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Bubenikova J, Plasil M, Futas J, Stejskalova K, Klumplerova M, Oppelt J, Suchentrunk F, Burger PA, Horin P. Diversity of major histocompatibility complex (MHC) and natural killer cell receptor (NKR) genes and their interactions in domestic horses. HLA 2024; 103:e15387. [PMID: 38358031 DOI: 10.1111/tan.15387] [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: 09/14/2023] [Revised: 01/03/2024] [Accepted: 01/28/2024] [Indexed: 02/16/2024]
Abstract
The immunogenome is the part of the genome that underlies immune mechanisms and evolves under various selective pressures. Two complex regions of the immunogenome, major histocompatibility complex (MHC) and natural killer cell receptor (NKR) genes, play an important role in the response to selective pressures of pathogens. Their importance is expressed by their genetic polymorphism at the molecular level, and their diversity associated with different types of diseases at the population level. Findings of associations between specific combinations of MHC/NKR haplotypes with different diseases in model species suggest that these gene complexes did not evolve independently. No such associations have been described in horses so far. The aim of the study was to detect associations between MHC and NKR gene/microsatellite haplotypes in three horse breed groups (Camargue, African, and Romanian) by statistical methods; chi-square test, Fisher's exact test, Pearson's goodness-of-fit test and logistic regression. Associations were detected for both MHC/NKR genes and microsatellites; the most significant associations were found between the most variable KLRA3 gene and the EQCA-1 or EQCA-2 genes. This finding supports the assumption that the KLRA3 is an important receptor for MHC I and that interactions of these molecules play important roles in the horse immunity and reproduction. Despite some limitations of the study such as low numbers of horses or lack of knowledge of the selected genes functions, the results were consistent across different statistical methods and remained significant even after overconservative Bonferroni corrections. We therefore consider them biologically plausible.
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Affiliation(s)
- Jana Bubenikova
- Research Group Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Martin Plasil
- Research Group Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Jan Futas
- Research Group Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Karla Stejskalova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czechia
| | - Marie Klumplerova
- Research Group Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Jan Oppelt
- Research Group Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Petr Horin
- Research Group Animal Immunogenomics, CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czechia
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2
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Zhu Z, You R, Li H, Feng S, Ma H, Tuo C, Meng X, Feng S, Peng Y. Multi-omics data integration reveals the complexity and diversity of host factors associated with influenza virus infection. PeerJ 2023; 11:e16194. [PMID: 37842064 PMCID: PMC10569165 DOI: 10.7717/peerj.16194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
Influenza viruses pose a significant and ongoing threat to human health. Many host factors have been identified to be associated with influenza virus infection. However, there is currently a lack of an integrated resource for these host factors. This study integrated human genes and proteins associated with influenza virus infections for 14 subtypes of influenza A viruses, as well as influenza B and C viruses, and built a database named H2Flu to store and organize these genes or proteins. The database includes 28,639 differentially expressed genes (DEGs), 1,850 differentially expressed proteins, and 442 proteins with differential posttranslational modifications after influenza virus infection, as well as 3,040 human proteins that interact with influenza virus proteins and 57 human susceptibility genes. Further analysis showed that the dynamic response of human cells to virus infection, cell type and strain specificity contribute significantly to the diversity of DEGs. Additionally, large heterogeneity was also observed in protein-protein interactions between humans and different types or subtypes of influenza viruses. Overall, the study deepens our understanding of the diversity and complexity of interactions between influenza viruses and humans, and provides a valuable resource for further studies on such interactions.
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Affiliation(s)
- Zhaozhong Zhu
- College of Biology, Hunan University, Changsha, China
- School of Public Health, University of South China, Hengyang, China
| | - Ruina You
- College of Biology, Hunan University, Changsha, China
| | - Huiru Li
- College of Biology, Hunan University, Changsha, China
| | - Shuidong Feng
- School of Public Health, University of South China, Hengyang, China
| | - Huan Ma
- College of Biology, Hunan University, Changsha, China
| | - Chaohao Tuo
- College of Biology, Hunan University, Changsha, China
| | | | - Song Feng
- Xiangya Hospital, Central South University, Changsha, China
| | - Yousong Peng
- College of Biology, Hunan University, Changsha, China
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3
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Phelan J, Gomez-Gonzalez PJ, Andreu N, Omae Y, Toyo-Oka L, Yanai H, Miyahara R, Nedsuwan S, de Sessions PF, Campino S, Sallah N, Parkhill J, Smittipat N, Palittapongarnpim P, Mushiroda T, Kubo M, Tokunaga K, Mahasirimongkol S, Hibberd ML, Clark TG. Genome-wide host-pathogen analyses reveal genetic interaction points in tuberculosis disease. Nat Commun 2023; 14:549. [PMID: 36725857 PMCID: PMC9892022 DOI: 10.1038/s41467-023-36282-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
The genetics underlying tuberculosis (TB) pathophysiology are poorly understood. Human genome-wide association studies have failed so far to reveal reproducible susceptibility loci, attributed in part to the influence of the underlying Mycobacterium tuberculosis (Mtb) bacterial genotype on the outcome of the infection. Several studies have found associations of human genetic polymorphisms with Mtb phylo-lineages, but studies analysing genome-genome interactions are needed. By implementing a phylogenetic tree-based Mtb-to-human analysis for 714 TB patients from Thailand, we identify eight putative genetic interaction points (P < 5 × 10-8) including human loci DAP and RIMS3, both linked to the IFNγ cytokine and host immune system, as well as FSTL5, previously associated with susceptibility to TB. Many of the corresponding Mtb markers are lineage specific. The genome-to-genome analysis reveals a complex interactome picture, supports host-pathogen adaptation and co-evolution in TB, and has potential applications to large-scale studies across many TB endemic populations matched for host-pathogen genomic diversity.
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Affiliation(s)
- Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Nuria Andreu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Yosuke Omae
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Licht Toyo-Oka
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideki Yanai
- Fukujuji Hospital and Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Reiko Miyahara
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | | | | | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Neneh Sallah
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nat Smittipat
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Prasit Palittapongarnpim
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | | | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Surakameth Mahasirimongkol
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom.
