1
|
Singh N, Nagar E, Roy D, Arora N. NLRP3/GSDMD mediated pyroptosis induces lung inflammation susceptibility in diesel exhaust exposed mouse strains. Gene 2024; 918:148459. [PMID: 38608794 DOI: 10.1016/j.gene.2024.148459] [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: 12/14/2023] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
BACKGROUND Genetic diversity among species influences the disease severity outcomes linked to air pollution. However, the mechanism responsible for this variability remain elusive and needs further investigation. OBJECTIVE To investigate the genetic factors and pathways linked with differential susceptibility in mouse strains associated with diesel exhaust exposure. METHODS C57BL/6 and Balb/c mice were exposed to diesel exhaust (DE) for 5 days/week for 30 min/day for 8 weeks. Body weight of mice was recorded every week and airway hyperresponsiveness towards DE exposure was recorded after 24 h of last exposure. Mice were euthanised to collect BALF, blood, lung tissues for immunobiochemical assays, structural integrity and genetic studies. RESULTS C57BL/6 mice showed significantly decreased body weight in comparison to Balb/c mice (p < 0.05). Both mouse strains showed lung resistance and damage to elastance upon DE exposure compared to respective controls (p < 0.05) with more pronounced effects in C57BL/6 mice. Lung histology showed increase in bronchiolar infiltration and damage to the wall in C57BL/6 mice (p < 0.05). DE exposure upregulated pro-inflammatory and Th2 cytokine levels in C57BL/6 in comparison to Balb/c mice. C57BL/6 mice showed increase in Caspase-1 and ASC expression confirming activation of downstream pathway. This showed significant activation of inflammasome pathway in C57BL/6 mice with ∼2-fold increase in NLRP3 and elevated IL-1β expression. Gasdermin-D levels were increased in C57BL/6 mice demonstrating induction of pyroptosis that corroborated with IL-1β secretion (p < 0.05). Genetic variability among both species was confirmed with sanger's sequencing suggesting presence of SNPs in 3'UTRs of IL-1β gene influencing expression between mouse strains. CONCLUSIONS C57BL/6 mice exhibited increased susceptibility to diesel exhaust in contrast to Balb/c mice via activation of NLRP3-related pyroptosis. Differential susceptibility between strains may be attributed via SNPs in the 3'UTRs of the IL-1β gene.
Collapse
Affiliation(s)
- Naresh Singh
- Allergy and Immunology Section, CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ekta Nagar
- Allergy and Immunology Section, CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Deepti Roy
- Allergy and Immunology Section, CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Naveen Arora
- Allergy and Immunology Section, CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
2
|
Burnham KL, Milind N, Lee W, Kwok AJ, Cano-Gamez K, Mi Y, Geoghegan CG, Zhang P, McKechnie S, Soranzo N, Hinds CJ, Knight JC, Davenport EE. eQTLs identify regulatory networks and drivers of variation in the individual response to sepsis. CELL GENOMICS 2024:100587. [PMID: 38897207 DOI: 10.1016/j.xgen.2024.100587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/27/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
Sepsis is a clinical syndrome of life-threatening organ dysfunction caused by a dysregulated response to infection, for which disease heterogeneity is a major obstacle to developing targeted treatments. We have previously identified gene-expression-based patient subgroups (sepsis response signatures [SRS]) informative for outcome and underlying pathophysiology. Here, we aimed to investigate the role of genetic variation in determining the host transcriptomic response and to delineate regulatory networks underlying SRS. Using genotyping and RNA-sequencing data on 638 adult sepsis patients, we report 16,049 independent expression (eQTLs) and 32 co-expression module (modQTLs) quantitative trait loci in this disease context. We identified significant interactions between SRS and genotype for 1,578 SNP-gene pairs and combined transcription factor (TF) binding site information (SNP2TFBS) and predicted regulon activity (DoRothEA) to identify candidate upstream regulators. Overall, these approaches identified putative mechanistic links between host genetic variation, cell subtypes, and the individual transcriptomic response to infection.
Collapse
Affiliation(s)
- Katie L Burnham
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nikhil Milind
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; University of Cambridge, Cambridge, UK
| | - Wanseon Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Andrew J Kwok
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kiki Cano-Gamez
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuxin Mi
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Ping Zhang
- Centre for Human Genetics, University of Oxford, Oxford, UK; Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
| | | | - Nicole Soranzo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Charles J Hinds
- Centre for Translational Medicine & Therapeutics, William Harvey Research Institute, Faculty of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Julian C Knight
- Centre for Human Genetics, University of Oxford, Oxford, UK; Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK.
| | | |
Collapse
|
3
|
Zhou Z, Shuai D. Disinfection and post-disinfection conditions drive bacterial and viral evolution across the environment and host. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134811. [PMID: 38850949 DOI: 10.1016/j.jhazmat.2024.134811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Water disinfection practices have long been established as a critical engineering intervention for controlling pathogen transmission and safeguarding individual and public health. However, recent discoveries have unveiled the significant role disinfection and post-disinfection play in accelerating the development of resistance to disinfectants and antimicrobial drugs within bacterial and viral communities in the environment. This phenomenon, in turn, may facilitate the emergence of persistent microbes and those with new genetic characteristics. These microbes may thrive in host environments with increased infectivity and resistance, posing challenges to current medical treatments and jeopardizing human health. In this perspective, we illuminate the intricate interplay between aquatic environments, microbes, and hosts and how microbial virulence evolves across the environment and host under the pressure of disinfection and post-disinfection conditions. We aim to draw attention to the previously overlooked potential risks associated with disinfection in driving the virulence evolution of bacteria and viruses, establish connections between pathogens in diverse environments and hosts within the overarching framework of the One Health concept, and ultimately provide guidelines for advancing future water disinfection technologies to effectively curb the spread of infectious diseases.
Collapse
Affiliation(s)
- Zhe Zhou
- Department of Civil and Environmental Engineering, The George Washington University, Washington, District of Columbia 20052, United States.
| | - Danmeng Shuai
- Department of Civil and Environmental Engineering, The George Washington University, Washington, District of Columbia 20052, United States.
| |
Collapse
|
4
|
Mentzer AJ, Dilthey AT, Pollard M, Gurdasani D, Karakoc E, Carstensen T, Muhwezi A, Cutland C, Diarra A, da Silva Antunes R, Paul S, Smits G, Wareing S, Kim H, Pomilla C, Chong AY, Brandt DYC, Nielsen R, Neaves S, Timpson N, Crinklaw A, Lindestam Arlehamn CS, Rautanen A, Kizito D, Parks T, Auckland K, Elliott KE, Mills T, Ewer K, Edwards N, Fatumo S, Webb E, Peacock S, Jeffery K, van der Klis FRM, Kaleebu P, Vijayanand P, Peters B, Sette A, Cereb N, Sirima S, Madhi SA, Elliott AM, McVean G, Hill AVS, Sandhu MS. High-resolution African HLA resource uncovers HLA-DRB1 expression effects underlying vaccine response. Nat Med 2024; 30:1384-1394. [PMID: 38740997 PMCID: PMC11108778 DOI: 10.1038/s41591-024-02944-5] [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: 02/08/2023] [Accepted: 03/25/2024] [Indexed: 05/16/2024]
Abstract
How human genetic variation contributes to vaccine effectiveness in infants is unclear, and data are limited on these relationships in populations with African ancestries. We undertook genetic analyses of vaccine antibody responses in infants from Uganda (n = 1391), Burkina Faso (n = 353) and South Africa (n = 755), identifying associations between human leukocyte antigen (HLA) and antibody response for five of eight tested antigens spanning pertussis, diphtheria and hepatitis B vaccines. In addition, through HLA typing 1,702 individuals from 11 populations of African ancestry derived predominantly from the 1000 Genomes Project, we constructed an imputation resource, fine-mapping class II HLA-DR and DQ associations explaining up to 10% of antibody response variance in our infant cohorts. We observed differences in the genetic architecture of pertussis antibody response between the cohorts with African ancestries and an independent cohort with European ancestry, but found no in silico evidence of differences in HLA peptide binding affinity or breadth. Using immune cell expression quantitative trait loci datasets derived from African-ancestry samples from the 1000 Genomes Project, we found evidence of differential HLA-DRB1 expression correlating with inferred protection from pertussis following vaccination. This work suggests that HLA-DRB1 expression may play a role in vaccine response and should be considered alongside peptide selection to improve vaccine design.
