1
|
Hujoel MLA, Handsaker RE, Sherman MA, Kamitaki N, Barton AR, Mukamel RE, Terao C, McCarroll SA, Loh PR. Protein-altering variants at copy number-variable regions influence diverse human phenotypes. Nat Genet 2024; 56:569-578. [PMID: 38548989 PMCID: PMC11018521 DOI: 10.1038/s41588-024-01684-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 02/08/2024] [Indexed: 04/09/2024]
Abstract
Copy number variants (CNVs) are among the largest genetic variants, yet CNVs have not been effectively ascertained in most genetic association studies. Here we ascertained protein-altering CNVs from UK Biobank whole-exome sequencing data (n = 468,570) using haplotype-informed methods capable of detecting subexonic CNVs and variation within segmental duplications. Incorporating CNVs into analyses of rare variants predicted to cause gene loss of function (LOF) identified 100 associations of predicted LOF variants with 41 quantitative traits. A low-frequency partial deletion of RGL3 exon 6 conferred one of the strongest protective effects of gene LOF on hypertension risk (odds ratio = 0.86 (0.82-0.90)). Protein-coding variation in rapidly evolving gene families within segmental duplications-previously invisible to most analysis methods-generated some of the human genome's largest contributions to variation in type 2 diabetes risk, chronotype and blood cell traits. These results illustrate the potential for new genetic insights from genomic variation that has escaped large-scale analysis to date.
Collapse
Affiliation(s)
- Margaux L A Hujoel
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Maxwell A Sherman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Serinus Biosciences Inc., New York, NY, USA
| | - Nolan Kamitaki
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Alison R Barton
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ronen E Mukamel
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
2
|
Kløve-Mogensen K, Terp SK, Steffensen R. Comparison of real-time quantitative PCR and two digital PCR platforms to detect copy number variation in FCGR3B. J Immunol Methods 2024; 526:113628. [PMID: 38331313 DOI: 10.1016/j.jim.2024.113628] [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: 11/06/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
The importance of structural genetic variants, such as copy number variations (CNVs), in modulating human disease is being increasingly recognized. Several clinical conditions require investigation of human neutrophil antigen (HNA-1), which is encoded by the Fc gamma receptor IIIb gene (FCGR3B), including suspicion of neutropenia, infections, and proactive testing of blood component donors to reduce the potential risk in transfusion. In this study, we compared real-time quantitative polymerase chain reaction (qPCR) with two digital PCR (dPCR) platforms, namely droplet digital PCR and an array-based platform, to determine copy numbers (CNs) in FCGR3B. We initially tested 400 anonymous blood donors with qPCR using a commercially available TaqMan probe assay (Applied Biosystems) on a Quant Studio 12 Flex. CNs was determined for all 400 tested individuals with CNs ranging from zero to four. Zero copies were detected in 0.2% (1/400), one copy was detected in 3.8% (15/400), two copies were detected in 87.8% (351/400), three copies were detected in 8.0% (32/400), and four copies were detected in 0.2% (1/400) of tested individuals. From this cohort, we selected 32 donors with CNs from zero to four for analyses with Digital Real-Time PCR (dPCR) using Lab on an array (LOAA) on an On-Point analyzer from Optolane Technologies Inc. and the Droplet Digital PCR (ddPCR) platform from Bio-Rad Laboratories. We compared the obtained CNs of FCGR3B on the three platforms and found full concordance between the CNs obtained. We therefore conclude that all three platforms can be used for quantification of CNs for FCGR3B, and although dPCR has some advantages over qPCR, it was not necessary for reliably estimating CNs of the FCGR3B gene.
