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Borghesi A. Life-threatening infections in human newborns: Reconciling age-specific vulnerability and interindividual variability. Cell Immunol 2024; 397-398:104807. [PMID: 38232634 DOI: 10.1016/j.cellimm.2024.104807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
In humans, the interindividual variability of clinical outcome following exposure to a microorganism is immense, ranging from silent infection to life-threatening disease. Age-specific immune responses partially account for the high incidence of infection during the first 28 days of life and the related high mortality at population level. However, the occurrence of life-threatening disease in individual newborns remains unexplained. By contrast, inborn errors of immunity and their immune phenocopies are increasingly being discovered in children and adults with life-threatening viral, bacterial, mycobacterial and fungal infections. There is a need for convergence between the fields of neonatal immunology, with its in-depth population-wide characterization of newborn-specific immune responses, and clinical immunology, with its investigations of infections in patients at the cellular and molecular levels, to facilitate identification of the mechanisms of susceptibility to infection in individual newborns and the design of novel preventive and therapeutic strategies.
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Affiliation(s)
- Alessandro Borghesi
- Neonatal Intensive Care Unit, San Matteo Research Hospital, Pavia, EU, Italy; School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland.
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2
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Dorfman B, Marcos-Hadad E, Tadmor-Levi R, David L. Disease resistance and infectivity of virus susceptible and resistant common carp strains. Sci Rep 2024; 14:4677. [PMID: 38409362 PMCID: PMC10897132 DOI: 10.1038/s41598-024-55133-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 02/20/2024] [Indexed: 02/28/2024] Open
Abstract
Infectious diseases challenge health and welfare of humans and animals. Unlike for humans, breeding of genetically resistant animals is a sustainable solution, also providing unique research opportunities. Chances to survive a disease are improved by disease resistance, but depend also on chances to get infected and infect others. Considerable knowledge exists on chances of susceptible and resistant animals to survive a disease, yet, almost none on their infectivity and if and how resistance and infectivity correlate. Common carp (Cyprinus carpio) is widely produced in aquaculture, suffering significantly from a disease caused by cyprinid herpes virus type 3 (CyHV-3). Here, the infectivity of disease-resistant and susceptible fish types was tested by playing roles of shedders (infecting) and cohabitants (infected) in all four type-role combinations. Resistant shedders restricted spleen viral load and survived more than susceptible ones. However, mortality of susceptible cohabitants infected by resistant shedders was lower than that of resistant cohabitants infected by susceptible shedders. Virus levels in water were lower in tanks with resistant shedders leading to lower spleen viral loads in cohabitants. Thus, we empirically demonstrated that disease resistant fish survive better and infect less, with implications to epidemiology in general and to the benefit of aquaculture production.
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Affiliation(s)
- Batya Dorfman
- Department of Animal Sciences, RH Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Evgeniya Marcos-Hadad
- Department of Animal Sciences, RH Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Roni Tadmor-Levi
- Department of Animal Sciences, RH Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Lior David
- Department of Animal Sciences, RH Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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3
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Tang X, Xiang L, Li Q, Shao Y, Wan L, Zhao D, Li X, Wu S, Wang H, Li D, Ding K. Molecular evolution in different subtypes of multifocal hepatocellular carcinoma. Hepatol Int 2023; 17:1429-1443. [PMID: 37273168 DOI: 10.1007/s12072-023-10551-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/07/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Multifocal hepatocellular carcinoma (MF-HCC) accounts for > 40% of HCCs, exhibiting a poor prognosis than single primary HCCs. Characterizing molecular features including dynamic changes of mutational signature along with clonal evolution, intrahepatic metastatic timing, and genetic footprint in the preneoplastic stage underlying different subtypes of MF-HCC are important for understanding their molecular evolution and developing a precision management strategy. METHODS We conducted whole-exome sequencing in 74 tumor samples from spatially distinct regions in 35 resected lesions and adjacent noncancerous tissues from 11 patients, 15 histologically confirmed preneoplastic lesions, and six samples from peripheral blood mononuclear cells. A previously published MF-HCC cohort (n = 9) was included as an independent validation dataset. We combined well-established approaches to investigate tumor heterogeneity, intrahepatic metastatic timing, and molecular footprints in different subtypes of MF-HCCs. RESULTS We classified MF-HCCs patients into three subtypes, including intrahepatic metastasis, multicentric occurrence, and mixed intrahepatic metastasis and multicentric occurrence. The dynamic changes in mutational signatures between tumor subclonal expansions demonstrated varied etiologies (e.g., aristolochic acid exposure) underlying the clonal progression in different MF-HCC subtypes. Furthermore, the clonal evolution in intrahepatic metastasis exhibited an early metastatic seeding at 10-4-0.01 cm3 in primary tumor volume (below the limits of clinical detection), further validated in an independent cohort. In addition, mutational footprints in the preneoplastic lesions for multicentric occurrence patients revealed common preneoplastic arising clones, evidently being ancestors of different tumor lesions. CONCLUSION Our study comprehensively characterized the varied tumor clonal evolutionary history underlying different subtypes of MF-HCC and provided important implications for optimizing personalized clinical management for MF-HCC.
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Affiliation(s)
- Xia Tang
- Shanghai Pudong Hospital and Pudong Medical Center of Fudan University, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Lei Xiang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Qingshu Li
- Department of Pathology, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Yue Shao
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Li Wan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Dachun Zhao
- Department of Pathology, Peking Union Medical College Hospital, Beijing, 100730, People's Republic of China
| | - Xiaoyuan Li
- Department of Oncology, Peking Union Medical College Hospital, Beijing, 100730, People's Republic of China
| | - Songfeng Wu
- Beijing Qinglian Biotech Co., Ltd, Beijing, 102206, People's Republic of China
| | - Haijian Wang
- Shanghai Pudong Hospital and Pudong Medical Center of Fudan University, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Dewei Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China.
- Hepatobiliary and Pancreatic Cancer Center, Chongqing University Cancer Hospital, Chongqing, 400030, People's Republic of China.
| | - Keyue Ding
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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Schulz VE, Tuff JF, Tough RH, Lewis L, Chimukangara B, Garrett N, Abdool Karim Q, Abdool Karim SS, McKinnon LR, Kharsany ABM, McLaren PJ. Host genetic variation at a locus near CHD1L impacts HIV sequence diversity in a South African population. J Virol 2023; 97:e0095423. [PMID: 37747237 PMCID: PMC10617395 DOI: 10.1128/jvi.00954-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/04/2023] [Indexed: 09/26/2023] Open
Abstract
IMPORTANCE It has been previously shown that genetic variants near CHD1L on chromosome 1 are associated with reduced HIV VL in African populations. However, the impact of these variants on viral diversity and how they restrict viral replication are unknown. We report on a regional association analysis in a South African population and show evidence of selective pressure by variants near CHD1L on HIV RT and gag. Our findings provide further insight into how genetic variability at this locus contributes to host control of HIV in a South African population.
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Affiliation(s)
- Vanessa E. Schulz
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jeffrey F. Tuff
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Riley H. Tough
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Lara Lewis
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Benjamin Chimukangara
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
- Department of Virology, University of KwaZulu-Natal, Durban, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Lyle R. McKinnon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Ayesha B. M. Kharsany
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Science, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Paul J. McLaren
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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D’Orso I, Forst CV. Mathematical Models of HIV-1 Dynamics, Transcription, and Latency. Viruses 2023; 15:2119. [PMID: 37896896 PMCID: PMC10612035 DOI: 10.3390/v15102119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/10/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
HIV-1 latency is a major barrier to curing infections with antiretroviral therapy and, consequently, to eliminating the disease globally. The establishment, maintenance, and potential clearance of latent infection are complex dynamic processes and can be best described with the help of mathematical models followed by experimental validation. Here, we review the use of viral dynamics models for HIV-1, with a focus on applications to the latent reservoir. Such models have been used to explain the multi-phasic decay of viral load during antiretroviral therapy, the early seeding of the latent reservoir during acute infection and the limited inflow during treatment, the dynamics of viral blips, and the phenomenon of post-treatment control. Finally, we discuss that mathematical models have been used to predict the efficacy of potential HIV-1 cure strategies, such as latency-reversing agents, early treatment initiation, or gene therapies, and to provide guidance for designing trials of these novel interventions.
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Affiliation(s)
- Iván D’Orso
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Christian V. Forst
- Department of Genetics and Genomic Sciences, Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Xu ZM, Naret O, Oumelloul MA, Fellay J. G2GSnake: a Snakemake workflow for host-pathogen genomic association studies. BIOINFORMATICS ADVANCES 2023; 3:vbad142. [PMID: 37840906 PMCID: PMC10576169 DOI: 10.1093/bioadv/vbad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023]
Abstract
Summary Joint analyses of paired host and pathogen genome sequences have the potential to enhance our understanding of host-pathogen interactions. A systematic approach to conduct such a joint analysis is through a "genome-to-genome" (G2G) association study, which involves testing for associations between all host and pathogen genetic variants. Significant associations reveal host genetic factors that might drive pathogen variation, highlighting biological mechanisms likely to be involved in host control and pathogen escape. Here, we present a Snakemake workflow that allows researchers to conduct G2G studies in a reproducible and scalable manner. In addition, we have developed an intuitive R Shiny application that generates custom summaries of the results, enabling users to derive relevant insights. Availability and implementation G2GSnake is freely available at: https://github.com/zmx21/G2GSnake under the MIT license.
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Affiliation(s)
- Zhi Ming Xu
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Olivier Naret
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Mariam Ait Oumelloul
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
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Movassagh M, Schiff SJ, Paulson JN. mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation. Bioinformatics 2023; 39:btad565. [PMID: 37707523 PMCID: PMC10516520 DOI: 10.1093/bioinformatics/btad565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/25/2023] [Accepted: 09/11/2023] [Indexed: 09/15/2023] Open
Abstract
MOTIVATION In recent years, significant strides have been made in the field of genomics, with the commencement of large-scale studies aimed at collecting host mutational profiles and microbiome data. The amalgamation of host gene mutational profiles in both healthy and diseased subjects with microbial abundance data holds immense promise in providing insights into several crucial research questions, including the development and progression of diseases, as well as individual responses to therapeutic interventions. With the advent of sequencing methods such as 16s ribosomal RNA (rRNA) sequencing and whole genome sequencing, there is increasing evidence of interplay of human genetics and microbial communities. Quantitative trait loci associated with microbial abundance (mbQTLs), are genetic variants that influence the abundance of microbial populations within the host. RESULTS Here, we introduce mbQTL, the first R package integrating 16S ribosomal RNA (rRNA) sequencing and single-nucleotide variation (SNV) and single-nucleotide polymorphism (SNP) data. We describe various statistical methods implemented for the identification of microbe-SNV pairs, relevant statistical measures, and plot functionality for interpretation. AVAILABILITY AND IMPLEMENTATION mbQTL is available on bioconductor at https://bioconductor.org/packages/mbQTL/.