Collapse
Affiliation(s)
- Alexander J Mentzer
- Centre for Human Genetics, University of Oxford, Oxford, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - Alexander T Dilthey
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital of Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | | | | | | | - Allan Muhwezi
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Clare Cutland
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Amidou Diarra
- Groupe de Recherche Action en Santé (GRAS) 06 BP 10248, Ouagadougou, Burkina Faso
| | | | - Sinu Paul
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Gaby Smits
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Susan Wareing
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
| | | | | | - Amanda Y Chong
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Debora Y C Brandt
- Department of Integrative Biology, University of California at Berkeley, California, CA, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California at Berkeley, California, CA, USA
| | - Samuel Neaves
- Avon Longitudinal Study of Parents and Children at University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Nicolas Timpson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Austin Crinklaw
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Anna Rautanen
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dennison Kizito
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Tom Parks
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Kate E Elliott
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tara Mills
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Katie Ewer
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Nick Edwards
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Segun Fatumo
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- The Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine London, London, UK
| | - Emily Webb
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine London, London, UK
| | - Sarah Peacock
- Tissue Typing Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Katie Jeffery
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | | | - Bjorn Peters
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Sodiomon Sirima
- Groupe de Recherche Action en Santé (GRAS) 06 BP 10248, Ouagadougou, Burkina Faso
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Alison M Elliott
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine London, London, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Adrian V S Hill
- Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Manjinder S Sandhu
- Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, UK.
| |
Collapse
|
5
|
Carlsson F, Råberg L. The germ theory revisited: A noncentric view on infection outcome. Proc Natl Acad Sci U S A 2024; 121:e2319605121. [PMID: 38578984 PMCID: PMC11047106 DOI: 10.1073/pnas.2319605121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
Abstract
The germ theory states that pathogenic microorganisms are responsible for causing infectious diseases. The theory is inherently microbe-centric and does not account for variability in disease severity among individuals and asymptomatic carriership-two phenomena indicating an important role for host variability in infection outcome. The basic tenet of the germ theory was recently challenged, and a radically host-centric paradigm referred to as the "full-blown host theory" was proposed. According to this view, the pathogen is reduced to a passive environmental trigger, and the development of disease is instead due to pre-existing immunodeficiencies of the host. Here, we consider the factors that determine disease severity using established knowledge concerning evolutionary biology, microbial pathogenesis, and host-pathogen interactions. We note that the available data support a noncentric view that recognizes key roles for both the causative microbe and the host in dictating infection outcome.
Collapse
Affiliation(s)
| | - Lars Råberg
- Department of Biology, Lund University, Lund223 62, Sweden
| |
Collapse
|
6
|
Jain A, Singam A, Mudiganti VNKS. Recent Advances in Immunomodulatory Therapy in Sepsis: A Comprehensive Review. Cureus 2024; 16:e57309. [PMID: 38690455 PMCID: PMC11059166 DOI: 10.7759/cureus.57309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 03/30/2024] [Indexed: 05/02/2024] Open
Abstract
Sepsis remains a critical healthcare challenge, characterized by dysregulated immune responses to infection, leading to organ dysfunction and high mortality rates. Traditional treatment strategies often fail to address the underlying immune dysregulation, necessitating exploring novel therapeutic approaches. Immunomodulatory therapy holds promise in sepsis management by restoring immune balance and mitigating excessive inflammation. This comprehensive review examines the pathophysiology of sepsis, current challenges in treatment, and recent advancements in immunomodulatory agents, including biologics, immunotherapy, and cellular therapies. Clinical trial outcomes, safety profiles, and future research and clinical practice implications are discussed. While immunomodulatory therapies show considerable potential in improving sepsis outcomes, their successful implementation requires further research, collaboration, and integration into standard clinical protocols.
Collapse
Affiliation(s)
- Abhishek Jain
- Critical Care Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Amol Singam
- Critical Care Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - V N K Srinivas Mudiganti
- Critical Care Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| |
Collapse
|
7
|
Garg E, Arguello-Pascualli P, Vishnyakova O, Halevy AR, Yoo S, Brooks JD, Bull SB, Gagnon F, Greenwood CMT, Hung RJ, Lawless JF, Lerner-Ellis J, Dennis JK, Abraham RJS, Garant JM, Thiruvahindrapuram B, Jones SJM, Strug LJ, Paterson AD, Sun L, Elliott LT. Canadian COVID-19 host genetics cohort replicates known severity associations. PLoS Genet 2024; 20:e1011192. [PMID: 38517939 PMCID: PMC10990181 DOI: 10.1371/journal.pgen.1011192] [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: 06/30/2023] [Revised: 04/03/2024] [Accepted: 02/22/2024] [Indexed: 03/24/2024] Open
Abstract
The HostSeq initiative recruited 10,059 Canadians infected with SARS-CoV-2 between March 2020 and March 2023, obtained clinical information on their disease experience and whole genome sequenced (WGS) their DNA. We analyzed the WGS data for genetic contributors to severe COVID-19 (considering 3,499 hospitalized cases and 4,975 non-hospitalized after quality control). We investigated the evidence for replication of loci reported by the International Host Genetics Initiative (HGI); analyzed the X chromosome; conducted rare variant gene-based analysis and polygenic risk score testing. Population stratification was adjusted for using meta-analysis across ancestry groups. We replicated two loci identified by the HGI for COVID-19 severity: the LZTFL1/SLC6A20 locus on chromosome 3 and the FOXP4 locus on chromosome 6 (the latter with a variant significant at P < 5E-8). We found novel significant associations with MRAS and WDR89 in gene-based analyses, and constructed a polygenic risk score that explained 1.01% of the variance in severe COVID-19. This study provides independent evidence confirming the robustness of previously identified COVID-19 severity loci by the HGI and identifies novel genes for further investigation.
