1
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Identification of shared molecular signatures between multiple sclerosis and Parkinson's disease using systems biology approach. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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2
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Complementary Experimental Methods in Genetics Open Up New Avenues of Research to Elucidate the Pathogenesis of Periodontitis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1373:209-227. [DOI: 10.1007/978-3-030-96881-6_11] [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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3
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Runaway multi-allelic copy number variation at the α-defensin locus in African and Asian populations. Sci Rep 2020; 10:9101. [PMID: 32499510 PMCID: PMC7272440 DOI: 10.1038/s41598-020-65675-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/04/2020] [Indexed: 12/15/2022] Open
Abstract
Alpha defensins are anti-microbial peptides of the innate immune system. The defensin A1 and A3 genes are located in a repeat array of variable copy number (the DEFA1A3 locus) and encode the human neutrophil peptides 1, 2 and 3. The possibility that copy number variation (CNV) may be associated with infection susceptibility and autoimmune pathology motivated the study of DEFA1A3 CNV across populations. We enhanced two existing methods (one qPCR-based and one sequencing-based) to enable copy number estimation that discriminates between DEFA1 and DEFA3 genes. We used these methods to quantify A1/A3 copy number variation in 2504 samples from the 1000 Genomes high-coverage dataset as well as performing FiberFISH assays on selected samples to visualize the haplotypes. These methods produce accurate estimates and show that there are substantial differences between populations. The African population is a clear outlier with a high frequency of the ancestral pure DEFA1 haplotype, but also harbours exceptionally long haplotypes of 24 copies of both DEFA1 and DEFA3, whilst the East Asian population displays the highest mean level of DEFA3 copy number. Further, our findings demonstrate that qPCR can be an accurate method for CNV estimation and that defensins substantially extend the known range of copy number variation for a human protein-coding gene.
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4
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Song X, Shao C, Guo Y, Wang Y, Cai J. Improved the expression level of active transglutaminase by directional increasing copy of mtg gene in Pichia pastoris. BMC Biotechnol 2019; 19:54. [PMID: 31362722 PMCID: PMC6668168 DOI: 10.1186/s12896-019-0542-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 07/05/2019] [Indexed: 12/31/2022] Open
Abstract
Background The microbial transglutaminase (MTG) is inactive when only the mature sequence is expressed in Pichia pastoris. Although co-expression of MTG and its N-terminal pro-peptide can obtain the active MTG, the enzyme activity was still low. One of the basic steps for strain improvement is to ensure a sufficient level of transcription of the heterologous gene, based on promoter strength and gene copy number. To date, high-copy-number recombinants of P. pastoris are achievable only by cloning of gene concatemers, so methods for rapid and reliable multicopy strains are therefore desirable. Results The coexpression strains harboring different copies mtg were obtained successfully by stepwise increasing Zeocin concentration based on the rDNA sequence of P. pastoris. The genome of coexpression strains with the highest enzyme activity was analyzed by real-time fluorescence quantitative PCR, and three copies of mtg gene (mtg-3c) was calculated according to the standard curve of gap and mtg genes (gap is regarded as the single-copy reference gene). The maximum enzyme activity of mtg-3c was up to 1.41 U/mL after being inducted for 72 h in 1 L flask under optimal culture conditions, and two protein bands were observed at the expected molecular weights (40 kDa and 5 kDa) by Western blot. Furthermore, among the strains detected, compared with mtg-2c, mtg-6c or mtg-8c, mtg-3c is the highest expression level and enzyme activity, implying that mtg-3c is the most suitable for co-expression pro-peptide and MTG. Conclusions This study provides an effective strategy for improving the expression level of active MTG by directional increasing of mtg copies in P. pastoris. Electronic supplementary material The online version of this article (10.1186/s12896-019-0542-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoping Song
- Department of Pharmacy, Anhui Medical College, Hefei, 230061, China. .,Anhui Engineering Research Center of Recombinant Protein Pharmaceutical Biotechnology, Hefei, 230022, China.