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Affiliation(s)
- Mercedeh Movassagh
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, United States
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, United States
| | - Steven J Schiff
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, United States
| | - Joseph N Paulson
- Department of Data Sciences, N-Power Medicine, Redwood City, CA 94063, United States
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8
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McLaren PJ. A new look at human leukocyte antigen variation in HIV; functional clustering to enhance power for discovery of host genetic associations. AIDS 2023; 37:1757-1758. [PMID: 37534725 DOI: 10.1097/qad.0000000000003636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Affiliation(s)
- Paul J McLaren
- Sexually Transmitted and Bloodborne Infections Division, National Microbiology Laboratories, Public Health Agency of Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
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Zucco AG, Bennedbæk M, Ekenberg C, Gabrielaite M, Leung P, Polizzotto MN, Kan V, Murray DD, Lundgren JD, MacPherson CR. Associations of functional human leucocyte antigen class I groups with HIV viral load in a heterogeneous cohort. AIDS 2023; 37:1643-1650. [PMID: 37534724 PMCID: PMC10399941 DOI: 10.1097/qad.0000000000003557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
OBJECTIVE Human leucocyte antigen (HLA) class I alleles are the main host genetic factors involved in controlling HIV-1 viral load (VL). Nevertheless, HLA diversity has proven a significant challenge in association studies. We assessed how accounting for binding affinities of HLA class I alleles to HIV-1 peptides facilitate association testing of HLA with HIV-1 VL in a heterogeneous cohort. DESIGN Cohort from the Strategic Timing of AntiRetroviral Treatment (START) study. METHODS We imputed HLA class I alleles from host genetic data (2546 HIV+ participants) and sampled immunopeptidomes from 2079 host-paired viral genomes (targeted amplicon sequencing). We predicted HLA class I binding affinities to HIV-1 and unspecific peptides, grouping alleles into functional clusters through consensus clustering. These functional HLA class I clusters were used to test associations with HIV VL. RESULTS We identified four clades totaling 30 HLA alleles accounting for 11.4% variability in VL. We highlight HLA-B∗57:01 and B∗57:03 as functionally similar but yet overrepresented in distinct ethnic groups, showing when combined a protective association with HIV+ VL (log, β -0.25; adj. P-value < 0.05). We further demonstrate only a slight power reduction when using unspecific immunopeptidomes, facilitating the use of the inferred functional HLA groups in other studies. CONCLUSION The outlined computational approach provides a robust and efficient way to incorporate HLA function and peptide diversity, aiding clinical association studies in heterogeneous cohorts. To facilitate access to the proposed methods and results we provide an interactive application for exploring data.
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Affiliation(s)
| | - Marc Bennedbæk
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut
| | | | - Migle Gabrielaite
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Mark N. Polizzotto
- Clinical Hub for Interventional Research, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Virginia Kan
- George Washington University, Veterans Affairs Medical Center, Washington, DC, USA
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Demirjian C, Vailleau F, Berthomé R, Roux F. Genome-wide association studies in plant pathosystems: success or failure? TRENDS IN PLANT SCIENCE 2023; 28:471-485. [PMID: 36522258 DOI: 10.1016/j.tplants.2022.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/28/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Harnessing natural genetic variation is an established alternative to artificial genetic variation for investigating the molecular dialog between partners in plant pathosystems. Herein, we review the successes of genome-wide association studies (GWAS) in both plants and pathogens. While GWAS in plants confirmed that the genetic architecture of disease resistance is polygenic, dynamic during the infection kinetics, and dependent on the environment, GWAS shortened the time of identification of quantitative trait loci (QTLs) and revealed both complex epistatic networks and a genetic architecture dependent upon the geographical scale. A similar picture emerges from the few GWAS in pathogens. In addition, the ever-increasing number of functionally validated QTLs has revealed new molecular plant defense mechanisms and pathogenicity determinants. Finally, we propose recommendations to better decode the disease triangle.
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Affiliation(s)
- Choghag Demirjian
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Fabienne Vailleau
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Richard Berthomé
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Fabrice Roux
- LIPME, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France.
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Gabrielaite M, Bennedbæk M, Rasmussen MS, Kan V, Furrer H, Flisiak R, Losso M, Lundgren JD, Marvig RL. Deep-sequencing of viral genomes from a large and diverse cohort of treatment-naive HIV-infected persons shows associations between intrahost genetic diversity and viral load. PLoS Comput Biol 2023; 19:e1010756. [PMID: 36595537 PMCID: PMC9838853 DOI: 10.1371/journal.pcbi.1010756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/13/2023] [Accepted: 11/23/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Infection with human immunodeficiency virus type 1 (HIV) typically results from transmission of a small and genetically uniform viral population. Following transmission, the virus population becomes more diverse because of recombination and acquired mutations through genetic drift and selection. Viral intrahost genetic diversity remains a major obstacle to the cure of HIV; however, the association between intrahost diversity and disease progression markers has not been investigated in large and diverse cohorts for which the majority of the genome has been deep-sequenced. Viral load (VL) is a key progression marker and understanding of its relationship to viral intrahost genetic diversity could help design future strategies for HIV monitoring and treatment. METHODS We analysed deep-sequenced viral genomes from 2,650 treatment-naive HIV-infected persons to measure the intrahost genetic diversity of 2,447 genomic codon positions as calculated by Shannon entropy. We tested for associations between VL and amino acid (AA) entropy accounting for sex, age, race, duration of infection, and HIV population structure. RESULTS We confirmed that the intrahost genetic diversity is highest in the env gene. Furthermore, we showed that mean Shannon entropy is significantly associated with VL, especially in infections of >24 months duration. We identified 16 significant associations between VL (p-value<2.0x10-5) and Shannon entropy at AA positions which in our association analysis explained 13% of the variance in VL. Finally, equivalent analysis based on variation in HIV consensus sequences explained only 2% of VL variance. CONCLUSIONS Our results elucidate that viral intrahost genetic diversity is associated with VL and could be used as a better disease progression marker than HIV consensus sequence variants, especially in infections of longer duration. We emphasize that viral intrahost diversity should be considered when studying viral genomes and infection outcomes. TRIAL REGISTRATION Samples included in this study were derived from participants who consented in the clinical trial, START (NCT00867048) (23), run by the International Network for Strategic Initiatives in Global HIV Trials (INSIGHT). All the participant sites are listed here: http://www.insight-trials.org/start/my_phpscript/participating.php?by=site.
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Affiliation(s)
- Migle Gabrielaite
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
- * E-mail: (MG); (MB)
| | - Marc Bennedbæk
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (MG); (MB)
| | - Malthe Sebro Rasmussen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
- Section of Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Virginia Kan
- Veterans Affairs Medical Center and The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, United States of America
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Bialystok, Bialystok, Poland
| | - Marcelo Losso
- Hospital General De Agudos J M Ramos Mejía, Buenos Aires, Argentina
| | - Jens D. Lundgren
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Rasmus L. Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
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Amandine C, Ebert D, Stukenbrock E, Rodríguez de la Vega RC, Tiffin P, Croll D, Tellier A. Unraveling coevolutionary dynamics using ecological genomics. Trends Genet 2022; 38:1003-1012. [PMID: 35715278 DOI: 10.1016/j.tig.2022.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
Abstract
Coevolutionary interactions, from the delicate co-dependency in mutualistic interactions to the antagonistic relationship of hosts and parasites, are a ubiquitous driver of adaptation. Surprisingly, little is known about the genomic processes underlying coevolution in an ecological context. However, species comprise genetically differentiated populations that interact with temporally variable abiotic and biotic environments. We discuss the recent advances in coevolutionary theory and genomics as well as shortcomings, to identify coevolving genes that take into account this spatial and temporal variability of coevolution, and propose a practical guide to understand the dynamic of coevolution using an ecological genomics lens.
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Affiliation(s)
- Cornille Amandine
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France.
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Eva Stukenbrock
- Max Planck Institute for Terrestrial Microbiology, Max Planck Research Group, Fungal Biodiversity, Marburg, Germany
| | | | - Peter Tiffin
- Department of Plant and Microbial Biology, 250 Biological Sciences, 1445 Gortner Ave., University of Minnesota, Saint Paul, MN 55108, USA
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland.
| | - Aurélien Tellier
- Population Genetics, Department of Life Science Systems, Technical University of Munich, Liesel-Beckman-Str. 2, 85354 Freising, Germany.
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13
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Hammer C, Mellman I. Coming of Age: Human Genomics and the Cancer-Immune Set Point. Cancer Immunol Res 2022; 10:674-679. [PMID: 35471657 PMCID: PMC9306278 DOI: 10.1158/2326-6066.cir-21-1017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/07/2022] [Accepted: 03/15/2022] [Indexed: 01/07/2023]
Abstract
Cancer is largely a disease of the tumor cell genome. As a result, the majority of genetics research in oncology has concentrated on the role of tumor somatic mutations, as well as inherited risk variants, in disease susceptibility and response to targeted treatments. The advent and success of cancer immunotherapies, however, have opened new perspectives for the investigation of the role of inherited genetic variation in codetermining outcome and safety. It is increasingly likely that the entirety of germline genetic variation involved in regulating immune responses accounts for a significant fraction of the observed variability in responses to cancer immunotherapies. Although germline genetic data from patients treated with cancer immunotherapies are still scarce, this line of research benefits from a vast body of knowledge derived from studies into autoimmune and infectious disease phenotypes, thus not requiring a start from a blank slate. Here, we discuss how a thorough investigation of genomic variation relevant for individuals' variability in (auto)immune responses can contribute to the discovery of novel treatment approaches and drug targets, and yield predictive biomarkers to stratify cancer patient populations in precision and personalized medicine settings.
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Affiliation(s)
- Christian Hammer
- Genentech, South San Francisco, California.,Corresponding Author: Christian Hammer, Genentech, Inc., South San Francisco, CA 94080. Phone: 650-452-9622; E-mail:
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14
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Muccini C, Guffanti M, Spagnuolo V, Cernuschi M, Galli L, Bigoloni A, Galli A, Poli A, Racca S, Castagna A. Association between low levels of HIV-1 DNA and HLA class I molecules in chronic HIV-1 infection. PLoS One 2022; 17:e0265348. [PMID: 35290394 PMCID: PMC8923435 DOI: 10.1371/journal.pone.0265348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/28/2022] [Indexed: 11/19/2022] Open
Abstract
Background HLA-B27 and -B57 were found in people with low levels of HIV-1 DNA, suggesting that HLA class I molecules may influence the size of HIV-1 reservoir. Aim of the study was to explore the association between HLA class I molecules and HIV-1 DNA in people with chronic HIV-1 infection. Methods Post-hoc analysis of the APACHE trial, on adults with chronic HIV-1 infection, prolonged suppressive antiretroviral therapy and good immunological profile. HIV-1 DNA was quantified in peripheral blood mononuclear cells (PBMCs); HLA-A, -B and -C were tested on genomic DNA. Crude odds ratios (OR) with their respective 95% Wald confidence intervals (95% CIs) were estimated by univariable logistic regression for HLAs with a p-value <0.10. Results We found 78 and 18 patients with HIV-1 DNA ≥100 copies/106PBMCs and with HIV-1 DNA <100 copies/106PBMCs, respectively. HLA-A24 was present in 21 (29.6%) participants among subjects with HIV-1 DNA ≥100 copies/106PBMCs and 1 (5.9%) among those with HIV-1 DNA <100 copies/106PBMCs (OR = 5.67, 95%CI = 0.79–46.03; p = 0.105); HLA-B39 was present in 1 (1.4%) with HIV-1 DNA ≥100 copies/106PBMCs and in 3 (17.6%) with HIV-1 DNA <100 copies/106PBMCs (OR = 13.71, 95%CI = 1.33–141.77; p = 0.028) and HLA-B55 in 3 (4.2%) and 3 (17.6%), respectively (OR = 4.43, 95%CI = 0.81–24.29; p = 0.087). All the three patients with HLA-B39 and HIV-1 DNA <100 copies/106PBMCs did not have HLA-A24. Conclusions In patients with HIV-1 infection who maintained a good virological and immunological profile, HLA-B39 and -B55 may be associated with lower levels of HIV-1 DNA.