Collapse
Affiliation(s)
- Elika Garg
- Department of Statistics and Actuarial Science, Simon Fraser University, Vancouver, British Columbia, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Paola Arguello-Pascualli
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Olga Vishnyakova
- Department of Statistics and Actuarial Science, Simon Fraser University, Vancouver, British Columbia, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Anat R. Halevy
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Samantha Yoo
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Jennifer D. Brooks
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Shelley B. Bull
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - France Gagnon
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Celia M. T. Greenwood
- Gerald Bronfman Department of Oncology, Department of Epidemiology, Biostatistics and Occupational Health, Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Rayjean J. Hung
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Jerald F. Lawless
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, Ontario, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jessica K. Dennis
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rohan J. S. Abraham
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jean-Michel Garant
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Steven J. M. Jones
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Lisa J. Strug
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Andrew D. Paterson
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Lei Sun
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Lloyd T. Elliott
- Department of Statistics and Actuarial Science, Simon Fraser University, Vancouver, British Columbia, Canada
| |
Collapse
|
8
|
Alamad B, Elliott K, Knight JC. Cross-population applications of genomics to understand the risk of multifactorial traits involving inflammation and immunity. CAMBRIDGE PRISMS. PRECISION MEDICINE 2024; 2:e3. [PMID: 38549844 PMCID: PMC10953767 DOI: 10.1017/pcm.2023.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/15/2023] [Accepted: 12/18/2023] [Indexed: 04/26/2024]
Abstract
The interplay between genetic and environmental factors plays a significant role in interindividual variation in immune and inflammatory responses. The availability of high-throughput low-cost genotyping and next-generation sequencing has revolutionized our ability to identify human genetic variation and understand how this varies within and between populations, and the relationship with disease. In this review, we explore the potential of genomics for patient benefit, specifically in the diagnosis, prognosis and treatment of inflammatory and immune-related diseases. We summarize the knowledge arising from genetic and functional genomic approaches, and the opportunity for personalized medicine. The review covers applications in infectious diseases, rare immunodeficiencies and autoimmune diseases, illustrating advances in diagnosis and understanding risk including use of polygenic risk scores. We further explore the application for patient stratification and drug target prioritization. The review highlights a key challenge to the field arising from the lack of sufficient representation of genetically diverse populations in genomic studies. This currently limits the clinical utility of genetic-based diagnostic and risk-based applications in non-Caucasian populations. We highlight current genome projects, initiatives and biobanks from diverse populations and how this is being used to improve healthcare globally by improving our understanding of genetic susceptibility to diseases and regional pathogens such as malaria and tuberculosis. Future directions and opportunities for personalized medicine and wider application of genomics in health care are described, for the benefit of individual patients and populations worldwide.
Collapse
Affiliation(s)
- Bana Alamad
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kate Elliott
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Julian C. Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| |
Collapse
|
9
|
Fam BSDO, Feira MF, Cadore NA, Sbruzzi R, Hünemeier T, Abel L, Zhang Q, Casanova JL, Vianna FSL. Human genetic determinants of COVID-19 in Brazil: challenges and future plans. Genet Mol Biol 2024; 46:e20230128. [PMID: 38226654 DOI: 10.1590/1678-4685-gmb-2023-0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 11/14/2023] [Indexed: 01/17/2024] Open
Abstract
COVID-19 pandemic represented a worldwide major challenge in different areas, and efforts undertaken by the scientific community led to the understanding of some of the genetic determinants that influence the different COVID-19 outcomes. In this paper, we review the studies about the role of human genetics in COVID-19 severity and how Brazilian studies also contributed to those findings. Rare variants in genes related to Inborn Errors of Immunity (IEI) in the type I interferons pathway, and its phenocopies, have been described as being causative of severe outcomes. IEI and its phenocopies are present in Brazil, not only in COVID-19 patients, but also in autoimmune conditions and severe reactions to yellow fever vaccine. In addition, studies focusing on common variants and GWAS studies encompassing worldwide patients have found several loci associated with COVID-19 severity. A GWAS study including only Brazilian COVID-19 patients identified a new locus 1q32.1 associated with COVID-19 severity. Thus, more comprehensive studies considering the Brazilian genomic diversity should be performed, since they can help to reveal not only what are the genetic determinants that contribute to the different outcomes for COVID-19 in the Brazilian population, but in the understanding of human genetics in different health conditions.
Collapse
Affiliation(s)
- Bibiana S de Oliveira Fam
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Marilea Furtado Feira
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Nathan Araujo Cadore
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Renan Sbruzzi
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Tábita Hünemeier
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas/Universitat Pompeu Fabra), Barcelona, Spain
| | - Laurent Abel
- The Rockefeller University, Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Qian Zhang
- The Rockefeller University, Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Jean-Laurent Casanova
- The Rockefeller University, Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- Necker Hospital for Sick Children, Department of Pediatrics, Paris, France
| | - Fernanda Sales Luiz Vianna
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| |
Collapse
|
10
|
Tilahun M, Gebresilase TT, Aseffa A, Haile K, Wogayehu T, Murale MT, Yntiso H, Munung NS, Bobosha K, Kaba M. Public perceptions of genomic studies and hereditary diseases in Aari community, South Omo Zone, Ethiopia. Trans R Soc Trop Med Hyg 2024; 118:51-60. [PMID: 38165197 DOI: 10.1093/trstmh/trad051] [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: 04/18/2023] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Genetic and genomic research is revolutionizing precision medicine; however, addressing ethical and cultural aspects is crucial to ensure ethical conduct and respect for community values and beliefs. This study explored the beliefs, perceptions and concerns of the Aari community in South Ethiopia regarding genetic concepts, hereditary diseases and ethical research practices related to sample collection, storage and sharing. METHODS In-depth interviews and focus group discussions were conducted with community elders, health officials, tuberculosis patients and apparently healthy individuals. Data were thematically analysed using MAXQDA software. RESULTS Participants identified diseases such as podoconiosis, leprosy, goitre and epilepsy as hereditary and perceived some as 'curses' due to generational impact and social stigma. Disease susceptibility was attributed to divine intervention or factors such as malnutrition and sanitation. Although hereditary diseases were considered unavoidable, in some cases environmental factors were acknowledged. Participants shared personal examples to demonstrate inheritance concepts. Blood held cultural significance, and concerns about its potential misuse resulted in scepticism towards giving samples. CONCLUSIONS This study emphasizes the significance of comprehending local beliefs and perceptions and stresses the need to establish effective communication, build trust and address underlying causes of hesitancy to improve recruitment and ensure ethical conduct.
Collapse
Affiliation(s)
- Melaku Tilahun
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Department of Biology, College of Natural and Computational Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Tewodros Tariku Gebresilase
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Kassa Haile
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Teklu Wogayehu
- Department of Biology, College of Natural and Computational Sciences, Arba Minch University, Arba Minch, Ethiopia
| | - Moi Top Murale
- Department of Psychology, Jinka University, Jinka, Ethiopia
| | - Hailu Yntiso
- South Aari Woreda Administration, Gazer, South Omo, Ethiopia
| | - Nchangwi Syntia Munung
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kidist Bobosha
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Mirgissa Kaba
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| |
Collapse
|
11
|
Shim SR, Lee Y, In SM, Lee KI, Kim I, Jeong H, Shin J, Kim JY. Increased risk of hearing loss associated with macrolide use: a systematic review and meta-analysis. Sci Rep 2024; 14:183. [PMID: 38167873 PMCID: PMC10762137 DOI: 10.1038/s41598-023-50774-1] [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: 07/20/2023] [Accepted: 12/25/2023] [Indexed: 01/05/2024] Open
Abstract
The increased risk of hearing loss with macrolides remains controversial. We aimed to systematically review and meta-analyze data on the clinical risk of hearing loss, tinnitus, and ototoxicity following macrolide use. A systematic search was conducted across PubMed, MEDLINE, Cochrane, and Embase databases from database inception to May 2023. Medical Subject Heading (MeSH) terms and text keywords were utilized, without any language restrictions. In addition to the electronic databases, two authors manually and independently searched for relevant studies in the US and European clinical trial registries and Google Scholar. Studies that involved (1) patients who had hearing loss, tinnitus, or ototoxicity after macrolide use, (2) intervention of use of macrolides such as azithromycin, clarithromycin, erythromycin, fidaxomicin, roxithromycin, spiramycin, and/or telithromycin, (3) comparisons with specified placebos or other antibiotics, (4) outcomes measured as odds ratio (OR), relative risk (RR), hazard ratio (HR), and mean difference for ototoxicity symptoms using randomized control trial (RCT)s and observational studies (case-control, cross-section, and cohort studies) were included. Data extraction was performed independently by two extractors, and a crosscheck was performed to identify any errors. ORs along with their corresponding 95% confidence intervals (CIs) were estimated using random-effects models. The Preferred Reporting Items for Systematic Reviews and Meta-analyses reporting guidelines for RCTs and Meta-Analysis of Observational Studies in Epidemiology guidelines for observational studies were followed. We assessed the hearing loss risk after macrolide use versus controls (placebos and other antibiotics). Based on data from 13 studies including 1,142,021 patients (n = 267,546 for macrolide and n = 875,089 for controls), the overall pooled OR was 1.25 (95% CI 1.07-1.47). In subgroup analysis by study design, the ORs were 1.37 (95% CI 1.08-1.73) for RCTs and 1.33 (95% CI 1.24-1.43) for case-control studies, indicating that RCT and case-control study designs showed a statistically significant higher risk of hearing loss. The group with underlying diseases such as multiple infectious etiologies (OR, 1.16 [95% CI 0.96-1.41]) had a statistically significant lower risk than the group without (OR, 1.53 [95% CI 1.38-1.70] P = .013). The findings from this systematic review and meta-analysis suggest that macrolide antibiotics increase the risk of hearing loss and that healthcare professionals should carefully consider this factor while prescribing macrolides.