| | - Changsheng Shao
- Anhui Engineering Research Center of Recombinant Protein Pharmaceutical Biotechnology, Hefei, 230022, China
| | - Yugang Guo
- Institute of advanced technology, University of Science and Technology of China, Hefei, 230031, China.,Anhui Engineering Research Center of Recombinant Protein Pharmaceutical Biotechnology, Hefei, 230022, China
| | - Yajie Wang
- Department of Pharmacy, Anhui Medical College, Hefei, 230061, China
| | - Jingjing Cai
- Department of Pharmacy, Anhui Medical College, Hefei, 230061, China
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5
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Abstract
IgA nephropathy (IgAN) represents a genetically complex multifactorial trait. Its prevalence and clinical features vary geographically, and the disease has a range of clinical presentations that suggest multiple subtypes. Although familial aggregation of IgAN has been reported and prior linkage studies have highlighted significant locus heterogeneity, specific genetic variants underlying familial IgAN have not yet been defined. Population-based genome-wide association studies (GWAS) have discovered nearly 20 IgAN risk loci, providing novel insights into disease epidemiology and molecular mechanisms, shifting old paradigms of the disease pathogenesis. Follow-up fine-mapping studies have identified specific causal variants, and genotype-phenotype correlation studies have begun to delineate clinical consequences of GWAS risk alleles. The association between IgAN and galactose-deficient IgA1 (Gd-IgA1), a validated serum biomarker of IgAN, presented another avenue for genetic discovery because elevated serum levels of Gd-IgA1 are highly heritable. Recent GWAS for serum Gd-IgA1 levels provided novel insights into genetic regulation of this trait, but the genetic link between Gd-IgA1 and IgAN has not yet been established. In this review, we discuss these developments in the broader context of modern genetic approaches to complex traits, and provide our perspective on the critical challenges that need to be addressed to advance the field.
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Affiliation(s)
- Y Dana Neugut
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY.
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6
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Schaefer AS. Genetics of periodontitis: Discovery, biology, and clinical impact. Periodontol 2000 2018; 78:162-173. [DOI: 10.1111/prd.12232] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Arne S Schaefer
- Department of Periodontology and Synoptic Dentistry; Institute for Dental and Craniofacial Sciences; Research Centre ImmunoSciences; Charité - University Medicine Berlin; Berlin Germany
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7
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Low-Copy Number Polymorphism in DEFA1/DEFA3 Is Associated with Susceptibility to Hospital-Acquired Infections in Critically Ill Patients. Mediators Inflamm 2018; 2018:2152650. [PMID: 29950924 PMCID: PMC5987315 DOI: 10.1155/2018/2152650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 03/25/2018] [Accepted: 04/19/2018] [Indexed: 01/19/2023] Open
Abstract
DEFA1/DEFA3, genes encoding human neutrophil peptides (HNP) 1-3, display wide-ranging copy number variations (CNVs) and is functionally associated with innate immunity and infections. To identify potential associations between DEFA1/DEFA3 CNV and hospital-acquired infections (HAIs), we enrolled 106 patients with HAIs and 109 controls in the intensive care unit (ICU) and examined their DEFA1/DEFA3 CNVs. DEFA1/DEFA3 copy number ranged from 2 to 16 per diploid genome in all 215 critically ill patients, with a median of 7 copies. In HAIs, DEFA1/DEFA3 CNV varied from 2 to 12 with a median of 6, which was significantly lower than that in controls (2 to 16 with a median of 8, p = 0.017). Patients with lower DEFA1/DEFA3 copy number (CNV < 7) were far more common in HAIs than in controls (52.8% in HAIs versus 35.8% in controls; p = 0.014; OR, 2.010; 95% CI, 1.164-3.472). The area under the receiver operating characteristic (AUROC) of DEFA1/DEFA3 CNV combined with clinical characteristics to predict the incidence of HAIs was 0.763 (95% CI 0.700-0.827), showing strong predictive ability. Therefore, lower DEFA1/DEFA3 copy number contributes to higher susceptibility to HAIs in critically ill patients, and DEFA1/DEFA3 CNV is a significant hereditary factor for predicting HAIs.
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8
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Park YJ, Lee HK. The Role of Skin and Orogenital Microbiota in Protective Immunity and Chronic Immune-Mediated Inflammatory Disease. Front Immunol 2018; 8:1955. [PMID: 29375574 PMCID: PMC5767596 DOI: 10.3389/fimmu.2017.01955] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/19/2017] [Indexed: 12/11/2022] Open
Abstract
The skin and orogenital mucosae, which constitute complex protective barriers against infection and injuries, are not only the first to come into contact with pathogens but are also colonized by a set of microorganisms that are essential to maintain a healthy physiological environment. Using 16S ribosomal RNA metagenomic sequencing, scientists recognized that the microorganism colonization has greater diversity and variability than previously assumed. These microorganisms, such as commensal bacteria, affect the host’s immune response against pathogens and modulate chronic inflammatory responses. Previously, a single pathogen was thought to cause a single disease, but current evidence suggests that dysbiosis of the tissue microbiota may underlie the disease status. Dysbiosis results in aberrant immune responses at the surface and furthermore, affects the systemic immune response. Hence, understanding the initial interaction between the barrier surface immune system and local microorganisms is important for understanding the overall systemic effects of the immune response. In this review, we describe current evidence for the basis of the interactions between pathogens, microbiota, and immune cells on surface barriers and offer explanations for how these interactions may lead to chronic inflammatory disorders.