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Affiliation(s)
- Camilla Muccini
- Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
- * E-mail:
| | - Monica Guffanti
- Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Vincenzo Spagnuolo
- Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Massimo Cernuschi
- Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Galli
- Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alba Bigoloni
- Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Galli
- Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Poli
- Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sara Racca
- Laboratory of Microbiology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Antonella Castagna
- Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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15
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The major genetic risk factor for severe COVID-19 is associated with protection against HIV. Proc Natl Acad Sci U S A 2022; 119:2116435119. [PMID: 35193979 PMCID: PMC8892305 DOI: 10.1073/pnas.2116435119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2022] [Indexed: 12/11/2022] Open
Abstract
There are genetic risk factors that influence the outcome of COVID-19 [COVID-19 Host Genetics Initiative, Nature 600, 472–477 (2021)]. The major genetic risk factor for severe COIVD-19 resides on chromosome 3 and is inherited from Neandertals [H. Zeberg, S. Pääbo, Nature 587, 610–612 (2020)]. The risk-associated DNA segment modulates the expression of several chemokine receptors, among them CCR5, a coreceptor for HIV which is down-regulated in carriers of the COVID-19 risk haplotype. Here I show that carriers of the risk variant have an ∼27% lower risk of HIV infection.
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16
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Buckley SJ, Harvey RJ. Lessons Learnt From Using the Machine Learning Random Forest Algorithm to Predict Virulence in Streptococcus pyogenes. Front Cell Infect Microbiol 2022; 11:809560. [PMID: 35004362 PMCID: PMC8739889 DOI: 10.3389/fcimb.2021.809560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
Group A Streptococcus is a globally significant human pathogen. The extensive variability of the GAS genome, virulence phenotypes and clinical outcomes, render it an excellent candidate for the application of genotype-phenotype association studies in the era of whole-genome sequencing. We have catalogued the distribution and diversity of the transcription regulators of GAS, and employed phylogenetics, concordance metrics and machine learning (ML) to test for associations. In this review, we communicate the lessons learnt in the context of the recent bacteria genotype-phenotype association studies of others that have utilised both genome-wide association studies (GWAS) and ML. We envisage a promising future for the application GWAS in bacteria genotype-phenotype association studies and foresee the increasing use of ML. However, progress in this field is hindered by several outstanding bottlenecks. These include the shortcomings that are observed when GWAS techniques that have been fine-tuned on human genomes, are applied to bacterial genomes. Furthermore, there is a deficit of easy-to-use end-to-end workflows, and a lag in the collection of detailed phenotype and clinical genomic metadata. We propose a novel quality control protocol for the collection of high-quality GAS virulence phenotype coupled to clinical outcome data. Finally, we incorporate this protocol into a workflow for testing genotype-phenotype associations using ML and ‘linked’ patient-microbe genome sets that better represent the infection event.
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Affiliation(s)
- Sean J Buckley
- School of Health and Behavioural Sciences, University of the Sunshine Coast, Maroochydore DC, QLD, Australia
| | - Robert J Harvey
- School of Health and Behavioural Sciences, University of the Sunshine Coast, Maroochydore DC, QLD, Australia.,Sunshine Coast Health Institute, Birtinya, QLD, Australia
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17
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Band G, Leffler EM, Jallow M, Sisay-Joof F, Ndila CM, Macharia AW, Hubbart C, Jeffreys AE, Rowlands K, Nguyen T, Gonçalves S, Ariani CV, Stalker J, Pearson RD, Amato R, Drury E, Sirugo G, d'Alessandro U, Bojang KA, Marsh K, Peshu N, Saelens JW, Diakité M, Taylor SM, Conway DJ, Williams TN, Rockett KA, Kwiatkowski DP. Malaria protection due to sickle haemoglobin depends on parasite genotype. Nature 2021; 602:106-111. [PMID: 34883497 PMCID: PMC8810385 DOI: 10.1038/s41586-021-04288-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022]
Abstract
Host genetic factors can confer resistance against malaria1, raising the question of whether this has led to evolutionary adaptation of parasite populations. Here we searched for association between candidate host and parasite genetic variants in 3,346 Gambian and Kenyan children with severe malaria caused by Plasmodium falciparum. We identified a strong association between sickle haemoglobin (HbS) in the host and three regions of the parasite genome, which is not explained by population structure or other covariates, and which is replicated in additional samples. The HbS-associated alleles include nonsynonymous variants in the gene for the acyl-CoA synthetase family member2–4PfACS8 on chromosome 2, in a second region of chromosome 2, and in a region containing structural variation on chromosome 11. The alleles are in strong linkage disequilibrium and have frequencies that covary with the frequency of HbS across populations, in particular being much more common in Africa than other parts of the world. The estimated protective effect of HbS against severe malaria, as determined by comparison of cases with population controls, varies greatly according to the parasite genotype at these three loci. These findings open up a new avenue of enquiry into the biological and epidemiological significance of the HbS-associated polymorphisms in the parasite genome and the evolutionary forces that have led to their high frequency and strong linkage disequilibrium in African P. falciparum populations. A strong association has been found between three regions of the Plasmodium falciparum genome and sickle haemoglobin in children with severe malaria, suggesting parasites have adapted to overcome natural host immunity.
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Affiliation(s)
- Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA.
| | - Ellen M Leffler
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Muminatou Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Edward Francis Small Teaching Hospital (formerly Royal Victoria Teaching Hospital), Independence Drive, Banjul, The Gambia
| | - Fatoumatta Sisay-Joof
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Carolyne M Ndila
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | | | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Anna E Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Kate Rowlands
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Thuy Nguyen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | - Jim Stalker
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Richard D Pearson
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA
| | | | | | - Giorgio Sirugo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Division of Translational Medicine and Human Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Umberto d'Alessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Kalifa A Bojang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Kevin Marsh
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya.,Nuffield Department of Medicine, NDM Research Building, Roosevelt Drive, Headington, Oxford, UK
| | - Norbert Peshu
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | - Joseph W Saelens
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Mahamadou Diakité
- Malaria Research and Training Center, University of Sciences, Techniques, and Technologies of Bamako, Bamako, Mali
| | - Steve M Taylor
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - David J Conway
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya.,Institute for Global Health Innovation, Department of Surgery and Cancer, Imperial College, London, London, UK
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK.
| | - Dominic P Kwiatkowski
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA.
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18
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Märkle H, John S, Cornille A, Fields PD, Tellier A. Novel genomic approaches to study antagonistic coevolution between hosts and parasites. Mol Ecol 2021; 30:3660-3676. [PMID: 34038012 DOI: 10.1111/mec.16001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/09/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
Host-parasite coevolution is ubiquitous, shaping genetic and phenotypic diversity and the evolutionary trajectory of interacting species. With the advances of high throughput sequencing technologies applicable to model and non-model organisms alike, it is now feasible to study in greater detail (a) the genetic underpinnings of coevolution, (b) the speed and type of dynamics at coevolving loci, and (c) the genomic consequences of coevolution. This review focuses on three recently developed approaches that leverage information from host and parasite full genome data simultaneously to pinpoint coevolving loci and draw inference on the coevolutionary history. First, co-genome-wide association study (co-GWAS) methods allow pinpointing the loci underlying host-parasite interactions. These methods focus on detecting associations between genetic variants and the outcome of experimental infection tests or on correlations between genomes of naturally infected hosts and their infecting parasites. Second, extensions to population genomics methods can detect genes under coevolution and infer the coevolutionary history, such as fitness costs. Third, correlations between host and parasite population size in time are indicative of coevolution, and polymorphism levels across independent spatially distributed populations of hosts and parasites can reveal coevolutionary loci and infer coevolutionary history. We describe the principles of these three approaches and discuss their advantages and limitations based on coevolutionary theory. We present recommendations for their application to various host (prokaryotes, fungi, plants, and animals) and parasite (viruses, bacteria, fungi, and macroparasites) species. We conclude by pointing out methodological and theoretical gaps to be filled to extract maximum information from full genome data and thereby to shed light on the molecular underpinnings of coevolution.
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Affiliation(s)
- Hanna Märkle
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Sona John
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Amandine Cornille
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Peter D Fields
- Department of Environmental Sciences, University of Basel, Zoology, Basel, Switzerland
| | - Aurélien Tellier
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
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19
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Gabrielaite M, Bennedbæk M, Zucco AG, Ekenberg C, Murray DD, Kan VL, Touloumi G, Vandekerckhove L, Turner D, Neaton J, Lane HC, Safo S, Arenas-Pinto A, Polizzotto MN, Günthard HF, Lundgren JD, Marvig RL. Human immunotypes impose selection on viral genotypes through viral epitope specificity. J Infect Dis 2021; 224:2053-2063. [PMID: 33974707 DOI: 10.1093/infdis/jiab253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/06/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Understanding the genetic interplay between human hosts and infectious pathogens is crucial for how we interpret virulence factors. Here, we tested for associations between HIV and host genetics, and interactive genetic effects on viral load (VL) in HIV+ ART-naive clinical trial participants. METHODS HIV genomes were sequenced and the encoded amino acid (AA) variants were associated with VL, human single nucleotide polymorphisms (SNPs) and imputed HLA alleles, using generalized linear models with Bonferroni correction. RESULTS Human (388,501 SNPs) and HIV (3,010 variants) genetic data was available for 2,122 persons. Four HIV variants were associated with VL (p-values<1.66×10 -5). Twelve HIV variants were associated with a range of 1-512 human SNPs (p-value<4.28×10 -11). We found 46 associations between HLA alleles and HIV variants (p-values<1.29×10 -7). We found HIV variants and immunotypes when analyzed separately, were associated with lower VL, whereas the opposite was true when analyzed in concert. Epitope binding prediction showed HLA alleles to be weaker binders of associated HIV AA variants relative to alternative variants on the same position. CONCLUSIONS Our results show the importance of immunotype specificity on viral antigenic determinants, and the identified genetic interplay puts emphasis that viral and human genetics should be studied in the context of each other.