Collapse
Affiliation(s)
- Sung Ryul Shim
- Department of Biomedical Informatics, College of Medicine, Konyang University, Daejeon, Republic of Korea
- Konyang Medical data Research group-KYMERA, Konyang University Hospital, Daejeon, Republic of Korea
| | - YungJin Lee
- Konyang Medical data Research group-KYMERA, Konyang University Hospital, Daejeon, Republic of Korea
- Department of Rehabilitation Medicine, College of Medicine, Konyang University, Daejeon, Republic of Korea
| | - Seung Min In
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Konyang University, Daejeon, Republic of Korea
| | - Ki-Il Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Konyang University, Daejeon, Republic of Korea
| | - Ikhee Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Konyang University, Daejeon, Republic of Korea
| | - Hyoyeon Jeong
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Konyang University, Daejeon, Republic of Korea
| | - Jieun Shin
- Department of Biomedical Informatics, College of Medicine, Konyang University, Daejeon, Republic of Korea.
- Konyang Medical data Research group-KYMERA, Konyang University Hospital, Daejeon, Republic of Korea.
| | - Jong-Yeup Kim
- Department of Biomedical Informatics, College of Medicine, Konyang University, Daejeon, Republic of Korea.
- Konyang Medical data Research group-KYMERA, Konyang University Hospital, Daejeon, Republic of Korea.
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Konyang University, Daejeon, Republic of Korea.
| |
Collapse
|
12
|
Cohen M, Laux J, Douagi I. Cytometry in High-Containment Laboratories. Methods Mol Biol 2024; 2779:425-456. [PMID: 38526798 DOI: 10.1007/978-1-0716-3738-8_20] [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] [Indexed: 03/27/2024]
Abstract
The emergence of new pathogens continues to fuel the need for advanced high-containment laboratories across the globe. Here we explore challenges and opportunities for integration of cytometry, a central technology for cell analysis, within high-containment laboratories. We review current applications in infectious disease, vaccine research, and biosafety. Considerations specific to cytometry within high-containment laboratories, such as biosafety requirements, and sample containment strategies are also addressed. We further tour the landscape of emerging technologies, including combination of cytometry with other omics, the application of automation, and artificial intelligence. Finally, we propose a framework to fast track the immersion of advanced technologies into the high-containment research setting to improve global preparedness for new emerging diseases.
Collapse
Affiliation(s)
- Melanie Cohen
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julie Laux
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
13
|
Tabll AA, Sohrab SS, Ali AA, Petrovic A, Steiner Srdarevic S, Siber S, Glasnovic M, Smolic R, Smolic M. Future Prospects, Approaches, and the Government's Role in the Development of a Hepatitis C Virus Vaccine. Pathogens 2023; 13:38. [PMID: 38251345 PMCID: PMC10820710 DOI: 10.3390/pathogens13010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
Developing a safe and effective vaccine against the hepatitis C virus (HCV) remains a top priority for global health. Despite recent advances in antiviral therapies, the high cost and limited accessibility of these treatments impede their widespread application, particularly in resource-limited settings. Therefore, the development of the HCV vaccine remains a necessity. This review article analyzes the current technologies, future prospects, strategies, HCV genomic targets, and the governmental role in HCV vaccine development. We discuss the current epidemiological landscape of HCV infection and the potential of HCV structural and non-structural protein antigens as vaccine targets. In addition, the involvement of government agencies and policymakers in supporting and facilitating the development of HCV vaccines is emphasized. We explore how vaccine development regulatory channels and frameworks affect research goals, funding, and public health policy. The significance of international and public-private partnerships in accelerating the development of an HCV vaccine is examined. Finally, the future directions for developing an HCV vaccine are discussed. In conclusion, the review highlights the urgent need for a preventive vaccine to fight the global HCV disease and the significance of collaborative efforts between scientists, politicians, and public health organizations to reach this important public health goal.
Collapse
Affiliation(s)
- Ashraf A. Tabll
- Microbial Biotechnology Department, Biotechnology Research Institute, National Research Centre, Cairo 12622, Egypt
- Egypt Centre for Research and Regenerative Medicine (ECRRM), Cairo 11517, Egypt
| | - Sayed S. Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed A. Ali
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Cairo 12622, Egypt;
| | - Ana Petrovic
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (A.P.); (S.S.S.); (S.S.); (M.G.); (R.S.)
| | - Sabina Steiner Srdarevic
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (A.P.); (S.S.S.); (S.S.); (M.G.); (R.S.)
| | - Stjepan Siber
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (A.P.); (S.S.S.); (S.S.); (M.G.); (R.S.)
| | - Marija Glasnovic
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (A.P.); (S.S.S.); (S.S.); (M.G.); (R.S.)
| | - Robert Smolic
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (A.P.); (S.S.S.); (S.S.); (M.G.); (R.S.)
| | - Martina Smolic
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (A.P.); (S.S.S.); (S.S.); (M.G.); (R.S.)
| |
Collapse
|
14
|
Namkoong H, Holland SM. Host Susceptibility to Nontuberculous Mycobacterial Pulmonary Disease. Clin Chest Med 2023; 44:723-730. [PMID: 37890911 PMCID: PMC10614071 DOI: 10.1016/j.ccm.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
Nontuberculous mycobacteria (NTM) pulmonary disease is a chronic progressive pulmonary infectious disease caused by low virulence pathogens. The existence of host susceptibility to NTM infection has been recognized from a high incidence among Asians compared to other populations in the United States, a high incidence among slender, middle-aged women, and the presence of familial clusters. Recent whole exome sequencing and genome-wide association studies have identified immune, CFTR, cilia, connective tissue and ion homeostasis genes as host susceptibility genes. Large-scale international collaborative studies and functional analyses are expected to elucidate host susceptibility in the future.