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Affiliation(s)
- Young Joon Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Heung Kyu Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.,KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
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9
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Munz M, Willenborg C, Richter GM, Jockel-Schneider Y, Graetz C, Staufenbiel I, Wellmann J, Berger K, Krone B, Hoffmann P, van der Velde N, Uitterlinden AG, de Groot LCPGM, Sawalha AH, Direskeneli H, Saruhan-Direskeneli G, Guzeldemir-Akcakanat E, Keceli HG, Laudes M, Noack B, Teumer A, Holtfreter B, Kocher T, Eickholz P, Meyle J, Doerfer C, Bruckmann C, Lieb W, Franke A, Schreiber S, Nohutcu RM, Erdmann J, Loos BG, Jepsen S, Dommisch H, Schaefer AS. A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis. Hum Mol Genet 2017; 26:2577-2588. [PMID: 28449029 DOI: 10.1093/hmg/ddx151] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/12/2017] [Indexed: 01/26/2023] Open
Abstract
Periodontitis is one of the most common inflammatory diseases, with a prevalence of 11% worldwide for the severe forms and an estimated heritability of 50%. The disease is characterized by destruction of the alveolar bone due to an aberrant host inflammatory response to a dysbiotic oral microbiome. Previous genome-wide association studies (GWAS) have reported several suggestive susceptibility loci. Here, we conducted a GWAS using a German and Dutch case-control sample of aggressive periodontitis (AgP, 896 cases, 7,104 controls), a rare but highly severe and early-onset form of periodontitis, validated the associations in a German sample of severe forms of the more moderate phenotype chronic periodontitis (CP) (993 cases, 1,419 controls). Positive findings were replicated in a Turkish sample of AgP (223 cases, 564 controls). A locus at SIGLEC5 (sialic acid binding Ig-like lectin 5) and a chromosomal region downstream of the DEFA1A3 locus (defensin alpha 1-3) showed association with both disease phenotypes and were associated with periodontitis at a genome-wide significance level in the pooled samples, with P = 1.09E-08 (rs4284742,-G; OR = 1.34, 95% CI = 1.21-1.48) and P = 5.48E-10 (rs2738058,-T; OR = 1.28, 95% CI = 1.18-1.38), respectively. SIGLEC5 is expressed in various myeloid immune cells and classified as an inhibitory receptor with the potential to mediate tyrosine phosphatases SHP-1/-2 dependent signaling. Alpha defensins are antimicrobial peptides with expression in neutrophils and mucosal surfaces and a role in phagocyte-mediated host defense. This study identifies the first shared genetic risk loci of AgP and CP with genome-wide significance and highlights the role of innate and adaptive immunity in the etiology of periodontitis.