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4
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Peloso GM, Tcheandjieu C, McGeary JE, Posner DC, Ho YL, Zhou JJ, Hilliard AT, Joseph J, O’Donnell CJ, Efird JT, Crawford DC, Wu WC, Arjomandi M, Sun YV, Assimes TL, Huffman JE. Genetic Loci Associated With COVID-19 Positivity and Hospitalization in White, Black, and Hispanic Veterans of the VA Million Veteran Program. Front Genet 2022; 12:777076. [PMID: 35222515 PMCID: PMC8864634 DOI: 10.3389/fgene.2021.777076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2 has caused symptomatic COVID-19 and widespread death across the globe. We sought to determine genetic variants contributing to COVID-19 susceptibility and hospitalization in a large biobank linked to a national United States health system. We identified 19,168 (3.7%) lab-confirmed COVID-19 cases among Million Veteran Program participants between March 1, 2020, and February 2, 2021, including 11,778 Whites, 4,893 Blacks, and 2,497 Hispanics. A multi-population genome-wide association study (GWAS) for COVID-19 outcomes identified four independent genetic variants (rs8176719, rs73062389, rs60870724, and rs73910904) contributing to COVID-19 positivity, including one novel locus found exclusively among Hispanics. We replicated eight of nine previously reported genetic associations at an alpha of 0.05 in at least one population-specific or the multi-population meta-analysis for one of the four MVP COVID-19 outcomes. We used rs8176719 and three additional variants to accurately infer ABO blood types. We found that A, AB, and B blood types were associated with testing positive for COVID-19 compared with O blood type with the highest risk for the A blood group. We did not observe any genome-wide significant associations for COVID-19 severity outcomes among those testing positive. Our study replicates prior GWAS findings associated with testing positive for COVID-19 among mostly White samples and extends findings at three loci to Black and Hispanic individuals. We also report a new locus among Hispanics requiring further investigation. These findings may aid in the identification of novel therapeutic agents to decrease the morbidity and mortality of COVID-19 across all major ancestral populations.
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Affiliation(s)
- Gina M. Peloso
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, United States
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - Catherine Tcheandjieu
- VA Palo Alto Healthcare System, Palo Alto, CA, United States
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, United States
| | - John E. McGeary
- Providence VA Healthcare System, Providence, RI, United States
- Department of Psychiatry and Human Behavior, Brown University, Providence, RI, United States
| | - Daniel C. Posner
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, United States
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, United States
| | - Jin J. Zhou
- Phoenix VA Health Care System, Phoenix, AZ, United States
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, United States
| | | | - Jacob Joseph
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, United States
- Cardiology Section, VA Boston Healthcare System, Boston, MA, United States
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Christopher J. O’Donnell
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, United States
- Cardiology Section, VA Boston Healthcare System, Boston, MA, United States
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Jimmy T. Efird
- Cooperative Studies Program Epidemiology Center-Durham, Durham VA Health Care System, Durham, NC, United States
| | - Dana C. Crawford
- Louis Stokes Cleveland VA Medical Center, Cleveland, OH, United States
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, United States
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, United States
| | - Wen-Chih Wu
- Providence VA Healthcare System, Providence, RI, United States
- Department of Medicine, Alpert Medical School, Brown University, Providence, RI, United States
| | - Mehrdad Arjomandi
- Medical Service, San Francisco VA Medical Center, San Francisco, CA, United States
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | | | - Yan V. Sun
- Atlanta VA Health Care System, Decatur, GA, United States
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, United States
| | - Themistocles L Assimes
- VA Palo Alto Healthcare System, Palo Alto, CA, United States
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, United States
| | - Jennifer E. Huffman
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, United States
- *Correspondence: Jennifer E. Huffman,
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5
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Westermann AJ, Vogel J. Cross-species RNA-seq for deciphering host-microbe interactions. Nat Rev Genet 2021; 22:361-378. [PMID: 33597744 DOI: 10.1038/s41576-021-00326-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2021] [Indexed: 02/08/2023]
Abstract
The human body is constantly exposed to microorganisms, which entails manifold interactions between human cells and diverse commensal or pathogenic bacteria. The cellular states of the interacting cells are decisive for the outcome of these encounters such as whether bacterial virulence programmes and host defence or tolerance mechanisms are induced. This Review summarizes how next-generation RNA sequencing (RNA-seq) has become a primary technology to study host-microbe interactions with high resolution, improving our understanding of the physiological consequences and the mechanisms at play. We illustrate how the discriminatory power and sensitivity of RNA-seq helps to dissect increasingly complex cellular interactions in time and space down to the single-cell level. We also outline how future transcriptomics may answer currently open questions in host-microbe interactions and inform treatment schemes for microbial disorders.
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Affiliation(s)
- Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany. .,Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany. .,Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.
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6
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Barkhash AV, Yurchenko AA, Yudin NS, Kozlova IV, Borishchuk IA, Smolnikova MV, Zaitseva OI, Pozdnyakova LL, Voevoda MI, Romaschenko AG. Association of ABCB9 and COL22A1 Gene Polymorphism with Human Predisposition to Severe Forms of Tick-Borne Encephalitis. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419030025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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7
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Abstract
In contemporary medical practice, approaches to infectious disease management have been primarily rooted in a pathogen-centered model. However, host genetics also contribute significantly to infectious disease burden. The fast expansion of bioinformatics techniques and the popularization of the genome-wide association study (GWAS) in recent decades have allowed for rapid and affordable high-throughput genomic analyses. This review focuses on the host model of infectious disease with particular emphasis placed on the genetic variations underlying observed infectious disease predisposition. First, we introduce observational twin-twin concordance studies of diseases such as poliomyelitis, tuberculosis, and hepatitis which suggest the important role of host genetics. We review the well-established links between specific genetic alterations and predisposition to malaria (P. falciparum and P. vivax), Creutzfeldt-Jacob disease (CJD), human immunodeficiency virus (HIV), and Norwalk virus. Finally, we discuss the novel findings yielded by modern GWAS studies, which suggest the strong contribution of immunologic variation in the major histocompatibility complex (MHC) to host genetic infectious disease susceptibility. Future large-scale genomic studies hold promise in providing insights into immunology-pathogen links and may allow for the development of personalized genomic approaches to infectious disease prevention and treatment.