Collapse
Affiliation(s)
- Ho Namkoong
- Department of Infectious Diseases, Keio University School of Medicine, 35 Shinanomachi Shinjyuku-ku, Tokyo 160-8582, Japan.
| | - Steven M Holland
- Division of Intramural Research, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), 10/11N248, MSC 1960, Bethesda, MD 20892-1960, USA
| |
Collapse
|
15
|
Pérez-Umphrey AA, Settlecowski AE, Elbers JP, Williams ST, Jonsson CB, Bonisoli-Alquati A, Snider AM, Taylor SS. Genetic variants associated with hantavirus infection in a reservoir host are related to regulation of inflammation and immune surveillance. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105525. [PMID: 37956745 DOI: 10.1016/j.meegid.2023.105525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/14/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023]
Abstract
The immunogenetics of wildlife populations influence the epidemiology and evolutionary dynamic of the host-pathogen system. Profiling immune gene diversity present in wildlife may be especially important for those species that, while not at risk of disease or extinction themselves, are host to diseases that are a threat to humans, other wildlife, or livestock. Hantaviruses (genus: Orthohantavirus) are globally distributed zoonotic RNA viruses with pathogenic strains carried by a diverse group of rodent hosts. The marsh rice rat (Oryzomys palustris) is the reservoir host of Orthohantavirus bayoui, a hantavirus that causes fatal cases of hantavirus cardiopulmonary syndrome in humans. We performed a genome wide association study (GWAS) using the rice rat "immunome" (i.e., all exons related to the immune response) to identify genetic variants associated with infection status in wild-caught rice rats naturally infected with their endemic strain of hantavirus. First, we created an annotated reference genome using 10× Chromium Linked Reads sequencing technology. This reference genome was used to create custom baits which were then used to target enrich prepared rice rat libraries (n = 128) and isolate their immunomes prior to sequencing. Top SNPs in the association test were present in four genes (Socs5, Eprs, Mrc1, and Il1f8) which have not been previously implicated in hantavirus infections. However, these genes correspond with other loci or pathways with established importance in hantavirus susceptibility or infection tolerance in reservoir hosts: the JAK/STAT, MHC, and NFκB. These results serve as informative markers for future exploration and highlight the importance of immune pathways that repeatedly emerge across hantavirus systems. Our work aids in creating cross-species comparisons for better understanding mechanisms of genetic susceptibility and host-pathogen coevolution in hantavirus systems.
Collapse
Affiliation(s)
- Anna A Pérez-Umphrey
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA.
| | - Amie E Settlecowski
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA
| | - Jean P Elbers
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA; Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Währinger Straße 10, 1090 Vienna, Austria
| | - S Tyler Williams
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA
| | - Colleen B Jonsson
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, University of Tennessee Health Science Center, University of Tennessee, 858 Madison Ave., Memphis, TN 38163, USA
| | - Andrea Bonisoli-Alquati
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA; Department of Biological Sciences, California State Polytechnic University-Pomona, Pomona, CA 91768, USA
| | - Allison M Snider
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA
| | - Sabrina S Taylor
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA
| |
Collapse
|
16
|
Angchagun K, Boonklang P, Chomkatekaew C, Pakdeerat S, Wongsuwan G, Amornchai P, Wuthiekanun V, Panapipat S, Ngernseng T, Waithira N, Walton S, Limmathurotsakul D, Surawong A, Siriboon S, Chamnan P, Chantratita N, Dunachie S, Corander J, Davenport EE, Knight J, Parkhill J, Peacock SJ, Thomson NR, Day NP, Chewapreecha C. BurkHostGEN: a study protocol for evaluating variations in the Burkholderia pseudomallei and host genomes associated with melioidosis infection. Wellcome Open Res 2023; 8:347. [PMID: 37928212 PMCID: PMC10624953 DOI: 10.12688/wellcomeopenres.19809.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2023] [Indexed: 11/07/2023] Open
Abstract
Background Melioidosis is a frequently fatal disease caused by an environmental bacterium Burkholderia pseudomallei. The disease is prevalent in northeast Thailand, particularly among rice field farmers who are at risk of bacterial exposure through contact with contaminated soil and water. However, not all exposure results in disease, and infection can manifest diverse outcomes. We postulate that genetic factors, whether from the bacterium, the host or the combination of both, may influence disease outcomes. To address this hypothesis, we aim to collect, sequence, and analyse genetic data from melioidosis patients and controls, along with isolates of B. pseudomallei obtained from patients. Additionally, we will study the metagenomics of the household water supply for both patients and controls, including the presence of B. pseudomallei. Methods BurkHostGEN is an ongoing observational study being conducted at Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand. We are obtaining consent from 600 melioidosis patients and 700 controls, spanning both sexes, to collect 1 mL of blood for host DNA analysis, 3 mL of blood for RNA analysis, as well as 5 L of household water supply for metagenomic analysis. Additionally, we are isolating B. pseudomallei from the melioidosis patients to obtain bacterial DNA. This comprehensive approach will allow us to identify B. pseudomallei and their paired host genetic factors associated with disease acquisition and severity. Ethical approvals have been obtained for BurkHostGEN. Host and bacterial genetic data will be uploaded to European Genome-Phenome Archive (EGA) and European Nucleotide Archive (ENA), respectively. Conclusions BurkHostGEN holds the potential to discover bacterial and host genetic factors associated with melioidosis infection and severity of illness. It can also support various study designs, including biomarker validation, disease pathogenesis, and epidemiological analysis not only for melioidosis but also for other infectious diseases.
Collapse
Affiliation(s)
- Kesorn Angchagun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Phumrapee Boonklang
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Chalita Chomkatekaew
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Sukritpong Pakdeerat
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Gumphol Wongsuwan
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Premjit Amornchai
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Salwaluk Panapipat
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Thatsanun Ngernseng
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Naomi Waithira
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Steve Walton
- Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UK
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Anoree Surawong
- Sunpasitthiprasong Regional Hospital, Ubon Ratchathani, 34000, Thailand
| | | | - Parinya Chamnan
- Sunpasitthiprasong Regional Hospital, Ubon Ratchathani, 34000, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Susie Dunachie
- Nuffield Department of Medicine, Centre of Tropical Medicine and Global Health, University of Oxford, Oxford, England, OX3 7LG, UK
| | - Jukka Corander
- Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UK
- Institute of Basic Medical Sciences, Faculty of Medcine, University of Oslo, Oslo, Oslo, 0317, Norway
| | | | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, England, OX3 7BN, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, England, CB3 0ES, UK
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Cambridge, England, CB2 0SP, UK
| | | | - Nicholas P.J. Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
- Nuffield Department of Medicine, Centre of Tropical Medicine and Global Health, University of Oxford, Oxford, England, OX3 7LG, UK
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
- Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UK
- Department of Clinical Medicine, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| |
Collapse
|
17
|
Serafim TD, Iniguez E, Barletta ABF, Cecilio P, Doehl JSP, Short M, Lack J, Nair V, Disotuar M, Wilson T, Coutinho-Abreu IV, Meneses C, Andersen J, Alves E Silva TL, Oliveira F, Vega-Rodriguez J, Barillas-Mury C, Ribeiro JMC, Beverley SM, Kamhawi S, Valenzuela JG. Leishmania genetic exchange is mediated by IgM natural antibodies. Nature 2023; 623:149-156. [PMID: 37880367 DOI: 10.1038/s41586-023-06655-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/19/2023] [Indexed: 10/27/2023]
Abstract
Host factors that mediate Leishmania genetic exchange are not well defined. Here we demonstrate that natural IgM (IgMn)1-4 antibodies mediate parasite genetic exchange by inducing the transient formation of a spherical parasite clump that promotes parasite fusion and hybrid formation. We establish that IgMn from Leishmania-free animals binds to the surface of Leishmania parasites to induce significant changes in the expression of parasite transcripts and proteins. Leishmania binding to IgMn is partially lost after glycosidase treatment, although parasite surface phosphoglycans, including lipophosphoglycan, are not required for IgMn-induced parasite clumping. Notably, the transient formation of parasite clumps is essential for Leishmania hybridization in vitro. In vivo, we observed a 12-fold increase in hybrid formation in sand flies provided a second blood meal containing IgMn compared with controls. Furthermore, the generation of recombinant progeny from mating hybrids and parental lines were only observed in sand flies provided with IgMn. Both in vitro and in vivo IgM-induced Leishmania crosses resulted in full genome hybrids that show equal patterns of biparental contribution. Leishmania co-option of a host natural antibody to facilitate mating in the insect vector establishes a new paradigm of parasite-host-vector interdependence that contributes to parasite diversity and fitness by promoting genetic exchange.