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Affiliation(s)
- Migle Gabrielaite
- Centre for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marc Bennedbæk
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Adrian G Zucco
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Christina Ekenberg
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Daniel D Murray
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Virginia L Kan
- Veterans Affairs Medical Center, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Giota Touloumi
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University; Ghent University Hospital, Ghent, Belgium
| | - Dan Turner
- Crusaid Kobler AIDS Center, Tel-Aviv Sourasky Medical Center, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - James Neaton
- School of Public Health, University of Minnesota, Minneapolis, USA
| | - H Clifford Lane
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Sandra Safo
- Division of Biostatistics, University of Minnesota, Minneapolis, USA
| | | | - Mark N Polizzotto
- Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, Australia
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, Zürich, Switzerland.,Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Jens D Lundgren
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Rasmus L Marvig
- Centre for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
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20
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Liu X, Ma Y, Wang J. Genetic variation and function: revealing potential factors associated with microbial phenotypes. BIOPHYSICS REPORTS 2021; 7:111-126. [PMID: 37288143 PMCID: PMC10235906 DOI: 10.52601/bpr.2021.200040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/09/2021] [Indexed: 06/09/2023] Open
Abstract
Innovations in sequencing technology have generated voluminous microbial and host genomic data, making it possible to detect these genetic variations and analyze the function influenced by them. Recently, many studies have linked such genetic variations to phenotypes through association or comparative analysis, which have further advanced our understanding of multiple microbial functions. In this review, we summarized the application of association analysis in microbes like Mycobacterium tuberculosis, focusing on screening of microbial genetic variants potentially associated with phenotypes such as drug resistance, pathogenesis and novel drug targets etc.; reviewed the application of additional comparative genomic or transcriptomic methods to identify genetic factors associated with functions in microbes; expanded the scope of our study to focus on host genetic factors associated with certain microbes or microbiome and summarized the recent host genetic variations associated with microbial phenotypes, including susceptibility and load after infection of HIV, presence/absence of different taxa, and quantitative traits of microbiome, and lastly, discussed the challenges that may be encountered and the apparent or potential viable solutions. Gene-function analysis of microbe and microbiome is still in its infancy, and in order to unleash its full potential, it is necessary to understand its history, current status, and the challenges hindering its development.
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Affiliation(s)
- Xiaolin Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Ma
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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21
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Thorball CW, Fellay J, Borghesi A. Immunological lessons from genome-wide association studies of infections. Curr Opin Immunol 2021; 72:87-93. [PMID: 33878603 DOI: 10.1016/j.coi.2021.03.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/24/2021] [Accepted: 03/27/2021] [Indexed: 02/06/2023]
Abstract
Over the past few years, genome-wide association studies (GWAS) have been increasingly applied to identify host genetic factors influencing clinical and laboratory traits related to immunity and infection, and to understand the interplay between the host and the microbial genomes. By screening large cohorts of individuals suffering from various infectious diseases, GWAS explored resistance against infection, natural history of the disease, development of life-threatening clinical signs, and innate and adaptive immune responses. These efforts provided fundamental insight on the role of major genes in the interindividual variability in the response to infection and on the mechanisms of the immune response against human pathogens both at the individual and population levels.
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Affiliation(s)
- Christian W Thorball
- Precision Medicine Unit, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- Precision Medicine Unit, Lausanne University Hospital (CHUV), University of Lausanne, Lausanne, Switzerland; School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alessandro Borghesi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
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22
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Bourgeois JS, Smith CM, Ko DC. These Are the Genes You're Looking For: Finding Host Resistance Genes. Trends Microbiol 2021; 29:346-362. [PMID: 33004258 PMCID: PMC7969353 DOI: 10.1016/j.tim.2020.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
Humanity's ongoing struggle with new, re-emerging and endemic infectious diseases serves as a frequent reminder of the need to understand host-pathogen interactions. Recent advances in genomics have dramatically advanced our understanding of how genetics contributes to host resistance or susceptibility to bacterial infection. Here we discuss current trends in defining host-bacterial interactions at the genome-wide level, including screens that harness CRISPR/Cas9 genome editing, natural genetic variation, proteomics, and transcriptomics. We report on the merits, limitations, and findings of these innovative screens and discuss their complementary nature. Finally, we speculate on future innovation as we continue to progress through the postgenomic era and towards deeper mechanistic insight and clinical applications.
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Affiliation(s)
- Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Duke Human Vaccine Institute, School of Medicine, Duke University Durham, NC, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC, USA.
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23
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Rüeger S, Hammer C, Loetscher A, McLaren PJ, Lawless D, Naret O, Khanna N, Bernasconi E, Cavassini M, Günthard HF, Kahlert CR, Rauch A, Depledge DP, Morfopoulou S, Breuer J, Zdobnov E, Fellay J. The influence of human genetic variation on Epstein-Barr virus sequence diversity. Sci Rep 2021; 11:4586. [PMID: 33633271 PMCID: PMC7907281 DOI: 10.1038/s41598-021-84070-7] [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: 12/02/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
Epstein-Barr virus (EBV) is one of the most common viruses latently infecting humans. Little is known about the impact of human genetic variation on the large inter-individual differences observed in response to EBV infection. To search for a potential imprint of host genomic variation on the EBV sequence, we jointly analyzed paired viral and human genomic data from 268 HIV-coinfected individuals with CD4 + T cell count < 200/mm3 and elevated EBV viremia. We hypothesized that the reactivated virus circulating in these patients could carry sequence variants acquired during primary EBV infection, thereby providing a snapshot of early adaptation to the pressure exerted on EBV by the individual immune response. We searched for associations between host and pathogen genetic variants, taking into account human and EBV population structure. Our analyses revealed significant associations between human and EBV sequence variation. Three polymorphic regions in the human genome were found to be associated with EBV variation: one at the amino acid level (BRLF1:p.Lys316Glu); and two at the gene level (burden testing of rare variants in BALF5 and BBRF1). Our findings confirm that jointly analyzing host and pathogen genomes can identify sites of genomic interactions, which could help dissect pathogenic mechanisms and suggest new therapeutic avenues.
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Affiliation(s)
- Sina Rüeger
- School of Life Sciences, EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Alexis Loetscher
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Paul J McLaren
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Dylan Lawless
- School of Life Sciences, EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Olivier Naret
- School of Life Sciences, EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nina Khanna
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christian R Kahlert
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St.Gallen, St.Gallen, Switzerland
- Childrens Hospital of Eastern Switzerland, St. Gallen, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Daniel P Depledge
- Division of Infection and Immunity, University College London, London, UK
| | - Sofia Morfopoulou
- Division of Infection and Immunity, University College London, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Evgeny Zdobnov
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Jacques Fellay
- School of Life Sciences, EPFL, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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24
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Ojwach DBA, Madlala P, Gordon M, Ndung'u T, Mann JK. Vulnerable targets in HIV-1 Pol for attenuation-based vaccine design. Virology 2021; 554:1-8. [PMID: 33316731 PMCID: PMC7931244 DOI: 10.1016/j.virol.2020.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 11/24/2022]
Abstract
Identification of viral immune escape mutations that compromise HIV's ability to replicate may aid rational attenuation-based vaccine design. Previously we reported amino acids associated with altered viral replication capacity (RC) from a sequence-function analysis of 487 patient-derived RT-integrase sequences. In this study, site-directed mutagenesis experiments were performed to validate the effect of these mutations on RC. Viral reverse transcripts were measured by quantitative PCR and structural modelling was performed to gain further insight into the effect of reverse transcriptase (RT) mutations on reverse transcription. RT-integrase variants in or flanking cytotoxic T cell epitopes in the RT palm (158S), RT thumb (241I and 257V) and integrase catalytic core domain (124N) were confirmed to significantly reduce RC. RT mutants showed a delayed initiation of viral DNA synthesis. Structural models provide insight into how these attenuating RT mutations may affect amino acid interactions in the helix clamp, primer grip and catalytic site regions.
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Affiliation(s)
- Doty B A Ojwach
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Paradise Madlala
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Michelle Gordon
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Africa Health Research Institute, Durban, South Africa; Max Planck Institute for Infection Biology, Berlin, Germany; Division of Infection and Immunity, University College London, London, UK
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.
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Abstract
Over the past four decades, research on the natural history of HIV infection has described how HIV wreaks havoc on human immunity and causes AIDS. HIV host genomic research, which aims to understand how human genetic variation affects our response to HIV infection, has progressed from early candidate gene studies to recent multi-omic efforts, benefiting from spectacular advances in sequencing technology and data science. In addition to invading cells and co-opting the host machinery for replication, HIV also stably integrates into our own genome. The study of the complex interactions between the human and retroviral genomes has improved our understanding of pathogenic mechanisms and suggested novel preventive and therapeutic approaches against HIV infection.
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Affiliation(s)
- Paul J. McLaren
- grid.415368.d0000 0001 0805 4386National HIV and Retrovirology Laboratory at the JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB Canada ,grid.21613.370000 0004 1936 9609Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB Canada
| | - Jacques Fellay
- grid.5333.60000000121839049School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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26
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Lorenzo-Redondo R, Ozer EA, Achenbach CJ, D'Aquila RT, Hultquist JF. Molecular epidemiology in the HIV and SARS-CoV-2 pandemics. Curr Opin HIV AIDS 2021; 16:11-24. [PMID: 33186230 PMCID: PMC7723008 DOI: 10.1097/coh.0000000000000660] [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] [Indexed: 12/20/2022]
Abstract
PURPOSE OF REVIEW The aim of this review was to compare and contrast the application of molecular epidemiology approaches for the improved management and understanding of the HIV versus SARS-CoV-2 epidemics. RECENT FINDINGS Molecular biology approaches, including PCR and whole genome sequencing (WGS), have become powerful tools for epidemiological investigation. PCR approaches form the basis for many high-sensitivity diagnostic tests and can supplement traditional contact tracing and surveillance strategies to define risk networks and transmission patterns. WGS approaches can further define the causative agents of disease, trace the origins of the pathogen, and clarify routes of transmission. When coupled with clinical datasets, such as electronic medical record data, these approaches can investigate co-correlates of disease and pathogenesis. In the ongoing HIV epidemic, these approaches have been effectively deployed to identify treatment gaps, transmission clusters and risk factors, though significant barriers to rapid or real-time implementation remain critical to overcome. Likewise, these approaches have been successful in addressing some questions of SARS-CoV-2 transmission and pathogenesis, but the nature and rapid spread of the virus have posed additional challenges. SUMMARY Overall, molecular epidemiology approaches offer unique advantages and challenges that complement traditional epidemiological tools for the improved understanding and management of epidemics.
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Affiliation(s)
- Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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27
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Ebert D, Fields PD. Host-parasite co-evolution and its genomic signature. Nat Rev Genet 2020; 21:754-768. [PMID: 32860017 DOI: 10.1038/s41576-020-0269-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2020] [Indexed: 01/14/2023]
Abstract
Studies in diverse biological systems have indicated that host-parasite co-evolution is responsible for the extraordinary genetic diversity seen in some genomic regions, such as major histocompatibility (MHC) genes in jawed vertebrates and resistance genes in plants. This diversity is believed to evolve under balancing selection on hosts by parasites. However, the mechanisms that link the genomic signatures in these regions to the underlying co-evolutionary process are only slowly emerging. We still lack a clear picture of the co-evolutionary concepts and of the genetic basis of the co-evolving phenotypic traits in the interacting antagonists. Emerging genomic tools that provide new options for identifying underlying genes will contribute to a fuller understanding of the co-evolutionary process.
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Affiliation(s)
- Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland. .,Wissenschaftskolleg zu Berlin, Berlin, Germany.