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8
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Ho EXP, Cheung CMG, Sim S, Chu CW, Wilm A, Lin CB, Mathur R, Wong D, Chan CM, Bhagarva M, Laude A, Lim TH, Wong TY, Cheng CY, Davila S, Hibberd M. Human pharyngeal microbiota in age-related macular degeneration. PLoS One 2018; 13:e0201768. [PMID: 30089174 PMCID: PMC6082546 DOI: 10.1371/journal.pone.0201768] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/20/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND While the aetiology of age-related macular degeneration (AMD)-a major blinding disease-remains unknown, the disease is strongly associated with variants in the complement factor H (CFH) gene. CFH variants also confer susceptibility to invasive infection with several bacterial colonizers of the nasopharyngeal mucosa. This shared susceptibility locus implicates complement deregulation as a common disease mechanism, and suggests the possibility that microbial interactions with host complement may trigger AMD. In this study, we address this possibility by testing the hypothesis that AMD is associated with specific microbial colonization of the human nasopharynx. RESULTS High-throughput Illumina sequencing of the V3-V6 region of the microbial 16S ribosomal RNA gene was used to comprehensively and accurately describe the human pharyngeal microbiome, at genus level, in 245 AMD patients and 386 controls. Based on mean and differential microbial abundance analyses, we determined an overview of the pharyngeal microbiota, as well as candidate genera (Prevotella and Gemella) suggesting an association towards AMD health and disease conditions. CONCLUSIONS Utilizing an extensive study population from Singapore, our results provided an accurate description of the pharyngeal microbiota profiles in AMD health and disease conditions. Through identification of candidate genera that are different between conditions, we provide preliminary evidence for the existence of microbial triggers for AMD. Ethical approval for this study was obtained through the Singapore Health Clinical Institutional Review Board, reference numbers R799/63/2010 and 2010/585/A.
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Affiliation(s)
| | - Chui Ming Gemmy Cheung
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Shuzhen Sim
- Genome Institute of Singapore,Singapore, Singapore
| | | | - Andreas Wilm
- Genome Institute of Singapore,Singapore, Singapore
| | | | - Ranjana Mathur
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Doric Wong
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Choi Mun Chan
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Mayuri Bhagarva
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore, Singapore
| | - Augustinus Laude
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tock Han Lim
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Ching Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Sonia Davila
- Genome Institute of Singapore,Singapore, Singapore
| | - Martin Hibberd
- Genome Institute of Singapore,Singapore, Singapore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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9
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Krause-Kyora B, Nutsua M, Boehme L, Pierini F, Pedersen DD, Kornell SC, Drichel D, Bonazzi M, Möbus L, Tarp P, Susat J, Bosse E, Willburger B, Schmidt AH, Sauter J, Franke A, Wittig M, Caliebe A, Nothnagel M, Schreiber S, Boldsen JL, Lenz TL, Nebel A. Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans. Nat Commun 2018; 9:1569. [PMID: 29717136 PMCID: PMC5931558 DOI: 10.1038/s41467-018-03857-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 03/16/2018] [Indexed: 01/26/2023] Open
Abstract
Leprosy, a chronic infectious disease caused by Mycobacterium leprae (M. leprae), was very common in Europe till the 16th century. Here, we perform an ancient DNA study on medieval skeletons from Denmark that show lesions specific for lepromatous leprosy (LL). First, we test the remains for M. leprae DNA to confirm the infection status of the individuals and to assess the bacterial diversity. We assemble 10 complete M. leprae genomes that all differ from each other. Second, we evaluate whether the human leukocyte antigen allele DRB1*15:01, a strong LL susceptibility factor in modern populations, also predisposed medieval Europeans to the disease. The comparison of genotype data from 69 M. leprae DNA-positive LL cases with those from contemporary and medieval controls reveals a statistically significant association in both instances. In addition, we observe that DRB1*15:01 co-occurs with DQB1*06:02 on a haplotype that is a strong risk factor for inflammatory diseases today. Leprosy, caused by infection with Mycobacterium leprae, was common in Europe in the Middle Ages. Here, Krause-Kyora et al. analyze ancient DNA from a medieval Danish leprosarium to assemble 10 complete bacterial genomes and perform association analysis of the DRB1*15:01 allele with risk of leprosy infection.
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Affiliation(s)
- Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany. .,Max Planck Institute for the Science of Human History, Jena, 07745, Germany.
| | - Marcel Nutsua
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | - Lisa Boehme
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | - Federica Pierini
- Department of Evolutionary Ecology, Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
| | - Dorthe Dangvard Pedersen
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, 5260, Denmark
| | | | - Dmitriy Drichel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931, Germany
| | - Marion Bonazzi
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | - Lena Möbus
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | - Peter Tarp
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, 5260, Denmark
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | - Esther Bosse
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | | | | | | | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | - Amke Caliebe
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, 24105, Germany
| | - Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany.,Clinic for Internal Medicine, University Hospital of Schleswig-Holstein, Kiel, 24105, Germany
| | - Jesper L Boldsen
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, 5260, Denmark
| | - Tobias L Lenz
- Department of Evolutionary Ecology, Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
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10
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Yudin NS, Barkhash AV, Maksimov VN, Ignatieva EV, Romaschenko AG. Human Genetic Predisposition to Diseases Caused by Viruses from Flaviviridae Family. Mol Biol 2018. [DOI: 10.1134/s0026893317050223] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Keeping Pace with the Red Queen: Identifying the Genetic Basis of Susceptibility to Infectious Disease. Genetics 2017; 208:779-789. [PMID: 29223971 PMCID: PMC5788537 DOI: 10.1534/genetics.117.300481] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 12/01/2017] [Indexed: 11/19/2022] Open
Abstract
The results of genome-wide association studies are known to be affected by epistasis and gene-by-environment interactions. Using a statistical model.... Genome-wide association studies are widely used to identify “disease genes” conferring resistance/susceptibility to infectious diseases. Using a combination of mathematical models and simulations, we demonstrate that genetic interactions between hosts and parasites [genotype-by-genotype (G × G) interactions] can drastically affect the results of these association scans and hamper our ability to detect genetic variation in susceptibility. When hosts and parasites coevolve, these G × G interactions often make genome-wide association studies unrepeatable over time or across host populations. Reanalyzing previously published data on Daphnia magna susceptibility to infection by Pasteuria ramosa, we identify genomic regions consistent with G × G interactions. We conclude by outlining possible avenues for designing more powerful and more repeatable association studies.