Collapse
Affiliation(s)
- Tiago D Serafim
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
| | - Eva Iniguez
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Ana Beatriz F Barletta
- Mosquito Immunity and Vector Competence Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Pedro Cecilio
- Vector Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Johannes S P Doehl
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Mara Short
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Vinod Nair
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Maria Disotuar
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Timothy Wilson
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Iliano V Coutinho-Abreu
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Claudio Meneses
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - John Andersen
- Vector Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Thiago Luiz Alves E Silva
- Molecular Parasitology and Entomology Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Fabiano Oliveira
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Joel Vega-Rodriguez
- Molecular Parasitology and Entomology Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Carolina Barillas-Mury
- Mosquito Immunity and Vector Competence Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - José M C Ribeiro
- Vector Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Stephen M Beverley
- Department of Molecular Microbiology, School of Medicine, Washington University, St Louis, MO, USA.
| | - Shaden Kamhawi
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
| | - Jesus G Valenzuela
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
| |
Collapse
|
18
|
Amarasinghe HE, Zhang P, Whalley JP, Allcock A, Migliorini G, Brown AC, Scozzafava G, Knight JC. Mapping the epigenomic landscape of human monocytes following innate immune activation reveals context-specific mechanisms driving endotoxin tolerance. BMC Genomics 2023; 24:595. [PMID: 37805492 PMCID: PMC10559536 DOI: 10.1186/s12864-023-09663-0] [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: 02/17/2023] [Accepted: 09/08/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND Monocytes are key mediators of innate immunity to infection, undergoing profound and dynamic changes in epigenetic state and immune function which are broadly protective but may be dysregulated in disease. Here, we aimed to advance understanding of epigenetic regulation following innate immune activation, acutely and in endotoxin tolerant states. METHODS We exposed human primary monocytes from healthy donors (n = 6) to interferon-γ or differing combinations of endotoxin (lipopolysaccharide), including acute response (2 h) and two models of endotoxin tolerance: repeated stimulations (6 + 6 h) and prolonged exposure to endotoxin (24 h). Another subset of monocytes was left untreated (naïve). We identified context-specific regulatory elements based on epigenetic signatures for chromatin accessibility (ATAC-seq) and regulatory non-coding RNAs from total RNA sequencing. RESULTS We present an atlas of differential gene expression for endotoxin and interferon response, identifying widespread context specific changes. Across assayed states, only 24-29% of genes showing differential exon usage are also differential at the gene level. Overall, 19.9% (6,884 of 34,616) of repeatedly observed ATAC peaks were differential in at least one condition, the majority upregulated on stimulation and located in distal regions (64.1% vs 45.9% of non-differential peaks) within which sequences were less conserved than non-differential peaks. We identified enhancer-derived RNA signatures specific to different monocyte states that correlated with chromatin accessibility changes. The endotoxin tolerance models showed distinct chromatin accessibility and transcriptomic signatures, with integrated analysis identifying genes and pathways involved in the inflammatory response, detoxification, metabolism and wound healing. We leveraged eQTL mapping for the same monocyte activation states to link potential enhancers with specific genes, identifying 1,946 unique differential ATAC peaks with 1,340 expression associated genes. We further use this to inform understanding of reported GWAS, for example involving FCHO1 and coronary artery disease. CONCLUSION This study reports context-specific regulatory elements based on transcriptomic profiling and epigenetic signatures for enhancer-derived RNAs and chromatin accessibility in immune tolerant monocyte states, and demonstrates the informativeness of linking such elements and eQTL to inform future mechanistic studies aimed at defining therapeutic targets of immunosuppression and diseases.
Collapse
Affiliation(s)
- Harindra E Amarasinghe
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK.
| | - Ping Zhang
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK
| | - Justin P Whalley
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Alice Allcock
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Gabriele Migliorini
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Andrew C Brown
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Giuseppe Scozzafava
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, UK.
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK.
| |
Collapse
|
19
|
Li B, Manan RS, Liang SQ, Gordon A, Jiang A, Varley A, Gao G, Langer R, Xue W, Anderson D. Combinatorial design of nanoparticles for pulmonary mRNA delivery and genome editing. Nat Biotechnol 2023; 41:1410-1415. [PMID: 36997680 PMCID: PMC10544676 DOI: 10.1038/s41587-023-01679-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/18/2023] [Indexed: 04/07/2023]
Abstract
The expanding applications of nonviral genomic medicines in the lung remain restricted by delivery challenges. Here, leveraging a high-throughput platform, we synthesize and screen a combinatorial library of biodegradable ionizable lipids to build inhalable delivery vehicles for messenger RNA and CRISPR-Cas9 gene editors. Lead lipid nanoparticles are amenable for repeated intratracheal dosing and could achieve efficient gene editing in lung epithelium, providing avenues for gene therapy of congenital lung diseases.
Collapse
Affiliation(s)
- Bowen Li
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Rajith Singh Manan
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shun-Qing Liang
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Akiva Gordon
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Allen Jiang
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew Varley
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Guangping Gao
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
- Horae Gene Therapy Center and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Anesthesiology, Boston Children's Hospital, Boston, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Daniel Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Anesthesiology, Boston Children's Hospital, Boston, MA, USA.
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
20
|
Giulieri SG, Guérillot R, Holmes NE, Baines SL, Hachani A, Hayes AS, Daniel DS, Seemann T, Davis JS, Van Hal S, Tong SYC, Stinear TP, Howden BP. A statistical genomics framework to trace bacterial genomic predictors of clinical outcomes in Staphylococcus aureus bacteremia. Cell Rep 2023; 42:113069. [PMID: 37703880 DOI: 10.1016/j.celrep.2023.113069] [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: 12/01/2022] [Revised: 06/29/2023] [Accepted: 08/18/2023] [Indexed: 09/15/2023] Open
Abstract
Outcomes of severe bacterial infections are determined by the interplay between host, pathogen, and treatments. While human genomics has provided insights into host factors impacting Staphylococcus aureus infections, comparatively little is known about S. aureus genotypes and disease severity. Building on the hypothesis that bacterial pathoadaptation is a key outcome driver, we developed a genome-wide association study (GWAS) framework to identify adaptive mutations associated with treatment failure and mortality in S. aureus bacteremia (1,358 episodes). Our research highlights the potential of vancomycin-selected mutations and vancomycin minimum inhibitory concentration (MIC) as key explanatory variables to predict infection severity. The contribution of bacterial variation was much lower for clinical outcomes (heritability <5%); however, GWASs allowed us to identify additional, MIC-independent candidate pathogenesis loci. Using supervised machine learning, we were able to quantify the predictive potential of these adaptive signatures. Our statistical genomics framework provides a powerful means to capture adaptive mutations impacting severe bacterial infections.