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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28
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Dickson LB, Merkling SH, Gautier M, Ghozlane A, Jiolle D, Paupy C, Ayala D, Moltini-Conclois I, Fontaine A, Lambrechts L. Exome-wide association study reveals largely distinct gene sets underlying specific resistance to dengue virus types 1 and 3 in Aedes aegypti. PLoS Genet 2020; 16:e1008794. [PMID: 32463828 PMCID: PMC7282673 DOI: 10.1371/journal.pgen.1008794] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/09/2020] [Accepted: 04/23/2020] [Indexed: 11/29/2022] Open
Abstract
Although specific interactions between host and pathogen genotypes have been well documented in invertebrates, the identification of host genes involved in discriminating pathogen genotypes remains a challenge. In the mosquito Aedes aegypti, the main dengue virus (DENV) vector worldwide, statistical associations between host genetic markers and DENV types or strains were previously detected, but the host genes underlying this genetic specificity have not been identified. In particular, it is unknown whether DENV type- or strain-specific resistance relies on allelic variants of the same genes or on distinct gene sets. Here, we investigated the genetic architecture of DENV resistance in a population of Ae. aegypti from Bakoumba, Gabon, which displays a stronger resistance phenotype to DENV type 1 (DENV-1) than to DENV type 3 (DENV-3) infection. Following experimental exposure to either DENV-1 or DENV-3, we sequenced the exomes of large phenotypic pools of mosquitoes that are either resistant or susceptible to each DENV type. Using variation in single-nucleotide polymorphism (SNP) frequencies among the pools, we computed empirical p values based on average gene scores adjusted for the differences in SNP counts, to identify genes associated with infection in a DENV type-specific manner. Among the top 5% most significant genes, 263 genes were significantly associated with resistance to both DENV-1 and DENV-3, 287 genes were only associated with DENV-1 resistance and 290 were only associated with DENV-3 resistance. The shared significant genes were enriched in genes with ATP binding activity and sulfur compound transmembrane transporter activity, whereas the genes uniquely associated with DENV-3 resistance were enriched in genes with zinc ion binding activity. Together, these results indicate that specific resistance to different DENV types relies on largely non-overlapping sets of genes in this Ae. aegypti population and pave the way for further mechanistic studies. Compatibility between hosts and pathogens is often genetically specific in invertebrates but host genes underlying this genetic specificity have not been elucidated. We investigated the genetic architecture of dengue virus type-specific resistance in the mosquito vector Aedes aegypti. We used a natural population of Ae. aegypti from Bakoumba, Gabon, which is differentially resistant to dengue virus type 1 and dengue virus type 3. We surveyed genetic variation in protein-coding regions of the mosquito genome and compared the frequency of genetic polymorphisms between groups of mosquitoes that are either resistant or susceptible to each dengue virus type. We found that the Ae. aegypti genes associated with resistance to dengue virus type 1 or dengue virus type 3 were largely non-overlapping. This finding indicates that different sets of host genes, rather than different variants of the same genes, confer pathogen-specific resistance in this population. This study is an important step towards identification of mechanisms underlying the genetic specificity of invertebrate host-pathogen interactions.
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Affiliation(s)
- Laura B. Dickson
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Sarah H. Merkling
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Amine Ghozlane
- Hub de Bioinformatique et Biostatistique–Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Davy Jiolle
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
- Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Christophe Paupy
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
- Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Diego Ayala
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
- Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Isabelle Moltini-Conclois
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - Albin Fontaine
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Louis Lambrechts
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- * E-mail:
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29
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Ekenberg C, Tang MH, Zucco AG, Murray DD, MacPherson CR, Hu X, Sherman BT, Losso MH, Wood R, Paredes R, Molina JM, Helleberg M, Jina N, Kityo CM, Florence E, Polizzotto MN, Neaton JD, Lane HC, Lundgren JD. Association Between Single-Nucleotide Polymorphisms in HLA Alleles and Human Immunodeficiency Virus Type 1 Viral Load in Demographically Diverse, Antiretroviral Therapy-Naive Participants From the Strategic Timing of AntiRetroviral Treatment Trial. J Infect Dis 2020; 220:1325-1334. [PMID: 31219150 DOI: 10.1093/infdis/jiz294] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/05/2019] [Indexed: 12/18/2022] Open
Abstract
The impact of variation in host genetics on replication of human immunodeficiency virus type 1 (HIV-1) in demographically diverse populations remains uncertain. In the current study, we performed a genome-wide screen for associations of single-nucleotide polymorphisms (SNPs) to viral load (VL) in antiretroviral therapy-naive participants (n = 2440) with varying demographics from the Strategic Timing of AntiRetroviral Treatment (START) trial. Associations were assessed using genotypic data generated by a customized SNP array, imputed HLA alleles, and multiple linear regression. Genome-wide significant associations between SNPs and VL were observed in the major histocompatibility complex class I region (MHC I), with effect sizes ranging between 0.14 and 0.39 log10 VL (copies/mL). Supporting the SNP findings, we identified several HLA alleles significantly associated with VL, extending prior observations that the (MHC I) is a major host determinant of HIV-1 control with shared genetic variants across diverse populations and underscoring the limitations of genome-wide association studies as being merely a screening tool.
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Affiliation(s)
- Christina Ekenberg
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Man-Hung Tang
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Adrian G Zucco
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Daniel D Murray
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Cameron Ross MacPherson
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Xiaojun Hu
- Laboratory of Human Retrovirology and Immunoinformatics, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Bethesda, Maryland
| | - Brad T Sherman
- Laboratory of Human Retrovirology and Immunoinformatics, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Bethesda, Maryland
| | - Marcelo H Losso
- Hospital General de Agudos JM Ramos, Buenos Aires, Argentina
| | - Robin Wood
- Desmond Tutu HIV Foundation Clinical Trials Unit, Cape Town, South Africa
| | - Roger Paredes
- Infectious Diseases Service and irsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Jean-Michel Molina
- Department of Infectious Diseases, University of Paris Diderot, Sorbonne Paris Cité, and Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, France
| | - Marie Helleberg
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Nureen Jina
- Clinical HIV Research Unit, Wits Health Consortium, Department of Medicine, University of the Witwatersrand, Helen Joseph Hospital, Themba Lethu Clinic, Johannesburg, South Africa
| | | | | | | | - James D Neaton
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis
| | - H Clifford Lane
- National Institute of Allergy and Infectious Diseases, Division of Clinical Research, Bethesda, Maryland
| | - Jens D Lundgren
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
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30
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Affiliation(s)
- Thomas Lengauer
- Max Planck Institute for Informatics Saarland Informatics Campus Campus E1 4 66123 Saarbrücken Germany
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31
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Saber MM, Shapiro BJ. Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes. Microb Genom 2020; 6:e000337. [PMID: 32100713 PMCID: PMC7200059 DOI: 10.1099/mgen.0.000337] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/23/2020] [Indexed: 11/18/2022] Open
Abstract
Genome-wide association studies (GWASs) have the potential to reveal the genetics of microbial phenotypes such as antibiotic resistance and virulence. Capitalizing on the growing wealth of bacterial sequence data, microbial GWAS methods aim to identify causal genetic variants while ignoring spurious associations. Bacteria reproduce clonally, leading to strong population structure and genome-wide linkage, making it challenging to separate true 'hits' (i.e. mutations that cause a phenotype) from non-causal linked mutations. GWAS methods attempt to correct for population structure in different ways, but their performance has not yet been systematically and comprehensively evaluated under a range of evolutionary scenarios. Here, we developed a bacterial GWAS simulator (BacGWASim) to generate bacterial genomes with varying rates of mutation, recombination and other evolutionary parameters, along with a subset of causal mutations underlying a phenotype of interest. We assessed the performance (recall and precision) of three widely used single-locus GWAS approaches (cluster-based, dimensionality-reduction and linear mixed models, implemented in plink, pyseer and gemma) and one relatively new multi-locus model implemented in pyseer, across a range of simulated sample sizes, recombination rates and causal mutation effect sizes. As expected, all methods performed better with larger sample sizes and effect sizes. The performance of clustering and dimensionality reduction approaches to correct for population structure were considerably variable according to the choice of parameters. Notably, the multi-locus elastic net (lasso) approach was consistently amongst the highest-performing methods, and had the highest power in detecting causal variants with both low and high effect sizes. Most methods reached the level of good performance (recall >0.75) for identifying causal mutations of strong effect size [log odds ratio (OR) ≥2] with a sample size of 2000 genomes. However, only elastic nets reached the level of reasonable performance (recall=0.35) for detecting markers with weaker effects (log OR ~1) in smaller samples. Elastic nets also showed superior precision and recall in controlling for genome-wide linkage, relative to single-locus models. However, all methods performed relatively poorly on highly clonal (low-recombining) genomes, suggesting room for improvement in method development. These findings show the potential for multi-locus models to improve bacterial GWAS performance. BacGWASim code and simulated data are publicly available to enable further comparisons and benchmarking of new methods.
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Affiliation(s)
- Morteza M. Saber
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
| | - B. Jesse Shapiro
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
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32
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Märkle H, Tellier A. Inference of coevolutionary dynamics and parameters from host and parasite polymorphism data of repeated experiments. PLoS Comput Biol 2020; 16:e1007668. [PMID: 32203545 PMCID: PMC7156111 DOI: 10.1371/journal.pcbi.1007668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 04/14/2020] [Accepted: 01/19/2020] [Indexed: 01/27/2023] Open
Abstract
There is a long-standing interest in understanding host-parasite coevolutionary dynamics and associated fitness effects. Increasing amounts of genomic data for both interacting species offer a promising source to identify candidate loci and to infer the main parameters of the past coevolutionary history. However, so far no method exists to perform the latter. By coupling a gene-for-gene model with coalescent simulations, we first show that three types of biological costs, namely, resistance, infectivity and infection, define the allele frequencies at the internal equilibrium point of the coevolution model. These in return determine the strength of selective signatures at the coevolving host and parasite loci. We apply an Approximate Bayesian Computation (ABC) approach on simulated datasets to infer these costs by jointly integrating host and parasite polymorphism data at the coevolving loci. To control for the effect of genetic drift on coevolutionary dynamics, we assume that 10 or 30 repetitions are available from controlled experiments or several natural populations. We study two scenarios: 1) the cost of infection and population sizes (host and parasite) are unknown while costs of infectivity and resistance are known, and 2) all three costs are unknown while populations sizes are known. Using the ABC model choice procedure, we show that for both scenarios, we can distinguish with high accuracy pairs of coevolving host and parasite loci from pairs of neutrally evolving loci, though the statistical power decreases with higher cost of infection. The accuracy of parameter inference is high under both scenarios especially when using both host and parasite data because parasite polymorphism data do inform on costs applying to the host and vice-versa. As the false positive rate to detect pairs of genes under coevolution is small, we suggest that our method complements recently developed methods to identify host and parasite candidate loci for functional studies.