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Affiliation(s)
- Matthias Munz
- Department of Periodontology and Synoptic Dentistry, Institute of Dental, Oral and Maxillary Medicine, Charité - University Medicine Berlin, Germany.,Institute for Integrative and Experimental Genomics, University Medical Center Schleswig-Holstein - Campus Lübeck, Germany
| | - Christina Willenborg
- Institute for Integrative and Experimental Genomics, University Medical Center Schleswig-Holstein - Campus Lübeck, Germany
| | - Gesa M Richter
- Department of Periodontology and Synoptic Dentistry, Institute of Dental, Oral and Maxillary Medicine, Charité - University Medicine Berlin, Germany
| | - Yvonne Jockel-Schneider
- Department of Periodontology, Clinic of Preventive Dentistry and Periodontology, University Medical Center of the Julius-Maximilians-University, Würzburg, Germany
| | - Christian Graetz
- Department of Operative Dentistry and Periodontology, University Medical Center Schleswig-Holstein, Campus Kiel, Germany
| | - Ingmar Staufenbiel
- Department of Conservative Dentistry, Periodontology and Preventive Dentistry, Hannover Medical School, Hannover, Germany
| | - Jürgen Wellmann
- Institute of Epidemiology and Social Medicine, University Münster, Germany
| | - Klaus Berger
- Institute of Epidemiology and Social Medicine, University Münster, Germany
| | - Bastian Krone
- Institute of Medical Informatics, Biometry and Epidemiology, University Clinic Essen, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Germany.,Human Genomics Research Group, Department of Biomedicine, University Hospital of Basel, Switzerland
| | - Nathalie van der Velde
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Internal Medicine Section of Geriatrics, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lisette C P G M de Groot
- Department of Epidemiology and the EMGO Institute of Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands
| | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.,Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, USA
| | - Haner Direskeneli
- Division of Rheumatology, Marmara University, School of Medicine, Istanbul, Turkey
| | | | | | - Huseyin Gencay Keceli
- Department of Periodontology, Faculty of Dentistry, Hacettepe University, Sihhiye, Ankara, Turkey
| | - Matthias Laudes
- Clinic of Internal Medicine, University Clinic Schleswig-Holstein, Kiel, Germany
| | - Barbara Noack
- Clinic of Conservational Dentistry, Center of Dental, Oral and Maxillary Medicine, University Medical Center Carl-Gustav-Carus, Technical University Dresden, Germany
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Germany
| | - Birte Holtfreter
- Unit of Periodontology, Department of Restorative Dentistry, Periodontology, Endodontology, Preventive Dentistry and Pedodontics, Dental School, University Medicine Greifswald, Germany
| | - Thomas Kocher
- Unit of Periodontology, Department of Restorative Dentistry, Periodontology, Endodontology, Preventive Dentistry and Pedodontics, Dental School, University Medicine Greifswald, Germany
| | - Peter Eickholz
- Department of Periodontology, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Jörg Meyle
- Department of Periodontology, University Medical Center Giessen and Marburg, Germany
| | - Christof Doerfer
- Department of Operative Dentistry and Periodontology, University Medical Center Schleswig-Holstein, Campus Kiel, Germany
| | - Corinna Bruckmann
- Department of Conservative Dentistry and Periodontology, Medical University Vienna, School of Dentistry, Vienna, Austria
| | - Wolfgang Lieb
- Institute of Epidemiology, Biobank PopGen, Christian-Albrechts-University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Stefan Schreiber
- Clinic of Internal Medicine, University Clinic Schleswig-Holstein, Kiel, Germany.,Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Rahime M Nohutcu
- Department of Periodontology, Faculty of Dentistry, Kocaeli University, Turkey
| | - Jeanette Erdmann
- Institute for Integrative and Experimental Genomics, University Medical Center Schleswig-Holstein - Campus Lübeck, Germany
| | - Bruno G Loos
- Department of Periodontology and Oral Biochemistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, The Netherlands
| | - Soeren Jepsen
- Department of Periodontology, Operative and Preventive Dentistry, University of Bonn, Bonn, Germany
| | - Henrik Dommisch
- Department of Periodontology and Synoptic Dentistry, Institute of Dental, Oral and Maxillary Medicine, Charité - University Medicine Berlin, Germany
| | - Arne S Schaefer
- Department of Periodontology and Synoptic Dentistry, Institute of Dental, Oral and Maxillary Medicine, Charité - University Medicine Berlin, Germany
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10
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Lin HT, Okumura T, Yatsuda Y, Ito S, Nakauchi H, Otsu M. Application of Droplet Digital PCR for Estimating Vector Copy Number States in Stem Cell Gene Therapy. Hum Gene Ther Methods 2017; 27:197-208. [PMID: 27763786 PMCID: PMC5111482 DOI: 10.1089/hgtb.2016.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Stable gene transfer into target cell populations via integrating viral vectors is widely used in stem cell gene therapy (SCGT). Accurate vector copy number (VCN) estimation has become increasingly important. However, existing methods of estimation such as real-time quantitative PCR are more restricted in practicality, especially during clinical trials, given the limited availability of sample materials from patients. This study demonstrates the application of an emerging technology called droplet digital PCR (ddPCR) in estimating VCN states in the context of SCGT. Induced pluripotent stem cells (iPSCs) derived from a patient with X-linked chronic granulomatous disease were used as clonable target cells for transduction with alpharetroviral vectors harboring codon-optimized CYBB cDNA. Precise primer–probe design followed by multiplex analysis conferred assay specificity. Accurate estimation of per-cell VCN values was possible without reliance on a reference standard curve. Sensitivity was high and the dynamic range of detection was wide. Assay reliability was validated by observation of consistent, reproducible, and distinct VCN clustering patterns for clones of transduced iPSCs with varying numbers of transgene copies. Taken together, use of ddPCR appears to offer a practical and robust approach to VCN estimation with a wide range of clinical and research applications.
