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Seddon JM, De D, Casazza W, Cheng SY, Punzo C, Daly M, Zhou D, Coss SL, Atkinson JP, Yu CY. Risk and protection of different rare protein-coding variants of complement component C4A in age-related macular degeneration. Front Genet 2024; 14:1274743. [PMID: 38348408 PMCID: PMC10859408 DOI: 10.3389/fgene.2023.1274743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/21/2023] [Indexed: 02/15/2024] Open
Abstract
Introduction: Age-related macular degeneration (AMD) is the leading cause of central vision loss in the elderly. One-third of the genetic contribution to this disease remains unexplained. Methods: We analyzed targeted sequencing data from two independent cohorts (4,245 cases, 1,668 controls) which included genomic regions of known AMD loci in 49 genes. Results: At a false discovery rate of <0.01, we identified 11 low-frequency AMD variants (minor allele frequency <0.05). Two of those variants were present in the complement C4A gene, including the replacement of the residues that contribute to the Rodgers-1/Chido-1 blood group antigens: [VDLL1207-1210ADLR (V1207A)] with discovery odds ratio (OR) = 1.7 (p = 3.2 × 10-5) which was replicated in the UK Biobank dataset (3,294 cases, 200,086 controls, OR = 1.52, p = 0.037). A novel variant associated with reduced risk for AMD in our discovery cohort was P1120T, one of the four C4A-isotypic residues. Gene-based tests yielded aggregate effects of nonsynonymous variants in 10 genes including C4A, which were associated with increased risk of AMD. In human eye tissues, immunostaining demonstrated C4A protein accumulation in and around endothelial cells of retinal and choroidal vasculature, and total C4 in soft drusen. Conclusion: Our results indicate that C4A protein in the complement activation pathways may play a role in the pathogenesis of AMD.
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Affiliation(s)
- Johanna M. Seddon
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Dikha De
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - William Casazza
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Shun-Yun Cheng
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Claudio Punzo
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Mark Daly
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Danlei Zhou
- Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Samantha L. Coss
- Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH, United States
| | - John P. Atkinson
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, Saint Louis, MO, United States
| | - Chack-Yung Yu
- Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH, United States
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Tomecki R, Drazkowska K, Kobylecki K, Tudek A. SKI complex: A multifaceted cytoplasmic RNA exosome cofactor in mRNA metabolism with links to disease, developmental processes, and antiviral responses. Wiley Interdiscip Rev RNA 2023; 14:e1795. [PMID: 37384835 DOI: 10.1002/wrna.1795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 07/01/2023]
Abstract
RNA stability and quality control are integral parts of gene expression regulation. A key factor shaping eukaryotic transcriptomes, mainly via 3'-5' exoribonucleolytic trimming or degradation of diverse transcripts in nuclear and cytoplasmic compartments, is the RNA exosome. Precise exosome targeting to various RNA molecules requires strict collaboration with specialized auxiliary factors, which facilitate interactions with its substrates. The predominant class of cytoplasmic RNA targeted by the exosome are protein-coding transcripts, which are carefully scrutinized for errors during translation. Normal, functional mRNAs are turned over following protein synthesis by the exosome or by Xrn1 5'-3'-exonuclease, acting in concert with Dcp1/2 decapping complex. In turn, aberrant transcripts are eliminated by dedicated surveillance pathways, triggered whenever ribosome translocation is impaired. Cytoplasmic 3'-5' mRNA decay and surveillance are dependent on the tight cooperation between the exosome and its evolutionary conserved co-factor-the SKI (superkiller) complex (SKIc). Here, we summarize recent findings from structural, biochemical, and functional studies of SKIc roles in controlling cytoplasmic RNA metabolism, including links to various cellular processes. Mechanism of SKIc action is illuminated by presentation of its spatial structure and details of its interactions with exosome and ribosome. Furthermore, contribution of SKIc and exosome to various mRNA decay pathways, usually converging on recycling of ribosomal subunits, is delineated. A crucial physiological role of SKIc is emphasized by describing association between its dysfunction and devastating human disease-a trichohepatoenteric syndrome (THES). Eventually, we discuss SKIc functions in the regulation of antiviral defense systems, cell signaling and developmental transitions, emerging from interdisciplinary investigations. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Rafal Tomecki
- Laboratory of RNA Processing and Decay, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Karolina Drazkowska
- Laboratory of Epitranscriptomics, Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Kamil Kobylecki
- Laboratory of RNA Processing and Decay, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Tudek
- Laboratory of RNA Processing and Decay, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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3
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Kulski JK, Suzuki S, Shiina T. Human leukocyte antigen super-locus: nexus of genomic supergenes, SNPs, indels, transcripts, and haplotypes. Hum Genome Var 2022; 9:49. [PMID: 36543786 DOI: 10.1038/s41439-022-00226-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
The human Major Histocompatibility Complex (MHC) or Human Leukocyte Antigen (HLA) super-locus is a highly polymorphic genomic region that encodes more than 140 coding genes including the transplantation and immune regulatory molecules. It receives special attention for genetic investigation because of its important role in the regulation of innate and adaptive immune responses and its strong association with numerous infectious and/or autoimmune diseases. In recent years, MHC genotyping and haplotyping using Sanger sequencing and next-generation sequencing (NGS) methods have produced many hundreds of genomic sequences of the HLA super-locus for comparative studies of the genetic architecture and diversity between the same and different haplotypes. In this special issue on 'The Current Landscape of HLA Genomics and Genetics', we provide a short review of some of the recent analytical developments used to investigate the SNP polymorphisms, structural variants (indels), transcription and haplotypes of the HLA super-locus. This review highlights the importance of using reference cell-lines, population studies, and NGS methods to improve and update our understanding of the mechanisms, architectural structures and combinations of human MHC genomic alleles (SNPs and indels) that better define and characterise haplotypes and their association with various phenotypes and diseases.