Collapse
Affiliation(s)
- Kirstine Kløve-Mogensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
| | - Simone Karlsson Terp
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark; Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark.
| | - Rudi Steffensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark.
| |
Collapse
|
3
|
Kløve-Mogensen K, Steffensen R, Masmas TN, Glenthøj A, Jensen CF, Haunstrup TM, Ratcliffe P, Höglund P, Hasle H, Nielsen KR. Genetic variations in low-to-medium-affinity Fcγ receptors and autoimmune neutropenia in early childhood in a Danish cohort. Int J Immunogenet 2023; 50:65-74. [PMID: 36754570 DOI: 10.1111/iji.12614] [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: 11/25/2022] [Revised: 01/09/2023] [Accepted: 01/22/2023] [Indexed: 02/10/2023]
Abstract
Autoimmune neutropenia (AIN) in early childhood is caused by autoantibodies directed against antigens on the neutrophil membrane and is a frequent cause of neutropenia in children. Association of AIN with Fcγ receptor (FCGR) 3B variants is well described. In this study, we investigate genetic variations in the FCGR locus and copy number variation of FCGR3B. A total of 130 antibody-positive AIN patients, 64 with specific anti-HNA-1a antibodies and 66 with broad-reacting anti-FcγRIIIb antibodies, were genotyped with a multiplex ligation probe assay and compared with healthy controls. Positive findings were confirmed with real-time q-PCR. We determined copy numbers of the FCGR2 and FCGR3 genes and the following SNPs: FCGR2A Q62W (rs201218628), FCGR2A H166R (rs1801274), FCGR2B I232T (rs1050501), FCGR3A V176F (rs396991), haplotypes for FCGR2B/C promoters (rs3219018/rs780467580), FCGR2C STOP/ORF and HNA-1 genotypes in FCGR3B (rs447536, rs448740, rs52820103, rs428888 and rs2290834). Generally, associations were antibody specific, with all associations being representative of the anti-HNA-1a-positive group, while the only association found in the anti-FcγRIIIb group was with the HNA-1 genotype. An increased risk of AIN was observed for patients with one copy of FCGR3B; the HNA genotypes HNA-1a, HNA-1aa or HNA-1aac; the FCGR2A 166H and FCGR2B 232I variations; and no copies of FCGR2B 2B.4. A decreased risk was observed for HNA genotype HNA-1bb; FCGR2A 166R; FCGR2B 232T; and one copy of FCGR2B promoter 2B.4. We conclude that in our Danish cohort, there was a strong association between variation in the FCGR locus and AIN. The findings of different genetic associations between autoantibody groups could indicate the presence of two different disease entities and disease heterogeneity.
Collapse
Affiliation(s)
- Kirstine Kløve-Mogensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Rudi Steffensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Tania Nicole Masmas
- Pediatric Hematopoietic Stem Cell Transplantation and Immunodeficiency, Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Andreas Glenthøj
- Department of Hematology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Christina Friis Jensen
- Department of Pediatrics and Adolescent Medicine, Aalborg University Hospital, Aalborg, Denmark
| | - Thure Mors Haunstrup
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Paul Ratcliffe
- Department of medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Petter Höglund
- Department of medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Henrik Hasle
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Kaspar René Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| |
Collapse
|
4
|
Juárez-Melchor D, Munguía-Realpozo P, Mendoza-Pinto C, Etchegaray-Morales I, Ayón-Aguilar J, Mendez-Martínez S, García-Carrasco M, Granados Arriola J. Genetic component of autoimmune rheumatological diseases. REUMATOLOGIA CLINICA 2022; 18:614-620. [PMID: 34953732 DOI: 10.1016/j.reumae.2021.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 06/14/2023]
Abstract
The purpose of this review is to present the main aspects of the genetic component of autoimmune rheumatic diseases, including the characteristics of the multifactorial or polygenic inheritance model, and its monogenic forms, as well as the main associated genes in both cases. The epigenetic changes involved, and the influence of the environment and sex that confer greater risk to women suffering from any of these diseases. Finally, to make known the advances that the study of omic sciences has allowed, opening the way to a new molecular classification of these diseases, aimed at personalized medicine. A review of the literature of the last 5 years, of English-language publications, in the PubMed database was performed and 28 review articles, and 19 original articles were included. Knowledge of the genetic factors involved in the aetiology of autoimmune rheumatic diseases, thanks to the availability of molecular studies, allows a better understanding of their pathophysiology and the possibility of diagnosis and treatment based on molecular markers in the future.
