the Major Histocompatibility Complex region is not a major contributor to these SLE manifestations among patients with SLE from admixed populations.
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Affiliation(s)
- Olivia Solomon
- University of California, Berkeley, Genetic Epidemiology and Genomic Laboratory
| | | | - Cameron Adams
- University of California, Berkeley, Genetic Epidemiology and Genomic Laboratory
| | - Joanne Nititham
- National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Kimberly E. Taylor
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco
| | - Sharon A. Chung
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco
| | - Jinoos Yazdany
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco
| | - Maria Dall’Era
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco
| | - Bernado A. Pons-Estel
- Centro Regional de Enfermedades Autoinmunes y Reumaticas (GO-CREAR), Rosario, Argentina
| | - Teresa Tusié-Luna
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán and Instituto de Investigaciones Biomédicas de la Universidad Nacional Autonoma de México, Mexico City, Mexico
| | - Betty Tsao
- Medical University of South Carolina, Charleston, South Carolina
| | - Eric Morand
- Monash University Faculty of Medicine, Nursing & Health Sciences, Melbourne, Australia
| | - Marta E. Alarcón-Riquelme
- Center for Genomics and Oncological Research (GENYO). Pfizer—University of Granada—Andalusian Government, Parque Tecnologico de la Salud, Granada, Spain
| | - Lisa F. Barcellos
- University of California, Berkeley, Genetic Epidemiology and Genomic Laboratory
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Fazel-Najafabadi M, Looger LL, Reddy-Rallabandi H, Nath SK. A multilayered post-GWAS analysis pipeline defines functional variants and target genes for systemic lupus erythematosus (SLE). MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.07.23288295. [PMID: 37066327 PMCID: PMC10104240 DOI: 10.1101/2023.04.07.23288295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Objectives Systemic lupus erythematosus (SLE), an autoimmune disease with incompletely understood etiology, has a strong genetic component. Although genome-wide association studies (GWAS) have revealed multiple SLE susceptibility loci and associated single nucleotide polymorphisms (SNPs), the precise causal variants, target genes, cell types, tissues, and mechanisms of action remain largely unknown. Methods Here, we report a comprehensive post-GWAS analysis using extensive bioinformatics, molecular modeling, and integrative functional genomic and epigenomic analyses to optimize fine-mapping. We compile and cross-reference immune cell-specific expression quantitative trait loci ( cis - and trans -eQTLs) with promoter-capture Hi-C, allele-specific chromatin accessibility, and massively parallel reporter assay data to define predisposing variants and target genes. We experimentally validate a predicted locus using CRISPR/Cas9 genome editing, qPCR, and Western blot. Results Anchoring on 452 index SNPs, we selected 9,931 high-linkage disequilibrium (r 2 >0.8) SNPs and defined 182 independent non-HLA SLE loci. 3,746 SNPs from 143 loci were identified as regulating 564 unique genes. Target genes are enriched in lupus-related tissues and associated with other autoimmune diseases. Of these, 329 SNPs (106 loci) showed significant allele-specific chromatin accessibility and/or enhancer activity, indicating regulatory potential. Using CRISPR/Cas9, we validated rs57668933 as a functional variant regulating multiple targets, including SLE risk gene ELF1 , in B-cells. Conclusion We demonstrate and validate post-GWAS strategies for utilizing multi-dimensional data to prioritize likely causal variants with cognate gene targets underlying SLE pathogenesis. Our results provide a catalog of significantly SLE-associated SNPs and loci, target genes, and likely biochemical mechanisms, to guide experimental characterization.
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Xiao Z, Luo S, Zhou Y, Pang H, Yin W, Qin J, Xie Z, Zhou Z. Association of the rs1990760, rs3747517, and rs10930046 polymorphisms in the IFIH1 gene with susceptibility to autoimmune diseases: a meta-analysis. Front Immunol 2023; 14:1051247. [PMID: 37426657 PMCID: PMC10327432 DOI: 10.3389/fimmu.2023.1051247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 06/08/2023] [Indexed: 07/11/2023] Open
Abstract
Objective Interferon induced with helicase C domain 1 (IFIH1) single-nucleotide polymorphisms (SNP) rs1990760, rs3747517, and rs10930046 have been shown to be closely related to the risk of autoimmune diseases. The aim of this study was firstly to examine the association of the rs1990760 with type 1 diabetes (T1D) in a Chinese population. Secondly, to assess the association of SNP rs1990760, rs3747517, and rs10930046 with autoimmune diseases susceptibility. Methods A total of 1,273 T1D patients and 1,010 healthy control subjects in a Chinese population were enrolled in this case-control study. Subsequently, we performed a meta-analysis on the association of the SNP rs1990760, rs3747517, and rs10930046 in the IFIH1 gene with susceptibility to autoimmune diseases. The random and fixed genetic effects models were used to evaluate the association and the effect sizes, including odds ratios (OR) and 95% confidence intervals (CI). Stratification analyses based on ethnicity and the type of autoimmune diseases were performed. Results IFIH1 SNP rs1990760 was not associated with a significant risk of T1D in the Chinese population in the case-control study. A total of 35 studies including 70,966 patients and 124,509 controls were identified and included in the meta-analysis. The results displayed significant associations between IFIH1 rs1990760 A allele and rs3747517 C allele and autoimmune diseases risk (OR=1.09, 95% CI: 1.01~1.17; OR=1.24, 95% CI: 1.15~1.25, respectively). Stratified analysis indicated a significant association rs1990760 and rs3747517 with autoimmune diseases risk in the Caucasian population (OR=1.11, 95% CI: 1.02~1.20, OR=1.29, 95% CI: 1.18~1.41, respectively). Conclusions This study revealed no association between IFIH1 SNP rs1990760 and T1D in Chinese. Furthermore, the meta-analysis indicated that rs1990760 and rs3747517 polymorphisms, confer susceptibility to autoimmune diseases, especially in the Caucasian population.
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Affiliation(s)
- Zilin Xiao
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Shuoming Luo
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yuemin Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Haipeng Pang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Wenfeng Yin
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jiabi Qin
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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Dieter C, de Almeida Brondani L, Lemos NE, Schaeffer AF, Zanotto C, Ramos DT, Girardi E, Pellenz FM, Camargo JL, Moresco KS, da Silva LL, Aubin MR, de Oliveira MS, Rech TH, Canani LH, Gerchman F, Leitão CB, Crispim D. Polymorphisms in ACE1, TMPRSS2, IFIH1, IFNAR2, and TYK2 Genes Are Associated with Worse Clinical Outcomes in COVID-19. Genes (Basel) 2022; 14:genes14010029. [PMID: 36672770 PMCID: PMC9858252 DOI: 10.3390/genes14010029] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/29/2022] [Accepted: 12/10/2022] [Indexed: 12/25/2022] Open
Abstract
Although advanced age, male sex, and some comorbidities impact the clinical course of COVID-19, these factors only partially explain the inter-individual variability in disease severity. Some studies have shown that genetic polymorphisms contribute to COVID-19 severity; however, the results are inconclusive. Thus, we investigated the association between polymorphisms in ACE1, ACE2, DPP9, IFIH1, IFNAR2, IFNL4, TLR3, TMPRSS2, and TYK2 and the clinical course of COVID-19. A total of 694 patients with COVID-19 were categorized as: (1) ward inpatients (moderate symptoms) or patients admitted at the intensive care unit (ICU; severe symptoms); and (2) survivors or non-survivors. In females, the rs1990760/IFIH1 T/T genotype was associated with risk of ICU admission and death. Moreover, the rs1799752/ACE1 Ins and rs12329760/TMPRSS2 T alleles were associated with risk of ICU admission. In non-white patients, the rs2236757/IFNAR2 A/A genotype was associated with risk of ICU admission, while the rs1799752/ACE1 Ins/Ins genotype, rs2236757/IFNAR2 A/A genotype, and rs12329760/TMPRSS2 T allele were associated with risk of death. Moreover, some of the analyzed polymorphisms interact in the risk of worse COVID-19 outcomes. In conclusion, this study shows an association of rs1799752/ACE1, rs1990760/IFIH1, rs2236757/IFNAR2, rs12329760/TMPRSS2, and rs2304256/TYK2 polymorphisms with worse COVID-19 outcomes, especially among female and non-white patients.
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Affiliation(s)
- Cristine Dieter
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
| | - Leticia de Almeida Brondani
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Natália Emerim Lemos
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Ariell Freires Schaeffer
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
| | - Caroline Zanotto
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Denise Taurino Ramos
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Eliandra Girardi
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Felipe Mateus Pellenz
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
| | - Joiza Lins Camargo
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
- Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Diabetes and Metabolism Group, Centro de Pesquisa Clínica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Karla Suzana Moresco
- Campus Realeza, Universidade Federal da Fronteira Sul, Realeza 85770-000, PR, Brazil
| | - Lucas Lima da Silva
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Mariana Rauback Aubin
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Mayara Souza de Oliveira
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
| | - Tatiana Helena Rech
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
- Diabetes and Metabolism Group, Centro de Pesquisa Clínica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Luís Henrique Canani
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
- Diabetes and Metabolism Group, Centro de Pesquisa Clínica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Fernando Gerchman
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
- Diabetes and Metabolism Group, Centro de Pesquisa Clínica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Cristiane Bauermann Leitão
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
- Diabetes and Metabolism Group, Centro de Pesquisa Clínica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Daisy Crispim
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
- Diabetes and Metabolism Group, Centro de Pesquisa Clínica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Correspondence:
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Solstad A, Hogaboam O, Forero A, Hemann EA. RIG-I-like Receptor Regulation of Immune Cell Function and Therapeutic Implications. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:845-854. [PMID: 36130131 PMCID: PMC9512390 DOI: 10.4049/jimmunol.2200395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/30/2022] [Indexed: 01/04/2023]
Abstract
Retinoic acid-inducible gene I-like receptors (RLRs) are cytosolic RNA sensors critical for initiation of antiviral immunity. Activation of RLRs following RNA recognition leads to production of antiviral genes and IFNs for induction of broad antiviral immunity. Although the RLRs are ubiquitously expressed, much of our understanding of these molecules comes from their study in epithelial cells and fibroblasts. However, RLR activation is critical for induction of immune function and long-term protective immunity. Recent work has focused on the roles of RLRs in immune cells and their contribution to programming of effective immune responses. This new understanding of RLR function in immune cells and immune programming has led to the development of vaccines and therapeutics targeting the RLRs. This review covers recent advances in our understanding of the contribution of RLRs to immune cell function during infection and the emerging RLR-targeting strategies for induction of immunity against cancer and viral infection.