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12
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Langlais D, Fodil N, Gros P. Genetics of Infectious and Inflammatory Diseases: Overlapping Discoveries from Association and Exome-Sequencing Studies. Annu Rev Immunol 2017; 35:1-30. [DOI: 10.1146/annurev-immunol-051116-052442] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David Langlais
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Nassima Fodil
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Philippe Gros
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
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Confounding effects of microbiome on the susceptibility of TNFSF15 to Crohn's disease in the Ryukyu Islands. Hum Genet 2017; 136:387-397. [PMID: 28197769 DOI: 10.1007/s00439-017-1764-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/08/2017] [Indexed: 12/30/2022]
Abstract
Crohn's disease (CD) involves chronic inflammation in the gastrointestinal tract due to dysregulation of the host immune response to the gut microbiome. Even though the host-microbiome interactions are likely contributors to the development of CD, a few studies have detected genetic variants that change bacterial compositions and increase CD risk. We focus on one of the well-replicated susceptible genes, tumor necrosis factor superfamily member 15 (TNFSF15), and apply statistical analyses for personal profiles of genotypes and salivary microbiota collected from CD cases and controls in the Ryukyu Islands, southernmost islands of the Japanese archipelago. Our association test confirmed the susceptibility of TNFSF15 in the Ryukyu Islands. We found that the recessive model was supported to fit the observed genotype frequency of risk alleles slightly better than the additive model, defining the genetic effect on CD if a pair of the chromosomes in an individual consists of all risk alleles. The combined analysis of haplotypes and salivary microbiome from a small set of samples showed a significant association of the genetic effect with the increase of Prevotella, which led to a significant increase of CD risk. However, the genetic effect on CD disappeared if the abundance of Prevotella was low, suggesting the genetic contribution to CD is conditionally independent given a fixed amount of Prevotella. Although our statistical power is limited due to the small sample size, these results support an idea that the genetic susceptibility of TNFSF15 to CD may be confounded, in part, by the increase of Prevotella.
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14
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MYD88 and functionally related genes are associated with multiple infections in a model population of Kenyan village dogs. Mol Biol Rep 2016; 43:1451-1463. [PMID: 27655108 DOI: 10.1007/s11033-016-4078-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 09/09/2016] [Indexed: 12/25/2022]
Abstract
The purpose of this study was to seek associations between immunity-related molecular markers and endemic infections in a model population of African village dogs from Northern Kenya with no veterinary care and no selective breeding. A population of village dogs from Northern Kenya composed of three sub-populations from three different areas (84, 50 and 55 dogs) was studied. Canine distemper virus (CDV), Hepatozoon canis, Microfilariae (Acantocheilonema dracunculoides, Acantocheilonema reconditum) and Neospora caninum were the pathogens studied. The presence of antibodies (CDV, Neospora), light microscopy (Hepatozoon) and diagnostic PCR (Microfilariae) were the methods used for diagnosing infection. Genes involved in innate immune mechanisms, NOS3, IL6, TLR1, TLR2, TLR4, TLR7, TLR9, LY96, MYD88, and three major histocompatibility genes class II genes were selected as candidates. Single nucleotide polymorphism (SNP) markers were detected by Sanger sequencing, next generation sequencing and PCR-RFLP. The Fisher´s exact test for additive and non-additive models was used for association analyses. Three SNPs within the MYD88 gene and one TLR4 SNP marker were associated with more than one infection. Combined genotypes and further markers identified by next generation sequencing confirmed associations observed for individual genes. The genes associated with infection and their combinations in specific genotypes match well our knowledge on their biological role and on the role of the relevant biological pathways, respectively. Associations with multiple infections observed between the MYD88 and TLR4 genes suggest their involvement in the mechanisms of anti-infectious defenses in dogs.
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15
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Barkhash AV, Babenko VN, Voevoda MI, Romaschenko AG. Association of IL28B and IL10 gene polymorphism with predisposition to tick-borne encephalitis in a Russian population. Ticks Tick Borne Dis 2016; 7:808-812. [PMID: 27068548 DOI: 10.1016/j.ttbdis.2016.03.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/22/2016] [Accepted: 03/30/2016] [Indexed: 12/30/2022]
Abstract
Genetic predisposition to tick-borne encephalitis (TBE) is rather poorly studied in human populations. Human genes encoding crucial components of antiviral immune response are most likely involved in protective mechanisms against TBE virus. Previously, several single nucleotide polymorphisms (SNPs) located in interleukin 28B (IL28B) and interleukin 10 (IL10) genes were associated with predisposition to chronic hepatitis C (caused by a structurally similar virus from the same Flaviviridae family) in a number of human populations. The aim of the present study was to estimate a possible association of the IL28B gene rs8103142 and rs12980275 SNPs and IL10 gene rs1800872, rs3021094, and rs3024498 SNPs with predisposition to TBE in a Russian population. Genotypic and allelic frequencies for these SNPs were analyzed in 132 non-immunized TBE patients (34 with fever, 60 with meningitis, and 38 with severe central nervous system disease) and compared with the population control (221 Novosibirsk citizens). The results obtained suggest that both studied IL28B gene SNPs, as well as the IL10 gene rs1800872 SNP are associated with predisposition to TBE in Russian population.