Collapse
Affiliation(s)
- Daniela Juárez-Melchor
- Departamento de Genética, Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico; Departamento de Genética, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Pamela Munguía-Realpozo
- Departamento de Reumatología, Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Claudia Mendoza-Pinto
- Departamento de Reumatología, Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico; Unidad de Investigación de Enfermedades Autoinmunes Sistémicas, CIBIOR-Hospital de Especialidades UMAE, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Ivet Etchegaray-Morales
- Departamento de Reumatología, Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Jorge Ayón-Aguilar
- Coordinador Médico de Investigación en Salud, Instituto Mexicano del Seguro Social, Delegación Puebla, Mexico
| | - Socorro Mendez-Martínez
- Coordinación de Planeación y Enlace Institucional, Instituto Mexicano del Seguro Social, Delegación Puebla, Mexico
| | - Mario García-Carrasco
- Departamento de Reumatología, Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico.
| | - Julio Granados Arriola
- División de Inmunogenética, Departamento de Trasplantes, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| |
Collapse
|
5
|
Association of Fc Gamma Receptor 3B Gene Copy Number Variation with Rheumatoid Arthritis Susceptibility. Genes (Basel) 2022; 13:genes13122238. [PMID: 36553504 PMCID: PMC9778311 DOI: 10.3390/genes13122238] [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: 10/13/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
Abstract
Structural variations such as copy number variants (CNVs) have been associated with multiple autoimmune diseases. In this study, we explored the association of the Fc gamma receptor 3B gene (FCGR3B) copy number variation (CNV) with rheumatoid arthritis (RA) susceptibility and related serological traits in the Pakistani population. We also performed a meta-analysis of four published FCGR3B CNV studies along with the current study. A total of 927 subjects (597 RA cases, 330 healthy controls) were recruited from three rheumatology centers in Pakistan. Anti-cyclic citrullinated peptide (anti-CCP) antibodies and rheumatoid factor (RF) were measured in RA patients. FCGR3B copy number was assayed using the TaqMan® CN assay (Hs04211858_cn, Applied Biosystems, Foster City, CA, USA) and the copy number was estimated by using CopyCaller® software (version 2.1; Applied Biosystems, USA). Logistic regression was applied to calculate the odds ratio (OR) of RA risk associated with FCGR3B CNV using sex and age as covariates in R. Meta-analysis on four previously published studies and the current study was performed using the random-effect model. We observed a significant association between FCGR3B copy number < 2 and RA susceptibility (OR = 1.53; 95% CI: 1.05 to 2.22; p = 0.0259) and anti-CCP seropositivity (OR 2.56; 95% CI: 1.34 to 4.89; p = 0.0045). A non-significant association of FCGR3B copy number < 2 was also observed between increased rheumatoid factor (RF) seropositivity (OR = 1.74; 95% CI:0.93 to 3.26; p = 0.0816). Meta-analysis on 13,915 subjects (7005 RA cases and 6907 controls) also showed significant association of copy number < 2 with the increased risk of RA (OR = 1.30; 95% CI: 1.07 to 1.56; p = 0.00671). FCGR3B copy number < 2 is associated with increased RA risk and anti-CCP seropositivity.
Collapse
|
6
|
Song RH, Gao CQ, Zhao J, Zhang JA. An Update Evolving View of Copy Number Variations in Autoimmune Diseases. Front Genet 2022; 12:794348. [PMID: 35126462 PMCID: PMC8810490 DOI: 10.3389/fgene.2021.794348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/06/2021] [Indexed: 02/01/2023] Open
Abstract
Autoimmune diseases (AIDs) usually share possible common mechanisms, i.e., a defect in the immune tolerance exists due to diverse causes from central and peripheral tolerance mechanisms. Some genetic variations including copy number variations (CNVs) are known to link to several AIDs and are of importance in the susceptibility to AIDs and the potential therapeutic responses to medicines. As an important source of genetic variants, DNA CNVs have been shown to be very common in AIDs, implying these AIDs may possess possible common mechanisms. In addition, some CNVs are differently distributed in various diseases in different ethnic populations, suggesting that AIDs may have their own different phenotypes and different genetic and/or environmental backgrounds among diverse populations. Due to the continuous advancement in genotyping technology, such as high-throughput whole-genome sequencing method, more susceptible variants have been found. Moreover, further replication studies should be conducted to confirm the results of studies with different ethnic cohorts and independent populations. In this review, we aim to summarize the most relevant data that emerged in the past few decades on the relationship of CNVs and AIDs and gain some new insights into the issue.