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Affiliation(s)
- Huan-Ting Lin
- 1 Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo , Tokyo, Japan .,2 Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo , Tokyo, Japan
| | - Takashi Okumura
- 2 Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo , Tokyo, Japan
| | | | - Satoru Ito
- 3 Life Science Division, Bio-Rad Laboratories , Tokyo, Japan
| | - Hiromitsu Nakauchi
- 1 Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo , Tokyo, Japan .,4 Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine , Stanford, California
| | - Makoto Otsu
- 1 Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo , Tokyo, Japan .,2 Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo , Tokyo, Japan
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11
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Abstract
Copy number variation (CNV), where a segment of DNA differs in copy number between different individuals, is an extensive and often underappreciated source of genetic variation within species. However, reliably determining copy number of a particular DNA sequence for a large number of samples can be challenging. Here, I describe and review the paralogue ratio test (PRT) in detail. PRT was developed to robustly type the CNV of the beta-defensin locus using small amounts of genomic DNA in a high-throughput manner, and has been applied successfully at many other loci. I discuss the strategies for designing successful PRT assays using both manual and bioinformatics methods, how to optimize experimental conditions, and approaches for analyzing the data. I discuss strengths and weaknesses of the approach, and how to troubleshoot results, as well as the range of problems to which PRT can be a potential solution.
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12
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Schwaderer AL, Wang H, Kim S, Kline JM, Liang D, Brophy PD, McHugh KM, Tseng GC, Saxena V, Barr-Beare E, Pierce KR, Shaikh N, Manak JR, Cohen DM, Becknell B, Spencer JD, Baker PB, Yu CY, Hains DS. Polymorphisms in α-Defensin-Encoding DEFA1A3 Associate with Urinary Tract Infection Risk in Children with Vesicoureteral Reflux. J Am Soc Nephrol 2016; 27:3175-3186. [PMID: 26940096 PMCID: PMC5042661 DOI: 10.1681/asn.2015060700] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 01/13/2016] [Indexed: 12/12/2022] Open
Abstract
The contribution of genetic variation to urinary tract infection (UTI) risk in children with vesicoureteral reflux is largely unknown. The innate immune system, which includes antimicrobial peptides, such as the α-defensins, encoded by DEFA1A3, is important in preventing UTIs but has not been investigated in the vesicoureteral reflux population. We used quantitative real-time PCR to determine DEFA1A3 DNA copy numbers in 298 individuals with confirmed UTIs and vesicoureteral reflux from the Randomized Intervention for Children with Vesicoureteral Reflux (RIVUR) Study and 295 controls, and we correlated copy numbers with outcomes. Outcomes studied included reflux grade, UTIs during the study on placebo or antibiotics, bowel and bladder dysfunction, and renal scarring. Overall, 29% of patients and 16% of controls had less than or equal to five copies of DEFA1A3 (odds ratio, 2.09; 95% confidence interval, 1.40 to 3.11; P<0.001). For each additional copy of DEFA1A3, the odds of recurrent UTI in patients receiving antibiotic prophylaxis decreased by 47% when adjusting for vesicoureteral reflux grade and bowel and bladder dysfunction. In patients receiving placebo, DEFA1A3 copy number did not associate with risk of recurrent UTI. Notably, we found that DEFA1A3 is expressed in renal epithelium and not restricted to myeloid-derived cells, such as neutrophils. In conclusion, low DEFA1A3 copy number associated with recurrent UTIs in subjects in the RIVUR Study randomized to prophylactic antibiotics, providing evidence that copy number polymorphisms in an antimicrobial peptide associate with UTI risk.