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Affiliation(s)
- Andrey V Barkhash
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 10 Lavrentyeva Ave., Novosibirsk 630090 Russia.
| | - Vladimir N Babenko
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 10 Lavrentyeva Ave., Novosibirsk 630090 Russia; Novosibirsk State University, 2 Pirogova str., Novosibirsk 630090 Russia
| | - Mikhail I Voevoda
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 10 Lavrentyeva Ave., Novosibirsk 630090 Russia; Novosibirsk State University, 2 Pirogova str., Novosibirsk 630090 Russia; Institute of Internal and Preventive Medicine, 175/1 B. Bogatkova str., Novosibirsk 630089 Russia
| | - Aida G Romaschenko
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 10 Lavrentyeva Ave., Novosibirsk 630090 Russia
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16
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17
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Croft SL. Neglected tropical diseases in the genomics era: re-evaluating the impact of new drugs and mass drug administration. Genome Biol 2016; 17:46. [PMID: 26975569 PMCID: PMC4791878 DOI: 10.1186/s13059-016-0916-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Simon Croft answers Genome Biology's questions on ways to approach neglected tropical diseases in the genomics era, including re-evaluating the impact of new drugs and mass drug administration.
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Affiliation(s)
- Simon L Croft
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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18
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Richardson IW, Berry DP, Wiencko HL, Higgins IM, More SJ, McClure J, Lynn DJ, Bradley DG. A genome-wide association study for genetic susceptibility to Mycobacterium bovis infection in dairy cattle identifies a susceptibility QTL on chromosome 23. Genet Sel Evol 2016; 48:19. [PMID: 26960806 PMCID: PMC4784436 DOI: 10.1186/s12711-016-0197-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 02/29/2016] [Indexed: 01/08/2023] Open
Abstract
Background Bovine tuberculosis (bTB) infection in cattle is a significant economic concern in many countries, with annual costs to the UK and Irish governments of approximately €190 million and €63 million, respectively, for bTB control. The existence of host additive and non-additive genetic components to bTB susceptibility has been established. Methods Two approaches i.e. single-SNP (single nucleotide polymorphism) regression and a Bayesian method were applied to genome-wide association studies (GWAS) using high-density SNP genotypes (n = 597,144 SNPs) from 841 dairy artificial insemination (AI) sires. Deregressed estimated breeding values for bTB susceptibility were used as the quantitative dependent variable. Network analysis was performed using the quantitative trait loci (QTL) that were identified as significant in the single-SNP regression and Bayesian analyses separately. In addition, an identity-by-descent analysis was performed on a subset of the most prolific sires in the dataset that showed contrasting prevalences of bTB infection in daughters. Results A significant QTL region was identified on BTA23 (P value >1 × 10−5, Bayes factor >10) across all analyses. Sires with the minor allele (minor allele frequency = 0.136) for this QTL on BTA23 had estimated breeding values that conferred a greater susceptibility to bTB infection than those that were homozygous for the major allele. Imputation of the regions that flank this QTL on BTA23 to full sequence indicated that the most significant associations were located within introns of the FKBP5 gene. Conclusions A genomic region on BTA23 that is strongly associated with host susceptibility to bTB infection was identified. This region contained FKBP5, a gene involved in the TNFα/NFκ-B signalling pathway, which is a major biological pathway associated with immune response. Although there is no study that validates this region in the literature, our approach represents one of the most powerful studies for the analysis of bTB susceptibility to
date. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0197-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ian W Richardson
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland. .,Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland.
| | - Donagh P Berry
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland.
| | - Heather L Wiencko
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland.
| | - Isabella M Higgins
- UCD Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Simon J More
- UCD Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | | | - David J Lynn
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland. .,South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, 5000, Australia. .,School of Medicine, Flinders University, Bedford Park, SA, 5042, Australia.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland.
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19
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Sim S, Hibberd ML. Caenorhabditis elegans susceptibility to gut Enterococcus faecalis infection is associated with fat metabolism and epithelial junction integrity. BMC Microbiol 2016; 16:6. [PMID: 26769134 PMCID: PMC4714453 DOI: 10.1186/s12866-016-0624-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/08/2016] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Gut bacteria-host interactions have been implicated in the pathogenesis of numerous human diseases, but few mechanisms have been described. The genetically tractable nematode worm Caenorhabditis elegans can be infected with pathogenic bacteria, such as the human gut commensal Enterococcus faecalis, via feeding, making it a good model for studying these interactions. RESULTS An RNAi screen of 17 worm candidate genes revealed that knockdown of the transcription factor nhr-49, a master regulator of fat metabolism, shortens worm lifespan upon infection with E. faecalis (and other potentially pathogenic bacteria) compared to Escherichia coli. The functional similarity of nhr-49 to the mammalian peroxisome proliferator-activated receptors (PPARs) suggests that this is mediated through a link between fatty acid metabolism and innate immunity. In addition, knockdown of either dlg-1 or ajm-1, which encode physically interacting proteins in the C. elegans epithelial junction, also reduces worm lifespan upon E. faecalis challenge, demonstrating the importance of the intestinal epithelium as an immune barrier. CONCLUSIONS The protective roles identified for nhr-49, dlg-1, and ajm-1 suggest mechanistic interactions between the gut microbiota, host fatty acid metabolism, innate immunity, and epithelial junction integrity that are remarkably similar to those implicated in human metabolic and inflammatory diseases.
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Affiliation(s)
- Shuzhen Sim
- Infectious Diseases, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore.
| | - Martin L Hibberd
- Infectious Diseases, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
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20
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Fodil N, Langlais D, Gros P. Primary Immunodeficiencies and Inflammatory Disease: A Growing Genetic Intersection. Trends Immunol 2016; 37:126-140. [PMID: 26791050 DOI: 10.1016/j.it.2015.12.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/10/2015] [Accepted: 12/13/2015] [Indexed: 02/08/2023]
Abstract
Recent advances in genome analysis have provided important insights into the genetic architecture of infectious and inflammatory diseases. The combined analysis of loci detected by genome-wide association studies (GWAS) in 22 inflammatory diseases has revealed a shared genetic core and associated biochemical pathways that play a central role in pathological inflammation. Parallel whole-exome sequencing studies have identified 265 genes mutated in primary immunodeficiencies (PID). Here, we examine the overlap between these two data sets, and find that it consists of genes essential for protection against infections and in which persistent activation causes pathological inflammation. Based on this intersection, we propose that, although strong or inactivating mutations (rare variants) in these genes may cause severe disease (PIDs), their more subtle modulation potentially by common regulatory/coding variants may contribute to chronic inflammation.