Collapse
|
7
|
Moraru M, Perez-Portilla A, Al-Akioui Sanz K, Blazquez-Moreno A, Arnaiz-Villena A, Reyburn HT, Vilches C. FCGR Genetic Variation in Two Populations From Ecuador Highlands-Extensive Copy-Number Variation, Distinctive Distribution of Functional Polymorphisms, and a Novel, Locally Common, Chimeric FCGR3B/A (CD16B/A) Gene. Front Immunol 2021; 12:615645. [PMID: 34108956 PMCID: PMC8183472 DOI: 10.3389/fimmu.2021.615645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/09/2021] [Indexed: 11/13/2022] Open
Abstract
Fcγ receptors (FcγR), cell-surface glycoproteins that bind antigen-IgG complexes, control both humoral and cellular immune responses. The FCGR locus on chromosome 1q23.3 comprises five homologous genes encoding low-affinity FcγRII and FcγRIII, and displays functionally relevant polymorphism that impacts on human health. Recurrent events of non-allelic homologous recombination across the FCGR locus result in copy-number variation of ~82.5 kbp-long fragments known as copy-number regions (CNR). Here, we characterize a recently described deletion that we name CNR5, which results in loss of FCGR3A, FCGR3B, and FCGR2C, and generation of a recombinant FCGR3B/A gene. We show that the CNR5 recombination spot lies at the beginning of the third FCGR3 intron. Although the FCGR3B/A-encoded hybrid protein CD16B/A reaches the plasma membrane in transfected cells, its possible natural expression, predictably restricted to neutrophils, could not be demonstrated in resting or interferon γ-stimulated cells. As the CNR5-deletion was originally described in an Ecuadorian family from Llano Grande (an indigenous community in North-Eastern Quito), we characterized the FCGR genetic variation in two populations from the highlands of Ecuador. Our results reveal that CNR5-deletion is relatively frequent in Llano Grande (5 carriers out of 36 donors). Furthermore, we found a high frequency of two strong-phagocytosis variants: the FCGR3B-NA1 haplotype and the CNR1 duplication, which translates into an increased FCGR3B and FCGR2C copy-number. CNR1 duplication was particularly increased in Llano Grande, 77.8% of the studied sample carrying at least one such duplication. In contrast, an extended haplotype CD16A-176V – CD32C-ORF+2B.2 – CD32B-2B.4 including strong activating and inhibitory FcγR variants was absent in Llano Grande and found at a low frequency (8.6%) in Ecuador highlands. This particular distribution of FCGR polymorphism, possibly a result of selective pressures, further confirms the importance of a comprehensive, joint analysis of all genetic variations in the locus and warrants additional studies on their putative clinical impact. In conclusion, our study confirms important ethnic variation at the FCGR locus; it shows a distinctive FCGR polymorphism distribution in Ecuador highlands; provides a molecular characterization of a novel CNR5-deletion associated with CD16A and CD16B deficiency; and confirms its presence in that population.