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Affiliation(s)
- Abigail Solstad
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, OH
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH
| | - Octavia Hogaboam
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, OH
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH
| | - Adriana Forero
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH
- Infectious Diseases Institute, The Ohio State University, Columbus, OH; and
| | - Emily A Hemann
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH;
- Infectious Diseases Institute, The Ohio State University, Columbus, OH; and
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9
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Nln I, Fernandez-Ruiz R, Muskardin TLW, Paredes JL, Blazer AD, Tuminello S, Attur M, Iturrate E, Petrilli CM, Abramson SB, Chakravarti A, Niewold TB. Interferon pathway lupus risk alleles modulate risk of death from acute COVID-19. Transl Res 2022; 244:47-55. [PMID: 35114420 PMCID: PMC8802623 DOI: 10.1016/j.trsl.2022.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 12/15/2022]
Abstract
Type I interferon (IFN) is critical in our defense against viral infections. Increased type I IFN pathway activation is a genetic risk factor for systemic lupus erythematosus (SLE), and a number of common risk alleles contribute to the high IFN trait. We hypothesized that these common gain-of-function IFN pathway alleles may be associated with protection from mortality in acute COVID-19. We studied patients admitted with acute COVID-19 (756 European-American and 398 African-American ancestry). Ancestral backgrounds were analyzed separately, and mortality after acute COVID-19 was the primary outcome. In European-American ancestry, we found that a haplotype of interferon regulatory factor 5 (IRF5) and alleles of protein kinase cGMP-dependent 1 (PRKG1) were associated with mortality from COVID-19. Interestingly, these were much stronger risk factors in younger patients (OR = 29.2 for PRKG1 in ages 45-54). Variants in the IRF7 and IRF8 genes were associated with mortality from COVID-19 in African-American subjects, and these genetic effects were more pronounced in older subjects. Combining genetic information with blood biomarker data such as C-reactive protein, troponin, and D-dimer resulted in significantly improved predictive capacity, and in both ancestral backgrounds the risk genotypes were most relevant in those with positive biomarkers (OR for death between 14 and 111 in high risk genetic/biomarker groups). This study confirms the critical role of the IFN pathway in defense against COVID-19 and viral infections, and supports the idea that some common SLE risk alleles exert protective effects in antiviral immunity.
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Affiliation(s)
- Ilona Nln
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, New York
| | - Ruth Fernandez-Ruiz
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, New York
| | | | - Jacqueline L Paredes
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, New York
| | - Ashira D Blazer
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, New York
| | - Stephanie Tuminello
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, New York
| | - Mukundan Attur
- Divison of Rheumatology, Department of Medicine, NYU Grossman School of Medicine, New York, New York
| | - Eduardo Iturrate
- Department of Medicine, NYU Grossman School of Medicine, New York, New York
| | | | - Steven B Abramson
- Department of Medicine, NYU Grossman School of Medicine, New York, New York
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, New York
| | - Timothy B Niewold
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, New York.
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10
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Lei Y, Fei P, Song B, Shi W, Luo C, Luo D, Li D, Chen W, Zheng J. A loosened gating mechanism of RIG-I leads to autoimmune disorders. Nucleic Acids Res 2022; 50:5850-5863. [PMID: 35580046 PMCID: PMC9177982 DOI: 10.1093/nar/gkac361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 11/12/2022] Open
Abstract
DDX58 encodes RIG-I, a cytosolic RNA sensor that ensures immune surveillance of nonself RNAs. Individuals with RIG-IE510V and RIG-IQ517H mutations have increased susceptibility to Singleton-Merten syndrome (SMS) defects, resulting in tissue-specific (mild) and classic (severe) phenotypes. The coupling between RNA recognition and conformational changes is central to RIG-I RNA proofreading, but the molecular determinants leading to dissociated disease phenotypes remain unknown. Herein, we employed hydrogen/deuterium exchange mass spectrometry (HDX-MS) and single molecule magnetic tweezers (MT) to precisely examine how subtle conformational changes in the helicase insertion domain (HEL2i) promote impaired ATPase and erroneous RNA proofreading activities. We showed that the mutations cause a loosened latch-gate engagement in apo RIG-I, which in turn gradually dampens its self RNA (Cap2 moiety:m7G cap and N1-2-2′-O-methylation RNA) proofreading ability, leading to increased immunopathy. These results reveal HEL2i as a unique checkpoint directing two specialized functions, i.e. stabilizing the CARD2-HEL2i interface and gating the helicase from incoming self RNAs; thus, these findings add new insights into the role of HEL2i in the control of antiviral innate immunity and autoimmunity diseases.
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Affiliation(s)
- Yixuan Lei
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.,The Drug Research Center of Immunological Diseases, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Panyu Fei
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,School of Mechanical Engineering, Zhejiang University, Hangzhou 310027, Zhejiang, China
| | - Bin Song
- The Drug Research Center of Immunological Diseases, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenjia Shi
- The Drug Research Center of Immunological Diseases, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China
| | - Cheng Luo
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,The Chemical Biology Center, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, Zhejiang, China
| | - Dahai Luo
- Lee Kong Chian School of Medicine, NTU Institute of Structural Biology, School of Biological Sciences, Nanyang Technological University, 636921, Singapore
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Wei Chen
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the MOE Frontier Science Center for Brain Science & Brain-Machine Integration, State Key Laboratory for Modern Optical Instrumentation Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jie Zheng
- The Drug Research Center of Immunological Diseases, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, Zhejiang, China
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11
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Chen YG, Hur S. Cellular origins of dsRNA, their recognition and consequences. Nat Rev Mol Cell Biol 2022; 23:286-301. [PMID: 34815573 PMCID: PMC8969093 DOI: 10.1038/s41580-021-00430-1] [Citation(s) in RCA: 143] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2021] [Indexed: 01/02/2023]
Abstract
Double-stranded RNA (dsRNA) is associated with most viral infections - it either constitutes the viral genome (in the case of dsRNA viruses) or is generated in host cells during viral replication. Hence, nearly all organisms have the capability of recognizing dsRNA and mounting a response, the primary aim of which is to mitigate the potential infection. In vertebrates, a set of innate immune receptors for dsRNA induce a multitude of cell-intrinsic and cell-extrinsic immune responses upon dsRNA recognition. Notably, recent studies showed that vertebrate cells can accumulate self-derived dsRNAs or dsRNA-like species upon dysregulation of several cellular processes, activating the very same immune pathways as in infected cells. On the one hand, such aberrant immune activation in the absence of infection can lead to pathogenesis of immune disorders, such as Aicardi-Goutières syndrome. On the other hand, the same innate immune reaction can be induced in a controlled setting for a therapeutic benefit, as occurs in immunotherapies. In this Review, we describe mechanisms by which immunostimulatory dsRNAs are generated in mammalian cells, either by viruses or by the host cells, and how cells respond to them, with the focus on recent developments regarding the role of cellular dsRNAs in immune modulation.
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Affiliation(s)
- Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
| | - Sun Hur
- Harvard Medical School & Boston Children's Hospital, Boston, MA, USA.
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12
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Harley ITW, Sawalha AH. Systemic lupus erythematosus as a genetic disease. Clin Immunol 2022; 236:108953. [PMID: 35149194 PMCID: PMC9167620 DOI: 10.1016/j.clim.2022.108953] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/12/2022]
Abstract
Systemic lupus erythematosus is the prototypical systemic autoimmune disease, as it is characterized both by protean multi-organ system manifestations and by the uniform presence of pathogenic autoantibodies directed against components of the nucleus. Prior to the modern genetic era, the diverse clinical manifestations of SLE suggested to many that SLE patients were unlikely to share a common genetic risk basis. However, modern genetic studies have revealed that SLE usually arises when an environmental exposure occurs in an individual with a collection of genetic risk variants passing a liability threshold. Here, we summarize the current state of the field aimed at: (1) understanding the genetic architecture of this complex disease, (2) synthesizing how this genetic risk architecture impacts cellular and molecular disease pathophysiology, (3) providing illustrative examples that highlight the rich complexity of the pathobiology of this prototypical autoimmune disease and (4) communicating this complex etiopathogenesis to patients.
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Affiliation(s)
- Isaac T W Harley
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; Human Immunology and Immunotherapy Initiative (HI(3)), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, USA; Rocky Mountain Regional Veteran's Administration Medical Center (VAMC), Medicine Service, Rheumatology Section, Aurora, CO, USA.
| | - Amr H Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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13
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Wang G, Wang Q, Wang Y, Liu C, Wang L, Chen H, Jiao T, Hu C, Lei X, Guo L, Ren L, Li M, Zhao Y, Zeng X, Zhang D, Cao B, Wang J. Presence of Anti-MDA5 Antibody and Its Value for the Clinical Assessment in Patients With COVID-19: A Retrospective Cohort Study. Front Immunol 2022; 12:791348. [PMID: 34987516 PMCID: PMC8720853 DOI: 10.3389/fimmu.2021.791348] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/01/2021] [Indexed: 02/05/2023] Open
Abstract
Background Striking similarities have been found between coronavirus disease 2019 (COVID-19) and anti-melanoma differentiation-associated gene 5 (MDA5) antibody (Ab)-related dermatomyositis, implying a shared autoinflammatory aberrance. Herein, we aim to investigate whether the anti-MDA5 Ab is present in COVID-19 and correlates with the severity and adverse outcome of COVID-19 patients. Methods and Findings We retrospectively recruited 274 adult inpatients with COVID-19 in this study, including 48, 164, and 62 cases of deaths, severe, and non-severe patients respectively. The anti-MDA5 Ab was determined by ELISA and verified by Western Blotting, which indicated that the positive rate of anti-MDA5 Ab in COVID-19 patients was 48.2% (132/274). The clinical and laboratory features, as well as outcomes between patients with positive and negative anti-MDA5 Ab were compared and we found that the anti-MDA5 Ab positive patients tended to represent severe disease (88.6% vs 66.9%, P<0.0001). We also demonstrated that the titer of anti-MDA5 Ab was significantly elevated in the non-survivals (5.95 ± 5.16 vs 8.22 ± 6.64, P=0.030) and the positive rate was also higher than that in the survivals (23.5% vs 12.0%, P=0.012). Regarding severe COVID-19 patients, we found that high titer of anti-MDA5 Ab (≥10.0 U/mL) was more prevalent in the non-survivals (31.2% vs 14.0%, P=0.006). Moreover, a dynamic analysis of anti-MDA5 Ab was conducted at different time-points of COVID-19, which revealed that early profiling of anti-MDA5 Ab could distinguish severe patients from those with non-severe ones. Conclusions Anti-MDA5 Ab was prevalent in the COVID-19 patients and high titer of this antibody is correlated with severe disease and unfavorable outcomes.
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Affiliation(s)
- Geng Wang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China.,National Health Commission of the People's Republic of China (NHC), Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qian Wang
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Yeming Wang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Department of Respiratory Medicine, Capital Medical University, Beijing, China
| | - Changzheng Liu
- National Health Commission of the People's Republic of China (NHC), Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Linghang Wang
- Laboratory of Infectious Diseases Center of Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Hong Chen
- The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tao Jiao
- National Health Commission of the People's Republic of China (NHC), Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chaojun Hu
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Xiaobo Lei
- National Health Commission of the People's Republic of China (NHC), Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Guo
- National Health Commission of the People's Republic of China (NHC), Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lili Ren
- National Health Commission of the People's Republic of China (NHC), Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengtao Li
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Yan Zhao
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Xiaofeng Zeng
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science & Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Dingyu Zhang
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology and Wuhan Jin Yin-Tan Hospital, China Academy of Sciences (CAS), Wuhan, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China.,Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Department of Respiratory Medicine, Capital Medical University, Beijing, China
| | - Jianwei Wang
- National Health Commission of the People's Republic of China (NHC), Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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14
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Ferreté-Bonastre AG, Cortés-Hernández J, Ballestar E. What can we learn from DNA methylation studies in lupus? Clin Immunol 2022; 234:108920. [PMID: 34973429 DOI: 10.1016/j.clim.2021.108920] [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: 11/03/2021] [Revised: 12/23/2021] [Accepted: 12/26/2021] [Indexed: 11/17/2022]
Abstract
During the past twenty years, a wide range of studies have established the existence of epigenetic alterations, particularly DNA methylation changes, in lupus. Epigenetic changes might have different contributions in children-onset versus adult-onset lupus. DNA methylation alterations have been identified and characterized in relation to disease activity and damage, different lupus subtypes and responses to drugs. However, to date there has been no practical application of these findings in the clinical milieu. In this article, we provide a review of key studies showing the relationship between DNA methylation and the many clinical aspects related to lupus. We also propose several options, in relation to the range of methodological developments and experimental design, that could optimize these findings and make them amenable for use in clinical practice.