Collapse
Affiliation(s)
- Stefano G Giulieri
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia.
| | - Romain Guérillot
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Natasha E Holmes
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Ashleigh S Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Diane S Daniel
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Torsten Seemann
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Joshua S Davis
- Department of Infectious Diseases, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia; Menzies School of Health Research, Charles Darwin University, Casuarina, NT 0810, Australia
| | - Sebastiaan Van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia
| | - Steven Y C Tong
- Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC 3084, Australia; Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC 3000, Australia
| |
Collapse
|
21
|
Adimulam T, Arumugam T, Naidoo A, Naidoo K, Ramsuran V. Polymorphisms within the SARS-CoV-2 Human Receptor Genes Associate with Variable Disease Outcomes across Ethnicities. Genes (Basel) 2023; 14:1798. [PMID: 37761938 PMCID: PMC10531089 DOI: 10.3390/genes14091798] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
The contribution of human genes to the variability of disease outcomes has been shown to be important across infectious diseases. Studies have shown mutations within specific human genes are associated with variable COVID-19 outcomes. We focused on the SARS-CoV-2 receptors/co-receptors to identify the role of specific polymorphisms within ACE2, TMPRSS2, NRP1 and CD147. Polymorphisms within ACE2 (rs2285666), TMPRSS2 (rs12329760), CD147 (rs8259) and NRP1 (rs10080) have been shown to associate with COVID-19 severity. Using cryopreserved samples from COVID-19-positive African, European and South Asian individuals within South Africa, we determined genotype frequencies. The genetic variant rs2285666 was associated with COVID-19 severity with an ethnic bias. African individuals with a CC genotype demonstrate more severe COVID-19 outcomes (OR = 7.5; 95% CI 1.164-80.89; p = 0.024) compared with those with a TT genotype. The expressions of ACE2 and SARS-CoV-2 viral load were measured using droplet digital PCR. Our results demonstrate rs2285666 and rs10080 were significantly associated with increased SARS-CoV-2 viral load and worse outcomes in certain ethnicities. This study demonstrates two important findings. Firstly, SARS-CoV-2 viral load is significantly lower in Africans compared with individuals of European and South Asian descent (p = 0.0002 and p < 0.0001). Secondly, SARS-CoV-2 viral load associates with specific SARS-CoV-2 receptor variants. A limited number of studies have examined the receptor/co-receptor genes within Africa. This study investigated genetic variants within the SARS-CoV-2 receptor/co-receptor genes and their association with COVID-19 severity and SARS-CoV-2 viral load across different ethnicities. We provide a genetic basis for differences in COVID-19 severity across ethnic groups in South Africa, further highlighting the importance of further investigation to determine potential therapeutic targets and to guide vaccination strategies that may prioritize specific genotypes.
Collapse
Affiliation(s)
- Theolan Adimulam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (T.A.); (T.A.)
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (T.A.); (T.A.)
| | - Anushka Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4041, South Africa; (A.N.); (K.N.)
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4041, South Africa; (A.N.); (K.N.)
- South African Medical Research Council (SAMRC), Durban 4013, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (T.A.); (T.A.)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4041, South Africa; (A.N.); (K.N.)
| |
Collapse
|
22
|
Lindsay-McGee V, Sanchez-Molano E, Banos G, Clark EL, Piercy RJ, Psifidi A. Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach. Genet Sel Evol 2023; 55:60. [PMID: 37592264 PMCID: PMC10436415 DOI: 10.1186/s12711-023-00827-w] [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: 11/23/2022] [Accepted: 07/07/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of these breeds. RESULTS The k-means clustering approach divided both the CP and WB populations into four genetic groups, among which the CP genetic group 1 (C1) associated with non-registered CP, C4 with US CP, WB genetic group 1 (W1) with Holsteiners, and W3 with Anglo European and British WB. Maximum and mean linkage disequilibrium (LD) varied significantly between the two breeds (mean from 0.077 to 0.130 for CP and from 0.016 to 0.370 for WB), but the rate of LD decay was generally slower in CP than WB. The LD block size distribution peaked at 225 kb for all genetic groups, with most of the LD blocks not exceeding 1 Mb. The top 0.5% harmonic mean pairwise fixation index (FST) values identified ontology terms related to cancer risk when the four CP genetic groups were compared. The four CP genetic groups were less inbred than the WB genetic groups, but C2, C3 and C4 had a lower proportion of shorter runs of homozygosity (ROH) (74 to 76% < 4 Mb) than the four WB genetic groups (80 to 85% < 4 Mb), indicating more recent inbreeding. The CP and WB genetic groups had a similar ratio of effective number of breeders (Neb) to effective population size (Ne). CONCLUSIONS Distinct genetic groups of individuals were revealed within each breed, and in WB these genetic groups reflected population substructure better than studbook or country of origin. Ontology terms associated with immune and inflammatory responses were identified from the signatures of selection between CP genetic groups, and while CP were less inbred than WB, the evidence pointed to a greater degree of recent inbreeding. The ratio of Neb to Ne was similar in CP and WB, indicating the influence of popular sires is similar in CP and WB.
Collapse
Affiliation(s)
- Victoria Lindsay-McGee
- Royal Veterinary College, London, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | | | | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | |
Collapse
|
23
|
Biswas S, Nain M, Ahmad SS, Sharma A. Role of Human Twin Studies to Identify Genetic Linkage of Malaria Pathogenesis and Outcomes. Am J Trop Med Hyg 2023; 109:241-247. [PMID: 37277110 PMCID: PMC10397443 DOI: 10.4269/ajtmh.23-0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/01/2023] [Indexed: 06/07/2023] Open
Abstract
Malaria remains a major public health challenge that needs attention, especially when the world is aiming at malaria elimination in the near future. It is crucial to understand the underlying genetic factors and epigenetics involved in malaria susceptibility and the dynamics of host immune responses that affect disease outcomes and relapses in Plasmodium vivax and Plasmodium ovale. Studies in newborn and adult twins can help in understanding the comparative roles of environmental and genetic factors on disease pathogenesis and outcome. These studies can help in providing insights into the factors responsible for malaria susceptibility, clinical presentation, responsiveness toward existing as well as candidate antimalarials, and even identification of novel therapeutic targets. The results and outcomes from twin studies can be further applied to the entire population. In the present manuscript, we analyze the available literature on malaria and human twins and discuss the significance and benefits of twin studies to help in better understanding malaria.