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Affiliation(s)
- Nassima Fodil
- Department of Biochemistry, Complex Traits Group, McGill University, Montreal, QC, Canada
| | - David Langlais
- Department of Biochemistry, Complex Traits Group, McGill University, Montreal, QC, Canada
| | - Philippe Gros
- Department of Biochemistry, Complex Traits Group, McGill University, Montreal, QC, Canada.
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21
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Dunstan SJ, Hue NT, Han B, Li Z, Tram TTB, Sim KS, Parry CM, Chinh NT, Vinh H, Lan NPH, Thieu NTV, Vinh PV, Koirala S, Dongol S, Arjyal A, Karkey A, Shilpakar O, Dolecek C, Foo JN, Phuong LT, Lanh MN, Do T, Aung T, Hon DN, Teo YY, Hibberd ML, Anders KL, Okada Y, Raychaudhuri S, Simmons CP, Baker S, de Bakker PIW, Basnyat B, Hien TT, Farrar JJ, Khor CC. Variation at HLA-DRB1 is associated with resistance to enteric fever. Nat Genet 2014; 46:1333-6. [PMID: 25383971 PMCID: PMC5099079 DOI: 10.1038/ng.3143] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 10/15/2014] [Indexed: 12/18/2022]
Abstract
Enteric fever affects more than 25 million people annually and results from systemic infection with Salmonella enterica serovar Typhi or Paratyphi pathovars A, B or C(1). We conducted a genome-wide association study of 432 individuals with blood culture-confirmed enteric fever and 2,011 controls from Vietnam. We observed strong association at rs7765379 (odds ratio (OR) for the minor allele = 0.18, P = 4.5 × 10(-10)), a marker mapping to the HLA class II region, in proximity to HLA-DQB1 and HLA-DRB1. We replicated this association in 595 enteric fever cases and 386 controls from Nepal and also in a second independent collection of 151 cases and 668 controls from Vietnam. Imputation-based fine-mapping across the extended MHC region showed that the classical HLA-DRB1*04:05 allele (OR = 0.14, P = 2.60 × 10(-11)) could entirely explain the association at rs7765379, thus implicating HLA-DRB1 as a major contributor to resistance against enteric fever, presumably through antigen presentation.
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Affiliation(s)
- Sarah J Dunstan
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [3] Nossal Institute of Global Health, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nguyen Thi Hue
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Faculty of Biology, University of Science, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Buhm Han
- 1] Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea. [2] Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA. [3] Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA. [4] Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, USA
| | - Zheng Li
- Genome Institute of Singapore, Singapore
| | - Trinh Thi Bich Tram
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | - Christopher M Parry
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Ha Vinh
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | - Nga Tran Vu Thieu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Phat Voong Vinh
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Samir Koirala
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Sciences, Patan Hospital, Patan, Nepal
| | - Sabina Dongol
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Sciences, Patan Hospital, Patan, Nepal
| | - Amit Arjyal
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Sciences, Patan Hospital, Patan, Nepal
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Sciences, Patan Hospital, Patan, Nepal
| | - Olita Shilpakar
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Sciences, Patan Hospital, Patan, Nepal
| | - Christiane Dolecek
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | | | | | | | - Tan Do
- Vietnam National Institute of Ophthalmology, Hanoi, Vietnam
| | - Tin Aung
- Singapore Eye Research Institute, Singapore
| | - Do Nu Hon
- Vietnam National Institute of Ophthalmology, Hanoi, Vietnam
| | - Yik Ying Teo
- 1] Department of Statistics and Applied Probability, National University of Singapore, Singapore. [2] Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Martin L Hibberd
- 1] Genome Institute of Singapore, Singapore. [2] London School of Tropical Medicine and Hygiene, London, UK
| | - Katherine L Anders
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Yukinori Okada
- 1] Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. [2] Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Soumya Raychaudhuri
- 1] Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA. [3] Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, USA. [4] Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, Massachusetts, USA. [5] Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Cameron P Simmons
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [3] Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen Baker
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [3] London School of Tropical Medicine and Hygiene, London, UK
| | - Paul I W de Bakker
- 1] Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands. [2] Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Buddha Basnyat
- Oxford University Clinical Research Unit-Nepal, Patan Academy of Health Sciences, Patan Hospital, Patan, Nepal
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Jeremy J Farrar
- 1] Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Chiea Chuen Khor
- 1] Genome Institute of Singapore, Singapore. [2] Singapore Eye Research Institute, Singapore. [3] Saw Swee Hock School of Public Health, National University of Singapore, Singapore. [4] Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore. [5] Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Sessa R, Pietro MD, Filardo S, Turriziani O. Infectious burden and atherosclerosis: A clinical issue. World J Clin Cases 2014; 2:240-249. [PMID: 25032197 PMCID: PMC4097149 DOI: 10.12998/wjcc.v2.i7.240] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 05/16/2014] [Accepted: 06/11/2014] [Indexed: 02/05/2023] Open
Abstract
Atherosclerotic cardiovascular diseases, chronic inflammatory diseases of multifactorial etiology, are the leading cause of death worldwide. In the last decade, more infectious agents, labeled as “infectious burden”, rather than any single pathogen, have been showed to contribute to the development of atherosclerosis through different mechanisms. Some microorganisms, such as Chlamydia pneumoniae (C. pneumoniae), human cytomegalovirus, etc. may act directly on the arterial wall contributing to endothelial dysfunction, foam cell formation, smooth muscle cell proliferation, platelet aggregation as well as cytokine, reactive oxygen specie, growth factor, and cellular adhesion molecule production. Others, such as Helicobacter pylori (H. pylori), influenza virus, etc. may induce a systemic inflammation which in turn may damage the vascular wall (e.g., by cytokines and proteases). Moreover, another indirect mechanism by which some infectious agents (such as H. pylori, C. pneumoniae, periodontal pathogens, etc.) may play a role in the pathogenesis of atherosclerosis is molecular mimicry. Given the complexity of the mechanisms by which each microorganism may contribute to atherosclerosis, defining the interplay of more infectious agents is far more difficult because the pro-atherogenic effect of each pathogen might be amplified. Clearly, continued research and a greater awareness will be helpful to improve our knowledge on the complex interaction between the infectious burden and atherosclerosis.