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Affiliation(s)
| | | | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain; Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, 200241, China.
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15
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Immunogenetics of Lupus Erythematosus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:213-257. [DOI: 10.1007/978-3-030-92616-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Nln I, Fernandez-Ruiz R, Wampler Muskardin TL, Paredes JL, Blazer AD, Tuminello S, Attur M, Iturrate E, Petrilli CM, Abramson SB, Chakravarti A, Niewold TB. Interferon pathway lupus risk alleles modulate risk of death from acute COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.11.01.21265766. [PMID: 34751274 PMCID: PMC8575145 DOI: 10.1101/2021.11.01.21265766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Type I interferon (IFN) is critical in our defense against viral infections. Increased type I IFN pathway activation is a genetic risk factor for systemic lupus erythematosus (SLE), and a number of common risk alleles contribute to the high IFN trait. We hypothesized that these common gain-of-function IFN pathway alleles may be associated with protection from mortality in acute COVID-19. We studied patients admitted with acute COVID-19 (756 European-American and 398 African-American ancestry). Ancestral backgrounds were analyzed separately, and mortality after acute COVID-19 was the primary outcome. In European-American ancestry, we found that a haplotype of interferon regulatory factor 5 (IRF5) and alleles of protein kinase cGMP-dependent 1 (PRKG1) were associated with mortality from COVID-19. Interestingly, these were much stronger risk factors in younger patients (OR=29.2 for PRKG1 in ages 45-54). Variants in the IRF7 and IRF8 genes were associated with mortality from COVID-19 in African-American subjects, and these genetic effects were more pronounced in older subjects. Combining genetic information with blood biomarker data such as C-reactive protein, troponin, and D-dimer resulted in significantly improved predictive capacity, and in both ancestral backgrounds the risk genotypes were most relevant in those with positive biomarkers (OR for death between 14 and 111 in high risk genetic/biomarker groups). This study confirms the critical role of the IFN pathway in defense against COVID-19 and viral infections, and supports the idea that some common SLE risk alleles exert protective effects in anti-viral immunity. BACKGROUND We find that a number of IFN pathway lupus risk alleles significantly impact mortality following COVID-19 infection. These data support the idea that type I IFN pathway risk alleles for autoimmune disease may persist in high frequency in modern human populations due to a benefit in our defense against viral infections. TRANSLATIONAL SIGNIFICANCE We develop multivariate prediction models which combine genetics and known biomarkers of severity to result in greatly improved prediction of mortality in acute COVID-19. The specific associated alleles provide some clues about key points in our defense against COVID-19.
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Affiliation(s)
- Ilona Nln
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY
| | - Ruth Fernandez-Ruiz
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY
| | | | | | - Ashira D Blazer
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY
| | - Stephanie Tuminello
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY
| | - Mukundan Attur
- Divison of Rheumatology, Department of Medicine, NYU Grossman School of Medicine, New York, NY
| | - Eduardo Iturrate
- Department of Medicine, NYU Grossman School of Medicine, New York, NY
| | | | - Steven B Abramson
- Department of Medicine, NYU Grossman School of Medicine, New York, NY
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY
| | - Timothy B Niewold
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY
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17
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Brinkmeyer-Langford C, Amstalden K, Konganti K, Hillhouse A, Lawley K, Perez-Gomez A, Young CR, Welsh CJ, Threadgill DW. Resilience in Long-Term Viral Infection: Genetic Determinants and Interactions. Int J Mol Sci 2021; 22:ijms222111379. [PMID: 34768809 PMCID: PMC8584141 DOI: 10.3390/ijms222111379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/16/2021] [Accepted: 10/20/2021] [Indexed: 02/06/2023] Open
Abstract
Virus-induced neurological sequelae resulting from infection by Theiler's murine encephalomyelitis virus (TMEV) are used for studying human conditions ranging from epileptic seizures to demyelinating disease. Mouse strains are typically considered susceptible or resistant to TMEV infection based on viral persistence and extreme phenotypes, such as demyelination. We have identified a broader spectrum of phenotypic outcomes by infecting strains of the genetically diverse Collaborative Cross (CC) mouse resource. We evaluated the chronic-infection gene expression profiles of hippocampi and thoracic spinal cords for 19 CC strains in relation to phenotypic severity and TMEV persistence. Strains were clustered based on similar phenotypic profiles and TMEV levels at 90 days post-infection, and we categorized distinct TMEV response profiles. The three most common profiles included "resistant" and "susceptible," as before, as well as a "resilient" TMEV response group which experienced both TMEV persistence and mild neurological phenotypes even at 90 days post-infection. Each profile had a distinct gene expression signature, allowing the identification of pathways and networks specific to each TMEV response group. CC founder haplotypes for genes involved in these pathways/networks revealed candidate response-specific alleles. These alleles demonstrated pleiotropy and epigenetic (miRNA) regulation in long-term TMEV infection, with particular relevance for resilient mouse strains.
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Affiliation(s)
- Candice Brinkmeyer-Langford
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA; (K.A.); (K.L.); (A.P.-G.); (C.R.Y.); (C.J.W.)
- Correspondence:
| | - Katia Amstalden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA; (K.A.); (K.L.); (A.P.-G.); (C.R.Y.); (C.J.W.)
| | - Kranti Konganti
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX 77843, USA; (K.K.); (A.H.); (D.W.T.)
| | - Andrew Hillhouse
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX 77843, USA; (K.K.); (A.H.); (D.W.T.)
| | - Koedi Lawley
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA; (K.A.); (K.L.); (A.P.-G.); (C.R.Y.); (C.J.W.)
| | - Aracely Perez-Gomez
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA; (K.A.); (K.L.); (A.P.-G.); (C.R.Y.); (C.J.W.)
| | - Colin R. Young
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA; (K.A.); (K.L.); (A.P.-G.); (C.R.Y.); (C.J.W.)
| | - C. Jane Welsh
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA; (K.A.); (K.L.); (A.P.-G.); (C.R.Y.); (C.J.W.)
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA
| | - David W. Threadgill
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX 77843, USA; (K.K.); (A.H.); (D.W.T.)
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX 77843, USA
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18
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Song B, Chen Y, Liu X, Yuan F, Tan EYJ, Lei Y, Song N, Han Y, Pascal BD, Griffin PR, Luo C, Wu B, Luo D, Zheng J. Ordered assembly of the cytosolic RNA-sensing MDA5-MAVS signaling complex via binding to unanchored K63-linked poly-ubiquitin chains. Immunity 2021; 54:2218-2230.e5. [PMID: 34644557 DOI: 10.1016/j.immuni.2021.09.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 05/05/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022]
Abstract
The RNA sensor MDA5 recruits the signaling adaptor MAVS to initiate type I interferon signaling and downstream antiviral responses, a process that requires K63-linked polyubiquitin chains. Here, we examined the mechanisms whereby K63-polyUb chain regulate MDA5 activation. Only long unanchored K63-polyUbn (n ≥ 8) could mediate tetramerization of the caspase activation and recruitment domains of MDA5 (MDA5CARDs). Cryoelectron microscopy structures of a polyUb13-bound MDA5CARDs tetramer and a polyUb11-bound MDA5CARDs-MAVSCARD assembly revealed a tower-like formation, wherein eight Ubs tethered along the outer rim of the helical shell, bridging MDA5CARDs and MAVSCARD tetramers into proximity. ATP binding and hydrolysis promoted the stabilization of RNA-bound MDA5 prior to MAVS activation via allosteric effects on CARDs-polyUb complex. Abundant ATP prevented basal activation of apo MDA5. Our findings reveal the ordered assembly of a MDA5 signaling complex competent to recruit and activate MAVS and highlight differences with RIG-I in terms of CARD orientation and Ub sensing that suggest different abilities to induce antiviral responses.
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Affiliation(s)
- Bin Song
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yun Chen
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xin Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Fei Yuan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Eddie Yong Jun Tan
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore
| | - Yixuan Lei
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ning Song
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yinqi Han
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | | | - Patrick R Griffin
- The Scripps Research Institute, Department of Molecular Medicine, Jupiter, FL 33458, USA
| | - Cheng Luo
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bin Wu
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore
| | - Jie Zheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.
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19
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Deng H, Yan X, Yuan L. Human genetic basis of coronavirus disease 2019. Signal Transduct Target Ther 2021; 6:344. [PMID: 34545062 PMCID: PMC8450706 DOI: 10.1038/s41392-021-00736-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/28/2021] [Accepted: 08/08/2021] [Indexed: 02/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in considerable morbidity and mortality worldwide. COVID-19 incidence, severity, and mortality rates differ greatly between populations, genders, ABO blood groups, human leukocyte antigen (HLA) genotypes, ethnic groups, and geographic backgrounds. This highly heterogeneous SARS-CoV-2 infection is multifactorial. Host genetic factors such as variants in the angiotensin-converting enzyme gene (ACE), the angiotensin-converting enzyme 2 gene (ACE2), the transmembrane protease serine 2 gene (TMPRSS2), along with HLA genotype, and ABO blood group help to explain individual susceptibility, severity, and outcomes of COVID-19. This review is focused on COVID-19 clinical and viral characteristics, pathogenesis, and genetic findings, with particular attention on genetic diversity and variants. The human genetic basis could provide scientific bases for disease prediction and targeted therapy to address the COVID-19 scourge.
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Affiliation(s)
- Hao Deng
- grid.216417.70000 0001 0379 7164Health Management Center, the Third Xiangya Hospital, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Disease Genome Research Center, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Xue Yan
- grid.216417.70000 0001 0379 7164Health Management Center, the Third Xiangya Hospital, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Disease Genome Research Center, Central South University, Changsha, China
| | - Lamei Yuan
- grid.216417.70000 0001 0379 7164Health Management Center, the Third Xiangya Hospital, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Disease Genome Research Center, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, China
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20
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Rychkov D, Neely J, Oskotsky T, Yu S, Perlmutter N, Nititham J, Carvidi A, Krueger M, Gross A, Criswell LA, Ashouri JF, Sirota M. Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis. Front Immunol 2021; 12:638066. [PMID: 34177888 PMCID: PMC8223752 DOI: 10.3389/fimmu.2021.638066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/17/2021] [Indexed: 01/20/2023] Open
Abstract
There is an urgent need to identify biomarkers for diagnosis and disease activity monitoring in rheumatoid arthritis (RA). We leveraged publicly available microarray gene expression data in the NCBI GEO database for whole blood (N=1,885) and synovial (N=284) tissues from RA patients and healthy controls. We developed a robust machine learning feature selection pipeline with validation on five independent datasets culminating in 13 genes: TNFAIP6, S100A8, TNFSF10, DRAM1, LY96, QPCT, KYNU, ENTPD1, CLIC1, ATP6V0E1, HSP90AB1, NCL and CIRBP which define the RA score and demonstrate its clinical utility: the score tracks the disease activity DAS28 (p = 7e-9), distinguishes osteoarthritis (OA) from RA (OR 0.57, p = 8e-10) and polyJIA from healthy controls (OR 1.15, p = 2e-4) and monitors treatment effect in RA (p = 2e-4). Finally, the immunoblotting analysis of six proteins on an independent cohort confirmed two proteins, TNFAIP6/TSG6 and HSP90AB1/HSP90.