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Izzi B, Thys C, Tirozzi A, Bezulska-Ditkowska M, De Reys M, Labarque V, Van Geet C, Peerlinck K, Freson K. Methylome analysis for haemophilia A intron 22 inversion patients with and without inhibitors: A pilot study. Haemophilia 2022; 28:e248-e250. [PMID: 35971883 DOI: 10.1111/hae.14651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/14/2022] [Accepted: 07/29/2022] [Indexed: 11/04/2022]
Affiliation(s)
- Benedetta Izzi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy
| | - Chantal Thys
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Alfonsina Tirozzi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy
| | - Martyna Bezulska-Ditkowska
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Mara De Reys
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Veerle Labarque
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium.,Paediatric Haemato-Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Chris Van Geet
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium.,Paediatric Haemato-Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Kathelijne Peerlinck
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium.,Vascular Medicine and Hemostasis, University Hospitals Leuven, Leuven, Belgium
| | - Kathleen Freson
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium.,KU Leuven Child and Youth Institute, KU Leuven, Leuven, Belgium
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Zhu XB, Hou YQ, Ye XY, Zou YX, Xia XS, Yang S, Huang P, Yu RB. Identifying and Exploring the Candidate Susceptibility Genes of Cirrhosis Using the Multi-Tissue Transcriptome-Wide Association Study. Front Genet 2022; 13:878607. [PMID: 35646080 PMCID: PMC9136150 DOI: 10.3389/fgene.2022.878607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/30/2022] [Indexed: 12/03/2022] Open
Abstract
Objective: We identify and explore the candidate susceptibility genes for cirrhosis and their underlying biological mechanism. Methods: We downloaded the genome-wide association studies summary data of 901 cirrhosis cases and 451,363 controls and integrated them with reference models of five potential tissues from the Genotype-Tissue Expression (GTEx) Project, including whole blood, liver, pancreas, spleen, and thyroid, to identify genes whose expression is predicted to be associated with cirrhosis. Then, we downloaded gene expression data of individuals with hepatocellular carcinoma from TCGA database to conduct differential expression analysis to validate these identified genes and explored their possible role in driving cirrhosis via functional enrichment and gene set enrichment analysis (GSEA). Results: We identified 10 significant genes (SKIV2L, JPH4, UQCC2, RP11-91I8.3, MAU2, ERAP1, PUS3, ZNF677, ARHGAP40, and SHANK3) associated with cirrhosis at a Bonferroni-corrected threshold of p < 0.01, among which two (SKIV2L and JPH4) were identified in the liver and five (SKIV2L, JPH4, MAU2, SHANK3, and UQCC2) were validated by differential expression analysis at an FDR-corrected threshold of p < 0.01. The enrichment analysis showed that the degradation process of RNA, which is enriched by 58 genes, is significantly under-enriched in liver cancer tissues (p = 0.0268). Conclusion: We have identified several candidate genes for cirrhosis in multiple tissues and performed differential genetic analysis using the liver cancer database to verify the significant genes. We found that the genes SKIV2L and JPH4 identified in the liver are of particular concern. Finally, through enrichment analysis, we speculate that the process of mRNA transcription and RNA degradation may play a role in cirrhosis.