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23
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Thompson P, Urayama K, Zheng J, Yang P, Ford M, Buffler P, Chokkalingam A, Lightfoot T, Taylor M. Differences in meiotic recombination rates in childhood acute lymphoblastic leukemia at an MHC class II hotspot close to disease associated haplotypes. PLoS One 2014; 9:e100480. [PMID: 24959916 PMCID: PMC4069019 DOI: 10.1371/journal.pone.0100480] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/20/2014] [Indexed: 12/20/2022] Open
Abstract
Childhood Acute Lymphoblastic Leukemia (ALL) is a malignant lymphoid disease of which B-cell precursor- (BCP) and T-cell- (T) ALL are subtypes. The role of alleles encoded by major histocompatibility loci (MHC) have been examined in a number of previous studies and results indicating weak, multi-allele associations between the HLA-DPB1 locus and BCP-ALL suggested a role for immunosusceptibility and possibly infection. Two independent SNP association studies of ALL identified loci approximately 37 kb from one another and flanking a strong meiotic recombination hotspot (DNA3), adjacent to HLA-DOA and centromeric of HLA-DPB1. To determine the relationship between this observation and HLA-DPB1 associations, we constructed high density SNP haplotypes of the 316 kb region from HLA-DMB to COL11A2 in childhood ALL and controls using a UK GWAS data subset and the software PHASE. Of four haplotype blocks identified, predicted haplotypes in Block 1 (centromeric of DNA3) differed significantly between BCP-ALL and controls (P = 0.002) and in Block 4 (including HLA-DPB1) between T-ALL and controls (P = 0.049). Of specific common (>5%) haplotypes in Block 1, two were less frequent in BCP-ALL, and in Block 4 a single haplotype was more frequent in T-ALL, compared to controls. Unexpectedly, we also observed apparent differences in ancestral meiotic recombination rates at DNA3, with BCP-ALL showing increased and T-ALL decreased levels compared to controls. In silico analysis using LDsplit sotware indicated that recombination rates at DNA3 are influenced by flanking loci, including SNPs identified in childhood ALL association studies. The observed differences in rates of meiotic recombination at this hotspot, and potentially others, may be a characteristic of childhood leukemia and contribute to disease susceptibility, alternatively they may reflect interactions between ALL-associated haplotypes in this region.
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Affiliation(s)
- Pamela Thompson
- Paediatric & Familial Cancer Research Group, Institute of Cancer Sciences, University of Manchester, St Mary's Hospital, Manchester, United Kingdom
| | - Kevin Urayama
- School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
- Department of Human Genetics and Disease Diversity, Tokyo Medical and Dental University, Tokyo, Japan
| | - Jie Zheng
- School of Computer Engineering, Nanyang Technological University, Singapore
- Genome Institute of Singapore, A*STAR (Agency for Science, Technology, and Research), Biopolis, Singapore
| | - Peng Yang
- Data Analytics Department, Institute for Infocomm Research, A*STAR, Singapore
| | - Matt Ford
- Research Computing Services, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom
| | - Patricia Buffler
- School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Anand Chokkalingam
- School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | | | - Malcolm Taylor
- Independent Researcher, Handforth, Cheshire, United Kingdom
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24
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Kaiser R. [After-care in general practice after tick-borne encephalitis]. MMW Fortschr Med 2014; 156:49-54. [PMID: 24938066 DOI: 10.1007/s15006-014-0003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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25
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Hall MD, Ebert D. The genetics of infectious disease susceptibility: has the evidence for epistasis been overestimated? BMC Biol 2013; 11:79. [PMID: 23855805 PMCID: PMC3711976 DOI: 10.1186/1741-7007-11-79] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 07/08/2013] [Indexed: 12/30/2022] Open
Abstract
Interactions amongst genes, known as epistasis, are assumed to make a substantial contribution to the genetic variation in infectious disease susceptibility, but this claim is controversial. Here, we focus on the debate surrounding the evolutionary importance of interactions between resistance loci and argue that its role in explaining overall variance in disease outcomes may have been overestimated.
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Affiliation(s)
- Matthew D Hall
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland.
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26
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Abstract
Vaccines are the most cost effective public health measure for preventing viral infection and limiting epidemic spread within susceptible populations. However, the efficacy of current protective vaccines is highly variable, particularly in aging populations. In addition, there have been a number of challenges in the development of new vaccines due to a lack of detailed understanding of the immune correlates of protection. To identify the mechanisms underlying the variability of the immune response to vaccines, system-level tools need to be developed that will further our understanding of virus-host interactions and correlates of vaccine efficacy. This will provide critical information for rational vaccine design and allow the development of an analog to the "precision medicine" framework (already acknowledged as a powerful approach in medicine and therapeutics) to be applied to vaccinology.
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Affiliation(s)
- Michael Mooney
- Division of Bioinformatics & Computational Biology, Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Oregon, United States
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Human genetics and respiratory syncytial virus disease: current findings and future approaches. Curr Top Microbiol Immunol 2013; 372:121-37. [PMID: 24362687 DOI: 10.1007/978-3-642-38919-1_6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Infection with respiratory syncytial virus (RSV) can result in a wide spectrum of pulmonary manifestations, from mild upper respiratory symptoms to severe bronchiolitis and pneumonia. Although there are several known risk factors for severe RSV disease, namely, premature birth, chronic lung disease, congenital heart disease, and T cell immunodeficiency, the majority of young children who develop severe RSV disease are otherwise healthy children. Genetic susceptibility to RSV infection is emerging as a complex trait, in which many different host genetic variants contribute to risk for distinct disease manifestations. Initially, host genetic studies focused on severe RSV disease using the candidate gene approach to interrogate common single nucleotide polymorphisms (SNPs). Many studies have reported genetic associations between severe RSV bronchiolitis and SNPs in genes within plausible biological pathways, such as in innate host defense genes (SPA, SPD, TLR4, and VDR), cytokine or chemokine response genes (CCR5, IFN, IL6, IL10, TGFB1), and altered Th1/Th2 immune responses (IL4, IL13). Due to the complexity of RSV susceptibility, genome studies done on a larger scale, such as genome-wide association studies have certainly identified more of the host factors that contribute to the development of severe RSV bronchiolitis or excessive pathology. Furthermore, whole-genome approaches can reveal robust associations between genetic markers and RSV disease susceptibility. Recent introduction of 'exome' genotyping or sequencing, which specifically analyzes the majority of coding variants, should be fruitful in sufficiently large, well-powered studies. The advent of new genomic technologies together with improved computational tools offer the promise of interrogating the host genome in search of genetic factors, rare, uncommon, or common that should give new insights into the underlying biology of susceptibility to or protection from severe RSV infection. Careful assessment of novel pathways and further identification of specific genes could identify new approaches for vaccine development and perhaps lead to effective risk modeling.
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Franzosa EA, Garamszegi S, Xia Y. Toward a three-dimensional view of protein networks between species. Front Microbiol 2012; 3:428. [PMID: 23267356 PMCID: PMC3528071 DOI: 10.3389/fmicb.2012.00428] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Accepted: 12/06/2012] [Indexed: 01/27/2023] Open
Abstract
General principles governing biomolecular interactions between species are expected to differ significantly from known principles governing the interactions within species, yet these principles remain poorly understood at the systems level. A key reason for this knowledge gap is the lack of a detailed three-dimensional (3D), atomistic view of biomolecular interaction networks between species. Recent progress in structural biology, systems biology, and computational biology has enabled accurate and large-scale construction of 3D structural models of nodes and edges for protein–protein interaction networks within and between species. The resulting within- and between-species structural interaction networks have provided new biophysical, functional, and evolutionary insights into species interactions and infectious disease. Here, we review the nascent field of between-species structural systems biology, focusing on interactions between host and pathogens such as viruses.
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Chen YT, Peng HL, Shia WC, Hsu FR, Ken CF, Tsao YM, Chen CH, Liu CE, Hsieh MF, Chen HC, Tang CY, Ku TH. Whole-genome sequencing and identification of Morganella morganii KT pathogenicity-related genes. BMC Genomics 2012; 13 Suppl 7:S4. [PMID: 23282187 PMCID: PMC3521468 DOI: 10.1186/1471-2164-13-s7-s4] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The opportunistic enterobacterium, Morganella morganii, which can cause bacteraemia, is the ninth most prevalent cause of clinical infections in patients at Changhua Christian Hospital, Taiwan. The KT strain of M. morganii was isolated during postoperative care of a cancer patient with a gallbladder stone who developed sepsis caused by bacteraemia. M. morganii is sometimes encountered in nosocomial settings and has been causally linked to catheter-associated bacteriuria, complex infections of the urinary and/or hepatobiliary tracts, wound infection, and septicaemia. M. morganii infection is associated with a high mortality rate, although most patients respond well to appropriate antibiotic therapy. To obtain insights into the genome biology of M. morganii and the mechanisms underlying its pathogenicity, we used Illumina technology to sequence the genome of the KT strain and compared its sequence with the genome sequences of related bacteria. RESULTS The 3,826,919-bp sequence contained in 58 contigs has a GC content of 51.15% and includes 3,565 protein-coding sequences, 72 tRNA genes, and 10 rRNA genes. The pathogenicity-related genes encode determinants of drug resistance, fimbrial adhesins, an IgA protease, haemolysins, ureases, and insecticidal and apoptotic toxins as well as proteins found in flagellae, the iron acquisition system, a type-3 secretion system (T3SS), and several two-component systems. Comparison with 14 genome sequences from other members of Enterobacteriaceae revealed different degrees of similarity to several systems found in M. morganii. The most striking similarities were found in the IS4 family of transposases, insecticidal toxins, T3SS components, and proteins required for ethanolamine use (eut operon) and cobalamin (vitamin B12) biosynthesis. The eut operon and the gene cluster for cobalamin biosynthesis are not present in the other Proteeae genomes analysed. Moreover, organisation of the 19 genes of the eut operon differs from that found in the other non-Proteeae enterobacterial genomes. CONCLUSIONS This is the first genome sequence of M. morganii, which is a clinically relevant pathogen. Comparative genome analysis revealed several pathogenicity-related genes and novel genes not found in the genomes of other members of Proteeae. Thus, the genome sequence of M. morganii provides important information concerning virulence and determinants of fitness in this pathogen.
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Affiliation(s)
- Yu-Tin Chen
- Department of Computer Science, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu, Taiwan
| | - Hwei-Ling Peng
- Department of Biological Science and Technology, National Chiao Tung University, 1001, University Road, Hsinchu, Taiwan
| | - Wei-Chung Shia
- Cancer Research Center, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Fang-Rong Hsu
- Master's Program in Biomedical Informatics and Biomedical Engineering, Feng Chia University, 100 Wenhwa Rd., Taichung, Taiwan
- Department of Information Engineering and Computer Sciences, Feng Chia University, 100 Wenhwa Rd., Taichung, Taiwan
| | - Chuian-Fu Ken
- Institute of Biotechnology, National Changhua University of Education, 2 Shi-Da Rd., Changhua, Taiwan
| | - Yu-Ming Tsao
- Department of Anesthesiology, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Chang-Hua Chen
- The Division of Infectious Diseases, Department of Internal Medicine, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Chun-Eng Liu
- The Division of Infectious Diseases, Department of Internal Medicine, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Ming-Feng Hsieh
- Department of Computer Science, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu, Taiwan
| | - Huang-Chi Chen
- Division of Critical Care Medicine, Department of Internal Medicine, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
| | - Chuan-Yi Tang
- Department of Computer Science, National Tsing Hua University, 101, Section 2, Kuang-Fu Rd., Hsinchu, Taiwan
- Department of Computer Science, Providence University, 200, Chung-Chi Rd., Taichung, Taiwan
| | - Tien-Hsiung Ku
- Department of Anesthesiology, Changhua Christian Hospital, 135, Nanhsiao St., Changhua, Taiwan
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