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Affiliation(s)
- Hanna Märkle
- Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Aurélien Tellier
- Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
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33
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Arora J, Pierini F, McLaren PJ, Carrington M, Fellay J, Lenz TL. HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation. Mol Biol Evol 2020; 37:639-650. [PMID: 31651980 PMCID: PMC7038656 DOI: 10.1093/molbev/msz249] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathogen-mediated balancing selection is regarded as a key driver of host immunogenetic diversity. A hallmark for balancing selection in humans is the heterozygote advantage at genes of the human leukocyte antigen (HLA), resulting in improved HIV-1 control. However, the actual mechanism of the observed heterozygote advantage is still elusive. HLA heterozygotes may present a broader array of antigenic viral peptides to immune cells, possibly resulting in a more efficient cytotoxic T-cell response. Alternatively, heterozygosity may simply increase the chance to carry the most protective HLA alleles, as individual HLA alleles are known to differ substantially in their association with HIV-1 control. Here, we used data from 6,311 HIV-1-infected individuals to explore the relative contribution of quantitative and qualitative aspects of peptide presentation in HLA heterozygote advantage against HIV. Screening the entire HIV-1 proteome, we observed that heterozygous individuals exhibited a broader array of HIV-1 peptides presented by their HLA class I alleles. In addition, viral load was negatively correlated with the breadth of the HIV-1 peptide repertoire bound by an individual's HLA variants, particularly at HLA-B. This suggests that heterozygote advantage at HLA-B is at least in part mediated by quantitative peptide presentation. We also observed higher HIV-1 sequence diversity among HLA-B heterozygous individuals, suggesting stronger evolutionary pressure from HLA heterozygosity. However, HLA heterozygotes were also more likely to carry certain HLA alleles, including the highly protective HLA-B*57:01 variant, indicating that HLA heterozygote advantage ultimately results from a combination of quantitative and qualitative effects in antigen presentation.
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Affiliation(s)
- Jatin Arora
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul J McLaren
- JC Wilt Infectious Diseases Research Center, National HIV and Retrovirology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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34
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Kiselev D, Matsvay A, Abramov I, Dedkov V, Shipulin G, Khafizov K. Current Trends in Diagnostics of Viral Infections of Unknown Etiology. Viruses 2020; 12:E211. [PMID: 32074965 PMCID: PMC7077230 DOI: 10.3390/v12020211] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022] Open
Abstract
Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.
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Affiliation(s)
- Daniel Kiselev
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- I.M. Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Alina Matsvay
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
| | - Ivan Abramov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Vladimir Dedkov
- Pasteur Institute, Federal Service on Consumers’ Rights Protection and Human Well-Being Surveillance, 197101 Saint-Petersburg, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - German Shipulin
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Kamil Khafizov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
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San JE, Baichoo S, Kanzi A, Moosa Y, Lessells R, Fonseca V, Mogaka J, Power R, de Oliveira T. Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls. Front Microbiol 2020; 10:3119. [PMID: 32082269 PMCID: PMC7002396 DOI: 10.3389/fmicb.2019.03119] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022] Open
Abstract
Microbial genome-wide association studies (mGWAS) are a new and exciting research field that is adapting human GWAS methods to understand how variations in microbial genomes affect host or pathogen phenotypes, such as drug resistance, virulence, host specificity and prognosis. Several computational tools and methods have been developed or adapted from human GWAS to facilitate the discovery of novel mutations and structural variations that are associated with the phenotypes of interest. However, no comprehensive, end-to-end, user-friendly tool is currently available. The development of a broadly applicable pipeline presents a real opportunity among computational biologists. Here, (i) we review the prominent and promising tools, (ii) discuss analytical pitfalls and bottlenecks in mGWAS, (iii) provide insights into the selection of appropriate tools, (iv) highlight the gaps that still need to be filled and how users and developers can work together to overcome these bottlenecks. Use of mGWAS research can inform drug repositioning decisions as well as accelerate the discovery and development of more effective vaccines and antimicrobials for pressing infectious diseases of global health significance, such as HIV, TB, influenza, and malaria.
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Affiliation(s)
- James Emmanuel San
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Shakuntala Baichoo
- Department of Digital Technologies, FoICDT, University of Mauritius, Réduit, Mauritius
| | - Aquillah Kanzi
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Yumna Moosa
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Vagner Fonseca
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - John Mogaka
- Discipline of Public Health, University of Kwazulu-Natal, Durban, South Africa
| | - Robert Power
- St Edmund Hall, Oxford University, Oxford, United Kingdom
| | - Tulio de Oliveira
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, United States
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36
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Fellay J, Pedergnana V. Exploring the interactions between the human and viral genomes. Hum Genet 2019; 139:777-781. [PMID: 31729546 DOI: 10.1007/s00439-019-02089-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/31/2019] [Indexed: 12/20/2022]
Abstract
Over the last decade, genome-wide association studies led to major advances in identifying human genetic variants associated with infectious disease susceptibility. On the pathogen side, comparable methods are now applied to identify disease-modulating pathogen variants. As host and pathogen variants jointly determine disease outcomes, the most recent development has been to explore simultaneously host and pathogen genomes, through so-called genome-to-genome studies. In this review, we provide some background on the development of genome-to-genome analysis and we detail the first wave of studies in this emerging field, which focused on patients chronically infected with HIV and hepatitis C virus. We also discuss the need for novel statistical methods to better tackle the issues of population stratification and multiple testing. Finally, we speculate on future research areas where genome-to-genome analysis may prove to be particularly effective.
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Affiliation(s)
- Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. .,Precision Medicine Unit, University Hospital and University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Vincent Pedergnana
- French National Center for Scientific Research (CNRS), Laboratory MIVEGEC (CNRS, IRD, UM), Montpellier, France
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37
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Vila Nova M, Durimel K, La K, Felten A, Bessières P, Mistou MY, Mariadassou M, Radomski N. Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale. BMC Genomics 2019; 20:814. [PMID: 31694533 PMCID: PMC6836353 DOI: 10.1186/s12864-019-6188-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/15/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Salmonella enterica subsp. enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mono- and multi-animal sources were selected from a curated and synthetized subset of Enterobase. The corresponding sequencing reads were downloaded from the European Nucleotide Archive (ENA) providing a balanced dataset of 440 Salmonella genomes in terms of serovars and sources (i). Secondly, the coregenome variants and accessory genes were detected (ii). Thirdly, single nucleotide polymorphisms and small insertions/deletions from the coregenome, as well as the accessory genes were associated to animal sources based on a microbial Genome Wide Association Study (GWAS) integrating an advanced correction of the population structure (iii). Lastly, a Gene Ontology Enrichment Analysis (GOEA) was applied to emphasize metabolic pathways mainly impacted by the pangenomic mutations associated to animal sources (iv). RESULTS Based on a genome dataset including Salmonella serovars from mono- and multi-animal sources (i), 19,130 accessory genes and 178,351 coregenome variants were identified (ii). Among these pangenomic mutations, 52 genomic signatures (iii) and 9 over-enriched metabolic signatures (iv) were associated to avian, bovine, swine and fish sources by GWAS and GOEA, respectively. CONCLUSIONS Our results suggest that the genetic and metabolic determinants of Salmonella adaptation to animal sources may have been driven by the natural feeding environment of the animal, distinct livestock diets modified by human, environmental stimuli, physiological properties of the animal itself, and work habits for health protection of livestock.
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Affiliation(s)
- Meryl Vila Nova
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
- Applied Mathematics and Computer Science, from Genomes to the Environment (MaIAGE), French National Institute for Agricultural Research (INRA), Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Kévin Durimel
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
| | - Kévin La
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
| | - Arnaud Felten
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
| | - Philippe Bessières
- Applied Mathematics and Computer Science, from Genomes to the Environment (MaIAGE), French National Institute for Agricultural Research (INRA), Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Michel-Yves Mistou
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France
| | - Mahendra Mariadassou
- Applied Mathematics and Computer Science, from Genomes to the Environment (MaIAGE), French National Institute for Agricultural Research (INRA), Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Nicolas Radomski
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety (LSAL), Paris-Est University, Maisons-Alfort, France.
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38
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Näpflin K, O'Connor EA, Becks L, Bensch S, Ellis VA, Hafer-Hahmann N, Harding KC, Lindén SK, Olsen MT, Roved J, Sackton TB, Shultz AJ, Venkatakrishnan V, Videvall E, Westerdahl H, Winternitz JC, Edwards SV. Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales. PeerJ 2019; 7:e8013. [PMID: 31720122 PMCID: PMC6839515 DOI: 10.7717/peerj.8013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022] Open
Abstract
Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.
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Affiliation(s)
- Kathrin Näpflin
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America
| | - Emily A O'Connor
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
| | - Lutz Becks
- Aquatic Ecology and Evolution, Limnological Institute University Konstanz, Konstanz, Germany
| | - Staffan Bensch
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
| | - Vincenzo A Ellis
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
| | - Nina Hafer-Hahmann
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Karin C Harding
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Sara K Lindén
- Department of Medical Chemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Morten T Olsen
- Section for Evolutionary Genomics, Natural History Museum of Denmark, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Roved
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
| | - Timothy B Sackton
- Informatics Group, Harvard University, Cambridge, MA, United States of America
| | - Allison J Shultz
- Ornithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Vignesh Venkatakrishnan
- Department of Medical Chemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Elin Videvall
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States of America
| | - Helena Westerdahl
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Lund, Sweden
| | - Jamie C Winternitz
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America.,Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
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39
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Houldcroft CJ. Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion. Pathogens 2019; 8:E186. [PMID: 31614759 PMCID: PMC6963362 DOI: 10.3390/pathogens8040186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 12/19/2022] Open
Abstract
The nine human herpesviruses are some of the most ubiquitous pathogens worldwide, causing life-long latent infection in a variety of different tissues. Human herpesviruses range from mild childhood infections to known tumour viruses and 'trolls of transplantation'. Epstein-Barr virus was the first human herpesvirus to have its whole genome sequenced; GenBank now includes thousands of herpesvirus genomes. This review will cover some of the recent advances in our understanding of herpesvirus diversity and disease that have come about as a result of new sequencing technologies, such as target enrichment and long-read sequencing. It will also look at the problem of resolving mixed-genotype infections, whether with short or long-read sequencing methods; and conclude with some thoughts on the future of the field as herpesvirus population genomics becomes a reality.
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Affiliation(s)
- Charlotte J Houldcroft
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambs CB2 0QQ UK.
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambs CB10 1SA, UK.
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40
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Thami PK, Chimusa ER. Population Structure and Implications on the Genetic Architecture of HIV-1 Phenotypes Within Southern Africa. Front Genet 2019; 10:905. [PMID: 31611910 PMCID: PMC6777512 DOI: 10.3389/fgene.2019.00905] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022] Open
Abstract
The interesting history of Southern Africa has put the region in the spotlight for population medical genetics. Major events including the Bantu expansion and European colonialism have imprinted unique genetic signatures within autochthonous populations of Southern Africa, this resulting in differential allele frequencies across the region. This genetic structure has potential implications on susceptibility and resistance to infectious diseases such as human immunodeficiency virus (HIV) infection. Southern Africa is the region affected worst by HIV. Here, we discuss advances made in genome-wide association studies (GWAS) of HIV-1 in the past 12 years and dissect population diversity within Southern Africa. Our findings accentuate that a plethora of factors such as migration, language and culture, admixture, and natural selection have profiled the genetics of the people of Southern Africa. Genetic structure has been observed among the Khoe-San, among Bantu speakers, and between the Khoe-San, Coloureds, and Bantu speakers. Moreover, Southern African populations have complex admixture scenarios. Few GWAS of HIV-1 have been conducted in Southern Africa, with only one of these identifying two novel variants (HCG22rs2535307 and CCNG1kgp22385164) significantly associated with HIV-1 acquisition and progression. High genetic diversity, multi-wave genetic mixture and low linkage disequilibrium of Southern African populations constitute a challenge in identifying genetic variants with modest risk or protective effect against HIV-1. We therefore posit that it is compelling to assess genome-wide contribution of ancestry to HIV-1 infection. We further suggest robust methods that can pin-point population-specific variants that may contribute to the control of HIV-1 in Southern Africa.