Collapse
Affiliation(s)
- Shibani Biswas
- ICMR-National Institute of Malaria Research, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Minu Nain
- ICMR-National Institute of Malaria Research, New Delhi, India
| | | | - Amit Sharma
- Academy of Scientific and Innovative Research, Ghaziabad, India
- Molecular Medicine, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| |
Collapse
|
24
|
Garg AD. The dynamic interface of genetics and immunity: toward future horizons in health & disease. Genes Immun 2023; 24:155-158. [PMID: 37464025 DOI: 10.1038/s41435-023-00213-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Affiliation(s)
- Abhishek D Garg
- Cell Stress & Immunity (CSI) Lab, Department for Cellular & Molecular Medicine (CMM), KU Leuven, Leuven, Belgium.
| |
Collapse
|
25
|
Nilsen SM, Valand J, Rogne T, Asheim A, Yin W, Metsälä J, Opdahl S, Døllner H, Damås JK, Kajantie E, Solligård E, Sandin S, Risnes K. Gestational age at birth and hospitalisations for infections among individuals aged 0-50 years in Norway: a longitudinal, register-based, cohort study. EClinicalMedicine 2023; 62:102108. [PMID: 37538542 PMCID: PMC10393616 DOI: 10.1016/j.eclinm.2023.102108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 08/05/2023] Open
Abstract
Background Preterm birth is associated with increased risk of childhood infections. Whether this risk persists into adulthood is unknown and limited information is available on risk patterns across the full range of gestational ages. Methods In this longitudinal, register-based, cohort study, we linked individual-level data on all individuals born in Norway (January 01, 1967-December 31, 2016) to nationwide hospital data (January 01, 2008-December 31, 2017). Gestational age was categorised as 23-27, 28-31, 32-33, 34-36, 37-38, 39-41, and 42-44 completed weeks. The analyses were stratified by age at follow-up: 0-11 months and 1-5, 6-14, 15-29, and 30-50 years. The primary outcome was hospitalisation due to any infectious disease, with major infectious disease groups as secondary outcomes. Adjusted hospitalisation rate ratios (RRs) for any infection and infectious disease groups were estimated using negative binomial regression. Models were adjusted for year of birth, maternal age at birth, parity, and sex, and included an offset parameter adjusted for person-time at risk. Findings Among 2,695,830 individuals with 313,940 hospitalisations for infections, we found a pattern of higher hospitalisation risk in lower gestational age groups, which was the strongest in childhood but still evident in adulthood. Comparing those born very preterm (28-31) and late preterm (34-36) to full-term (39-41 weeks), RRs (95% confidence interval) for hospitalisation for any infectious disease at ages 1-5 were 3.3 (3.0-3.7) and 1.7 (1.6-1.8), respectively. At 30-50 years, the corresponding estimates were 1.4 (1.2-1.7) and 1.2 (1.1-1.3). The patterns were similar for the infectious disease groups, including bacterial and viral infections, respiratory tract infections (RTIs), and infections not attributable to RTIs. Interpretation Increasing risk of hospitalisations for infections in lower gestational age groups was most prominent in children but still evident in adolescents and adults. Possible mechanisms and groups that could benefit from vaccinations and other prevention strategies should be investigated. Funding St. Olav's University Hospital and Norwegian University of Science and Technology, Norwegian Research Council, Liaison Committee for education, research and innovation in Central Norway, European Commission, Academy of Finland, Sigrid Jusélius Foundation, Foundation for Pediatric Research, and Signe and Ane Gyllenberg Foundation.
Collapse
Affiliation(s)
- Sara Marie Nilsen
- Center for Health Care Improvement, St. Olav's University Hospital, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jonas Valand
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tormod Rogne
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
- Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, CT, USA
- Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Andreas Asheim
- Center for Health Care Improvement, St. Olav's University Hospital, Norway
- Department of Mathematical Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Weiyao Yin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Metsälä
- Department of Public Health and Welfare, Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Signe Opdahl
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Henrik Døllner
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Children's Clinic, St. Olav's University Hospital, Trondheim, Norway
| | - Jan K. Damås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Clinic of Medicine, Department of Infectious Diseases, St Olav's University Hospital, Trondheim, Norway
| | - Eero Kajantie
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Public Health and Welfare, Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
- Clinical Medicine Research Unit, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Erik Solligård
- Department of Circulation and Medical Imaging, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Research and Development, Møre and Romsdal Hospital Trust, Ålesund, Norway
| | - Sven Sandin
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
- Seaver Center for Autism Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kari Risnes
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Children's Clinic, St. Olav's University Hospital, Trondheim, Norway
| |
Collapse
|
26
|
Scholtz D, Jooste T, Möller M, van Coller A, Kinnear C, Glanzmann B. Challenges of Diagnosing Mendelian Susceptibility to Mycobacterial Diseases in South Africa. Int J Mol Sci 2023; 24:12119. [PMID: 37569495 PMCID: PMC10418440 DOI: 10.3390/ijms241512119] [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: 06/29/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Inborn errors of immunity (IEI) are genetic disorders with extensive clinical presentations. They can range from increased susceptibility to infections to significant immune dysregulation that results in immune impairment. While IEI cases are individually rare, they collectively represent a significant burden of disease, especially in developing countries such as South Africa, where infectious diseases like tuberculosis (TB) are endemic. This is particularly alarming considering that certain high penetrance mutations that cause IEI, such as Mendelian Susceptibility to Mycobacterial Disease (MSMD), put individuals at higher risk for developing TB and other mycobacterial diseases. MSMD patients in South Africa often present with different clinical phenotypes than those from the developed world, therefore complicating the identification of disease-associated variants in this setting with a high burden of infectious diseases. The lack of available data, limited resources, as well as variability in clinical phenotype are the reasons many MSMD cases remain undetected or misdiagnosed. This article highlights the challenges in diagnosing MSMD in South Africa and proposes the use of transcriptomic analysis as a means of potentially identifying dysregulated pathways in affected African populations.
Collapse
Affiliation(s)
- Denise Scholtz
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; (D.S.); (T.J.); (M.M.); (C.K.)
| | - Tracey Jooste
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; (D.S.); (T.J.); (M.M.); (C.K.)
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; (D.S.); (T.J.); (M.M.); (C.K.)
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Ansia van Coller
- South African Medical Research Council (SAMRC) Genomics Platform, Cape Town 7505, South Africa;
| | - Craig Kinnear
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; (D.S.); (T.J.); (M.M.); (C.K.)
- South African Medical Research Council (SAMRC) Genomics Platform, Cape Town 7505, South Africa;
| | - Brigitte Glanzmann
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; (D.S.); (T.J.); (M.M.); (C.K.)
- South African Medical Research Council (SAMRC) Genomics Platform, Cape Town 7505, South Africa;
| |
Collapse
|
27
|
Khadzhieva MB, Gracheva AS, Belopolskaya OB, Kolobkov DS, Kashatnikova DA, Redkin IV, Kuzovlev AN, Grechko AV, Salnikova LE. COVID-19 severity: does the genetic landscape of rare variants matter? Front Genet 2023; 14:1152768. [PMID: 37456666 PMCID: PMC10339319 DOI: 10.3389/fgene.2023.1152768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023] Open
Abstract
Rare variants affecting host defense against pathogens may be involved in COVID-19 severity, but most rare variants are not expected to have a major impact on the course of COVID-19. We hypothesized that the accumulation of weak effects of many rare functional variants throughout the exome may contribute to the overall risk in patients with severe disease. This assumption is consistent with the omnigenic model of the relationship between genetic and phenotypic variation in complex traits, according to which association signals tend to spread across most of the genome through gene regulatory networks from genes outside the major pathways to disease-related genes. We performed whole-exome sequencing and compared the burden of rare variants in 57 patients with severe and 29 patients with mild/moderate COVID-19. At the whole-exome level, we observed an excess of rare, predominantly high-impact (HI) variants in the group with severe COVID-19. Restriction to genes intolerant to HI or damaging missense variants increased enrichment for these classes of variants. Among various sets of genes, an increased signal of rare HI variants was demonstrated predominantly for primary immunodeficiency genes and the entire set of genes associated with immune diseases, as well as for genes associated with respiratory diseases. We advocate taking the ideas of the omnigenic model into account in COVID-19 studies.
Collapse
Affiliation(s)
- Maryam B. Khadzhieva
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- The Laboratory of Molecular Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alesya S. Gracheva
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
- The Department of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Olesya B. Belopolskaya
- The Resource Center “Bio-bank Center”, Research Park of St. