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Canzian F, Rizzato C, Stein A, Flores-Luna L, Camorlinga-Ponce M, Mendez-Tenorio A, Chen W, Kasamatsu E, Bravo MM, Torres J, Muñoz N, Kato I. Phylogenetic origin of Helicobacter pylori pathogenicity island and risk of stomach cancer and high-grade premalignant gastric lesions. Eur J Cancer Prev 2023; 32:301-304. [PMID: 36719829 PMCID: PMC10073236 DOI: 10.1097/cej.0000000000000779] [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] [Indexed: 02/01/2023]
Abstract
Infection by Helicobacter pylori (Hp) has been causally linked to risk of gastric cancer (GC). The coevolution of Hp and humans shaped the risk of GC as our species left Africa and migrated to the other continents. Latin America (LatAm) is a high GC incidence region where Hp evolved uniquely in the 500 years since European colonization. Differential virulence of the Hp cagA -pathogenicity island (cagPAI) by ancestral origin has been reported. We hypothesized that Hp phylogenetic origin might play a role in determining GC risk in LatAm. We used genotypes of 50 Hp genetic variants mapping to the Hp cagPAI, studied in 1220 subjects from Venezuela, Colombia, Mexico and Paraguay, who were infected with cagA-positive Hp, including 150 GC, 177 high-grade premalignant lesions (HGPMLs) and 893 low-grade premalignant lesions. We estimated the phylogenetic origin of Hp cagPAI in all study subjects by use of the STRUCTURE software and principal component analysis (PCA) and tested whether the estimated African ancestry percentage was associated with the risk of GC or HGPML. African ancestral component estimates by STRUCTURE and PCA were highly correlated. STRUCTURE-based African origin estimate was not significantly associated with the risk of HGPML, but it was inversely associated with GC risk: the OR associated with the continuous values of African component was 0.09 (95% CI, 0.01-0.85; P = 0.035). Similar trends were observed for GC with PCA-based estimates, but the association was not statistically significant. These results suggest that Hp ancestral origin may play a role in gastric carcinogenesis.
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Affiliation(s)
- Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cosmeri Rizzato
- Department of Translation Research and of New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Angelika Stein
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lourdes Flores-Luna
- Center for Public Health Research, National Institute of Public Health, Cuernavaca
| | - Margarita Camorlinga-Ponce
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social
| | - Alfonso Mendez-Tenorio
- Laboratorio de Biotecnología y Bioinformática Genómica, ENCB, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Wei Chen
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Elena Kasamatsu
- Instituto de Investigaciones en Ciencias de la Salud, National University of Asunción, Asunción, Paraguay
| | - Maria Mercedes Bravo
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social
| | - Nubia Muñoz
- Cancer Institute of Colombia, Bogotá, Colombia
| | - Ikuko Kato
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan, USA
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Quan Y, Zhang KX, Zhang HY. The gut microbiota links disease to human genome evolution. Trends Genet 2023; 39:451-461. [PMID: 36872184 DOI: 10.1016/j.tig.2023.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 03/06/2023]
Abstract
A large number of studies have established a causal relationship between the gut microbiota and human disease. In addition, the composition of the microbiota is substantially influenced by the human genome. Modern medical research has confirmed that the pathogenesis of various diseases is closely related to evolutionary events in the human genome. Specific regions of the human genome known as human accelerated regions (HARs) have evolved rapidly over several million years since humans diverged from a common ancestor with chimpanzees, and HARs have been found to be involved in some human-specific diseases. Furthermore, the HAR-regulated gut microbiota has undergone rapid changes during human evolution. We propose that the gut microbiota may serve as an important mediator linking diseases to human genome evolution.
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Affiliation(s)
- Yuan Quan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ke-Xin Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Hong-Yu Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China.
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3
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Singh S, Sharma P, Mahant S, Das K, Som A, Das R. Analysis of Functional Status of Genetically Diverse OipA Gene in Indian Patients with Distinct Gastrointestinal Disease. Curr Microbiol 2022; 80:35. [PMID: 36512098 DOI: 10.1007/s00284-022-03137-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022]
Abstract
Helicobacter pylori (H. pylori,) a genetically diversified bacteria which colonizes human gastric epithelium, is now established causative agent for gastric cancer worldwide. Outer membrane protein (OMP)-coding genes of H. pylori are responsible for attachment and colonization of bacteria. These genes which code proteins on outer membrane of H. pylori is a group of 33 genes which with other virulent genes are causative of giving rise to disease-causing factors in the host. OipA (Outer inflammatory protein A), a participant of Hop family of OMP, is effective in acting as a biomarker for studying progression of diseases like gastric cancer. The functionality of oipA gene is regulated by phase variation within CT repeat pattern. It is the expression, i.e., "on"/"off" of oipA gene which is related with the development of distinct gastric diseases. 40 amplified DNA sequences were studied to investigate functional status of oipA. Our results reveal 57.2% isolates with functional oipA along with significant association with cagA (P = 0.0011) and vacAs1m1/s1m2 (P = 0.0034, P = 0.0093) genotypes, respectively. In conclusion, our results indicate diversity in CT repeat pattern among Indian H. pylori strains. The prevalence of functional oipA gene was found to be ranging between 50% and 64.2% though it did not show significant correlation between functional oipA and disease outcome.
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Affiliation(s)
- Sarika Singh
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, UP, India
| | - Prateek Sharma
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, UP, India
| | - Shweta Mahant
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, UP, India
| | - Kunal Das
- Department of Gastroenterology, Yashoda Superspeciality Hospital, Ghaziabad, UP, India
| | - Anup Som
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj, 211002, UP, India
| | - Rajashree Das
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, UP, India.
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Guevara-Tique AA, Torres RC, Bravo MM, Carvajal Carmona LG, Echeverry de Polanco MM, Bohórquez ME, Torres J. Recombination events drives the emergence of Colombian Helicobacter pylori subpopulations with self-identity ancestry. Virulence 2022; 13:1146-1160. [PMID: 35838227 PMCID: PMC9291697 DOI: 10.1080/21505594.2022.2095737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Helicobacter pylori have coevolved with mankind since its origins, adapting to different human groups. In America, H. pylori has evolved into several subpopulations. We analysed the genome of 154 Colombian strains along with 1,091 strains from worldwide populations to discern the ancestry and adaption to Colombian people. Population structure and ancestry was inferred with FineStructure and ChromoPainter. Phylogenetic relationship and the relative effect of recombination were analysing the core SNPs. Also, a Fst index was calculated to identify the gene variants with the strongest fixation in the Colombian subpopulations compared to their parent population hspSWEurope. FineStructure allowed the identification of two Colombian subpopulations, the previously described hspSWEuropeColombia and a novel subpopulation named hspColombia, that included three subgroups following their geographic origin. Colombian subpopulations represent an admixture of European, African and Indigenous ancestry; although some genomes showed a high proportion of self identity, suggesting an advanced adaption to these mestizo Colombian groups. We found that recombination is more important that punctual mutations in H. pylori genome diversity, 13.9 more important in hspSWEurope, 12.5 in hspSWEColombia and 10.5 in hspColombia, reflecting the divergence of these subpopulations. Fst analysis identified 82 SNPs fixed in 26 genes of the hspColombia subpopulation that encode for outer membrane and central metabolism proteins. Strongest fixation indexes were identified in genes encoding HofC, HopE, FrpB-4 and Sialidase A. These findings demonstrate that H. pylori has evolved in Colombia to give rise to subpopulations with a self identity ancestry, reflected in allele changes on genes encoding for outer membrane proteins.
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Affiliation(s)
- Alix A Guevara-Tique
- Grupo de Investigación en Citogenética, Filogenia y Evolución de Poblaciones, Departamento de Ciencias y Ciencias de la Salud, Universidad del Tolima, Tolima, Colombia
| | - Roberto C Torres
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Maria M Bravo
- Laboratorio de Inmunología, Instituto Nacional de Cancerología, Bogotá, D. C., Colombia
| | - Luis G Carvajal Carmona
- Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine-University of California, Davis, California, USA
| | - María M Echeverry de Polanco
- Grupo de Investigación en Citogenética, Filogenia y Evolución de Poblaciones, Departamento de Ciencias y Ciencias de la Salud, Universidad del Tolima, Tolima, Colombia
| | - Mabel E Bohórquez
- Grupo de Investigación en Citogenética, Filogenia y Evolución de Poblaciones, Departamento de Ciencias y Ciencias de la Salud, Universidad del Tolima, Tolima, Colombia.,Medicine Program, Department of Health Sciences, Tolima University, Tolima, Colombia
| | - Javier Torres
- c Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatria, Instituto Mexicano del Seguro Social, México
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Leontiadis GI, Longstreth GF. Evolutionary Medicine Perspectives: Helicobacter pylori, Lactose Intolerance, and 3 Hypotheses for Functional and Inflammatory Gastrointestinal and Hepatobiliary Disorders. Am J Gastroenterol 2022; 117:721-728. [PMID: 35169106 DOI: 10.14309/ajg.0000000000001681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/10/2022] [Indexed: 12/11/2022]
Abstract
Many clinicians have suboptimal knowledge of evolutionary medicine. This discipline integrates social and basic sciences, epidemiology, and clinical medicine, providing explanations, especially ultimate causes, for many conditions. Principles include genetic variation from population bottleneck and founder effects, evolutionary trade-offs, and coevolution. For example, host-microbe coevolution contributes to the inflammatory and carcinogenic variability of Helicobacter pylori. Antibiotic-resistant strains are evolving, but future therapy could target promutagenic proteins. Ancient humans practicing dairying achieved survival and reproduction advantages of postweaning lactase persistence and passed this trait to modern descendants, delegitimizing lactose intolerance as "disease" in people with lactase nonpersistence. Three evolutionary hypotheses are each relevant to multiple diseases: (i) the polyvagal hypothesis posits that prehistoric adaptation of autonomic nervous system reactions to stress is beneficial acutely but, when continued chronically, predisposes individuals to painful functional gastrointestinal disorders, in whom it may be a biomarker; (ii) the thrifty gene hypothesis proposes genetic adaptation to feast-famine cycles among Pleistocene migrants to America, which is mismatched with Indigenous Americans' current diet and physical activity, predisposing them to obesity, nonalcoholic fatty liver disease, and gallstones and their complications; and (iii) the hygiene hypothesis proposes alteration of the gut microbiome, with which humans have coevolved, in allergic and autoimmune disease pathogenesis; for example, association of microbiome-altering proton pump inhibitor use with pediatric eosinophilic esophagitis, early-life gastrointestinal infection with celiac disease, and infant antibiotic use and an economically advanced environment with inflammatory bowel disease. Evolutionary perspectives broaden physicians' understanding of disease processes, improve care, and stimulate research.
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Affiliation(s)
- Grigorios I Leontiadis
- Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - George F Longstreth
- Section of Gastroenterology, Veterans Administration San Diego Healthcare System, San Diego, California, USA
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Guo S, Lei S, Palittapongarnpim P, McNeil E, Chaiprasert A, Li J, Chen H, Ou W, Surachat K, Qin W, Zhang S, Luo R, Chongsuvivatwong V. Association between Mycobacterium tuberculosis genotype and diabetes mellitus/hypertension: a molecular study. BMC Infect Dis 2022; 22:401. [PMID: 35462543 PMCID: PMC9035274 DOI: 10.1186/s12879-022-07344-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background A paucity of studies focused on the genetic association that tuberculosis (TB) patients with non-communicable diseases (NCDs) are more likely to be infected with Mycobacterium tuberculosis (MTB) with more potent virulence on anti-TB drug resistance than those without NCDs. The study aimed to document the predominant genotype, determine the association between MTB genotypes and NCD status and drug resistance. Methods We conducted a molecular study in 105 TB patients based on a cross-sectional study focused on the comorbid relationship between chronic conditions and TB among 1773 subjects from September 1, 2019 to August 30, 2020 in Guizhou, China. The participants were investigated through face-to-face interviews, followed by NCDs screening. The DNA of MTB isolates was extracted prior to genotyping using 24 loci MIRU-VNTR. The subsequent evaluations were performed by phylogenetic trees, combined with tests of statistical power, Chi-square or Fisher and multivariate logistic regression analysis. Results The Beijing family of Lineage 2 (East Asia) was the predominant genotype accounting for 43.8% (46/105), followed by Lineage 4 (Euro-America) strains, including Uganda I (34.3%, 36/105), and the NEW-1 (9.5%, 10/105). The proportion of Beijing strain in patients with and without NCDS was 28.6% (8/28) and 49.4% (38/77), respectively, with a statistical power test value of 24.3%. No significant association was detected between MTB genotype and NCD status. A low clustering rate (2.9%) was identified, consisting of two clusters. The rates of global, mono-, poly- and multi-drug resistance were 16.2% (17/105), 14.3% (15/105), 1.0% (1/105) and 4.8% (5/105), respectively. The drug-resistant rates of rifampicin, isoniazid, and streptomycin, were 6.7% (7/105), 11.4% (12/105) and 5.7% (6/105), respectively. Isoniazid resistance was significantly associated with the Beijing genotype of Lineage 2 (19.6% versus 5.1%). Conclusions The Lineage 2 East Asia/Beijing genotype is the dominant genotype of the local MTB with endogenous infection preponderating. Not enough evidence is detected to support the association between the MTB genotype and diabetes/hypertension. Isoniazid resistance is associated with the Lineage 2 East Asia/Beijing strain. Supplementary information The online version contains supplementary material available at 10.1186/s12879-022-07344-z.
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Kato I, Zhang J, Sun J. Bacterial-Viral Interactions in Human Orodigestive and Female Genital Tract Cancers: A Summary of Epidemiologic and Laboratory Evidence. Cancers (Basel) 2022; 14:425. [PMID: 35053587 PMCID: PMC8773491 DOI: 10.3390/cancers14020425] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Infectious agents, including viruses, bacteria, fungi, and parasites, have been linked to pathogenesis of human cancers, whereas viruses and bacteria account for more than 99% of infection associated cancers. The human microbiome consists of not only bacteria, but also viruses and fungi. The microbiome co-residing in specific anatomic niches may modulate oncologic potentials of infectious agents in carcinogenesis. In this review, we focused on interactions between viruses and bacteria for cancers arising from the orodigestive tract and the female genital tract. We examined the interactions of these two different biological entities in the context of human carcinogenesis in the following three fashions: (1) direct interactions, (2) indirect interactions, and (3) no interaction between the two groups, but both acting on the same host carcinogenic pathways, yielding synergistic or additive effects in human cancers, e.g., head and neck cancer, liver cancer, colon cancer, gastric cancer, and cervical cancer. We discuss the progress in the current literature and summarize the mechanisms of host-viral-bacterial interactions in various human cancers. Our goal was to evaluate existing evidence and identify gaps in the knowledge for future directions in infection and cancer.
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Affiliation(s)
- Ikuko Kato
- Department of Oncology and Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Jilei Zhang
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Jun Sun
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
- UIC Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
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Avalueva EB, Serkova MY, Sitkin SI. <i>Helicobacter pylori</i>. The survival strategy of a commensal symbiont in the <i>Homo sapiens</i> population. EXPERIMENTAL AND CLINICAL GASTROENTEROLOGY 2021:102-108. [DOI: 10.31146/1682-8658-ecg-193-9-102-108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Несмотря на крайне высокую степень инфицированности Helicobacter pylori в популяции Homo sapiens, подавляющее большинство инфицированных являются бессимптомными носителями. Широкое распространение инфекции H. pylori среди лиц без признаков патологии и низкая заболеваемость при хронической колонизации слизистой оболочки желудка указывают на то, что H. pylori с большей вероятностью является условно-патогенным микроорганизмом или патобионтом. Популяционная ликвидация инфекции H. pylori существенно снизила заболеваемость инфекцией H. pylori, однако появление устойчивости к противомикробным препаратам привело к их неэффективности.
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Affiliation(s)
- E. B. Avalueva
- North-Western state medical University named after I. I. Mechnikov, Ministry of health of the Russian Federation
| | - M. Yu. Serkova
- North-Western state medical University named after I. I. Mechnikov, Ministry of health of the Russian Federation
| | - S. I. Sitkin
- North-Western state medical University named after I. I. Mechnikov, Ministry of health of the Russian Federation; Almazov National Medical Research Centre
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McHenry ML, Wampande EM, Joloba ML, Malone LL, Mayanja-Kizza H, Bush WS, Boom WH, Williams SM, Stein CM. Interaction between M. tuberculosis Lineage and Human Genetic Variants Reveals Novel Pathway Associations with Severity of TB. Pathogens 2021; 10:pathogens10111487. [PMID: 34832643 PMCID: PMC8617877 DOI: 10.3390/pathogens10111487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/01/2021] [Accepted: 11/10/2021] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis (TB) remains a major public health threat globally, especially in sub-Saharan Africa. Both human and Mycobacterium tuberculosis (MTBC) genetic variation affect TB outcomes, but few studies have examined if and how the two genomes interact to affect disease. We hypothesize that long-term coexistence between human genomes and MTBC lineages modulates disease to affect its severity. We examined this hypothesis in our TB household contact study in Kampala, Uganda, in which we identified three MTBC lineages, of which one, L4.6-Uganda, is clearly derived and hence recent. We quantified TB severity using the Bandim TBscore and examined the interaction between MTBC lineage and human single-nucleotide polymorphisms (SNPs) genome-wide, in two independent cohorts of TB cases (n = 149 and n = 127). We found a significant interaction between an SNP in PPIAP2 and the Uganda lineage (combined p = 4 × 10−8). PPIAP2 is a pseudogene that is highly expressed in immune cells. Pathway and eQTL analyses indicated potential roles between coevolving SNPs and cellular replication and metabolism as well as platelet aggregation and coagulation. This finding provides further evidence that host–pathogen interactions affect clinical presentation differently than host and pathogen genetic variation independently, and that human–MTBC coevolution is likely to explain patterns of disease severity.
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Affiliation(s)
- Michael L. McHenry
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44016, USA; (M.L.M.); (W.S.B.); (S.M.W.)
| | - Eddie M. Wampande
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; (E.M.W.); (M.L.J.)
| | - Moses L. Joloba
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; (E.M.W.); (M.L.J.)
| | - LaShaunda L. Malone
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (L.L.M.); (W.H.B.)
| | - Harriet Mayanja-Kizza
- Department of Medicine and Mulago Hospital, School of Medicine, Makerere University, Kampala, Uganda;
| | - William S. Bush
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44016, USA; (M.L.M.); (W.S.B.); (S.M.W.)
| | - W. Henry Boom
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (L.L.M.); (W.H.B.)
| | - Scott M. Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44016, USA; (M.L.M.); (W.S.B.); (S.M.W.)
| | - Catherine M. Stein
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44016, USA; (M.L.M.); (W.S.B.); (S.M.W.)
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; (E.M.W.); (M.L.J.)
- Correspondence:
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Mekonnen D, Derbie A, Mihret A, Yimer SA, Tønjum T, Gelaw B, Nibret E, Munshae A, Waddell SJ, Aseffa A. Lipid droplets and the transcriptome of Mycobacterium tuberculosis from direct sputa: a literature review. Lipids Health Dis 2021; 20:129. [PMID: 34602073 PMCID: PMC8487580 DOI: 10.1186/s12944-021-01550-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/09/2021] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the main etiology of tuberculosis (TB), is predominantly an intracellular pathogen that has caused infection, disease and death in humans for centuries. Lipid droplets (LDs) are dynamic intracellular organelles that are found across the evolutionary tree of life. This review is an evaluation of the current state of knowledge regarding Mtb-LD formation and associated Mtb transcriptome directly from sputa.Based on the LD content, Mtb in sputum may be classified into three groups: LD positive, LD negative and LD borderline. However, the clinical and evolutionary importance of each state is not well elaborated. Mounting evidence supports the view that the presence of LD positive Mtb bacilli in sputum is a biomarker of slow growth, low energy state, towards lipid degradation, and drug tolerance. In Mtb, LD may serve as a source of chemical energy, scavenger of toxic compounds, prevent destruction of Mtb through autophagy, delay trafficking of lysosomes towards the phagosome, and contribute to Mtb persistence. It is suggest that LD is a key player in the induction of a spectrum of phenotypic and metabolic states of Mtb in the macrophage, granuloma and extracellular sputum microenvironment. Tuberculosis patients with high proportion of LD positive Mtb in pretreatment sputum was associated with higher rate of poor treatment outcome, indicating that LD may have a clinical application in predicting treatment outcome.The propensity for LD formation among Mtb lineages is largely unknown. The role of LD on Mtb transmission and disease phenotype (pulmonary TB vs extra-pulmonary TB) is not well understood. Thus, further studies are needed to understand the relationships between LD positivity and Mtb lineage, Mtb transmission and clinical types.
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Affiliation(s)
- Daniel Mekonnen
- Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia.
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Awoke Derbie
- Department of Medical Microbiology, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- The Centre for Innovative Drug Development and Therapeutic Trials for Africa (CDT-Africa), Addis Ababa University, Addis Ababa, Ethiopia
| | - Adane Mihret
- Armauer Hansen Research Institute, Jimma Road, ALERT Compound, PO Box 1005, Addis Ababa, Ethiopia
- Department of Medical Microbiology, Immunology and Parasitology, College of Medicine and Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Abebe Yimer
- Department of Microbiology, University of Oslo, PO Box 1071, Blindern, NO-0316, Oslo, Norway
- Coalition for Epidemic Preparedness Innovations, CEPI, P.O. Box 123, Torshov, 0412, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, PO Box 1071, Blindern, NO-0316, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, PO Box 4950, Nydalen, NO-0424, Oslo, Norway
| | - Baye Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Endalkachew Nibret
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abaineh Munshae
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Simon J Waddell
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Jimma Road, ALERT Compound, PO Box 1005, Addis Ababa, Ethiopia
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Ornithine decarboxylase (ODC1) gene variant (rs2302615) is associated with gastric cancer independently of Helicobacter pylori CagA serostatus. Oncogene 2021; 40:5963-5969. [PMID: 34376808 PMCID: PMC8692072 DOI: 10.1038/s41388-021-01981-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/08/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023]
Abstract
The primary cause of gastric cancer is chronic infection with Helicobacter pylori (H. pylori), particularly the high-risk genotype cagA, and risk modification by human genetic variants. We studied 94 variants in 54 genes for association with gastric cancer, including rs2302615 in ornithine decarboxylase (ODC1), which may affect response to chemoprevention with the ODC inhibitor, eflornithine (difluoromethylornithine; DFMO). Our population-based, case-control study included 1366 individuals (664 gastric cancer cases and 702 controls) from Western Honduras, a high incidence region of Latin America. CagA seropositivity was strongly associated with cancer (OR = 3.6; 95% CI: 2.6, 5.1). The ODC1 variant rs2302615 was associated with gastric cancer (OR = 1.36; p = 0.018) in a model adjusted for age, sex, and CagA serostatus. Two additional single nucleotide polymorphisms (SNPs) in CASP1 (rs530537) and TLR4 (rs1927914) genes were also associated with gastric cancer in univariate models as well as models adjusted for age, sex, and CagA serostatus. The ODC1 SNP association with gastric cancer was stronger in individuals who carried the TT genotype at the associating TLR4 polymorphism, rs1927914 (OR = 1.77; p = 1.85 × 10-3). In conclusion, the ODC1 variant, rs2302615, is associated with gastric cancer and supports chemoprevention trials with DFMO, particularly in individuals homozygous for the T allele at rs1927914.
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Miller AK, Williams SM. Helicobacter pylori infection causes both protective and deleterious effects in human health and disease. Genes Immun 2021; 22:218-226. [PMID: 34244666 PMCID: PMC8390445 DOI: 10.1038/s41435-021-00146-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/18/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023]
Abstract
Infection with Helicobacter pylori (H. pylori) is necessary but not sufficient for the development of gastric cancer, the third leading cause of cancer death globally. H. pylori infection affects over half of people globally; however, it does not affect populations uniformly. H. pylori infection rates are declining in western industrialized countries but are plateauing in developing and newly industrialized countries where gastric cancer is most prevalent. Despite H. pylori infection being the primary causative agent for gastric cancer, H. pylori infection can also cause other effects, detrimental or beneficial, throughout an individual's life, with the beneficial effects often being seen in childhood and the deleterious effects in adulthood. H. pylori is an ancient bacterium and its likelihood of affecting disease or health is dependent on both human and bacterial genetics that have co-evolved over millennia. In this review, we focus on the impact of infection and its genetic bases in different populations and diseases throughout an individual's lifespan, highlighting the benefits of individualized treatment and argue that universal eradication of H. pylori in its host may cause more harm than good for those infected with H. pylori.
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Affiliation(s)
- Anna K Miller
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH
| | - Scott M Williams
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH
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13
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Shedding Light on the African Enigma: In Vitro Testing of Homo sapiens-Helicobacter pylori Coevolution. Microorganisms 2021; 9:microorganisms9020240. [PMID: 33503840 PMCID: PMC7912213 DOI: 10.3390/microorganisms9020240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/27/2022] Open
Abstract
The continuous characterization of genome-wide diversity in population and case–cohort samples, allied to the development of new algorithms, are shedding light on host ancestry impact and selection events on various infectious diseases. Especially interesting are the long-standing associations between humans and certain bacteria, such as the case of Helicobacter pylori, which could have been strong drivers of adaptation leading to coevolution. Some evidence on admixed gastric cancer cohorts have been suggested as supporting Homo-Helicobacter coevolution, but reliable experimental data that control both the bacterium and the host ancestries are lacking. Here, we conducted the first in vitro coinfection assays with dual human- and bacterium-matched and -mismatched ancestries, in African and European backgrounds, to evaluate the genome wide gene expression host response to H. pylori. Our results showed that: (1) the host response to H. pylori infection was greatly shaped by the human ancestry, with variability on innate immune system and metabolism; (2) African human ancestry showed signs of coevolution with H. pylori while European ancestry appeared to be maladapted; and (3) mismatched ancestry did not seem to be an important differentiator of gene expression at the initial stages of infection as assayed here.
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14
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Pedro N, Pinto RJ, Cavadas B, Pereira L. Sub-Saharan African information potential to unveil adaptations to infectious disease. Hum Mol Genet 2021; 30:R138-R145. [PMID: 33461217 DOI: 10.1093/hmg/ddab001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/10/2020] [Accepted: 01/05/2021] [Indexed: 12/09/2022] Open
Abstract
Sub-Saharan Africa is the most promising region of the world to conduct high-throughput studies to unveil adaptations to infectious diseases due to several reasons, namely, the longest evolving time-depth in the Homo sapiens phylogenetic tree (at least two-third older than any other worldwide region); the continuous burden of infectious diseases (still number one in health/life threat); and the coexistence of populations practising diverse subsistence modes (nomadic or seminomadic hunter-gatherers and agropastoralists, and sedentary agriculturalists, small urban and megacity groups). In this review, we will present the most up-to-date results that shed light on three main hypotheses related with this adaptation. One is the hypothesis of coevolution between host and pathogen, given enough time for the establishment of this highly dynamic relationship. The second hypothesis enunciates that the agricultural transition was responsible for the increase of the infectious disease burden, due to the huge expansion of the sedentary human population and the cohabitation with domesticates as main reservoirs of pathogens. The third hypothesis states that the boosting of our immune system against pathogens by past selection may have resulted in maladaptation of the developed hygienic societies, leading to an increase of allergic, inflammatory and autoimmune disorders. Further work will enlighten the biological mechanisms behind these main adaptations, which can be insightful for translation into diagnosis, prognosis and treatment interventions.
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Affiliation(s)
- Nicole Pedro
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Ricardo J Pinto
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Bruno Cavadas
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Luisa Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
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15
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McHenry ML, Williams SM, Stein CM. Genetics and evolution of tuberculosis pathogenesis: New perspectives and approaches. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 81:104204. [PMID: 31981609 PMCID: PMC7192760 DOI: 10.1016/j.meegid.2020.104204] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 12/11/2022]
Abstract
Tuberculosis is the most lethal infectious disease globally, but the vast majority of people who are exposed to the primary causative pathogen, Mycobacterium tuberculosis (MTB), do not develop active disease. Most people do, however, show signs of infection that remain throughout their lifetimes. In this review, we develop a framework that describes several possible transitions from pathogen exposure to TB disease and reflect on the genetics studies to address many of these. The evidence strongly supports a human genetic component for both infection and active disease, but many of the existing studies, including some of our own, do not clearly delineate what transition(s) is being explicitly examined. This can make interpretation difficult in terms of why only some people develop active disease. Nonetheless, both linkage peaks and associations with either active disease or latent infection have been identified. For transition to active disease, pathways defined as active TB altered T and B cell signaling in rheumatoid arthritis and T helper cell differentiation are significantly associated. Pathways that affect transition from exposure to infection are less clear-cut, as studies of this phenotype are less common, and a primary response, if it exists, is not yet well defined. Lastly, we discuss the role that interaction between the MTB lineage and human genetics can play in TB disease, especially severity. Severity of TB is at present the only way to study putative co-evolution between MTB and humans as it is impossible in the absence of disease to know the MTB lineage(s) to which an individual has been exposed. In addition, even though severity has been defined in multiple heterogeneous ways, it appears that MTB-human co-evolution may shape pathogenicity. Further analysis of co-evolution, requiring careful analysis of paired samples, may be the best way to completely assess the genetic basis of TB.
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Affiliation(s)
- Michael L McHenry
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America; Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, United States of America.
| | - Catherine M Stein
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America; Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
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16
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Fitak RR, Antonides JD, Baitchman EJ, Bonaccorso E, Braun J, Kubiski S, Chiu E, Fagre AC, Gagne RB, Lee JS, Malmberg JL, Stenglein MD, Dusek RJ, Forgacs D, Fountain-Jones NM, Gilbertson MLJ, Worsley-Tonks KEL, Funk WC, Trumbo DR, Ghersi BM, Grimaldi W, Heisel SE, Jardine CM, Kamath PL, Karmacharya D, Kozakiewicz CP, Kraberger S, Loisel DA, McDonald C, Miller S, O'Rourke D, Ott-Conn CN, Páez-Vacas M, Peel AJ, Turner WC, VanAcker MC, VandeWoude S, Pecon-Slattery J. The Expectations and Challenges of Wildlife Disease Research in the Era of Genomics: Forecasting with a Horizon Scan-like Exercise. J Hered 2020; 110:261-274. [PMID: 31067326 DOI: 10.1093/jhered/esz001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 01/08/2019] [Indexed: 12/14/2022] Open
Abstract
The outbreak and transmission of disease-causing pathogens are contributing to the unprecedented rate of biodiversity decline. Recent advances in genomics have coalesced into powerful tools to monitor, detect, and reconstruct the role of pathogens impacting wildlife populations. Wildlife researchers are thus uniquely positioned to merge ecological and evolutionary studies with genomic technologies to exploit unprecedented "Big Data" tools in disease research; however, many researchers lack the training and expertise required to use these computationally intensive methodologies. To address this disparity, the inaugural "Genomics of Disease in Wildlife" workshop assembled early to mid-career professionals with expertise across scientific disciplines (e.g., genomics, wildlife biology, veterinary sciences, and conservation management) for training in the application of genomic tools to wildlife disease research. A horizon scanning-like exercise, an activity to identify forthcoming trends and challenges, performed by the workshop participants identified and discussed 5 themes considered to be the most pressing to the application of genomics in wildlife disease research: 1) "Improving communication," 2) "Methodological and analytical advancements," 3) "Translation into practice," 4) "Integrating landscape ecology and genomics," and 5) "Emerging new questions." Wide-ranging solutions from the horizon scan were international in scope, itemized both deficiencies and strengths in wildlife genomic initiatives, promoted the use of genomic technologies to unite wildlife and human disease research, and advocated best practices for optimal use of genomic tools in wildlife disease projects. The results offer a glimpse of the potential revolution in human and wildlife disease research possible through multi-disciplinary collaborations at local, regional, and global scales.
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Affiliation(s)
| | - Jennifer D Antonides
- Department of Forestry & Natural Resources, Purdue University, West Lafayette, IN
| | - Eric J Baitchman
- The Zoo New England Division of Animal Health and Conservation, Boston, MA
| | - Elisa Bonaccorso
- The Instituto BIOSFERA and Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, vía Interoceánica y Diego de Robles, Quito, Ecuador
| | - Josephine Braun
- The Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Steven Kubiski
- The Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Elliott Chiu
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Anna C Fagre
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Roderick B Gagne
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Justin S Lee
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Jennifer L Malmberg
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Mark D Stenglein
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Robert J Dusek
- The U. S. Geological Survey, National Wildlife Health Center, Madison, WI
| | - David Forgacs
- The Interdisciplinary Graduate Program of Genetics, Texas A&M University, College Station, TX
| | | | - Marie L J Gilbertson
- The Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN
| | | | - W Chris Funk
- The Department of Biology, Colorado State University, Fort Collins, CO
| | - Daryl R Trumbo
- The Department of Biology, Colorado State University, Fort Collins, CO
| | | | | | - Sara E Heisel
- The Odum School of Ecology, University of Georgia, Athens, GA
| | - Claire M Jardine
- The Department of Pathobiology, Canadian Wildlife Health Cooperative, University of Guelph, Guelph, Ontario, Canada
| | - Pauline L Kamath
- The School of Food and Agriculture, University of Maine, Orono, ME
| | | | | | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ
| | - Dagan A Loisel
- The Department of Biology, Saint Michael's College, Colchester, VT
| | - Cait McDonald
- The Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY (McDonald)
| | - Steven Miller
- The Department of Biology, Drexel University, Philadelphia, PA
| | | | - Caitlin N Ott-Conn
- The Michigan Department of Natural Resources, Wildlife Disease Laboratory, Lansing, MI
| | - Mónica Páez-Vacas
- The Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Machala y Sabanilla, Quito, Ecuador
| | - Alison J Peel
- The Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Wendy C Turner
- The Department of Biological Sciences, University at Albany, State University of New York, Albany, NY
| | - Meredith C VanAcker
- The Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY
| | - Sue VandeWoude
- The College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Jill Pecon-Slattery
- The Center for Species Survival, Smithsonian Conservation Biology Institute-National Zoological Park, Front Royal, VA
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17
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Genome Sequences of Three Colombian Helicobacter pylori Strains Isolated from Tolimense Patients. Microbiol Resour Announc 2020; 9:9/18/e00117-20. [PMID: 32354968 PMCID: PMC7193923 DOI: 10.1128/mra.00117-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We present the complete genome sequences of three Helicobacter pylori strains isolated from patients who resided in Tolima Department, Colombia, diagnosed with chronic gastritis. The genomes present an average length of 1.6 Mbp and 1,546 genes and correspond to different H. pylori subpopulations. We present the complete genome sequences of three Helicobacter pylori strains isolated from patients who resided in Tolima Department, Colombia, diagnosed with chronic gastritis. The genomes present an average length of 1.6 Mbp and 1,546 genes and correspond to different H. pylori subpopulations.
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18
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McHenry ML, Bartlett J, Igo RP, Wampande EM, Benchek P, Mayanja-Kizza H, Fluegge K, Hall NB, Gagneux S, Tishkoff SA, Wejse C, Sirugo G, Boom WH, Joloba M, Williams SM, Stein CM. Interaction between host genes and Mycobacterium tuberculosis lineage can affect tuberculosis severity: Evidence for coevolution? PLoS Genet 2020; 16:e1008728. [PMID: 32352966 PMCID: PMC7217476 DOI: 10.1371/journal.pgen.1008728] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 05/12/2020] [Accepted: 03/20/2020] [Indexed: 12/16/2022] Open
Abstract
Genetic studies of both the human host and Mycobacterium tuberculosis (MTB) demonstrate independent association with tuberculosis (TB) risk. However, neither explains a large portion of disease risk or severity. Based on studies in other infectious diseases and animal models of TB, we hypothesized that the genomes of the two interact to modulate risk of developing active TB or increasing the severity of disease, when present. We examined this hypothesis in our TB household contact study in Kampala, Uganda, in which there were 3 MTB lineages of which L4-Ugandan (L4.6) is the most recent. TB severity, measured using the Bandim TBscore, was modeled as a function of host SNP genotype, MTB lineage, and their interaction, within two independent cohorts of TB cases, N = 113 and 121. No association was found between lineage and severity, but association between multiple polymorphisms in IL12B and TBscore was replicated in two independent cohorts (most significant rs3212227, combined p = 0.0006), supporting previous associations of IL12B with TB susceptibility. We also observed significant interaction between a single nucleotide polymorphism (SNP) in SLC11A1 and the L4-Ugandan lineage in both cohorts (rs17235409, meta p = 0.0002). Interestingly, the presence of the L4-Uganda lineage in the presence of the ancestral human allele associated with more severe disease. These findings demonstrate that IL12B is associated with severity of TB in addition to susceptibility, and that the association between TB severity and human genetics can be due to an interaction between genes in the two species, consistent with host-pathogen coevolution in TB.
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Affiliation(s)
- Michael L. McHenry
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Jacquelaine Bartlett
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Robert P. Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Eddie M. Wampande
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Penelope Benchek
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Harriet Mayanja-Kizza
- Department of Medicine and Mulago Hospital, School of Medicine, Makerere University, Kampala, Uganda
| | - Kyle Fluegge
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Noemi B. Hall
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sarah A. Tishkoff
- Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Christian Wejse
- Department of Infectious Diseases and Center for Global Health, Aarhus University, Aarhus, Denmark
- Bandim Health Project, INDEPTH Network, Bissau, Guinea Bissau
| | - Giorgio Sirugo
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, Unites States of America
| | - W. Henry Boom
- Tuberculosis Research Unit, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Moses Joloba
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Scott M. Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- * E-mail: (SMW); (CMS)
| | - Catherine M. Stein
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Tuberculosis Research Unit, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- * E-mail: (SMW); (CMS)
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19
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BCG Vaccinations Upregulate Myc, a Central Switch for Improved Glucose Metabolism in Diabetes. iScience 2020; 23:101085. [PMID: 32380424 PMCID: PMC7205768 DOI: 10.1016/j.isci.2020.101085] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 04/03/2020] [Accepted: 04/15/2020] [Indexed: 12/11/2022] Open
Abstract
Myc has emerged as a pivotal transcription factor for four metabolic pathways: aerobic glycolysis, glutaminolysis, polyamine synthesis, and HIF-1α/mTOR. Each of these pathways accelerates the utilization of sugar. The BCG vaccine, a derivative of Mycobacteria-bovis, has been shown to trigger a long-term correction of blood sugar levels to near normal in type 1 diabetics (T1D). Here we reveal the underlying mechanisms behind this beneficial microbe-host interaction. We show that baseline glucose transport is deficient in T1D monocytes but is improved by BCG in vitro and in vivo. We then show, using RNAseq in monocytes and CD4 T cells, that BCG treatment over 56 weeks in humans is associated with upregulation of Myc and activation of nearly two dozen Myc-target genes underlying the four metabolic pathways. This is the first documentation of BCG induction of Myc and its association with systemic blood sugar control in a chronic disease like diabetes. T1D has insufficient aerobic glycolysis; this causes insufficient sugar utilization BCG vaccine lowers blood sugar levels in T1D by augmenting aerobic glycolysis BCG-induced shift to aerobic glycolysis is associated with Myc activation Host-microbe BCG interactions through Myc activate sugar-regulating genes in T1D
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20
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Azad AK, Lloyd C, Sadee W, Schlesinger LS. Challenges of Immune Response Diversity in the Human Population Concerning New Tuberculosis Diagnostics, Therapies, and Vaccines. Front Cell Infect Microbiol 2020; 10:139. [PMID: 32322562 PMCID: PMC7156588 DOI: 10.3389/fcimb.2020.00139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/17/2020] [Indexed: 11/13/2022] Open
Abstract
Universal approaches to the prevention and treatment of human diseases fail to take into account profound immune diversity resulting from genetic variations across populations. Personalized or precision medicine takes into account individual lifestyle, environment, and biology (genetics and immune status) and is being adopted in several disease intervention strategies such as cancer and heart disease. However, its application in infectious diseases, particularly global diseases such as tuberculosis (TB), is far more complex and in a state of infancy. Here, we discuss the impact of human genetic variations on immune responses and how they relate to failures seen in current TB diagnostic, therapy, and vaccine approaches across populations. We offer our perspective on the challenges and potential for more refined approaches going forward.
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Affiliation(s)
- Abul K Azad
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Christopher Lloyd
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Wolfgang Sadee
- Department of Cancer Biology and Genetics, Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Larry S Schlesinger
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, United States
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21
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Sukhan DS, Vernygorodskyi SV, Haidukov NV, Ludkevich HP. Molecular and Genetic Aspects of Helicobacter pylori Interaction with Cells of Gastric Mucosa. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720020139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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22
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Petti S, Lodi G. The controversial natural history of oral herpes simplex virus type 1 infection. Oral Dis 2019; 25:1850-1865. [PMID: 31733122 DOI: 10.1111/odi.13234] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/29/2019] [Accepted: 11/10/2019] [Indexed: 02/06/2023]
Abstract
The natural history of oral herpes simplex virus type 1 (HSV-1) infection in the immunocompetent host is complex and rich in controversial phenomena, namely the role of unapparent transmission in primary infection acquisition, the high frequency of asymptomatic primary and recurrent infections, the lack of immunogenicity of HSV-1 internalized in the soma (cell body) of the sensory neurons of the trigeminal ganglion, the lytic activity of HSV-1 in the soma of neurons that is inhibited in the sensory neurons of the trigeminal ganglion and often uncontrolled in the other neurons, the role of keratin in promoting the development of recurrence episodes in immunocompetent hosts, the virus-host Nash equilibrium, the paradoxical HSV-1-seronegative individuals who shed HSV-1 through saliva, the limited efficacy of anti-HSV vaccines, and why the oral route of infection is the least likely to produce severe complications. The natural history of oral HSV-1 infection is also a history of symbiosis between humans and virus that may switch from mutualism to parasitism and vice versa. This balance is typical of microorganisms that are highly coevolved with humans, and its knowledge is essential to oral healthcare providers to perform adequate diagnosis and provide proper individual-based HSV-1 infection therapy.
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Affiliation(s)
- Stefano Petti
- Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Giovanni Lodi
- Department of Biomedical, Surgical, and Dental Sciences, University of Milan, Milan, Italy
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23
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Corvalán AH, Ruedlinger J, de Mayo T, Polakovicova I, Gonzalez-Hormazabal P, Aguayo F. The Phylogeographic Diversity of EBV and Admixed Ancestry in the Americas⁻Another Model of Disrupted Human-Pathogen Co-Evolution. Cancers (Basel) 2019; 11:cancers11020217. [PMID: 30769835 PMCID: PMC6406347 DOI: 10.3390/cancers11020217] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 12/24/2022] Open
Abstract
Epstein-Barr virus (EBV) is an etiological agent for gastric cancer with significant worldwide variations. Molecular characterizations of EBV have shown phylogeographical variations among healthy populations and in EBV-associated diseases, particularly the cosegregated BamHI-I fragment and XhoI restriction site of exon 1 of the LMP-1 gene. In the Americas, both cosegregated variants are present in EBV carriers, which aligns with the history of Asian and European human migration to this continent. Furthermore, novel recombinant variants have been found, reflecting the genetic makeup of this continent. However, in the case of EBV-associated gastric cancer (EBV-associated GC), the cosegregated European BamHI-“i” fragment and XhoI restriction site strain prevails. Thus, we propose that a disrupted coevolution between viral phylogeographical strains and mixed human ancestry in the Americas might explain the high prevalence of this particular gastric cancer subtype. This cosegregated region contains two relevant transcripts for EBV-associated GC, the BARF-1 and miR-BARTs. Thus, genome-wide association studies (GWAS) or targeted sequencing of both transcripts may be required to clarify their role as a potential source of this disrupted coevolution.
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Affiliation(s)
- Alejandro H Corvalán
- Department of Hematology and Oncology, Pontificia Universidad Catolica de Chile, Santiago 8330034, Chile.
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Catolica de Chile, Santiago 8330034, Chile.
| | - Jenny Ruedlinger
- Department of Hematology and Oncology, Pontificia Universidad Catolica de Chile, Santiago 8330034, Chile.
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Catolica de Chile, Santiago 8330034, Chile.
| | - Tomas de Mayo
- Department of Hematology and Oncology, Pontificia Universidad Catolica de Chile, Santiago 8330034, Chile.
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Catolica de Chile, Santiago 8330034, Chile.
- Faculty of Sciences, School of Medicine, Universidad Mayor, Santiago 7510041, Chile.
| | - Iva Polakovicova
- Department of Hematology and Oncology, Pontificia Universidad Catolica de Chile, Santiago 8330034, Chile.
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Catolica de Chile, Santiago 8330034, Chile.
| | - Patricio Gonzalez-Hormazabal
- Program of Human Genetics, Instituto Ciencias Biomedicas, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile.
| | - Francisco Aguayo
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Catolica de Chile, Santiago 8330034, Chile.
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile.
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Nagashima H, Yamaoka Y. Importance of Toll-like Receptors in Pro-inflammatory and Anti-inflammatory Responses by Helicobacter pylori Infection. Curr Top Microbiol Immunol 2019; 421:139-158. [PMID: 31123888 DOI: 10.1007/978-3-030-15138-6_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Infectious diseases have been paramount among the threats to human health and survival throughout evolutionary history. Bacterial cell-surface molecules are key factors in the microorganism-host crosstalk, as they can interact with host pattern-recognition receptors (PRRs) of the gastrointestinal mucosa. The best-studied PRRs are toll-like receptors (TLRs). Because TLRs play an important key role in host defense, they have received increasing interest in the evolutionary and population genetics literature, and their variation represents a potential target of adaptive evolution. Helicobacter pylori is one of the commensal bacteria in our body and can have pathogenic properties in a subset of infected people. The history of H. pylori research indicated that humans and bacteria co-evolved during evolution. A genome-wide association study (GWAS) has opened the way for investigating the genomic evolution of bacterial pathogens during the colonization and infection of humans. Recent GWAS research emphasized the importance of TLRs, especially TLR10 during pathogenesis in H. pylori infection. We demonstrated that TLR10, whose ligand was unknown for a long time, can recognize H. pylori LPS. Our results of H. pylori research suggest that TLR10 might play an important role to also recognize other commensal bacteria. In this review, we discuss the importance of TLRs in pro-inflammatory and anti-inflammatory responses by H. pylori infection. Especially, we highlight the TLR10 interaction with H. pylori infection, providing new insights about TLR10 signaling.
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Affiliation(s)
- Hiroyuki Nagashima
- Department of Gastroenterology, Hokkaido Cancer Center, Sapporo, Hokkaido, Japan.,Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita, 879-5593, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita, 879-5593, Japan. .,Department of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA.
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25
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Tavera G, Morgan DR, Williams SM. Tipping the Scale Toward Gastric Disease: A Host-Pathogen Genomic Mismatch? CURRENT GENETIC MEDICINE REPORTS 2018; 6:199-207. [PMID: 30775159 PMCID: PMC6373874 DOI: 10.1007/s40142-018-0153-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW Chronic infection with Helicobacter pylori infection is necessary but not sufficient to initiate development of intestinal-type gastric adenocarcinoma. It is not clear what additional factors tip the scale from commensal bacteria towards a pathogen that facilitates development of gastric cancer. Genetic variants in both the pathogen and host have been implicated, but neither alone explains a substantial portion of disease risk. RECENT FINDINGS In this review, we consider studies that address the important role of human and bacterial genetics, ancestry and their interactions in determining gastric disease risk. We observe gaps in the current literature that should guide future work to confirm the hypothesis of the interacting roles of host and bacterial genetics that will be necessary to translate these findings into clinically relevant information. SUMMARY We summarize genetic risk factors for gastric disease in both H. pylori and human hosts. However, genetic variation of one or the other organism in isolation insufficiently explains gastric disease risk. The most promising models of gastric disease risk simultaneously consider the genetic variation of both the H. pylori and human host, under a co-evolution model.
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Affiliation(s)
- Gloria Tavera
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Douglas R Morgan
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
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26
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Li Y, Cai Q, Lin L, Xu C. MiR-875 and miR-3144 switch the human papillomavirus 16 E6/E6* mRNA ratio through the EGFR pathway and a direct targeting effect. Gene 2018; 679:389-397. [PMID: 30205176 DOI: 10.1016/j.gene.2018.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/03/2018] [Accepted: 09/07/2018] [Indexed: 01/06/2023]
Abstract
By employing bioinformatics scanning approaches and luciferase reporter, our previous study showed that two less common human miRNAs, miR-875 and miR-3144, target a conserved site in the genomes of most high-risk human papillomaviruses (HR-HPVs). In this study, we found that the site targeted by miR-875 and miR-3144 overlapped with the 5' alternative splice site of E6E7 transcripts in HPV16. Using HPV16+ SiHa cells, we showed that high levels of miR-875 and miR-3144 reduced the abundance of unspliced E6, while they promoted three E6* spliced transcripts and decreased the expression levels of E6/E7 oncoproteins and epidermal growth factor receptor (EGFR). A potential miR-875 target site was predicted in EGFR. Meanwhile, depletion of EGFR resulted in a failure to promote E6* but maintained the suppression of unspliced E6 driven by miR-875 and miR-3144. The data suggest that these two miRNAs switch the E6/E6* ratio through both the EGFR pathway and direct targeting. Here, we demonstrate for the first time that human miRNAs regulate the HPV splice isoforms. Furthermore, miRNA-875 and miRNA-3144 are only found in vertebrates and Homo sapiens, and the binding site in EGFR is highly conserved in Boreoeutheria. Our findings highlight the tumour-suppressing effect of miRNAs that possibly appeared in the late stage of biological evolution. ABBREVIATIONS
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Affiliation(s)
- Yanyun Li
- Obstetrics and Gynaecology Hospital, Fudan University, Shanghai 200011, China.
| | - Qingqing Cai
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Lin Lin
- Obstetrics and Gynaecology Hospital, Fudan University, Shanghai 200011, China
| | - Congjian Xu
- Obstetrics and Gynaecology Hospital, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China; Department of Obstetrics and Gynaecology of Shanghai Medical School, Fudan University, Shanghai 200032, China; Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China.
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27
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Farzi N, Yadegar A, Aghdaei HA, Yamaoka Y, Zali MR. Genetic diversity and functional analysis of oipA gene in association with other virulence factors among Helicobacter pylori isolates from Iranian patients with different gastric diseases. INFECTION GENETICS AND EVOLUTION 2018; 60:26-34. [PMID: 29452293 DOI: 10.1016/j.meegid.2018.02.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 01/29/2018] [Accepted: 02/12/2018] [Indexed: 12/15/2022]
Abstract
Helicobacter pylori (H. pylori) is one of the most genetically diverse bacterial pathogens that persistently colonizes the human gastric epithelium. This remarkable genomic plasticity may act as a driving force for successful adaptation and persistence of the bacteria in the harsh gastric environment. Outer inflammatory protein A (OipA) encoded by oipA gene (HP0638/hopH) is a member of the outer membrane proteins (OMPs) of H. pylori involved in induction of IL-8 secretion and is associated with development of peptic ulcer and gastric cancer. Expression of OipA is regulated by phase variation within a CT dinucleotide repeat motif of the oipA gene. In this study we carried out direct DNA sequence analysis of 53 amplified fragments to investigate the oipA "On/Off" status among Iranian H. pylori isolates from patients with various gastric diseases. The prevalence of cagL, cagA, EPIYA motifs, vacA alleles, babA2 and sabA genotypes as well as cagPAI integrity of the isolates were determined by PCR. Our results demonstrated a high prevalence of strains with functional oipA status (79%) and significant associations were found between functional oipA and cagA (P = 0.027) and vacA s1m1 (P = 0.022) genotypes. The vacA s1m2 genotype was also found to be statistically associated with PUD (P = 0.0001). Interestingly, we showed that H. pylori strains with intact cagPAI co-expressed oipA gene in a significant synergistic relationship (P < 0.01). However, no significant association was observed between the functional oipA status and clinical outcomes (P > 0.05). In conclusion, our findings denotes great diversity in the number and pattern of CT dinucleotide repeats of oipA among Iranian H. pylori strains. The synergistic link between functional oipA and other important virulence factors is proposed to be critical in the pathogenesis of H. pylori, which needs further studies with a larger number of samples.
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Affiliation(s)
- Nastaran Farzi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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28
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Delahay RM, Croxall NJ, Stephens AD. Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements. Mob DNA 2018; 9:5. [PMID: 29416569 PMCID: PMC5785829 DOI: 10.1186/s13100-018-0109-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/15/2018] [Indexed: 12/12/2022] Open
Abstract
Background The genome of the gastric pathogen Helicobacter pylori is characterised by considerable variation of both gene sequence and content, much of which is contained within three large genomic islands comprising the cag pathogenicity island (cagPAI) and two mobile integrative and conjugative elements (ICEs) termed tfs3 and tfs4. All three islands are implicated as virulence factors, although whereas the cagPAI is well characterised, understanding of how the tfs elements influence H. pylori interactions with different human hosts is significantly confounded by limited definition of their distribution, diversity and structural representation in the global H. pylori population. Results To gain a global perspective of tfs ICE population dynamics we established a bioinformatics workflow to extract and precisely define the full tfs pan-gene content contained within a global collection of 221 draft and complete H. pylori genome sequences. Complete (ca. 35-55kbp) and remnant tfs ICE clusters were reconstructed from a dataset comprising > 12,000 genes, from which orthologous gene complements and distinct alleles descriptive of different tfs ICE types were defined and classified in comparative analyses. The genetic variation within defined ICE modular segments was subsequently used to provide a complete description of tfs ICE diversity and a comprehensive assessment of their phylogeographic context. Our further examination of the apparent ICE modular types identified an ancient and complex history of ICE residence, mobility and interaction within particular H. pylori phylogeographic lineages and further, provided evidence of both contemporary inter-lineage and inter-species ICE transfer and displacement. Conclusions Our collective results establish a clear view of tfs ICE diversity and phylogeographic representation in the global H. pylori population, and provide a robust contextual framework for elucidating the functional role of the tfs ICEs particularly as it relates to the risk of gastric disease associated with different tfs ICE genotypes. Electronic supplementary material The online version of this article (10.1186/s13100-018-0109-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robin M Delahay
- 1Nottingham Digestive Diseases Centre and National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Nicola J Croxall
- 1Nottingham Digestive Diseases Centre and National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Amberley D Stephens
- 1Nottingham Digestive Diseases Centre and National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK.,2Present Address: Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcette Drive, West Cambridge, Cambridge, CB3 0AS UK
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29
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Bullock KK, Shaffer CL, Brooks AW, Secka O, Forsyth MH, McClain MS, Cover TL. Genetic signatures for Helicobacter pylori strains of West African origin. PLoS One 2017; 12:e0188804. [PMID: 29186206 PMCID: PMC5706691 DOI: 10.1371/journal.pone.0188804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 11/13/2017] [Indexed: 01/22/2023] Open
Abstract
Helicobacter pylori is a genetically diverse bacterial species that colonizes the stomach in about half of the human population. Most persons colonized by H. pylori remain asymptomatic, but the presence of this organism is a risk factor for gastric cancer. Multiple populations and subpopulations of H. pylori with distinct geographic distributions are recognized. Genetic differences among these populations might be a factor underlying geographic variation in gastric cancer incidence. Relatively little is known about the genomic features of African H. pylori strains compared to other populations of strains. In this study, we first analyzed the genomes of H. pylori strains from seven globally distributed populations or subpopulations and identified encoded proteins that exhibited the highest levels of sequence divergence. These included secreted proteins, an LPS glycosyltransferase, fucosyltransferases, proteins involved in molybdopterin biosynthesis, and Clp protease adaptor (ClpS). Among proteins encoded by the cag pathogenicity island, CagA and CagQ exhibited the highest levels of sequence diversity. We then identified proteins in strains of Western African origin (classified as hspWAfrica by MLST analysis) with sequences that were highly divergent compared to those in other populations of strains. These included ATP-dependent Clp protease, ClpS, and proteins of unknown function. Three of the divergent proteins sequences identified in West African strains were characterized by distinct insertions or deletions up to 8 amino acids in length. These polymorphisms in rapidly evolving proteins represent robust genetic signatures for H. pylori strains of West African origin.
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Affiliation(s)
- Kennady K. Bullock
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Carrie L. Shaffer
- Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Andrew W. Brooks
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Ousman Secka
- Medical Research Council Unit The Gambia, Banjul, The Gambia
| | - Mark H. Forsyth
- Department of Biology, The College of William and Mary, Williamsburg, Virginia, United States of America
| | - Mark S. McClain
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Timothy L. Cover
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, United States of America
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30
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Brites D, Gagneux S. The Nature and Evolution of Genomic Diversity in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:1-26. [DOI: 10.1007/978-3-319-64371-7_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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31
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Stein CM, Sausville L, Wejse C, Sobota RS, Zetola NM, Hill PC, Boom WH, Scott WK, Sirugo G, Williams SM. Genomics of human pulmonary tuberculosis: from genes to pathways. CURRENT GENETIC MEDICINE REPORTS 2017; 5:149-166. [PMID: 29805915 DOI: 10.1007/s40142-017-0130-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Purpose of review Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), remains a major public health threat globally. Several lines of evidence support a role for host genetic factors in resistance/susceptibility to TB disease and MTB infection. However, results across candidate gene and genome-wide association studies (GWAS) are largely inconsistent, so a cohesive genetic model underlying TB risk has not emerged. Recent Findings Despite the difficulties in identifying consistent genetic associations, genetic studies of TB and MTB infection have revealed a few well-documented loci. These well validated genes are presented in this review, but there remains a large gap in how these genes translate into better understanding of TB. To address this, we present a pathway based extension of standard association analyses, seeding the results with the best validated genes from candidate gene and GWAS studies. Summary Several pathways were significantly enriched using pathway analyses that may help to explain population patterns of TB risk. In conclusion, we advocate for novel approaches to the study of host genetic analysis of TB that extend traditional association approaches.
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Affiliation(s)
- Catherine M Stein
- Department of Population and Quantitative Health Sciences, Cleveland, OH.,Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH
| | - Lindsay Sausville
- Department of Population and Quantitative Health Sciences, Cleveland, OH
| | - Christian Wejse
- Dept of Infectious Diseases/Center for Global Health, Aarhus University, Aarhus, Denmark
| | - Rafal S Sobota
- The Ken and Ruth Davee Department of Neurology, Northwestern University, Chicago, IL
| | - Nicola M Zetola
- Division of Infectious Diseases, University of Pennsylvania, Philadelphia, PA 19104, USA.,Botswana-UPenn Partnership, Gaborone, Botswana.,Department of Medicine, University of Botswana, Gaborone, Botswana
| | - Philip C Hill
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - W Henry Boom
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH
| | - William K Scott
- Department of Human Genetics and Genomics, University of Miami School of Medicine, Miami, FL
| | - Giorgio Sirugo
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Cleveland, OH
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32
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Carrasco-Avino G, Riquelme I, Padilla O, Villaseca M, Aguayo FR, Corvalan AH. The conundrum of the Epstein-Barr virus-associated gastric carcinoma in the Americas. Oncotarget 2017; 8:75687-75698. [PMID: 29088902 PMCID: PMC5650457 DOI: 10.18632/oncotarget.18497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/29/2017] [Indexed: 02/07/2023] Open
Abstract
Epstein-Barr virus-associated gastric carcinoma shows a higher prevalence in the Americas than Asia. We summarize all studies of Epstein Barr virus-associated gastric carcinoma in the Americas, focusing on host characteristics, environmental associations and phylogeographic diversity of Epstein-Barr virus strains. In the Americas, the prevalence of Epstein Barr virus-associated gastric carcinoma is 11.4%, more frequent in males and portray predominantly diffuse-type histology. EBERs, EBNAs, BARTs and LMP are the highest expressed genes; their variations in healthy individuals may explain the phylogeographic diversity of Epstein-Barr virus across the region. Gastric cancer cases harbor exclusively the western genotype (subtype D and kept Xho I site), suggesting a disrupted co-evolution between the pathogen and its host. Epstein-Barr virus-associated gastric carcinoma molecular subtype cases from The Cancer Genome Atlas display PIK3CA gene mutations, amplification of JAK2, PD-L1 and PD-L2 and CpG island methylator phenotype, leading to more extensive methylation of host and viral genomes than any other subtypes from the study. Environmental conditions include negative- and positive- associations with being firstborn child and smoking, respectively. A marginal association with H. pylori has also been reported. Lymphoepithelioma-like carcinoma is associated with Epstein Barr virus in 80%-86% of cases, most of which have been included as part of Epstein Barr virus-associated gastric carcinoma series (prevalence 1.1%-7.6%). Whether these cases represent a variant of Epstein-Barr virus-associated gastric carcinoma is discussed. We propose novel research strategies to solve the conundrum of the high prevalence of Epstein-Barr virus-associated gastric carcinoma in the Americas.
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Affiliation(s)
- Gonzalo Carrasco-Avino
- Advanced Center for Chronic Diseases (ACCDIS), Pontificia Universidad Catolica de Chile, Santiago, Chile
- Department of Pathology, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Ismael Riquelme
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de la Frontera, Temuco, Chile
- Department of Pathology, Universidad de la Frontera, Temuco, Chile
| | - Oslando Padilla
- Department of Public Health, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Miguel Villaseca
- Department of Pathology, Universidad de la Frontera, Temuco, Chile
| | - Francisco R. Aguayo
- Advanced Center for Chronic Diseases (ACCDIS), Pontificia Universidad Catolica de Chile, Santiago, Chile
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Alejandro H. Corvalan
- Advanced Center for Chronic Diseases (ACCDIS), Pontificia Universidad Catolica de Chile, Santiago, Chile
- UC-Center for Investigational Oncology (CITO), Pontificia Universidad Catolica de Chile, Santiago, Chile
- Department of Hematology and Oncology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile
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33
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Nutrition and Helicobacter pylori: Host Diet and Nutritional Immunity Influence Bacterial Virulence and Disease Outcome. Gastroenterol Res Pract 2016; 2016:3019362. [PMID: 27688750 PMCID: PMC5027306 DOI: 10.1155/2016/3019362] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/03/2016] [Indexed: 12/19/2022] Open
Abstract
Helicobacter pylori colonizes the stomachs of greater than 50% of the world's human population making it arguably one of the most successful bacterial pathogens. Chronic H. pylori colonization results in gastritis in nearly all patients; however in a subset of people, persistent infection with H. pylori is associated with an increased risk for more severe disease outcomes including B-cell lymphoma of mucosal-associated lymphoid tissue (MALT lymphoma) and invasive adenocarcinoma. Research aimed at elucidating determinants that mediate disease progression has revealed genetic differences in both humans and H. pylori which increase the risk for developing gastric cancer. Furthermore, host diet and nutrition status have been shown to influence H. pylori-associated disease outcomes. In this review we will discuss how H. pylori is able to create a replicative niche within the hostile host environment by subverting and modifying the host-generated immune response as well as successfully competing for limited nutrients such as transition metals by deploying an arsenal of metal acquisition proteins and virulence factors. Lastly, we will discuss how micronutrient availability or alterations in the gastric microbiome may exacerbate negative disease outcomes associated with H. pylori colonization.
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34
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Sobota RS, Kodaman N, Mera R, Piazuelo MB, Bravo LE, Pazos A, Zabaleta J, Delgado AG, El-Rifai W, Morgan DR, Wilson KT, Correa P, Williams SM, Schneider BG. Epigenetic and genetic variation in GATA5 is associated with gastric disease risk. Hum Genet 2016; 135:895-906. [PMID: 27225266 PMCID: PMC4947561 DOI: 10.1007/s00439-016-1687-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/17/2016] [Indexed: 12/12/2022]
Abstract
Gastric cancer incidence varies considerably among populations, even those with comparable rates of Helicobacter pylori infection. To test the hypothesis that genetic variation plays a role in gastric disease, we assessed the relationship between genotypes and gastric histopathology in a Colombian study population, using a genotyping array of immune-related single nucleotide polymorphisms (SNPs). Two synonymous SNPs (rs6061243 and rs6587239) were associated with progression of premalignant gastric lesions in a dominant-effects model after correction for multiple comparisons (p = 2.63E-07 and p = 7.97E-07, respectively); effect sizes were β = -0.863 and β = -0.815, respectively, where β is an estimate of effect on histopathology scores, which ranged from 1 (normal) to 5 (dysplasia). In our replication cohort, a second Colombian population, both SNPs were associated with histopathology when additively modeled (β = -0.256, 95 % CI = -0.47, -0.039; and β = -0.239, 95 % CI = -0.45, -0.024), and rs6587239 was significantly associated in a dominant-effects model (β = -0.330, 95 % CI = -0.66, 0.00). Because promoter methylation of GATA5 has previously been associated with gastric cancer, we also tested for the association of methylation status with more advanced histopathology scores in our samples and found a significant relationship (p = 0.001). A multivariate regression model revealed that the effects of both the promoter methylation and the exonic SNPs in GATA5 were independent. A SNP-by-methylation interaction term was also significant. This interaction between GATA5 variants and GATA5 promoter methylation indicates that the association of either factor with gastric disease progression is modified by the other.
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Affiliation(s)
- Rafal S Sobota
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nuri Kodaman
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Robertino Mera
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - M Blanca Piazuelo
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - Luis E Bravo
- Department of Pathology, School of Medicine, Universidad del Valle, Cali 760043, Colombia
| | - Alvaro Pazos
- Department of Biology, University of Nariño, Pasto 520002, Colombia
| | - Jovanny Zabaleta
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Alberto G Delgado
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - Wael El-Rifai
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs, Veterans Affairs Tennessee Valley Healthcare System and Office of Medical Research, Nashville, TN, USA
| | - Douglas R Morgan
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - Keith T Wilson
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN 37232, USA
- Department of Veterans Affairs, Veterans Affairs Tennessee Valley Healthcare System and Office of Medical Research, Nashville, TN, USA
| | - Pelayo Correa
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - Scott M Williams
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Barbara G Schneider
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN 37232, USA
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Influenza A Virus and Influenza B Virus Can Induce Apoptosis via Intrinsic or Extrinsic Pathways and Also via NF-κB in a Time and Dose Dependent Manner. Biochem Res Int 2016; 2016:1738237. [PMID: 27042352 PMCID: PMC4793101 DOI: 10.1155/2016/1738237] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/07/2016] [Indexed: 12/22/2022] Open
Abstract
Influenza viruses are able to cause annual epidemics and pandemics due to their mutation rates and reassortment capabilities leading to antigenic shifts and drifts. To identify host response to influenza A and B viruses on A549 and MDCK II cells at low and high MOIs, expressions of MxA and caspases 3, 8, and 9 and BAD, TNFα, and IκBα genes were measured in the cells supernatants. H1N1 and H3N2 prefer to initially enhance the intrinsic pathway, determined by higher caspase 9 activity in MDCK II cells compared to caspase 8 activity and vice versa in A549 cells at different MOIs, while INF B prefers extrinsic pathway in A549 cells according to significant low or undetectable caspase 9 activity and high activity of caspase 8 but also can induce intrinsic pathway in MDCK II cells as determined by significant low or undetectable activity of caspase 8 and high caspase 9 activity at different MOIs; the considerable MxA expression was found in influenza A and B viruses infected A549 and MDCK II cells at low MOIs. In conclusion, influenza A and B viruses induced extrinsic and intrinsic apoptosis in parallel, and the induction was associated with viral infection in a dose dependent manner.
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Amieva M, Peek RM. Pathobiology of Helicobacter pylori-Induced Gastric Cancer. Gastroenterology 2016; 150:64-78. [PMID: 26385073 PMCID: PMC4691563 DOI: 10.1053/j.gastro.2015.09.004] [Citation(s) in RCA: 553] [Impact Index Per Article: 69.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/01/2015] [Accepted: 09/03/2015] [Indexed: 02/07/2023]
Abstract
Colonization of the human stomach by Helicobacter pylori and its role in causing gastric cancer is one of the richest examples of a complex relationship among human cells, microbes, and their environment. It is also a puzzle of enormous medical importance given the incidence and lethality of gastric cancer worldwide. We review recent findings that have changed how we view these relationships and affected the direction of gastric cancer research. For example, recent data have indicated that subtle mismatches between host and microbe genetic traits greatly affect the risk of gastric cancer. The ability of H pylori and its oncoprotein CagA to reprogram epithelial cells and activate properties of stemness show the sophisticated relationship between H pylori and progenitor cells in the gastric mucosa. The observation that cell-associated H pylori can colonize the gastric glands and directly affect precursor and stem cells supports these observations. The ability to mimic these interactions in human gastric organoid cultures as well as animal models will allow investigators to more fully unravel the extent of H pylori control on the renewing gastric epithelium. Finally, our realization that external environmental factors, such as dietary components and essential micronutrients, as well as the gastrointestinal microbiota, can change the balance between H pylori's activity as a commensal or a pathogen has provided direction to studies aimed at defining the full carcinogenic potential of this organism.
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Affiliation(s)
- Manuel Amieva
- Department of Microbiology and Immunology, Stanford University, Palo Alto, CA,Department of Pediatrics, Stanford University, Palo Alto, CA
| | - Richard M. Peek
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University, Nashville, TN,Department of Cancer Biology, Vanderbilt University, Nashville, TN
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37
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Abstract
The causative agent of human tuberculosis (TB), Mycobacterium tuberculosis, is an obligate pathogen that evolved to exclusively persist in human populations. For M. tuberculosis to transmit from person to person, it has to cause pulmonary disease. Therefore, M. tuberculosis virulence has likely been a significant determinant of the association between M. tuberculosis and humans. Indeed, the evolutionary success of some M. tuberculosis genotypes seems at least partially attributable to their increased virulence. The latter possibly evolved as a consequence of human demographic expansions. If co-evolution occurred, humans would have counteracted to minimize the deleterious effects of M. tuberculosis virulence. The fact that human resistance to infection has a strong genetic basis is a likely consequence of such a counter-response. The genetic architecture underlying human resistance to M. tuberculosis remains largely elusive. However, interactions between human genetic polymorphisms and M. tuberculosis genotypes have been reported. Such interactions are consistent with local adaptation and allow for a better understanding of protective immunity in TB. Future 'genome-to-genome' studies, in which locally associated human and M. tuberculosis genotypes are interrogated in conjunction, will help identify new protective antigens for the development of better TB vaccines.
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Affiliation(s)
- Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute and University of Basel, Basel, Switzerland
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38
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Shelburne SA, Ajami NJ, Chibucos MC, Beird HC, Tarrand J, Galloway-Peña J, Albert N, Chemaly RF, Ghantoji SS, Marsh L, Pemmaraju N, Andreeff M, Shpall EJ, Wargo JA, Rezvani K, Alousi A, Bruno VM, Futreal PA, Petrosino JF, Kontoyiannis DP. Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis. PLoS One 2015; 10:e0139851. [PMID: 26556047 PMCID: PMC4640583 DOI: 10.1371/journal.pone.0139851] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 09/17/2015] [Indexed: 12/19/2022] Open
Abstract
Disease can be conceptualized as the result of interactions between infecting microbe and holobiont, the combination of a host and its microbial communities. It is likely that genomic variation in the host, infecting microbe, and commensal microbiota are key determinants of infectious disease clinical outcomes. However, until recently, simultaneous, multiomic investigation of infecting microbe and holobiont components has rarely been explored. Herein, we characterized the infecting microbe, host, micro- and mycobiomes leading up to infection onset in a leukemia patient that developed invasive mucormycosis. We discovered that the patient was infected with a strain of the recently described Mucor velutinosus species which we determined was hypervirulent in a Drosophila challenge model and has a predisposition for skin dissemination. After completing the infecting M. velutinosus genome and genomes from four other Mucor species, comparative pathogenomics was performed and assisted in identifying 66 M. velutinosus-specific putatively secreted proteins, including multiple novel secreted aspartyl proteinases which may contribute to the unique clinical presentation of skin dissemination. Whole exome sequencing of the patient revealed multiple non-synonymous polymorphisms in genes critical to control of fungal proliferation, such as TLR6 and PTX3. Moreover, the patient had a non-synonymous polymorphism in the NOD2 gene and a missense mutation in FUT2, which have been linked to microbial dysbiosis and microbiome diversity maintenance during physiologic stress, respectively. In concert with host genetic polymorphism data, the micro- and mycobiome analyses revealed that the infection developed amid a dysbiotic microbiome with low α-diversity, dominated by staphylococci. Additionally, longitudinal mycobiome data showed that M. velutinosus DNA was detectable in oral samples preceding disease onset. Our genome-level study of the host-infecting microbe-commensal triad extends the concept of personalized genomic medicine to the holobiont-infecting microbe interface thereby offering novel opportunities for using synergistic genetic methods to increase understanding of infectious diseases pathogenesis and clinical outcomes.
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Affiliation(s)
- Samuel A. Shelburne
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Nadim J. Ajami
- The Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Marcus C. Chibucos
- Department of Microbiology & Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Hannah C. Beird
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jeffrey Tarrand
- Department of Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jessica Galloway-Peña
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Nathan Albert
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Roy F. Chemaly
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Shashank S. Ghantoji
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Lisa Marsh
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Naveen Pemmaraju
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Michael Andreeff
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Elizabeth J. Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jennifer A. Wargo
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Amin Alousi
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Vincent M. Bruno
- The Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Phillip A. Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- The Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Dimitrios P. Kontoyiannis
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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Patarčić I, Gelemanović A, Kirin M, Kolčić I, Theodoratou E, Baillie KJ, de Jong MD, Rudan I, Campbell H, Polašek O. The role of host genetic factors in respiratory tract infectious diseases: systematic review, meta-analyses and field synopsis. Sci Rep 2015; 5:16119. [PMID: 26524966 PMCID: PMC4630784 DOI: 10.1038/srep16119] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/09/2015] [Indexed: 12/17/2022] Open
Abstract
Host genetic factors have frequently been implicated in respiratory infectious diseases, often with inconsistent results in replication studies. We identified 386 studies from the total of 24,823 studies identified in a systematic search of four bibliographic databases. We performed meta-analyses of studies on tuberculosis, influenza, respiratory syncytial virus, SARS-Coronavirus and pneumonia. One single-nucleotide polymorphism from IL4 gene was significant for pooled respiratory infections (rs2070874; 1.66 [1.29–2.14]). We also detected an association of TLR2 gene with tuberculosis (rs5743708; 3.19 [2.03–5.02]). Subset analyses identified CCL2 as an additional risk factor for tuberculosis (rs1024611; OR = 0.79 [0.72–0.88]). The IL4-TLR2-CCL2 axis could be a highly interesting target for translation towards clinical use. However, this conclusion is based on low credibility of evidence - almost 95% of all identified studies had strong risk of bias or confounding. Future studies must build upon larger-scale collaborations, but also strictly adhere to the highest evidence-based principles in study design, in order to reduce research waste and provide clinically translatable evidence.
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Affiliation(s)
- Inga Patarčić
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Andrea Gelemanović
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Mirna Kirin
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Ivana Kolčić
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Evropi Theodoratou
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
| | - Kenneth J Baillie
- Roslin Institute, University of Edinburgh, Midlothian, UK.,Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Menno D de Jong
- Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
| | - Ozren Polašek
- Department of Public Health, University of Split School of Medicine, Split, Croatia.,Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
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40
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Helicobacter pylori: Genomic Insight into the Host-Pathogen Interaction. Int J Genomics 2015; 2015:386905. [PMID: 25722969 PMCID: PMC4334614 DOI: 10.1155/2015/386905] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/09/2015] [Indexed: 12/18/2022] Open
Abstract
The advent of genomic analyses has revolutionized the study of human health. Infectious disease research in particular has experienced an explosion of bacterial genomic, transcriptomic, and proteomic data complementing the phenotypic methods employed in traditional bacteriology. Together, these techniques have revealed novel virulence determinants in numerous pathogens and have provided information for potential chemotherapeutics. The bacterial pathogen, Helicobacter pylori, has been recognized as a class 1 carcinogen and contributes to chronic inflammation within the gastric niche. Genomic analyses have uncovered remarkable coevolution between the human host and H. pylori. Perturbation of this coevolution results in dysregulation of the host-pathogen interaction, leading to oncogenic effects. This review discusses the relationship of H. pylori with the human host and environment and the contribution of each of these factors to disease progression, with an emphasis on features that have been illuminated by genomic tools.
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41
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Hill JM, Clement C, Zhao Y, Lukiw WJ. Induction of the pro-inflammatory NF-kB-sensitive miRNA-146a by human neurotrophic viruses. Front Microbiol 2015; 6:43. [PMID: 25691883 PMCID: PMC4315103 DOI: 10.3389/fmicb.2015.00043] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 01/12/2015] [Indexed: 01/13/2023] Open
Affiliation(s)
- James M Hill
- Departments of Microbiology and Pharmacology, Louisiana State University Health Science Center New Orleans, LA, USA ; LSU Neuroscience Center and Department of Ophthalmology, Louisiana State University Health Science Center New Orleans, LA, USA
| | - Christian Clement
- Infectious Diseases, Experimental Therapeutics and Human Toxicology Lab, Department of Natural Sciences, Southern University at New Orleans New Orleans, LA, USA
| | - Yuhai Zhao
- LSU Neuroscience Center and Department of Ophthalmology, Louisiana State University Health Science Center New Orleans, LA, USA
| | - Walter J Lukiw
- LSU Neuroscience Center and Department of Ophthalmology, Louisiana State University Health Science Center New Orleans, LA, USA ; Department of Neurology, Louisiana State University Health Science Center New Orleans, LA, USA
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42
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Coscolla M, Gagneux S. Consequences of genomic diversity in Mycobacterium tuberculosis. Semin Immunol 2014; 26:431-44. [PMID: 25453224 PMCID: PMC4314449 DOI: 10.1016/j.smim.2014.09.012] [Citation(s) in RCA: 291] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 11/29/2022]
Abstract
The causative agent of human tuberculosis, Mycobacterium tuberculosis complex (MTBC), comprises seven phylogenetically distinct lineages associated with different geographical regions. Here we review the latest findings on the nature and amount of genomic diversity within and between MTBC lineages. We then review recent evidence for the effect of this genomic diversity on mycobacterial phenotypes measured experimentally and in clinical settings. We conclude that overall, the most geographically widespread Lineage 2 (includes Beijing) and Lineage 4 (also known as Euro-American) are more virulent than other lineages that are more geographically restricted. This increased virulence is associated with delayed or reduced pro-inflammatory host immune responses, greater severity of disease, and enhanced transmission. Future work should focus on the interaction between MTBC and human genetic diversity, as well as on the environmental factors that modulate these interactions.
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Affiliation(s)
- Mireia Coscolla
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland; University of Basel, Petersplatz 1, Basel 4003, Switzerland.
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43
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Álvarez-Castro JM, Yang RC. One century later: dissecting genetic effects for looking over old paradigms. Front Genet 2014; 5:396. [PMID: 25429301 PMCID: PMC4228978 DOI: 10.3389/fgene.2014.00396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 10/27/2014] [Indexed: 11/17/2022] Open
Affiliation(s)
| | - Rong-Cai Yang
- Department of Agricultural, Food and Nutritional Science, University of AlbertaEdmonton, AB, Canada
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44
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Alfaro-Núñez A, Frost Bertelsen M, Bojesen AM, Rasmussen I, Zepeda-Mendoza L, Tange Olsen M, Gilbert MTP. Global distribution of Chelonid fibropapilloma-associated herpesvirus among clinically healthy sea turtles. BMC Evol Biol 2014; 14:206. [PMID: 25342462 PMCID: PMC4219010 DOI: 10.1186/s12862-014-0206-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 09/21/2014] [Indexed: 01/09/2023] Open
Abstract
Background Fibropapillomatosis (FP) is a neoplastic disease characterized by cutaneous tumours that has been documented to infect all sea turtle species. Chelonid fibropapilloma-associated herpesvirus (CFPHV) is believed to be the aetiological agent of FP, based principally on consistent PCR-based detection of herpesvirus DNA sequences from FP tumours. We used a recently described PCR-based assay that targets 3 conserved CFPHV genes, to survey 208 green turtles (Chelonia mydas). This included both FP tumour exhibiting and clinically healthy individuals. An additional 129 globally distributed clinically healthy individual sea turtles; representing four other species were also screened. Results CFPHV DNA sequences were obtained from 37/37 (100%) FP exhibiting green turtles, and 45/300 (15%) clinically healthy animals spanning all five species. Although the frequency of infected individuals per turtle population varied considerably, most global populations contained at least one CFPHV positive individual, with the exception of various turtle species from the Arabian Gulf, Northern Indian Ocean and Puerto Rico. Haplotype analysis of the different gene markers clustered the CFPHV DNA sequences for two of the markers (UL18 and UL22) in turtles from Turks and Caicos separate to all others, regardless of host species or geographic origin. Conclusion Presence of CFPHV DNA within globally distributed samples for all five species of sea turtle was confirmed. While 100% of the FP exhibiting green turtles yielded CFPHV sequences, surprisingly, so did 15% of the clinically healthy turtles. We hypothesize that turtle populations with zero (0%) CFPHV frequency may be attributed to possible environmental differences, diet and/or genetic resistance in these individuals. Our results provide first data on the prevalence of CFPHV among seemingly healthy turtles; a factor that may not be directly correlated to the disease incidence, but may suggest of a long-term co-evolutionary latent infection interaction between CFPHV and its turtle-host across species. Finally, computational analysis of amino acid variants within the Turks and Caicos samples suggest potential functional importance in a substitution for marker UL18 that encodes the major capsid protein gene, which potentially could explain differences in pathogenicity. Nevertheless, such a theory remains to be validated by further research. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0206-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alonzo Alfaro-Núñez
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | | | - Anders Miki Bojesen
- Department of Veterinary Disease Biology, Veterinary Clinical Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Isabel Rasmussen
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | - Lisandra Zepeda-Mendoza
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | - Morten Tange Olsen
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
| | - Marcus Thomas Pius Gilbert
- Centre for GeoGenetics, Section for Evolutionary Genomics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark. .,Trace and Environmental DNA Laboratory, School of Environment and Agriculture, Curtin University, Perth, Western Australia, 6845, Australia.
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