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Affiliation(s)
| | - Huanyu Wang
- The Centers for Clinical and Translational Medicine and
| | | | | | - Dong Liang
- Innate Immunity Translational Research Center, Children's Foundation Research Institute at Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Pat D Brophy
- Division of Nephrology, Department of Pediatrics, University of Iowa Children's Hospital, Iowa City, Iowa
| | - Kirk M McHugh
- Division of Anatomy, The Ohio State University, Columbus, Ohio
| | | | - Vijay Saxena
- The Centers for Clinical and Translational Medicine and
| | | | - Keith R Pierce
- Innate Immunity Translational Research Center, Children's Foundation Research Institute at Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Nader Shaikh
- Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - J Robert Manak
- Departments of Biology and Pediatrics, University of Iowa, Iowa; and
| | | | | | | | - Peter B Baker
- Department of Pathology, Nationwide Children's Hospital, Columbus, Ohio
| | - Chack-Yung Yu
- Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - David S Hains
- Innate Immunity Translational Research Center, Children's Foundation Research Institute at Le Bonheur Children's Hospital, Memphis, Tennessee; Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
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13
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Ai Z, Li M, Liu W, Foo JN, Mansouri O, Yin P, Zhou Q, Tang X, Dong X, Feng S, Xu R, Zhong Z, Chen J, Wan J, Lou T, Yu J, Zhou Q, Fan J, Mao H, Gale D, Barratt J, Armour JAL, Liu J, Yu X. Low α-defensin gene copy number increases the risk for IgA nephropathy and renal dysfunction. Sci Transl Med 2016; 8:345ra88. [PMID: 27358498 DOI: 10.1126/scitranslmed.aaf2106] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 06/10/2016] [Indexed: 12/12/2022]
Abstract
Although a major source of genetic variation, copy number variations (CNVs) and their involvement in disease development have not been well studied. Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulonephritis worldwide. We performed association analysis of the DEFA1A3 CNV locus in two independent IgAN cohorts of southern Chinese Han (total of 1189 cases and 1187 controls). We discovered three independent copy number associations within the locus: DEFA1A3 [P = 3.99 × 10−9; odds ratio (OR), 0.88], DEFA3 (P = 6.55 × 10−5; OR, 0.82), and a noncoding deletion variant (211bp) (P = 3.50 × 10−16; OR, 0.75) (OR per copy, fixed-effects meta-analysis). While showing strong association with an increased risk for IgAN (P = 9.56 × 10−20), low total copy numbers of the three variants also showed significant association with renal dysfunction in patients with IgAN (P = 0.03; hazards ratio, 3.69; after controlling for the effects of known prognostic factors) and also with increased serum IgA1 (P = 0.02) and galactose-deficient IgA1 (P = 0.03). For replication, we confirmed the associations of DEFA1A3 (P = 4.42 × 10−4; OR, 0.82) and DEFA3 copy numbers (P = 4.30 × 10−3; OR, 0.74) with IgAN in a Caucasian cohort (531 cases and 198 controls) and found the 211bp variant to be much rarer in Caucasians. We also observed an association of the 211bp copy number with membranous nephropathy (P = 1.11 × 10−7; OR, 0.74; in 493 Chinese cases and 500 matched controls), but not with diabetic kidney disease (in 806 Chinese cases and 786 matched controls). By explaining 4.96% of disease risk and influencing renal dysfunction in patients with IgAN, the DEFA1A3 CNV locus may be a potential therapeutic target for developing treatments for this disease.
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Affiliation(s)
- Zhen Ai
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China
| | - Ming Li
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China
| | - Wenting Liu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China
| | - Jia-Nee Foo
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Omniah Mansouri
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Peiran Yin
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China
| | - Qian Zhou
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China
| | - Xueqing Tang
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China
| | - Xiuqing Dong
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China
| | - Shaozhen Feng
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China
| | - Ricong Xu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China
| | - Zhong Zhong
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China
| | - Jian Chen
- Department of Nephrology, Fuzhou General Hospital of Nanjing Military Command, Fuzhou, Fujian 350025, China
| | - Jianxin Wan
- Department of Nephrology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Tanqi Lou
- Department of Nephrology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Jianwen Yu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China
| | - Qin Zhou
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China
| | - Jinjin Fan
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China
| | - Haiping Mao
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China
| | - Daniel Gale
- University College London Centre for Nephrology, Royal Free Hospital, London NW3 2PF, UK
| | - Jonathan Barratt
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK
| | - John A L Armour
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Jianjun Liu
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore. School of Biological Sciences, Anhui Medical University, Hefei, Anhui 230032, China. Saw Swee Hock School of Public Health, National University of Singapore, Singapore 119077, Singapore.
| | - Xueqing Yu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China. Key Laboratory of Nephrology, Ministry of Health and Guangdong Province, Guangzhou, Guangdong 510080, China.