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Affiliation(s)
- Dmitry Rychkov
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, United States
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States
| | - Jessica Neely
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States
| | - Tomiko Oskotsky
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, United States
| | - Steven Yu
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, United States
| | - Noah Perlmutter
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Joanne Nititham
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Alexander Carvidi
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Melissa Krueger
- Department of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Andrew Gross
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Lindsey A. Criswell
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
- Institute for Human Genetics (IHG), University of California San Francisco, San Francisco, CA, United States
- Department of Medicine, University of California San Francisco, San Francisco, CA, United States
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, United States
| | - Judith F. Ashouri
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, United States
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States
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21
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Singh B, Maiti GP, Zhou X, Fazel-Najafabadi M, Bae SC, Sun C, Terao C, Okada Y, Chua KH, Kochi Y, Guthridge JM, Zhang H, Weirauch M, James JA, Harley JB, Varshney GK, Looger LL, Nath SK. Lupus susceptibility region containing CDKN1B rs34330 mechanistically influences expression and function of multiple target genes, also linked to proliferation and apoptosis. Arthritis Rheumatol 2021; 73:2303-2313. [PMID: 33982894 DOI: 10.1002/art.41799] [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] [Received: 08/26/2020] [Accepted: 05/04/2021] [Indexed: 11/10/2022]
Abstract
OBJECTIVE A recent genome-wide association study (GWAS) reported a significant genetic association between rs34330 of cyclin-dependent kinase inhibitor 1B (CDKN1B) and risk of systemic lupus erythematosus (SLE) in Han Chinese. This study aims to validate the reported association and elucidate the biochemical mechanisms underlying the variant's effect. METHODS We performed allelic association with SLE followed by meta-analysis across 11 independent cohorts (n=28,872). We applied in silico bioinformatics and experimental validation in SLE-relevant cell lines to determine the functional consequences of rs34330. RESULTS We replicated genetic association between SLE and rs34330 (Pmeta =5.29x10-22 , OR (95% CI)=0.84 (0.81-0.87)). Follow-up bioinformatics and eQTL analysis suggest that rs34330 is located in active chromatin and potentially regulates several target genes. Using luciferase and ChIP-qPCR, we demonstrated substantial allele-specific promoter and enhancer activity, and allele-specific binding of three histone marks (H3K27ac, H3K4me3, H3K4me1), RNA pol II, CTCF, and a critical immune transcription factor (IRF-1). Chromosome conformation capture (3C) detected long-range chromatin interactions between rs34330 and the promoters of neighboring genes APOLD1 and DDX47, and effects on CDKN1B and the other target genes were directly validated by CRISPR-based genome editing. Finally, CRISPR-dCas9-based epigenetic activation/silencing confirmed these results. Gene-edited cell lines also showed higher levels of proliferation and apoptosis. CONCLUSION Collectively, these findings suggest a mechanism whereby the rs34330 risk allele (C) influences the presence of histone marks, RNA pol II, and the IRF-1 transcription factor to regulate expression of several target genes linked to proliferation and apoptosis, which potentially underlie the association of rs34330 with SLE.
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Affiliation(s)
- Bhupinder Singh
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Guru P Maiti
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Xujie Zhou
- Renal Division, Peking University First Hospital, Peking University, Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
| | - Mehdi Fazel-Najafabadi
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Republic of Korea
| | - Celi Sun
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan.,Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Joel M Guthridge
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University, Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
| | - Matthew Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE), Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, and the US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Judith A James
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, and the US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Gaurav K Varshney
- Genes and Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Loren L Looger
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
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22
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Lai D, Kapoor M, Wetherill L, Schwandt M, Ramchandani VA, Goldman D, Chao M, Almasy L, Bucholz K, Hart RP, Kamarajan C, Meyers JL, Nurnberger JI, Tischfield J, Edenberg HJ, Schuckit M, Goate A, Scott DM, Porjesz B, Agrawal A, Foroud T. Genome-wide admixture mapping of DSM-IV alcohol dependence, criterion count, and the self-rating of the effects of ethanol in African American populations. Am J Med Genet B Neuropsychiatr Genet 2021; 186:151-161. [PMID: 32652861 PMCID: PMC9376735 DOI: 10.1002/ajmg.b.32805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/06/2020] [Accepted: 06/01/2020] [Indexed: 12/15/2022]
Abstract
African Americans (AA) have lower prevalence of alcohol dependence and higher subjective response to alcohol than European Americans. Genome-wide association studies (GWAS) have identified genes/variants associated with alcohol dependence specifically in AA; however, the sample sizes are still not large enough to detect variants with small effects. Admixture mapping is an alternative way to identify alcohol dependence genes/variants that may be unique to AA. In this study, we performed the first admixture mapping of DSM-IV alcohol dependence diagnosis, DSM-IV alcohol dependence criterion count, and two scores from the self-rating of effects of ethanol (SRE) as measures of response to alcohol: the first five times of using alcohol (SRE-5) and average of SRE across three times (SRE-T). Findings revealed a region on chromosome 4 that was genome-wide significant for SRE-5 (p value = 4.18E-05). Fine mapping did not identify a single causal variant to be associated with SRE-5; instead, conditional analysis concluded that multiple variants collectively explained the admixture mapping signal. PPARGC1A, a gene that has been linked to alcohol consumption in previous studies, is located in this region. Our finding suggests that admixture mapping is a useful tool to identify genes/variants that may have been missed by current GWAS approaches in admixed populations.
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Affiliation(s)
- Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Manav Kapoor
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Melanie Schwandt
- Office of the Clinical Director, National Institute on Alcohol Abuse & Alcoholism, Bethesda, MD
| | - Vijay A. Ramchandani
- Section on Human Psychopharmacology, Division of Intramural Clinical and Biological Research, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD
| | - David Goldman
- Office of the Clinical Director, National Institute on Alcohol Abuse & Alcoholism, Bethesda, MD
| | - Michael Chao
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Kathleen Bucholz
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
| | - Ronald P. Hart
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ
| | - Chella Kamarajan
- Henri Begleiter Neurodynamics Lab, Department of Psychiatry, State University of New York, Downstate Medical Center, Brooklyn, NY
| | - Jacquelyn L. Meyers
- Henri Begleiter Neurodynamics Lab, Department of Psychiatry, State University of New York, Downstate Medical Center, Brooklyn, NY
| | - John I. Nurnberger
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN
| | - Jay Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ
| | - Howard J. Edenberg
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
| | - Marc Schuckit
- Department of Psychiatry, University of California, San Diego Medical School, San Diego, CA
| | - Alison Goate
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY
| | - Denise M. Scott
- Departments of Pediatrics and Human Genetics, Howard University, Washington, DC
| | - Bernice Porjesz
- Henri Begleiter Neurodynamics Lab, Department of Psychiatry, State University of New York, Downstate Medical Center, Brooklyn, NY
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
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23
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Grolmusz VK, Bozsik A, Papp J, Patócs A. Germline Genetic Variants of Viral Entry and Innate Immunity May Influence Susceptibility to SARS-CoV-2 Infection: Toward a Polygenic Risk Score for Risk Stratification. Front Immunol 2021; 12:653489. [PMID: 33763088 PMCID: PMC7982482 DOI: 10.3389/fimmu.2021.653489] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 02/16/2021] [Indexed: 12/15/2022] Open
Abstract
The ongoing COVID-19 pandemic caused by the novel coronavirus, SARS-CoV-2 has affected all aspects of human society with a special focus on healthcare. Although older patients with preexisting chronic illnesses are more prone to develop severe complications, younger, healthy individuals might also exhibit serious manifestations. Previous studies directed to detect genetic susceptibility factors for earlier epidemics have provided evidence of certain protective variations. Following SARS-CoV-2 exposure, viral entry into cells followed by recognition and response by the innate immunity are key determinants of COVID-19 development. In the present review our aim was to conduct a thorough review of the literature on the role of single nucleotide polymorphisms (SNPs) as key agents affecting the viral entry of SARS-CoV-2 and innate immunity. Several SNPs within the scope of our approach were found to alter susceptibility to various bacterial and viral infections. Additionally, a multitude of studies confirmed genetic associations between the analyzed genes and autoimmune diseases, underlining the versatile immune consequences of these variants. Based on confirmed associations it is highly plausible that the SNPs affecting viral entry and innate immunity might confer altered susceptibility to SARS-CoV-2 infection and its complex clinical consequences. Anticipating several COVID-19 genomic susceptibility loci based on the ongoing genome wide association studies, our review also proposes that a well-established polygenic risk score would be able to clinically leverage the acquired knowledge.
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Affiliation(s)
- Vince Kornél Grolmusz
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
- Hereditary Tumors Research Group, Eötvös Loránd Research Network—Semmelweis University, Budapest, Hungary
| | - Anikó Bozsik
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
- Hereditary Tumors Research Group, Eötvös Loránd Research Network—Semmelweis University, Budapest, Hungary
| | - János Papp
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
- Hereditary Tumors Research Group, Eötvös Loránd Research Network—Semmelweis University, Budapest, Hungary
| | - Attila Patócs
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
- Hereditary Tumors Research Group, Eötvös Loránd Research Network—Semmelweis University, Budapest, Hungary
- Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
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24
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Zhang S, Chu C, Wu Z, Liu F, Xie J, Yang Y, Qiu H. IFIH1 Contributes to M1 Macrophage Polarization in ARDS. Front Immunol 2021; 11:580838. [PMID: 33519803 PMCID: PMC7841399 DOI: 10.3389/fimmu.2020.580838] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/02/2020] [Indexed: 12/22/2022] Open
Abstract
Accumulated evidence has demonstrated that the macrophage phenotypic switch from M0 to M1 is crucial in the initiation of the inflammatory process of acute respiratory distress syndrome (ARDS). Better insight into the molecular control of M1 macrophages in ARDS may identify potential therapeutic targets. In the current study, 36 candidate genes associated with the severity of ARDS and simultaneously involved in M1-polarized macrophages were first screened through a weighted network algorithm on all gene expression profiles from the 26 ARDS patients and empirical Bayes analysis on the gene expression profiles of macrophages. STAT1, IFIH1, GBP1, IFIT3, and IRF1 were subsequently identified as hub genes according to connectivity degree analysis and multiple external validations. Among these candidate genes, IFIH1 had the strongest connection with ARDS through the RobustRankAggreg algorithm. It was selected as a crucial gene for further investigation. For in vitro validation, the RAW264.7 cell line and BMDMs were transfected with shIFIH1 lentivirus and plasmid expression vectors of IFIH1. Cellular experimental studies further confirmed that IFIH1 was a novel regulator for promoting M1 macrophage polarization. Moreover, gene set enrichment analysis (GSEA) and in vitro validations indicated that IFIH1 regulated M1 polarization by activating IRF3. In addition, previous studies demonstrated that activation of IFIH1-IRF3 was stimulated by viral RNAs or RNA mimics. Surprisingly, the current study found that LPS could also induce IFIH1-IRF3 activation via a MyD88-dependent mechanism. We also found that only IFIH1 expression without LPS or RNA mimic stimulation could not affect IRF3 activation and M1 macrophage polarization. These findings were validated on two types of macrophages, RAW264.7 cells and BMDMs, which expanded the knowledge on the inflammatory roles of IFIH1 and IRF3, suggesting IFIH1 as a potential target for ARDS treatment.