Collapse
Affiliation(s)
- Manuela Moraru
- Immunogenetics & Histocompatibility Lab, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Spain
| | - Adriana Perez-Portilla
- Department of Immunology and Oncology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Karima Al-Akioui Sanz
- Immunogenetics & Histocompatibility Lab, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Spain
| | - Alfonso Blazquez-Moreno
- Department of Immunology and Oncology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | | | - Hugh T Reyburn
- Department of Immunology and Oncology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Carlos Vilches
- Immunogenetics & Histocompatibility Lab, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Spain
| |
Collapse
|
8
|
Chen Y, Li H, Lai L, Feng Q, Shen J. Identification of Common Differentially Expressed Genes and Potential Therapeutic Targets in Ulcerative Colitis and Rheumatoid Arthritis. Front Genet 2020; 11:572194. [PMID: 33262784 PMCID: PMC7686785 DOI: 10.3389/fgene.2020.572194] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Ulcerative colitis (UC) and rheumatoid arthritis (RA) are immune-mediated inflammatory diseases (IMIDs) with similar symptoms and common genomics. However, the relationship between UC and RA has not been investigated thoroughly. Therefore, this study aimed to establish the differentially expressed genes (DEGs) and potential therapeutic targets in UC and RA. Three microarray datasets (GSE38713, GSE1919, and GSE12251) were selected from the Gene Expression Omnibus (GEO) database for analysis. We used R software to identify the DEGs and performed enrichment analyses. Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Cytoscape software were used to construct the protein-protein interaction (PPI) network and identify the hub genes. A regulatory network based on the constructed PPI was generated using StarBase and PROMO databases. We identified a total of 1542 and 261 DEGs in UC and RA. There were 169 common DEGs identified in both UC and RA, including 63 upregulated genes (DEGs1) and nine downregulated genes (DEGs2). The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of DEGs1 and DEGs2 in the PPI network revealed that the genes enriched were involved in immunity. A total of 45 hub genes were selected based on high scores of correlation; three hub genes (SRGN, PLEK, and FCGR3B) were found to be upregulated in UC and RA, and downregulated in UC patients with response to infliximab treatment. The identification of novel DEGs and hub genes in the current study contributes to a novel perception for latent functional mechanisms and presents potential prognostic indicators and therapeutic targets in UC and RA.
Collapse
Affiliation(s)
- Yueying Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Hanyang Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Lijie Lai
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qi Feng
- Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Shen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| |
Collapse
|
9
|
Nagelkerke SQ, Schmidt DE, de Haas M, Kuijpers TW. Genetic Variation in Low-To-Medium-Affinity Fcγ Receptors: Functional Consequences, Disease Associations, and Opportunities for Personalized Medicine. Front Immunol 2019; 10:2237. [PMID: 31632391 PMCID: PMC6786274 DOI: 10.3389/fimmu.2019.02237] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/04/2019] [Indexed: 12/23/2022] Open
Abstract
Fc-gamma receptors (FcγR) are the cellular receptors for Immunoglobulin G (IgG). Upon binding of complexed IgG, FcγRs can trigger various cellular immune effector functions, thereby linking the adaptive and innate immune systems. In humans, six classic FcγRs are known: one high-affinity receptor (FcγRI) and five low-to-medium-affinity FcγRs (FcγRIIA, -B and -C, FcγRIIIA and -B). In this review we describe the five genes encoding the low-to-medium -affinity FcγRs (FCGR2A, FCGR2B, FCGR2C, FCGR3A, and FCGR3B), including well-characterized functionally relevant single nucleotide polymorphisms (SNPs), haplotypes as well as copy number variants (CNVs), which occur in distinct copy number regions across the locus. The evolution of the locus is also discussed. Importantly, we recommend a consistent nomenclature of genetic variants in the FCGR2/3 locus. Next, we focus on the relevance of genetic variation in the FCGR2/3 locus in auto-immune and auto-inflammatory diseases, highlighting pathophysiological insights that are informed by genetic association studies. Finally, we illustrate how specific FcγR variants relate to variation in treatment responses and prognosis amongst autoimmune diseases, cancer and transplant immunology, suggesting novel opportunities for personalized medicine.