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Mehlotra RK, Zimmerman PA, Weinberg A. Defensin gene variation and HIV/AIDS: a comprehensive perspective needed. J Leukoc Biol 2016; 99:687-92. [PMID: 26957215 DOI: 10.1189/jlb.6ru1215-560r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/02/2016] [Indexed: 01/24/2023] Open
Abstract
Both α- and β-defensins have anti-human immunodeficiency virus activity. These defensins achieve human immunodeficiency virus inhibition through a variety of mechanisms, including direct binding with virions, binding to and modulation of host cell-surface receptors with disruption of intracellular signaling, and functioning as chemokines or cytokines to augment and alter adaptive immune responses. Polymorphisms in the defensin genes have been associated with susceptibility to human immunodeficiency virus infection and disease progression. However, the roles that these defensins and their genetic polymorphisms have in influencing human immunodeficiency virus/acquired immunodeficiency syndrome outcomes are not straightforward and, at times, appear contradictory. Differences in populations, study designs, and techniques for genotyping defensin gene polymorphisms may have contributed to this lack of clarity. In addition, a comprehensive approach, where both subfamilies of defensins and their all-inclusive genetic polymorphism profiles are analyzed, is lacking. Such an approach may reveal whether the human immunodeficiency virus inhibitory activities of α- and β-defensins are based on parallel or divergent mechanisms and may provide further insights into how the genetic predisposition for susceptibility or resistance to human immunodeficiency virus/acquired immunodeficiency syndrome is orchestrated between these molecules.
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Affiliation(s)
- Rajeev K Mehlotra
- Center for Global Health and Diseases, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Peter A Zimmerman
- Center for Global Health and Diseases, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Aaron Weinberg
- Department of Biological Sciences, Case Western Reserve University School of Dental Medicine, Cleveland, Ohio, USA
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15
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Identification of new susceptibility loci for IgA nephropathy in Han Chinese. Nat Commun 2015; 6:7270. [PMID: 26028593 PMCID: PMC4458882 DOI: 10.1038/ncomms8270] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 04/23/2015] [Indexed: 12/20/2022] Open
Abstract
IgA nephropathy (IgAN) is one of the most common primary glomerulonephritis. Previously identified genome-wide association study (GWAS) loci explain only a fraction of disease risk. To identify novel susceptibility loci in Han Chinese, we conduct a four-stage GWAS comprising 8,313 cases and 19,680 controls. Here, we show novel associations at ST6GAL1 on 3q27.3 (rs7634389, odds ratio (OR)=1.13, P=7.27 × 10(-10)), ACCS on 11p11.2 (rs2074038, OR=1.14, P=3.93 × 10(-9)) and ODF1-KLF10 on 8q22.3 (rs2033562, OR=1.13, P=1.41 × 10(-9)), validate a recently reported association at ITGAX-ITGAM on 16p11.2 (rs7190997, OR=1.22, P=2.26 × 10(-19)), and identify three independent signals within the DEFA locus (rs2738058, P=1.15 × 10(-19); rs12716641, P=9.53 × 10(-9); rs9314614, P=4.25 × 10(-9), multivariate association). The risk variants on 3q27.3 and 11p11.2 show strong association with mRNA expression levels in blood cells while allele frequencies of the risk variants within ST6GAL1, ACCS and DEFA correlate with geographical variation in IgAN prevalence. Our findings expand our understanding on IgAN genetic susceptibility and provide novel biological insights into molecular mechanisms underlying IgAN.
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16
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Machado LR, Ottolini B. An evolutionary history of defensins: a role for copy number variation in maximizing host innate and adaptive immune responses. Front Immunol 2015; 6:115. [PMID: 25852686 PMCID: PMC4364288 DOI: 10.3389/fimmu.2015.00115] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/01/2015] [Indexed: 12/21/2022] Open
Abstract
Defensins represent an evolutionary ancient family of antimicrobial peptides that play diverse roles in human health and disease. Defensins are cationic cysteine-containing multifunctional peptides predominantly expressed by epithelial cells or neutrophils. Defensins play a key role in host innate immune responses to infection and, in addition to their classically described role as antimicrobial peptides, have also been implicated in immune modulation, fertility, development, and wound healing. Aberrant expression of defensins is important in a number of inflammatory diseases as well as modulating host immune responses to bacteria, unicellular pathogens, and viruses. In parallel with their role in immunity, in other species, defensins have evolved alternative functions, including the control of coat color in dogs. Defensin genes reside in complex genomic regions that are prone to structural variations and some defensin family members exhibit copy number variation (CNV). Structural variations have mediated, and continue to influence, the diversification and expression of defensin family members. This review highlights the work currently being done to better understand the genomic architecture of the β-defensin locus. It evaluates current evidence linking defensin CNV to autoimmune disease (i.e., Crohn’s disease and psoriasis) as well as the contribution CNV has in influencing immune responses to HIV infection.