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Affiliation(s)
- Shi Zhang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Cuilin Chu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Zongsheng Wu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Feng Liu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Jianfeng Xie
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Yi Yang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Haibo Qiu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
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25
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Braegelmann C, Fetter T, Niebel D, Dietz L, Bieber T, Wenzel J. Immunostimulatory Endogenous Nucleic Acids Perpetuate Interface Dermatitis-Translation of Pathogenic Fundamentals Into an In Vitro Model. Front Immunol 2021; 11:622511. [PMID: 33505404 PMCID: PMC7831152 DOI: 10.3389/fimmu.2020.622511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Interface dermatitis is a histopathological pattern mirroring a distinct cytotoxic immune response shared by a number of clinically diverse inflammatory skin diseases amongst which lichen planus and cutaneous lupus erythematosus are considered prototypic. Interface dermatitis is characterized by pronounced cytotoxic immune cell infiltration and necroptotic keratinocytes at the dermoepidermal junction. The initial inflammatory reaction is established by cytotoxic immune cells that express CXC chemokine receptor 3 and lesional keratinocytes that produce corresponding ligands, CXC motif ligands 9/10/11, recruiting the effector cells to the site of inflammation. During the resulting anti-epithelial attack, endogenous immune complexes and nucleic acids are released from perishing keratinocytes, which are then perceived by the innate immune system as danger signals. Keratinocytes express a distinct signature of pattern recognition receptors and binding of endogenous nucleic acid motifs to these receptors results in interferon-mediated immune responses and further enhancement of CXC chemokine receptor 3 ligand production. In this perspective article, we will discuss the role of innate nucleic acid sensing as a common mechanism in the perpetuation of clinically heterogeneous diseases featuring interface dermatitis based on own data and a review of the literature. Furthermore, we will introduce a keratinocyte-specific in vitro model of interface dermatitis as follows: Stimulation of human keratinocytes with endogenous nucleic acids alone and in combination with interferon gamma leads to pronounced production of distinct cytokines, which are essential in the pathogenesis of interface dermatitis. This experimental approach bears the capability to investigate potential therapeutics in this group of diseases with unmet medical need.
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Affiliation(s)
| | - Tanja Fetter
- Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany
| | - Dennis Niebel
- Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany
| | - Lara Dietz
- Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany
| | - Thomas Bieber
- Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany
| | - Joerg Wenzel
- Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany
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26
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Kirsch-Volders M, Bolognesi C, Ceppi M, Bruzzone M, Fenech M. Micronuclei, inflammation and auto-immune disease. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 786:108335. [PMID: 33339583 DOI: 10.1016/j.mrrev.2020.108335] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/28/2020] [Accepted: 09/03/2020] [Indexed: 12/16/2022]
Abstract
Auto-immune diseases (AUD) are characterized by an immune response to antigenic components of the host itself. The etiology of AUD is not well understood. The available evidence points to an interaction between genetic, epigenetic, environmental, infectious and life-style factors. AUD are more prevalent in women than in men; sex hormones play a crucial role in this sex bias. Micronuclei (MN) emerged as a new player in the induction of AUD, based on the capacity of DNA-sensors to detect self-DNA that leaks into the cytoplasm from disrupted MN and induce the cGAS-STING pathway triggering an innate auto-immune response and chronic inflammation. It was found that inflammation can induce MN and MN can induce inflammation, leading to a vicious inflammation-oxidative-DNA damage-MN-formation-chromothripsis cycle. MN originating from sex chromosome-loss may induce inflammation and AUD. We performed a systematic review of studies reporting MN in patients with systemic or organ-specific AUD. A meta-analysis was performed on lymphocyte MN in diabetes mellitus (10 studies, 457 patients/290 controls) and Behcet's disease (3 studies, 100 patients/70 controls) and for buccal MN in diabetes mellitus (11 studies, 507 patients/427 controls). A statistically significant increase in patients compared to controls was found in the meta-analyses providing an indication of an association between MN and AUD. A 36%-higher mean-MRi in buccal cells (3.8+/-0.7) was found compared to lymphocytes (2.8+/-0.7)(P = 0.01). The meta-MRi in lymphocytes and buccal cells (1.7 and 3.0 respectively) suggest that buccal cells may be more sensitive. To assess their relative sensitivity, studies with measurements from the same subjects would be desirable. It is important that future studies (i) investigate, in well-designed powered studies, the prospective association of MN-formation with AUD and (ii) explore the molecular mechanisms by which chromosome shattering in MN and the release of chromatin fragments from MN lead to the formation of auto-antibodies.
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Affiliation(s)
- Micheline Kirsch-Volders
- Laboratory for Cell Genetics, Department Biology, Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Claudia Bolognesi
- Environmental Carcinogenesis Unit, Ospedale Policlinico San Martino, 16132 Genoa, Italy.
| | - Marcello Ceppi
- Unit of Clinical Epidemiology, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Marco Bruzzone
- Unit of Clinical Epidemiology, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Michael Fenech
- Genome Health Foundation, North Brighton, 5048, Australia; Clinical and Health Sciences, University of South Australia, SA 5000, Australia
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27
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Maiti AK. The African-American population with a low allele frequency of SNP rs1990760 (T allele) in IFIH1 predicts less IFN-beta expression and potential vulnerability to COVID-19 infection. Immunogenetics 2020; 72:387-391. [PMID: 32737579 PMCID: PMC7394703 DOI: 10.1007/s00251-020-01174-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/23/2020] [Indexed: 12/13/2022]
Abstract
Covid-19 has caused worldwide devastation. IFIH1 is a pattern recognition receptor that senses coronavirus RNA and triggers interferon production as a first line of viral immune defense. The role of IFIH1 polymorphism, rs1990760 (C>T; aaA946T) in the epidemiology of viral infection is well studied, and the minor allele T resists viral infection. Knock-in mice with mutated IFIH1 protein (946T) for this allele have enhanced interferon production and protection from lethal viral infection. The minor allele frequency (Tmaf) varies widely from Africans (0.06 to 0.35) to Chinese (0.19 to 0.23) to Caucasians (0.56 to 0.69). During the initial days of infection when the social restrictions were not imposed, I show that the infection rate in Italy was lower as expected from its higher Tmaf (0.56) than that in China (Tmaf for southern China, 0.23). The infection rate in the USA and Spain was intermediate between those two countries despite higher Caucasian overall Tmaf (0.69), perhaps due to a more admixed African population in these countries. These analyses suggest that African-Americans and Chinese with low Tmaf of rs1990760 are more vulnerable to SARS-COV2 infection, apart from other genetic factors or socioeconomic conditions in these population. Taken together, an IFN-beta supplement might aid in preventing COVID-19 infection and help in development of herd immunity.
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Affiliation(s)
- Amit K Maiti
- Department of Genetics and Genomics, Mydnavar, 2645 Somerset Boulevard, Troy, MI, 48084, USA.
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28
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Liu G, Gack MU. Distinct and Orchestrated Functions of RNA Sensors in Innate Immunity. Immunity 2020; 53:26-42. [PMID: 32668226 PMCID: PMC7367493 DOI: 10.1016/j.immuni.2020.03.017] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/07/2020] [Accepted: 03/07/2020] [Indexed: 12/21/2022]
Abstract
Faithful maintenance of immune homeostasis relies on the capacity of the cellular immune surveillance machinery to recognize "nonself", such as the presence of pathogenic RNA. Several families of pattern-recognition receptors exist that detect immunostimulatory RNA and then induce cytokine-mediated antiviral and proinflammatory responses. Here, we review the distinct features of bona fide RNA sensors, Toll-like receptors and retinoic-acid inducible gene-I (RIG-I)-like receptors in particular, with a focus on their functional specificity imposed by cell-type-dependent expression, subcellular localization, and ligand preference. Furthermore, we highlight recent advances on the roles of nucleotide-binding oligomerization domain (NOD)-like receptors and DEAD-box or DEAH-box RNA helicases in an orchestrated RNA-sensing network and also discuss the relevance of RNA sensor polymorphisms in human disease.
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Affiliation(s)
- GuanQun Liu
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Michaela U Gack
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA.
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29
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Ziyatdinov A, Parker MM, Vaysse A, Beaty TH, Kraft P, Cho MH, Aschard H. Mixed-model admixture mapping identifies smoking-dependent loci of lung function in African Americans. Eur J Hum Genet 2020; 28:656-668. [PMID: 31836859 PMCID: PMC7171162 DOI: 10.1038/s41431-019-0545-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 11/08/2022] Open
Abstract
Admixture mapping has led to the discovery of many genes associated with differential disease risk by ancestry, highlighting the importance of ancestry-based approaches to association studies. However, the potential of admixture mapping in deciphering the interplay between genes and environment exposures has been seldom explored. Here we performed a genome-wide screening of local ancestry-smoking interactions for five spirometric lung function phenotypes in 3300 African Americans from the COPDGene study. To account for population structure and outcome heterogeneity across exposure groups, we developed a multi-component linear mixed model for mapping gene-environment interactions and empirically showed its robustness and increased power. When applied to the COPDGene study, our approach identified two 11p15.2-3 and 2q37 loci, exhibiting local ancestry-smoking interactions at genome-wide significant level, which would have been missed by standard single-nucleotide polymorphism analyses. These two loci harbor the PARVA and RAB17 genes previously recognized to be involved in smoking behavior. Overall, our study provides the first evidence for potential synergistic effects between African ancestry and smoking on pulmonary function, and underlines the importance of ethnic diversity in genetic studies.
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Affiliation(s)
- Andrey Ziyatdinov
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Amaury Vaysse
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
| | - Terri H Beaty
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Hugues Aschard
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
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30
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Abstract
PURPOSE OF REVIEW Lupus nephritis (LN) is a serious manifestation of systemic lupus erythematosus and is characterized by proteinuria and renal failure. Proteinuria is a marker of poor prognosis and is attributed to podocyte loss and dysfunction. It is often debated whether these cells are innocent bystanders or active participants in the pathogenesis of glomerulonephritis. RECENT FINDINGS Podocytes share many elements of the innate and adaptive immune system. Specifically, they produce and express complement components and receptors which when dysregulated appear to contribute to podocyte damage and LN. In parallel, podocytes express major histocompatibility complex and co-stimulatory molecules which may be involved in local immune events. Podocyte-specific cytotoxic cells and possibly other immune cells contribute to glomerular damage. Autoantibodies present in lupus sera enter podocytes to upregulate calcium/calmodulin kinase which in turn compromises their structure and function. SUMMARY More recent studies point to the restoration of podocyte function using cell targeted approaches to prevent and treat LN. These strategies along with podocyte involvement in the pathogenesis of LN will be addressed in this review.