Collapse
Affiliation(s)
- Sietse Q Nagelkerke
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - David E Schmidt
- Sanquin Research and Landsteiner Laboratory, Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Masja de Haas
- Sanquin Diagnostic Services, Department of Immunohematology Diagnostics, Amsterdam, Netherlands.,Sanquin Research, Center for Clinical Transfusion Research, Leiden, Netherlands.,Jon J. van Rood Center for Clinical Transfusion Science, Leiden University Medical Center, Leiden, Netherlands.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Taco W Kuijpers
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
10
|
Barbosa FB, Simioni M, Wiezel CEV, Torres FR, Molck MC, Bonilla MM, de Araujo TK, Donadi EA, Gil-da-Silva-Lopes VL, Lemos B, Simões AL. Copy number variation in the susceptibility to systemic lupus erythematosus. PLoS One 2018; 13:e0206683. [PMID: 30485348 PMCID: PMC6261406 DOI: 10.1371/journal.pone.0206683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/30/2018] [Indexed: 11/23/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong genetic component and etiology characterized by chronic inflammation and autoantibody production. The purpose of this study was to ascertain copy number variation (CNV) in SLE using a case-control design in an admixed Brazilian population. The whole-genome detection of CNV was performed using Cytoscan HD array in SLE patients and healthy controls. The best CNV candidates were then evaluated by quantitative real-time PCR in a larger cohort or validated using droplet digital PCR. Logistic regression models adjusted for sex and ancestry covariates was applied to evaluate the association between CNV with SLE susceptibility. The data showed a synergistic effect between the FCGR3B and ADAM3A loci with the presence of deletions in both loci significantly increasing the risk to SLE (5.9-fold) compared to the deletion in the single FCGR3B locus (3.6-fold). In addition, duplications in these genes were indeed more frequent in healthy subjects, suggesting that high FCGR3B/ADAM3A gene copy numbers are protective factors against to disease development. Overall, 21 rare CNVs were identified in SLE patients using a four-step pipeline created for identification of rare variants. Furthermore, heterozygous deletions overlapping the CFHR4, CFHR5 and HLA-DPB2 genes were described for the first time in SLE patients. Here we present the first genome-wide CNV study of SLE patients in a tri-hybrid population. The results show that novel susceptibility loci to SLE can be found once the distribution of structural variants is analyzed throughout the whole genome.
Collapse
Affiliation(s)
| | - Milena Simioni
- Department of Medical Genetics, Faculty of Medical Sciences, UNICAMP, Campinas, SP, Brazil
| | | | - Fábio Rossi Torres
- Department of Medical Genetics, Faculty of Medical Sciences, UNICAMP, Campinas, SP, Brazil
| | - Miriam Coelho Molck
- Department of Medical Genetics, Faculty of Medical Sciences, UNICAMP, Campinas, SP, Brazil
| | - Melvin M. Bonilla
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | | | - Eduardo Antônio Donadi
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, USP, Ribeirão Preto, SP, Brazil
| | | | - Bernardo Lemos
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Aguinaldo Luiz Simões
- Department of Genetics, Ribeirão Preto Medical School, USP, Ribeirão Preto, SP, Brazil
| |
Collapse
|
11
|
Kaifu T, Nakamura A. Polymorphisms of immunoglobulin receptors and the effects on clinical outcome in cancer immunotherapy and other immune diseases: a general review. Int Immunol 2018; 29:319-325. [PMID: 28910969 DOI: 10.1093/intimm/dxx041] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/10/2017] [Indexed: 12/15/2022] Open
Abstract
Receptors for the Fc domain of immunoglobulins [Fc receptors (FcRs)] are essential for the maintenance of antibody-mediated immune responses. FcRs consist of activating- and inhibitory-type receptors that regulate adequate thresholds for various immune cells. In particular, polymorphisms and/or gene copy-number variations of FcRs for IgG (FcγRs) are closely associated with the development of inflammatory disorders, including autoimmune diseases. Recent evidence has implicated polymorphisms of FcRs in the efficacy of monoclonal antibody (mAb)-mediated therapy. This review provides an overview of genetic variations in human FcγRs and the clinical contribution of FcγR polymorphisms in mAb treatments for cancer, autoimmune diseases and allergies.