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Affiliation(s)
- Prisca K Thami
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa.,Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
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41
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Chaturvedi N, Svarovskaia ES, Mo H, Osinusi AO, Brainard DM, Subramanian GM, McHutchison JG, Zeuzem S, Fellay J. Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes. eLife 2019; 8:e42542. [PMID: 31478832 PMCID: PMC6721370 DOI: 10.7554/elife.42542] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 05/31/2019] [Indexed: 12/21/2022] Open
Abstract
Genetic polymorphism in the interferon lambda (IFN-λ) region is associated with spontaneous clearance of hepatitis C virus (HCV) infection and response to interferon-based treatment. Here, we evaluate associations between IFN-λ polymorphism and HCV variation in 8729 patients (Europeans 77%, Asians 13%, Africans 8%) infected with various viral genotypes, predominantly 1a (41%), 1b (22%) and 3a (21%). We searched for associations between rs12979860 genotype and variants in the NS3, NS4A, NS5A and NS5B HCV proteins. We report multiple associations in all tested proteins, including in the interferon-sensitivity determining region of NS5A. We also assessed the combined impact of human and HCV variation on pretreatment viral load and report amino acids associated with both IFN-λ polymorphism and HCV load across multiple viral genotypes. By demonstrating that IFN-λ variation leaves a large footprint on the viral proteome, we provide evidence of pervasive viral adaptation to innate immune pressure during chronic HCV infection.
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Affiliation(s)
- Nimisha Chaturvedi
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | | | - Hongmei Mo
- Gilead Sciences IncFoster CityUnited States
| | | | | | | | | | | | - Jacques Fellay
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
- Precision Medicine UnitLausanne University HospitalLausanneSwitzerland
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42
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Ramírez de Arellano E, Díez-Fuertes F, Aguilar F, de la Torre Tarazona HE, Sánchez-Lara S, Lao Y, Vicario JL, García F, González-Garcia J, Pulido F, Gutierrez-Rodero F, Moreno S, Iribarren JA, Viciana P, Vilches C, Ramos M, Capa L, Alcamí J, Del Val M. Novel association of five HLA alleles with HIV-1 progression in Spanish long-term non progressor patients. PLoS One 2019; 14:e0220459. [PMID: 31393887 PMCID: PMC6687284 DOI: 10.1371/journal.pone.0220459] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 07/16/2019] [Indexed: 12/12/2022] Open
Abstract
Certain host genetic variants, especially in the human leucocyte antigen (HLA) region, are associated with different progression of HIV-1-induced diseases and AIDS. Long term non progressors (LTNP) represent only the 2% of infected patients but are especially relevant because of their efficient HIV control. In this work we present a global analysis of genetic data in the large national multicenter cohort of Spanish LTNP, which is compared with seronegative individuals and HIV-positive patients. We have analyzed whether several single-nucleotide polymorphisms (SNPs) including in key genes and certain HLA-A and B alleles could be associated with a specific HIV phenotype. A total of 846 individuals, 398 HIV-1-positive patients (213 typical progressors, 55 AIDS patients, and 130 LTNPs) and 448 HIV-negative controls, were genotyped for 15 polymorphisms and HLA-A and B alleles. Significant differences in the allele frequencies among the studied populations identified 16 LTNP-associated genetic factors, 5 of which were defined for the first time as related to LTNP phenotype: the protective effect of HLA-B39, and the detrimental impact of HLA-B18, -A24, -B08 and –A29. The remaining eleven polymorphisms confirmed previous publications, including the protective alleles HLA-B57, rs2395029 (HCP5), HLA bw4 homozygosity, HLA-B52, HLA-B27, CCR2 V64I, rs9264942 (HLA-C) and HLA-A03; and the risk allele HLA bw6 homozygosity. Notably, individual Spanish HIV-negative individuals had an average of 0.12 protective HLA alleles and SNPs, compared with an average of 1.43 protective alleles per LTNP patient, strongly suggesting positive selection of LTNP. Finally, stratification of LTNP according to viral load showed a proportional relationship between the frequency of protective alleles with control of viral load. Interestingly, no differences in the frequency of protection/risk polymorphisms were found between elite controllers and LTNPs maintaining viral loads <2.000 copies/mL throughout the follow-up.
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Affiliation(s)
- Eva Ramírez de Arellano
- National Center for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- * E-mail:
| | - Francisco Díez-Fuertes
- National Center for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Infectious Diseases Unit, IBIDAPS, HIVACAT, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Francisco Aguilar
- National Center for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | | | - Susana Sánchez-Lara
- National Center for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Viral Immunology, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - Yolanda Lao
- National Center for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - José Luis Vicario
- Departamento de Histocompatibilidad, Centro de Transfusión de Madrid, Madrid, Spain
| | - Felipe García
- Infectious Diseases Unit, IBIDAPS, HIVACAT, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | | | - Federico Pulido
- HIV Unit, Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
| | - Félix Gutierrez-Rodero
- Servicio de Medicina Interna, Unidad de Enfermedades Infecciosas, Hospital General Universitario de Elche, Alicante, Spain
| | | | | | - Pompeyo Viciana
- Laboratory of Immunovirology, Biomedicine Institute of Sevilla, Virgen del Rocío University Hospital, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, IBIS/CSIC/SAS/University of Sevilla, Sevilla, Spain
| | - Carlos Vilches
- Inmunogenética e Histocompatibilidad, Instituto de Investigación Sanitaria Puerta de Hierro, Majadahonda, Madrid, Spain
| | - Manuel Ramos
- National Center for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Viral Immunology, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - Laura Capa
- National Center for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - José Alcamí
- National Center for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Infectious Diseases Unit, IBIDAPS, HIVACAT, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Margarita Del Val
- National Center for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Viral Immunology, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
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43
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Large-scale viral genome analysis identifies novel clinical associations between hepatitis B virus and chronically infected patients. Sci Rep 2019; 9:10529. [PMID: 31324819 PMCID: PMC6642195 DOI: 10.1038/s41598-019-46609-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/25/2019] [Indexed: 12/16/2022] Open
Abstract
Despite the high global prevalence of chronic hepatitis B (CHB) infection, datasets covering the whole hepatitis B viral genome from large patient cohorts are lacking, greatly limiting our understanding of the viral genetic factors involved in this deadly disease. We performed deep sequencing of viral samples from patients chronically infected with HBV to investigate the association between viral genome variation and patients' clinical characteristics. We discovered novel viral variants strongly associated with viral load and HBeAg status. Patients with viral variants C1817T and A1838G had viral loads nearly three orders of magnitude lower than patients without those variants. These patients consequently experienced earlier viral suppression while on treatment. Furthermore, we identified novel variants that either independently or in combination with precore mutation G1896A were associated with the transition from HBeAg positive to the negative phase of infection. These observations are consistent with the hypothesis that mutation of the HBeAg open reading frame is an important factor driving CHB patient's HBeAg status. This analysis provides a detailed picture of HBV genetic variation in the largest patient cohort to date and highlights the diversity of plausible molecular mechanisms through which viral variation affects clinical phenotype.
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44
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Balasubramaniam M, Pandhare J, Dash C. Immune Control of HIV. JOURNAL OF LIFE SCIENCES (WESTLAKE VILLAGE, CALIF.) 2019; 1:4-37. [PMID: 31468033 PMCID: PMC6714987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The human immunodeficiency virus (HIV) infection of the immune cells expressing the cluster of differentiation 4 cell surface glycoprotein (CD4+ cells) causes progressive decline of the immune system and leads to the acquired immunodeficiency syndrome (AIDS). The ongoing global HIV/AIDS pandemic has already claimed over 35 million lives. Even after 37 years into the epidemic, neither a cure is available for the 37 million people living with HIV (PLHIV) nor is a vaccine discovered to avert the millions of new HIV infections that continue to occur each year. If left untreated, HIV infection typically progresses to AIDS and, ultimately, causes death in a majority of PLHIV. The recommended combination antiretroviral therapy (cART) suppresses virus replication and viremia, prevents or delays progression to AIDS, reduces transmission rates, and lowers HIV-associated mortality and morbidity. However, because cART does not eliminate HIV, and an enduring pool of infected resting memory CD4+ T cells (latent HIV reservoir) is established early on, any interruption to cART leads to a relapse of viremia and disease progression. Hence, strict adherence to a life-long cART regimen is mandatory for managing HIV infection in PLHIV. The HIV-1-specific cytotoxic T cells expressing the CD8 glycoprotein (CD8+ CTL) limit the virus replication in vivo by recognizing the viral antigens presented by human leukocyte antigen (HLA) class I molecules on the infected cell surface and killing those cells. Nevertheless, CTLs fail to durably control HIV-1 replication and disease progression in the absence of cART. Intriguingly, <1% of cART-naive HIV-infected individuals called elite controllers/HIV controllers (HCs) exhibit the core features that define a HIV-1 "functional cure" outcome in the absence of cART: durable viral suppression to below the limit of detection, long-term non-progression to AIDS, and absence of viral transmission. Robust HIV-1-specific CTL responses and prevalence of protective HLA alleles associated with enduring HIV-1 control have been linked to the HC phenotype. An understanding of the molecular mechanisms underlying the CTL-mediated suppression of HIV-1 replication and disease progression in HCs carrying specific protective HLA alleles may yield promising insights towards advancing the research on HIV cure and prophylactic HIV vaccine.
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Affiliation(s)
- Muthukumar Balasubramaniam
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN – 37208. USA
- Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, TN – 37208. USA
| | - Jui Pandhare
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN – 37208. USA
- School of Graduate Studies and Research, Meharry Medical College, Nashville, TN – 37208. USA
| | - Chandravanu Dash
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN – 37208. USA
- Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, TN – 37208. USA
- School of Graduate Studies and Research, Meharry Medical College, Nashville, TN – 37208. USA
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45
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Lees JA, Ferwerda B, Kremer PHC, Wheeler NE, Serón MV, Croucher NJ, Gladstone RA, Bootsma HJ, Rots NY, Wijmega-Monsuur AJ, Sanders EAM, Trzciński K, Wyllie AL, Zwinderman AH, van den Berg LH, van Rheenen W, Veldink JH, Harboe ZB, Lundbo LF, de Groot LCPGM, van Schoor NM, van der Velde N, Ängquist LH, Sørensen TIA, Nohr EA, Mentzer AJ, Mills TC, Knight JC, du Plessis M, Nzenze S, Weiser JN, Parkhill J, Madhi S, Benfield T, von Gottberg A, van der Ende A, Brouwer MC, Barrett JC, Bentley SD, van de Beek D. Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis. Nat Commun 2019; 10:2176. [PMID: 31092817 PMCID: PMC6520353 DOI: 10.1038/s41467-019-09976-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/11/2019] [Indexed: 12/21/2022] Open
Abstract
Streptococcus pneumoniae is a common nasopharyngeal colonizer, but can also cause life-threatening invasive diseases such as empyema, bacteremia and meningitis. Genetic variation of host and pathogen is known to play a role in invasive pneumococcal disease, though to what extent is unknown. In a genome-wide association study of human and pathogen we show that human variation explains almost half of variation in susceptibility to pneumococcal meningitis and one-third of variation in severity, identifying variants in CCDC33 associated with susceptibility. Pneumococcal genetic variation explains a large amount of invasive potential (70%), but has no effect on severity. Serotype alone is insufficient to explain invasiveness, suggesting other pneumococcal factors are involved in progression to invasive disease. We identify pneumococcal genes involved in invasiveness including pspC and zmpD, and perform a human-bacteria interaction analysis. These genes are potential candidates for the development of more broadly-acting pneumococcal vaccines.