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31
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Pang H, Luo S, Huang G, Xia Y, Xie Z, Zhou Z. Advances in Knowledge of Candidate Genes Acting at the Beta-Cell Level in the Pathogenesis of T1DM. Front Endocrinol (Lausanne) 2020; 11:119. [PMID: 32226409 PMCID: PMC7080653 DOI: 10.3389/fendo.2020.00119] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/24/2020] [Indexed: 12/12/2022] Open
Abstract
T1DM (type 1 diabetes mellitus), which results from the irreversible elimination of beta-cells mediated by autoreactive T cells, is defined as an autoimmune disease. It is widely accepted that T1DM is caused by a combination of genetic and environmental factors, but the precise underlying molecular mechanisms are still unknown. To date, more than 50 genetic risk regions contributing to the pathogenesis of T1DM have been identified by GWAS (genome-wide association studies). Notably, more than 60% of the identified candidate genes are expressed in islets and beta-cells, which makes it plausible that these genes act at the beta-cell level and play a key role in the pathogenesis of T1DM. In this review, we focus on the current status of candidate genes that act at the beta-cell level by regulating the innate immune response and antiviral activity, affecting susceptibility to proapoptotic stimuli and influencing the pancreatic beta-cell phenotype.
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Affiliation(s)
- Haipeng Pang
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Diseases, Changsha, China
| | - Shuoming Luo
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Diseases, Changsha, China
| | - Gan Huang
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Diseases, Changsha, China
| | - Ying Xia
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Diseases, Changsha, China
| | - Zhiguo Xie
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Diseases, Changsha, China
- *Correspondence: Zhiguo Xie
| | - Zhiguang Zhou
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Diseases, Changsha, China
- Zhiguang Zhou
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32
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Keskitalo S, Haapaniemi E, Einarsdottir E, Rajamäki K, Heikkilä H, Ilander M, Pöyhönen M, Morgunova E, Hokynar K, Lagström S, Kivirikko S, Mustjoki S, Eklund K, Saarela J, Kere J, Seppänen MRJ, Ranki A, Hannula-Jouppi K, Varjosalo M. Novel TMEM173 Mutation and the Role of Disease Modifying Alleles. Front Immunol 2019; 10:2770. [PMID: 31866997 PMCID: PMC6907089 DOI: 10.3389/fimmu.2019.02770] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/12/2019] [Indexed: 02/02/2023] Open
Abstract
Upon binding to pathogen or self-derived cytosolic nucleic acids cyclic GMP-AMP synthase (cGAS) triggers the production of cGAMP that further activates transmembrane protein STING. Upon activation STING translocates from ER via Golgi to vesicles. Monogenic STING gain-of-function mutations cause early-onset type I interferonopathy, with disease presentation ranging from fatal vasculopathy to mild chilblain lupus. Molecular mechanisms underlying the variable phenotype-genotype correlation are presently unclear. Here, we report a novel gain-of-function G207E STING mutation causing a distinct phenotype with alopecia, photosensitivity, thyroid dysfunction, and features of STING-associated vasculopathy with onset in infancy (SAVI), such as livedo reticularis, skin vasculitis, nasal septum perforation, facial erythema, and bacterial infections. Polymorphism in TMEM173 and IFIH1 showed variable penetrance in the affected family, implying contribution to varying phenotype spectrum. The G207E mutation constitutively activates inflammation-related pathways in vitro, and causes aberrant interferon signature and inflammasome activation in patient PBMCs. Treatment with Janus kinase 1 and 2 (JAK1/2) inhibitor baricitinib was beneficiary for a vasculitic ulcer, induced hair regrowth and improved overall well-being in one patient. Protein-protein interactions propose impaired cellular trafficking of G207E mutant. These findings reveal the molecular landscape of STING and propose common polymorphisms in TMEM173 and IFIH1 as likely modifiers of the phenotype.
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Affiliation(s)
- Salla Keskitalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Emma Haapaniemi
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, University of Helsinki, Helsinki, Finland.,Department of Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Elisabet Einarsdottir
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Kristiina Rajamäki
- Faculty of Medicine, University of Helsinki, Clinicum, Helsinki, Finland
| | - Hannele Heikkilä
- Department of Dermatology and Allergology, Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Mette Ilander
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Minna Pöyhönen
- Department of Clinical Genetics, University of Helsinki, Helsinki University Hospital, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Ekaterina Morgunova
- Department of Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Kati Hokynar
- Clinical Research Institute HUCH Ltd., Helsinki, Finland
| | - Sonja Lagström
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Sirpa Kivirikko
- Department of Clinical Genetics, University of Helsinki, Helsinki University Hospital, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.,Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Kari Eklund
- Faculty of Medicine, University of Helsinki, Clinicum, Helsinki, Finland.,Department of Rheumatology, Helsinki University Hospital, Helsinki, Finland
| | - Janna Saarela
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Juha Kere
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, United Kingdom
| | - Mikko R J Seppänen
- Rare Disease Center, Children's Hospital, University of Helsinki, Helsinki University Hospital, Helsinki, Finland.,Immunodeficiency Unit, Inflammation Center, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Annamari Ranki
- Department of Dermatology and Allergology, Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Katariina Hannula-Jouppi
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland.,Department of Dermatology and Allergology, Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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33
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Hamilton JA, Hsu HC, Mountz JD. Autoreactive B cells in SLE, villains or innocent bystanders? Immunol Rev 2019; 292:120-138. [PMID: 31631359 PMCID: PMC6935412 DOI: 10.1111/imr.12815] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/12/2019] [Accepted: 09/23/2019] [Indexed: 12/14/2022]
Abstract
The current concepts for development of autoreactive B cells in SLE (systemic lupus erythematosus) focus on extrinsic stimuli and factors that provoke B cells into tolerance loss. Traditionally, major tolerance loss pathways are thought to be regulated by factors outside the B cell including autoantigen engagement of the B-cell receptor (BCR) with simultaneous type I interferon (IFN) produced by dendritic cells, especially plasmacytoid dendritic cells (pDCs). Later, in autoreactive follicles, B-cells encounter T-follicular helper cells (Tfh) that produce interleukin (IL)-21, IL-4 and pathogenic cytokines, IL-17 and IFN gamma (IFNɣ). This review discusses these mechanisms and also highlights recent advances pointing to the peripheral transitional B-cell stage as a major juncture where transient autocrine IFNβ expression by developing B-cells imprints a heightened susceptibility to external factors favoring differentiation into autoantibody-producing plasmablasts. Recent studies highlight transitional B-cell heterogeneity as a determinant of intrinsic resistance or susceptibility to tolerance loss through the shaping of B-cell responsiveness to cytokines and other environment factors.
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Affiliation(s)
| | - Hui-Chen Hsu
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - John D Mountz
- University of Alabama at Birmingham, Birmingham, AL, USA
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34
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Refae S, Gal J, Brest P, Milano G. Germinal immunogenetics as a predictive factor for immunotherapy. Crit Rev Oncol Hematol 2019; 141:146-152. [PMID: 31301542 DOI: 10.1016/j.critrevonc.2019.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/19/2019] [Accepted: 06/23/2019] [Indexed: 01/17/2023] Open
Abstract
Clinical response to checkpoint inhibitors-based (CPIs) therapies can vary among tumor types and between patients. This led to a significant amount of pre-clinical and clinical research into biomarker identification. Biomarkers have been found to cover both the tumor itself and the tumor microenvironment. Entering host-related parameters into the equation should provide a valuable strategy for identifying not only factors predictive of treatment efficacy but also of treatment-related toxicity. It is clear that germline variants can offer efficient and easily-assessable indicators (blood DNA) to enlarge the spectrum of predictive markers for CPI-based treatment. A major issue concerns the real functional significance of the reported single-nucleotide polymorphisms (SNPs) linked to CPI-treatment outcome. Powered calculations should lead to an optimal trade-off between sample size and allele frequency. New molecular technologies and new analytical methods should provide opportunities to bridge the knowledge gap between SNP-CPI treatment associations and the functional impact of these SNPs.
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Affiliation(s)
- Sadal Refae
- Centre Antoine Lacassagne, Medical Oncology Department, University Côte d'Azur, Nice, F-06189, France
| | - Jocelyn Gal
- Centre Antoine Lacassagne, Epidemiology and Biostatistics Department, University Côte d'Azur, Nice, F-06189, France
| | - Patrick Brest
- Centre Antoine Lacassagne, Cnrs, Inserm, Ircan, FHU-Oncoage, University Côte d'Azur, Nice, F-06189, France
| | - Gerard Milano
- Centre Antoine Lacassagne, Oncopharmacology Unit, University Côte d'Azur, Nice, F-06189, France.
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35
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ONAN D, YORULMAZ A, EZGÜ FS, HAYRAN KM, KÜLCÜ S, ARTÜZ RF, YALÇIN B. The role of IFIH1 gene rs1990760 and rs2111485 single-nucleotide polymorphisms in generalized vitiligo predisposition. Turk J Med Sci 2019; 49:206-211. [PMID: 30761886 PMCID: PMC7350844 DOI: 10.3906/sag-1808-63] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Background/aim Interferon-induced helicase (IFIH1) is a gene locus that has been recently defined as a candidate for susceptibility to generalized vitiligo (GV). The objectives of this study were to assess the association of IFIH1 gene, rs2111485, and rs1990760 single-nucleotide polymorphisms (SNP) with susceptibility to GV and the autoimmune diseases accompanying GV. Materials and methods We prospectively studied GV patients and frequency-matched healthy controls by age and sex. The genotypes of the participants were determined for rs1990760 and rs2111485 SNPs of IFIH1. Dominant, recessive, and additive models were evaluated for each SNP adjusted for age and sex. Results The patients and their controls were observed to be in the Hardy–Weinberg equilibrium for SNP1 (2q24.2, rs1990760, IFIH1, T/C) and SNP2 (2q24.2, rs2111485, IFIH1, G/A), respectively (all P > 0.7). For SNP1, every T allel addition was significantly associated with 1.53 times protectiveness in terms of vitiligo risk (P = 0.033). As for SNP2, every G allel addition was associated with 1.42 times protectiveness, close to statistical significance (P = 0.100). Conclusions: We detected that for SNP1, each T allel and for SNP2, each G allel are protective in terms of vitiligo development. Hereby, we confirmed that IFIH1 gene locus has a role in GV susceptibility.