Collapse
Affiliation(s)
- Tomonori Kaifu
- Division of Immunology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsushima, Aoba-ku, Sendai 981-8558, Japan
| | - Akira Nakamura
- Division of Immunology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsushima, Aoba-ku, Sendai 981-8558, Japan
| |
Collapse
|
12
|
Abstract
PURPOSE OF REVIEW Copy number variation (CNV) disorders arise from the dosage imbalance of one or more gene(s), resulting from deletions, duplications or other genomic rearrangements that lead to the loss or gain of genetic material. Several disorders, characterized by multiple birth defects and neurodevelopmental abnormalities, have been associated with relatively large (>1 Mb) and often recurrent CNVs. CNVs have also been implicated in the etiology of neuropsychiatric disorders including autism and schizophrenia as well as other common complex diseases. Thus, CNVs have a significant impact on human health and disease. RECENT FINDINGS The use of increasingly higher resolution, genomewide analysis has greatly enhanced the detection of genetic variation, including CNVs. Furthermore, the availability of comprehensive genetic variation data from large cohorts of healthy controls has the potential to greatly improve the identification of disease associated genetic variants in patient samples. SUMMARY This review discusses the current knowledge about CNV disorders, including the mechanisms underlying their formation and phenotypic outcomes, and the advantages and limitations of current methods of detection and disease association.
Collapse
Affiliation(s)
- Tamim H. Shaikh
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, CO 80045
| |
Collapse
|
13
|
Zuccherato LW, Schneider S, Tarazona-Santos E, Hardwick RJ, Berg DE, Bogle H, Gouveia MH, Machado LR, Machado M, Rodrigues-Soares F, Soares-Souza GB, Togni DL, Zamudio R, Gilman RH, Duarte D, Hollox EJ, Rodrigues MR. Population genetics of immune-related multilocus copy number variation in Native Americans. J R Soc Interface 2017; 14:rsif.2017.0057. [PMID: 28356540 DOI: 10.1098/rsif.2017.0057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/02/2017] [Indexed: 12/22/2022] Open
Abstract
While multiallelic copy number variation (mCNV) loci are a major component of genomic variation, quantifying the individual copy number of a locus and defining genotypes is challenging. Few methods exist to study how mCNV genetic diversity is apportioned within and between populations (i.e. to define the population genetic structure of mCNV). These inferences are critical in populations with a small effective size, such as Amerindians, that may not fit the Hardy-Weinberg model due to inbreeding, assortative mating, population subdivision, natural selection or a combination of these evolutionary factors. We propose a likelihood-based method that simultaneously infers mCNV allele frequencies and the population structure parameter f, which quantifies the departure of homozygosity from the Hardy-Weinberg expectation. This method is implemented in the freely available software CNVice, which also infers individual genotypes using information from both the population and from trios, if available. We studied the population genetics of five immune-related mCNV loci associated with complex diseases (beta-defensins, CCL3L1/CCL4L1, FCGR3A, FCGR3B and FCGR2C) in 12 traditional Native American populations and found that the population structure parameters inferred for these mCNVs are comparable to but lower than those for single nucleotide polymorphisms studied in the same populations.
Collapse
Affiliation(s)
- Luciana W Zuccherato
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Silvana Schneider
- Departamento de Estatística, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Douglas E Berg
- Department of Molecular Microbiology, Washington University in Saint Louis School of Medicine, St Louis, MO, USA.,Department of Medicine, University of California San Diego, CA, USA
| | - Helen Bogle
- Department of Genetics, University of Leicester, Leicester, UK
| | - Mateus H Gouveia
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lee R Machado
- Department of Genetics, University of Leicester, Leicester, UK.,School of Health, University of Northampton, Northampton, UK
| | - Moara Machado
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fernanda Rodrigues-Soares
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Giordano B Soares-Souza
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Diego L Togni
- Departamento de Estatística, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Roxana Zamudio
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Robert H Gilman
- Johns Hopkins School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Asociación Benéfica PRISMA, Lima, Peru.,Universidade Peruana Cayetano Heredia, Lima, Peru
| | - Denise Duarte
- Departamento de Estatística, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Edward J Hollox
- Department of Genetics, University of Leicester, Leicester, UK
| | - Maíra R Rodrigues
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| |
Collapse
|