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Affiliation(s)
- John A Lees
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Bart Ferwerda
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Philip H C Kremer
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Nicole E Wheeler
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- The Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Mercedes Valls Serón
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK
| | | | - Hester J Bootsma
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Nynke Y Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Alienke J Wijmega-Monsuur
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Elisabeth A M Sanders
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, 3508 AB, The Netherlands
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, 3508 AB, The Netherlands
| | - Anne L Wyllie
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, 3508 AB, The Netherlands
- Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Aeilko H Zwinderman
- Amsterdam UMC, University of Amsterdam, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Wouter van Rheenen
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, 3584 CG, The Netherlands
| | - Zitta B Harboe
- Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, DK-2300, Denmark
| | - Lene F Lundbo
- Department of Infectious Diseases, Hvidovre Hospital, University of Copenhagen, Hvidovre, 2650, Denmark
| | - Lisette C P G M de Groot
- Department of Human Nutrition, Wageningen University, P.O. Box 17, 6700 AA, Wageningen, The Netherlands
| | - Natasja M van Schoor
- Amsterdam UMC, VU University, Department of Epidemiology and Biostatistics, Amsterdam Public Health, Van der Boechorststraat 7, Amsterdam, 1007 MB, The Netherlands
| | - Nathalie van der Velde
- Amsterdam UMC, University of Amsterdam, Department of Internal Medicine, Geriatrics, Amsterdam Public Health, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Centre Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Lars H Ängquist
- Center for Clinical Research and Disease Prevention, Bispebjerg and Frederiksberg Hospitals, The Capital Region, Copenhagen, DK-2000, Denmark
| | - Thorkild I A Sørensen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Copenhagen, DK-2200, Denmark
- The Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK-1014, Denmark
| | - Ellen A Nohr
- Institute of Clinical Research, University of Southern Denmark, Odense, DK-5000, Denmark
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Tara C Mills
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Mignon du Plessis
- School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2000, South Africa
| | - Susan Nzenze
- School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2000, South Africa
| | - Jeffrey N Weiser
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016, USA
| | - Julian Parkhill
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Shabir Madhi
- National Institute for Communicable Diseases, Johannesburg, 2192, South Africa
| | - Thomas Benfield
- Department of Infectious Diseases, Hvidovre Hospital, University of Copenhagen, Hvidovre, 2650, Denmark
| | - Anne von Gottberg
- School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, 2000, South Africa
- National Institute for Communicable Diseases, Johannesburg, 2192, South Africa
| | - Arie van der Ende
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam Infection and Immunity, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
- Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam UMC/RIVM, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Matthijs C Brouwer
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands
| | - Jeffrey C Barrett
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Genomics Plc, East Road, Cambridge, CB1 1BH, UK
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.
| | - Diederik van de Beek
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands.
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46
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López-Galíndez C. HIV long-term non-progressors elite controllers: an interplay between host, immune and viral factors. Future Virol 2019. [DOI: 10.2217/fvl-2018-0207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
There is a rare group of HIV-1-infected individuals who show permanent control of clinical progression for over 10 years, maintain CD4+ cells >500 μl and have undetectable viral loads; they are designated long-term non-progressors elite controllers (LTNPs ECs). Multiple studies have demonstrated the necessary contribution of at least two of host, immune and viral factors to the LTNP phenotype. This group of individuals is not homogenous because of the different involvement of these factors. We will review the role of each of these and their combinations to the LTNP EC phenotype. LTNP EC individuals offer an opportunity for the investigation into the mechanisms for the spontaneous control of HIV infection.
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Affiliation(s)
- Cecilio López-Galíndez
- Unidad de Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
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47
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Bertels F, Marzel A, Leventhal G, Mitov V, Fellay J, Günthard HF, Böni J, Yerly S, Klimkait T, Aubert V, Battegay M, Rauch A, Cavassini M, Calmy A, Bernasconi E, Schmid P, Scherrer AU, Müller V, Bonhoeffer S, Kouyos R, Regoes RR. Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T-Cell Decline, and Per-Parasite Pathogenicity. Mol Biol Evol 2019; 35:27-37. [PMID: 29029206 PMCID: PMC5850767 DOI: 10.1093/molbev/msx246] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Pathogen strains may differ in virulence because they attain different loads in their hosts, or because they induce different disease-causing mechanisms independent of their load. In evolutionary ecology, the latter is referred to as “per-parasite pathogenicity”. Using viral load and CD4+ T-cell measures from 2014 HIV-1 subtype B-infected individuals enrolled in the Swiss HIV Cohort Study, we investigated if virulence—measured as the rate of decline of CD4+ T cells—and per-parasite pathogenicity are heritable from donor to recipient. We estimated heritability by donor–recipient regressions applied to 196 previously identified transmission pairs, and by phylogenetic mixed models applied to a phylogenetic tree inferred from HIV pol sequences. Regressing the CD4+ T-cell declines and per-parasite pathogenicities of the transmission pairs did not yield heritability estimates significantly different from zero. With the phylogenetic mixed model, however, our best estimate for the heritability of the CD4+ T-cell decline is 17% (5–30%), and that of the per-parasite pathogenicity is 17% (4–29%). Further, we confirm that the set-point viral load is heritable, and estimate a heritability of 29% (12–46%). Interestingly, the pattern of evolution of all these traits differs significantly from neutrality, and is most consistent with stabilizing selection for the set-point viral load, and with directional selection for the CD4+ T-cell decline and the per-parasite pathogenicity. Our analysis shows that the viral genotype affects virulence mainly by modulating the per-parasite pathogenicity, while the indirect effect via the set-point viral load is minor.
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Affiliation(s)
- Frederic Bertels
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Alex Marzel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Venelin Mitov
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Division of Infectious Diseases, Laboratory of Virology, Geneva University Hospital, Geneva, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine - Petersplatz, University of Basel, Basel, Switzerland
| | - Vincent Aubert
- Division of Immunology and Allergy, University Hospital Lausanne, Lausanne, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Berne University Hospital and University of Berne, Berne, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, Lausanne, Switzerland
| | - Alexandra Calmy
- HIV/AIDS Unit, Infectious Disease Service, Geneva University Hospital, Geneva, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, Budapest, Hungary.,Evolutionary Systems Research Group, MTA Centre for Ecological Research, Tihany, Hungary
| | | | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roland R Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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48
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HIV peptidome-wide association study reveals patient-specific epitope repertoires associated with HIV control. Proc Natl Acad Sci U S A 2019; 116:944-949. [PMID: 30602460 DOI: 10.1073/pnas.1812548116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Genetic variation in the peptide-binding groove of the highly polymorphic HLA class I molecules has repeatedly been associated with HIV-1 control and progression to AIDS, accounting for up to 12% of the variation in HIV-1 set point viral load (spVL). This suggests a key role in disease control for HLA presentation of HIV-1 epitopes to cytotoxic T cells. However, a comprehensive understanding of the relevant HLA-bound HIV epitopes is still elusive. Here we describe a peptidome-wide association study (PepWAS) approach that integrates HLA genotypes and spVL data from 6,311 HIV-infected patients to interrogate the entire HIV-1 proteome (3,252 unique peptides) for disease-relevant peptides. This PepWAS approach predicts a core set of epitopes associated with spVL, including known epitopes but also several previously uncharacterized disease-relevant peptides. More important, each patient presents only a small subset of these predicted core epitopes through their individual HLA-A and HLA-B variants. Eventually, the individual differences in these patient-specific epitope repertoires account for the variation in spVL that was previously associated with HLA genetic variation. PepWAS thus enables a comprehensive functional interpretation of the robust but little-understood association between HLA and HIV-1 control, prioritizing a short list of disease-associated epitopes for the development of targeted therapy.
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49
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Chen QY, Hu YL, Wang XY, Harrison TJ, Wang C, Hu LP, Yang QL, Ren CC, Jia HH, Fang AZL. Locus 5p13.1 may be associated with the selection of cancer-related HBV core promoter mutations. Int J Med Sci 2019; 16:990-997. [PMID: 31341412 PMCID: PMC6643130 DOI: 10.7150/ijms.34297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/21/2019] [Indexed: 11/16/2022] Open
Abstract
Background: The basal core promoter (BCP) double mutations (A1762T and G1764A) of hepatitis B virus (HBV) have been reported to be an aetiological factor of hepatocellular carcinoma (HCC). What distinguishes the subset of HBV carriers in whom these mutations are selected? Methods: A genome-wide association study (GWAS) was carried out on 218 asymptomatic HBsAg carriers infected with HBV with BCP double mutations and 191 controls infected with HBV with the wild type BCP. The highest ranking nucleotide polymorphisms (SNPs) were validated with other study subjects, 203 cases and 181 controls. The expression of the gene nearest a SNP found to be significant was examined using RT-PCR. Results: Forty-five candidate SNPs were identified in the GWAS. Three SNPs were found to be associated with the selection of HBV BCP double mutations in the replication stage, including rs7717457 at 5p13.1, rs670011 at 17q21.2, rs2071611 at 6p22.2. Especially, rs7717457 (P= 4.57×10-5 combined P) reached the potential GWAS significance level. The expression of gene complement component 7 (C7), nearest to SNP rs7717457, differed significantly between the case and control groups (t=2.045, P=0.04), suggesting that SNP rs7717457 was associated with the expression of its nearest gene. Conclusions: SNP rs7717457 is associated with the selection of HBV BCP double mutations, providing an important clue to understanding the mechanisms of oncogenesis of HBV BCP double mutations.
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Affiliation(s)
- Qin-Yan Chen
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Yan-Ling Hu
- Center for Genomic and Personalized Medicine, Guangxi Medical University, 22 ShuangYong Road, Nanning, Guangxi 530021, China
| | - Xue-Yan Wang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | | | - Chao Wang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Li-Ping Hu
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Qing-Li Yang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Chuang-Chuang Ren
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China.,School of Preclinical Medicine, Guangxi Medical University, 22 ShuangYong Road, Nanning, Guangxi 530021, China
| | - Hui-Hua Jia
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China.,School of Preclinical Medicine, Guangxi Medical University, 22 ShuangYong Road, Nanning, Guangxi 530021, China
| | - And Zhong-Liao Fang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
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50
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Abstract
Although the idea of coevolution was first presented 150 years ago, we still only vaguely understand the genetic basis of its workings. Identifying the genes responsible for coevolutionary interactions would enable us to distinguish between fundamentally different models of coevolution and would represent a milestone in population genetics and genomics.
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Affiliation(s)
- Dieter Ebert
- Department of Environmental Sciences, University of Basel, Zoology, Vesalgasse 1, 4051, Basel, Switzerland.
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