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Affiliation(s)
- Duru ONAN
- Department of Dermatology, Ankara Numune Training and Research Hospital, University of Health Sciences, AnkaraTurkey
- * To whom correspondence should be addressed. E-mail:
| | - Ahu YORULMAZ
- Department of Dermatology, Ankara Numune Training and Research Hospital, University of Health Sciences, AnkaraTurkey
| | - Fatih Süheyl EZGÜ
- Department of Pediatric Genetics, Faculty of Medicine, Gazi University, AnkaraTurkey
| | - Kadir Mutlu HAYRAN
- Department of Preventive Oncology, Cancer Institute, Hacettepe University, AnkaraTurkey
| | - Seray KÜLCÜ
- Department of Dermatology, Ankara Numune Training and Research Hospital, University of Health Sciences, AnkaraTurkey
| | - Refika Ferda ARTÜZ
- Department of Dermatology, Ankara Numune Training and Research Hospital, University of Health Sciences, AnkaraTurkey
| | - Başak YALÇIN
- Department of Dermatology, Ankara Numune Training and Research Hospital, University of Health Sciences, AnkaraTurkey
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36
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Fike AJ, Elcheva I, Rahman ZSM. The Post-GWAS Era: How to Validate the Contribution of Gene Variants in Lupus. Curr Rheumatol Rep 2019; 21:3. [DOI: 10.1007/s11926-019-0801-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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37
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Comprehensive assessment of the association between genes on JAK-STAT pathway (IFIH1, TYK2, IL-10) and systemic lupus erythematosus: a meta-analysis. Arch Dermatol Res 2018; 310:711-728. [DOI: 10.1007/s00403-018-1858-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 08/19/2018] [Accepted: 08/26/2018] [Indexed: 12/12/2022]
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38
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Zhang J, Liu X, Meng Y, Wu H, Wu Y, Yang B, Wang L. Autoimmune disease associated IFIH1 single nucleotide polymorphism related with IL-18 serum levels in Chinese systemic lupus erythematosus patients. Sci Rep 2018; 8:9442. [PMID: 29930297 PMCID: PMC6013496 DOI: 10.1038/s41598-018-27782-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 06/08/2018] [Indexed: 02/05/2023] Open
Abstract
Systemic lupus erythematosus (SLE) has heterogeneous clinical manifestations. IFIH1 (interferon induced with helicase C domain 1) as one of antiviral helicase genes mediating type I interferon production, plays an essential role in the pathogenesis of SLE. The gene variants in IFIH1 could abnormally activate antiviral defenses and increased type I interferon signaling. The present study aimed to validate associations between single nucleotide polymorphisms (SNP) in IFIH1 and the pathogenesis of SLE. In total, rs1990760, rs3747517 and rs10930046 in IFIH1 are genotyped in 400 SLE patients and 659 health controls in Chinese cohort by an improved multiplex ligation detection reaction (iMLDR) technique. Significant associations were observed between alleles of IFIH1 (rs1990760 C > T, P = 0.005, OR = 1.36, 95%CI = 1.10–1.69; rs3747517 T > C, P = 0.004, OR = 1.31, 95%CI = 1.09–1.58, respectively) and SLE susceptibility. IFIH1 rs1990760 TT genotype carriers had lower serum levels of IL-18 (P < 0.001) and granzyme B (P < 0.001) than CC and CT genotype carriers. IFIH1 rs1990760 CT genotype carriers had higher anti-dsDNA–positive than CC and TT genotype carriers. In conclusion, IFIH1 polymorphisms (rs1990760 and rs3747517) were associated with SLE susceptibility and rs1990760 risk T allele related with IL-18 and granzyme B serum levels in SLE patients.
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Affiliation(s)
- Junlong Zhang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Xinle Liu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yanming Meng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Hengxu Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yongkang Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Bin Yang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
| | - Lanlan Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
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Abstract
When apoptotic cells are not cleared in an efficient and timely manner, they progress to secondary necrosis and lose their membrane integrity. This results in a leakage of immunostimulatory, danger associated molecular patterns (DAMPs), similar to accidental (or primary) necrosis. However, primary necrosis is a sudden event with an inadvertent release of almost unmodified DAMPs. Secondary necrotic cells, in contrast, have gone through various modifications during the process of apoptosis. Recent research revealed that the molecules released from the cytoplasm or exposed on the cell surface differ between primary necrosis, secondary necrosis, and regulated necrosis such as necroptosis. This review gives an overview of these differences and focusses their effects on the immune response. The implications to human physiology and diseases are manifold and will be discussed in the context of cancer, neurodegenerative disorders and autoimmunity.
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Affiliation(s)
- Monika Sachet
- Surgical Research Laboratories, Department of Surgery and Comprehensive Cancer Center, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Ying Yu Liang
- Surgical Research Laboratories, Department of Surgery and Comprehensive Cancer Center, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.,Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Rudolf Oehler
- Surgical Research Laboratories, Department of Surgery and Comprehensive Cancer Center, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
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Evaluation of Impact of Interferon-Induced Helicase C Domain-Containing Protein 1 Gene in Egyptian Systemic Lupus Erythematosus Patients and its Relationship With Vascular Manifestations of the Disease. Arch Rheumatol 2018; 33:181-189. [PMID: 30207578 DOI: 10.5606/archrheumatol.2018.6476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/25/2017] [Indexed: 01/02/2023] Open
Abstract
Objectives This study aims to investigate the impact of interferon-induced helicase C domain-containing protein 1 (IFIH1) gene single nucleotide polymorphism on interferon pathway signaling in systemic lupus erythematosus (SLE) patients specifically with vascular affection. Patients and methods The cross-sectional study included 30 consecutive SLE patients (2 males, 28 females; mean age 28±3.4 years; range 16 to 40 years) diagnosed according to the American College of Rheumatology revised criteria and 10 healthy age- and sex-matched controls (2 males, 8 females; mean age 27±2.5 years; range 22 to 23 years). SLE patients and controls were compared in terms of quantitative reverse transcriptase polymerase chain reaction gene expression of IFIH1 gene, von Willebrand factor, carotid intima-media thickness, and ankle brachial index. Results Interferon-induced helicase C domain-containing protein 1 gene expression was significantly higher in SLE patients than controls (1.7±0.6 and 0.5±0.2, respectively) (p<0.0001). IFIH1 gene expression was highly related to vascular complication with a cutoff point at 1.74 and it positively correlated with other endothelial dysfunction markers. Conclusion Interferon-induced helicase C domain-containing protein 1 gene (single nucleotide polymorphism 1990670) is associated with SLE in Egyptian patients. Expression of IFIH1 gene is related to disease activity and may serve as a novel predictor of vascular affection in SLE.
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41
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Schmidt RE, Grimbacher B, Witte T. Autoimmunity and primary immunodeficiency: two sides of the same coin? Nat Rev Rheumatol 2017; 14:7-18. [PMID: 29255211 DOI: 10.1038/nrrheum.2017.198] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Autoimmunity and immunodeficiency were previously considered to be mutually exclusive conditions; however, increased understanding of the complex immune regulatory and signalling mechanisms involved, coupled with the application of genetic analysis, is revealing the complex relationships between primary immunodeficiency syndromes and autoimmune diseases. Single-gene defects can cause rare diseases that predominantly present with autoimmune symptoms. Such genetic defects also predispose individuals to recurrent infections (a hallmark of immunodeficiency) and can cause primary immunodeficiencies, which can also lead to immune dysregulation and autoimmunity. Moreover, risk factors for polygenic rheumatic diseases often exist in the same genes as the mutations that give rise to primary immunodeficiency syndromes. In this Review, various primary immunodeficiency syndromes are presented, along with their pathogenetic mechanisms and relationship to autoimmune diseases, in an effort to increase awareness of immunodeficiencies that occur concurrently with autoimmune diseases and to highlight the need to initiate appropriate genetic tests. The growing knowledge of various genetically determined pathologic mechanisms in patients with immunodeficiencies who have autoimmune symptoms opens up new avenues for personalized molecular therapies that could potentially treat immunodeficiency and autoimmunity at the same time, and that could be further explored in the context of autoimmune rheumatic diseases.
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Affiliation(s)
- Reinhold E Schmidt
- Klinik für Immunologie und Rheumatologie, Medizinische Hochschule Hannover (MHH), Carl-Neuberg Straße 1, D-30625 Hannover, Germany
| | - Bodo Grimbacher
- Centre for Chronic Immunodeficiency, University Medical Centre, University of Freiburg, Faculty of Medicine, Breisacher Straße 115, D-79106 Freiburg, Germany
| | - Torsten Witte
- Klinik für Immunologie und Rheumatologie, Medizinische Hochschule Hannover (MHH), Carl-Neuberg Straße 1, D-30625 Hannover, Germany
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42
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Abstract
PURPOSE OF REVIEW Our understanding on genetic basis of SLE has been advanced through genome-wide association studies. We review recent progress in lupus genetics with a focus on SLE-associated loci that have been functionally characterized, and discuss the potential for clinical translation of genetics data. RECENT FINDINGS Over 100 loci have been confirmed to show robust association with SLE and many share with other immune-mediated diseases. Although causative variants captured at these established loci are limited, they guide biological studies of gene targets for functional characterization which highlight the importance of aberrant recognition of self-nucleic acid, type I interferon overproduction, and defective immune cell signaling underlying the pathogenesis of SLE. Increasing examples illustrate a predictive value of genetic findings in susceptibility/prognosis prediction, clinical classification, and pharmacological implication. Genetic findings provide a foundation for better understanding of disease pathogenic mechanisms and opportunities for target selection in lupus drug development.
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43
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Zaki M, Thoenes M, Kawalia A, Nürnberg P, Kaiser R, Heller R, Bolz HJ. Recurrent and Prolonged Infections in a Child with a Homozygous IFIH1 Nonsense Mutation. Front Genet 2017; 8:130. [PMID: 29018476 PMCID: PMC5614965 DOI: 10.3389/fgene.2017.00130] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 09/04/2017] [Indexed: 01/02/2023] Open
Abstract
In an Egyptian girl born to consanguineous parents, whole-exome sequencing (WES) identified a homozygous mutation in PHGDH, c.1273G>A (p.Val425Met), indicating 3-phosphoglycerate dehydrogenase deficiency. This diagnosis was compatible with the patient's microcephaly, severe psychomotor retardation, seizures and cataracts. However, she additionally suffered from recurrent (at least monthly) episodes of prolonged and severe chest infections requiring hospitalization, suggesting a secondary, predisposing and potentially Mendelian, condition. A local reactivation of an EBV infection in the respiratory tract was detected after a recent chest infection, likely representing an opportunistic infection based on a compromised immune system. Further inspection of WES data revealed a homozygous nonsense mutation, c.2665A>T (p.Lys889∗), in IFIH1, encoding MDA5. MDA5 detects long viral double-stranded RNA that is generated during replication of picorna viruses, and thereby activates the type I interferon signaling pathway. The results of Western blot analysis of protein from cultured fibroblasts of the patient indicates absence of wild type MDA5/IFIH1, compatible with NMD. We propose that, analogous to the severe course of primary influenza infection due to biallelic deficiency of a downstream effector, IRF7, homozygous loss of IFIH1 defines a novel Mendelian immunodeficiency disorder that increases susceptibility to severe viral infections. This is contrasted to heterozygous gain-of-function IFIH1 mutations in autoimmune diseases. Our findings highlight the potential of comprehensive genomic investigations in patients from consanguineous families to identify monogenic predispositions to severe infections.