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Affiliation(s)
- Lee R Machado
- Institute of Health and Wellbeing, School of Health, University of Northampton , Northampton , UK
| | - Barbara Ottolini
- Department of Cancer Studies, University of Leicester , Leicester , UK
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17
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Black HA, Khan FF, Tyson J, Armour JAL. Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus. BMC Genomics 2014; 15:614. [PMID: 25048054 PMCID: PMC4117965 DOI: 10.1186/1471-2164-15-614] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/14/2014] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The determination of structural haplotypes at copy number variable regions can indicate the mechanisms responsible for changes in copy number, as well as explain the relationship between gene copy number and expression. However, obtaining spatial information at regions displaying extensive copy number variation, such as the DEFA1A3 locus, is complex, because of the difficulty in the phasing and assembly of these regions. The DEFA1A3 locus is intriguing in that it falls within a region of high linkage disequilibrium, despite its high variability in copy number (n = 3-16); hence, the mechanisms responsible for changes in copy number at this locus are unclear. RESULTS In this study, a region flanking the DEFA1A3 locus was sequenced across 120 independent haplotypes with European ancestry, identifying five common classes of DEFA1A3 haplotype. Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry. The features of each DEFA1A3 class, for example, the associated DEFA1A3 copy numbers, were initially assessed in a European cohort (n = 599) and replicated in the 1000 Genomes samples, showing within-class similarity, but between-class and between-population differences in the features of the DEFA1A3 locus. Emulsion haplotype fusion-PCR was used to generate 61 structural haplotypes at the DEFA1A3 locus, showing a high within-class similarity in structure. CONCLUSIONS Structural haplotypes across the DEFA1A3 locus indicate that intra-allelic rearrangement is the predominant mechanism responsible for changes in DEFA1A3 copy number, explaining the conservation of linkage disequilibrium across the locus. The identification of common structural haplotypes at the DEFA1A3 locus could aid studies into how DEFA1A3 copy number influences expression, which is currently unclear.
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Affiliation(s)
- Holly A Black
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, NG7 2UH UK
| | - Fayeza F Khan
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, NG7 2UH UK
| | - Jess Tyson
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, NG7 2UH UK
| | - John AL Armour
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, NG7 2UH UK
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18
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Human gene copy number variation and infectious disease. Hum Genet 2014; 133:1217-33. [PMID: 25110110 DOI: 10.1007/s00439-014-1457-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/20/2014] [Indexed: 01/05/2023]
Abstract
Variability in the susceptibility to infectious disease and its clinical manifestation can be determined by variation in the environment and by genetic variation in the pathogen and the host. Despite several successes based on candidate gene studies, defining the host variation affecting infectious disease has not been as successful as for other multifactorial diseases. Both single nucleotide variation and copy number variation (CNV) of the host contribute to the host's susceptibility to infectious disease. In this review we focus on CNV, particularly on complex multiallelic CNV that is often not well characterised either directly by hybridisation methods or indirectly by analysis of genotypes and flanking single nucleotide variants. We summarise the well-known examples, such as α-globin deletion and susceptibility to severe malaria, as well as more recent controversies, such as the extensive CNV of the chemokine gene CCL3L1 and HIV infection. We discuss the potential biological mechanisms that could underly any genetic association and reflect on the extensive complexity and functional variation generated by a combination of CNV and sequence variation, as illustrated by the Fc gamma receptor genes FCGR3A, FCGR3B and FCGR2C. We also highlight some understudied areas that might prove fruitful areas for further research.
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Abstract
IgA nephropathy (IgAN) represents the leading cause of kidney failure among East Asian populations and the most frequent form of primary glomerulonephritis among Europeans. Patients with IgAN develop characteristic IgA1-containing immune complexes that deposit in the glomerular mesangium, producing progressive kidney injury. Recent studies define IgAN as an autoimmune trait of complex architecture with a strong genetic determination. This Review summarizes new insights into the role of the O-glycosylation pathway, anti-glycan immune response, mucosal immunity, antigen processing and presentation, and the alternative complement pathway in the pathogenesis of IgAN.
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