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Affiliation(s)
- Xiao-Bo Zhu
- The People’s Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, China
| | - Yu-Qing Hou
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiang-Yu Ye
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yi-Xin Zou
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xue-Shan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Sheng Yang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Peng Huang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- *Correspondence: Peng Huang, ; Rong-Bin Yu,
| | - Rong-Bin Yu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- *Correspondence: Peng Huang, ; Rong-Bin Yu,
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6
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Zhou D, Rudnicki M, Chua GT, Lawrance SK, Zhou B, Drew JL, Barbar-Smiley F, Armstrong TK, Hilt ME, Birmingham DJ, Passler W, Auletta JJ, Bowden SA, Hoffman RP, Wu YL, Jarjour WN, Mok CC, Ardoin SP, Lau YL, Yu CY. Human Complement C4B Allotypes and Deficiencies in Selected Cases With Autoimmune Diseases. Front Immunol 2021; 12:739430. [PMID: 34764957 PMCID: PMC8577214 DOI: 10.3389/fimmu.2021.739430] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/24/2021] [Indexed: 11/13/2022] Open
Abstract
Human complement C4 is one of the most diverse but heritable effectors for humoral immunity. To help understand the roles of C4 in the defense and pathogenesis of autoimmune and inflammatory diseases, we determined the bases of polymorphisms including the frequent genetic deficiency of C4A and/or C4B isotypes. We demonstrated the diversities of C4A and C4B proteins and their gene copy number variations (CNVs) in healthy subjects and patients with autoimmune disease, such as type 1 diabetes, systemic lupus erythematosus (SLE) and encephalitis. We identified subjects with (a) the fastest migrating C4B allotype, B7, or (b) a deficiency of C4B protein caused by genetic mutation in addition to gene copy-number variation. Those variants and mutants were characterized, sequenced and specific techniques for detection developed. Novel findings were made in four case series. First, the amino acid sequence determinant for C4B7 was likely the R729Q variation at the anaphylatoxin-like region. Second, in healthy White subject MS630, a C-nucleotide deletion at codon-755 led to frameshift mutations in his single C4B gene, which was a private mutation. Third, in European family E94 with multiplex lupus-related mortality and low serum C4 levels, the culprit was a recurrent haplotype with HLA-A30, B18 and DR7 that segregated with two defective C4B genes and identical mutations at the donor splice site of intron-28. Fourth, in East-Asian subject E133P with anti-NMDA receptor encephalitis, the C4B gene had a mutation that changed tryptophan-660 to a stop-codon (W660x), which was present in a haplotype with HLA-DRB1*04:06 and B*15:27. The W660x mutation is recurrent among East-Asians with a frequency of 1.5% but not detectable among patients with SLE. A meticulous annotation of C4 sequences revealed clusters of variations proximal to sites for protein processing, activation and inactivation, and binding of interacting molecules.
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Affiliation(s)
- Danlei Zhou
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Michael Rudnicki
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | - Gilbert T Chua
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong, SAR China
| | - Simon K Lawrance
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Biology & Earth Science, Otterbein University, Westerville, OH, United States
| | - Bi Zhou
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Joanne L Drew
- Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Fatima Barbar-Smiley
- Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University, Columbus, OH, United States
| | - Taylor K Armstrong
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, United States
| | - Miranda E Hilt
- Department of Biology & Earth Science, Otterbein University, Westerville, OH, United States
| | - Daniel J Birmingham
- Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Werner Passler
- Division of Nephrology and Dialysis, City Hospital, Bolzano, Italy
| | - Jeffrey J Auletta
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States.,Division of Hematology/Oncology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Sasigarn A Bowden
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States.,Division of Endocrinology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Robert P Hoffman
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States.,Division of Endocrinology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Yee Ling Wu
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, United States
| | - Wael N Jarjour
- Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Chi Chiu Mok
- Department of Medicine, Tuen Mun Hospital, Hong Kong, Hong Kong, SAR China
| | - Stacy P Ardoin
- Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University, Columbus, OH, United States.,Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong, SAR China
| | - Chack Yung Yu
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University, Columbus, OH, United States
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Abstract
Here we review data suggestive of a role for RNA-binding proteins in vertebrate immunity. We focus on the products of genes found in the class III region of the Major Histocompatibility Complex. Six of these genes, DDX39B (aka BAT1), DXO, LSM2, NELFE, PRRC2A (aka BAT2), and SKIV2L, encode RNA-binding proteins with clear roles in post-transcriptional gene regulation and RNA surveillance. These genes are likely to have important functions in immunity and are associated with autoimmune diseases.
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Affiliation(s)
- Geraldine Schott
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.,Biochemistry and Molecular Biology Graduate Program, University of Texas Medical Branch, Galveston, Texas, USA
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.,Programme in Infectious Diseases, Duke-NUS Medical School, Singapore.,Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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8
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Kulski JK, Shiina T, Dijkstra JM. Genomic Diversity of the Major Histocompatibility Complex in Health and Disease. Cells 2019; 8:E1270. [PMID: 31627481 DOI: 10.3390/cells8101270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 12/20/2022] Open
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