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Affiliation(s)
- Maha Zaki
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research CentreCairo, Egypt
| | - Michaela Thoenes
- Institute of Human Genetics, University Hospital of CologneCologne, Germany
| | - Amit Kawalia
- Cologne Center for Genomics, University of CologneCologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of CologneCologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of CologneCologne, Germany
| | - Rolf Kaiser
- Institute of Virology, University Hospital of CologneCologne, Germany
| | - Raoul Heller
- Institute of Human Genetics, University Hospital of CologneCologne, Germany
| | - Hanno J Bolz
- Institute of Human Genetics, University Hospital of CologneCologne, Germany
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44
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Abstract
PURPOSE OF REVIEW To describe the recent studies on the genetics of systemic lupus erythematosus (SLE) and Sjögren's syndrome. RECENT FINDINGS We overview the most recent findings on the genetic susceptibility of the diseases and provide information on their genetic similarities and differences. SUMMARY SLE and Sjögren's syndrome are two closely related systemic autoimmune diseases that share multiple clinical and molecular aspects, including a significant number of susceptibility genes. Several genome-wide association studies were recently published in different populations that provide a better picture of their molecular mechanisms. It is becoming clear that their genetic architecture is quite well established, but more information is required on expression quantitative trait loci, epigenetic genome-wide analyses, gene × gene interactions and the role of rare variants.
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45
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Tsokos GC, Lo MS, Costa Reis P, Sullivan KE. New insights into the immunopathogenesis of systemic lupus erythematosus. Nat Rev Rheumatol 2017; 12:716-730. [PMID: 27872476 DOI: 10.1038/nrrheum.2016.186] [Citation(s) in RCA: 762] [Impact Index Per Article: 108.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The aetiology of systemic lupus erythematosus (SLE) is multifactorial, and includes contributions from the environment, stochastic factors, and genetic susceptibility. Great gains have been made in understanding SLE through the use of genetic variant identification, mouse models, gene expression studies, and epigenetic analyses. Collectively, these studies support the concept that defective clearance of immune complexes and biological waste (such as apoptotic cells), neutrophil extracellular traps, nucleic acid sensing, lymphocyte signalling, and interferon production pathways are all central to loss of tolerance and tissue damage. Increased understanding of the pathogenesis of SLE is driving a renewed interest in targeted therapy, and researchers are now on the verge of developing targeted immunotherapy directed at treating either specific organ system involvement or specific subsets of patients with SLE. Accordingly, this Review places these insights within the context of our current understanding of the pathogenesis of SLE and highlights pathways that are ripe for therapeutic targeting.
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Affiliation(s)
- George C Tsokos
- Division of Rheumatology, Beth Israel Deaconess Medical Center, Harvard Medical School, 110 Francis Street, Boston, Massachusetts 02215, USA
| | - Mindy S Lo
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Patricia Costa Reis
- Department of Pediatrics, Lisbon Medical School, Lisbon University, Santa Maria Hospital, Avenida Professor Egas Moniz, 1649-035 Lisbon, Portugal
| | - Kathleen E Sullivan
- Division of Allergy and Immunology, The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, 3615 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
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46
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Abstract
RIG-I-like receptors (RLRs) are cytosolic innate immune sensors that detect pathogenic RNA and induce a systemic antiviral response. During the last decade, many studies focused on their molecular characterization and the identification of RNA agonists. Therefore, it became more and more clear that RLR activation needs to be carefully regulated, because constitutive signaling or detection of endogenous RNA through loss of specificity is detrimental. Here, we review the current understanding of RLR activation and selectivity. We specifically focus upon recent findings on the function of the helicase domain in discriminating between different RNAs, and whose malfunctioning causes serious autoimmune diseases.
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Affiliation(s)
- Charlotte Lässig
- From the Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, 81377 Munich and
| | - Karl-Peter Hopfner
- From the Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, 81377 Munich and
- the Center for Integrated Protein Sciences, 81377 Munich, Germany
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47
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Karol SE, Larsen E, Cheng C, Cao X, Yang W, Ramsey LB, Fernandez CA, McCorkle JR, Paugh SW, Autry RJ, Lopez-Lopez E, Diouf B, Jeha S, Pui CH, Raetz EA, Winick NJ, Carroll WL, Hunger SP, Loh ML, Devidas M, Evans WE, Yang JJ, Relling MV. Genetics of ancestry-specific risk for relapse in acute lymphoblastic leukemia. Leukemia 2017; 31:1325-1332. [PMID: 28096535 PMCID: PMC5462853 DOI: 10.1038/leu.2017.24] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/16/2016] [Accepted: 01/09/2017] [Indexed: 02/06/2023]
Abstract
The causes of individual relapses in children with acute lymphoblastic leukemia (ALL) remain incompletely understood. We evaluated the contribution of germline genetic factors to relapse in 2225 children treated on Children's Oncology Group trial AALL0232. We identified 302 germline single-nucleotide polymorphisms (SNPs) associated with relapse after adjusting for treatment and ancestry and 715 additional SNPs associated with relapse in an ancestry-specific manner. We tested for replication of these relapse-associated SNPs in external data sets of antileukemic drug pharmacokinetics and pharmacodynamics and an independent clinical cohort. 224 SNPs were associated with rapid drug clearance or drug resistance, and 32 were replicated in the independent cohort. The adverse risk associated with black and Hispanic ancestries was attenuated by addition of the 4 SNPs most strongly associated with relapse in these populations (for blacks: model without SNPs hazard ratio (HR)=2.32, P=2.27 × 10-4, model with SNPs HR=1.07, P=0.79; for Hispanics: model without SNPs HR=1.7, P=8.23 × 10-5, model with SNPs HR=1.31, P=0.065). Relapse SNPs associated with asparaginase resistance or allergy were overrepresented among SNPs associated with relapse in the more asparaginase intensive treatment arm (20/54 in Capizzi-methorexate arm vs 8/54 in high-dose methotrexate arm, P=0.015). Inherited genetic variation contributes to race-specific and treatment-specific relapse risk.
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Affiliation(s)
- S E Karol
- Comprehensive Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - E Larsen
- Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - C Cheng
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - X Cao
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - W Yang
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - L B Ramsey
- Department of Pharmacy Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - C A Fernandez
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - J R McCorkle
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - S W Paugh
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - R J Autry
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - E Lopez-Lopez
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - B Diouf
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - S Jeha
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - C-H Pui
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - E A Raetz
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - N J Winick
- Department of Pediatrics, University of Texas, Southwestern Medical Center, Dallas, TX, USA
| | - W L Carroll
- Perlmutter Cancer Center, Department of Pediatrics and Pathology, New York University Langone Medical Center, New York, NY, USA
| | - S P Hunger
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - M L Loh
- Department of Pediatrics, University of California School of Medicine, San Francisco, CA, USA
| | - M Devidas
- Department of Biostatistics, Colleges of Medicine, Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - W E Evans
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - J J Yang
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - M V Relling
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
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48
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Molineros JE, Yang W, Zhou XJ, Sun C, Okada Y, Zhang H, Heng Chua K, Lau YL, Kochi Y, Suzuki A, Yamamoto K, Ma J, Bang SY, Lee HS, Kim K, Bae SC, Zhang H, Shen N, Looger LL, Nath SK. Confirmation of five novel susceptibility loci for systemic lupus erythematosus (SLE) and integrated network analysis of 82 SLE susceptibility loci. Hum Mol Genet 2017; 26:1205-1216. [PMID: 28108556 DOI: 10.1093/hmg/ddx026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/13/2017] [Indexed: 01/13/2023] Open
Abstract
We recently identified ten novel SLE susceptibility loci in Asians and uncovered several additional suggestive loci requiring further validation. This study aimed to replicate five of these suggestive loci in a Han Chinese cohort from Hong Kong, followed by meta-analysis (11,656 cases and 23,968 controls) on previously reported Asian and European populations, and to perform bioinformatic analyses on all 82 reported SLE loci to identify shared regulatory signatures. We performed a battery of analyses for these five loci, as well as joint analyses on all 82 SLE loci. All five loci passed genome-wide significance: MYNN (rs10936599, Pmeta = 1.92 × 10-13, OR = 1.14), ATG16L2 (rs11235604, Pmeta = 8.87 × 10 -12, OR = 0.78), CCL22 (rs223881, Pmeta = 5.87 × 10-16, OR = 0.87), ANKS1A (rs2762340, Pmeta = 4.93 × 10-15, OR = 0.87) and RNASEH2C (rs1308020, Pmeta = 2.96 × 10-19, OR = 0.84) and co-located with annotated gene regulatory elements. The novel loci share genetic signatures with other reported SLE loci, including effects on gene expression, transcription factor binding, and epigenetic characteristics. Most (56%) of the correlated (r2 > 0.8) SNPs from the 82 SLE loci were implicated in differential expression (9.81 × 10-198 < P < 5 × 10-3) of cis-genes. Transcription factor binding sites for p53, MEF2A and E2F1 were significantly (P < 0.05) over-represented in SLE loci, consistent with apoptosis playing a critical role in SLE. Enrichment analysis revealed common pathways, gene ontology, protein domains, and cell type-specific expression. In summary, we provide evidence of five novel SLE susceptibility loci. Integrated bioinformatics using all 82 loci revealed that SLE susceptibility loci share many gene regulatory features, suggestive of conserved mechanisms of SLE etiopathogenesis.
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Affiliation(s)
- Julio E Molineros
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Xu-Jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, and Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Huoru Zhang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yu-Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan.,Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jianyang Ma
- Joint Molecular Rheumatology Laboratory of the Institute of Health Sciences and Shanghai Renji Hospital, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul 02447, Korea
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, and Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - Nan Shen
- Joint Molecular Rheumatology Laboratory of the Institute of Health Sciences and Shanghai Renji Hospital, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
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49
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Kato H, Oh SW, Fujita T. RIG-I-Like Receptors and Type I Interferonopathies. J Interferon Cytokine Res 2017; 37:207-213. [PMID: 28475461 PMCID: PMC5439449 DOI: 10.1089/jir.2016.0095] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 12/28/2016] [Indexed: 12/24/2022] Open
Abstract
Type I interferon (IFN) production by the proper activation of nucleic acid sensors is essential for hosts to eliminate invading viruses. Among these sensors, RIG-I-like receptors (RLRs) are well-known viral RNA sensors in the cytoplasm that recognize the nonself signatures of viral RNAs to trigger IFN responses. Recent accumulating evidence has clarified that some specific and atypical self-RNAs also cause activation of RLRs independently of virus infection. Importantly, when RLR-activation by these RNAs or a conformational change via missense mutations is sustained, the resulting continuous production of type I IFN will lead to autoimmune disorders. We, herein, focus on autoimmune diseases caused by chronic activation of RLRs and discuss possible mechanisms of their onset.
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Affiliation(s)
- Hiroki Kato
- Laboratory of Molecular Genetics, Institute for Virus Research, Kyoto University , Kyoto, Japan
| | - Seong-Wook Oh
- Laboratory of Molecular Genetics, Institute for Virus Research, Kyoto University , Kyoto, Japan
| | - Takashi Fujita
- Laboratory of Molecular Genetics, Institute for Virus Research, Kyoto University , Kyoto, Japan
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50
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Langlais D, Fodil N, Gros P. Genetics of Infectious and Inflammatory Diseases: Overlapping Discoveries from Association and Exome-Sequencing Studies. Annu Rev Immunol 2017; 35:1-30. [DOI: 10.1146/annurev-immunol-051116-052442] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David Langlais
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Nassima Fodil
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Philippe Gros
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
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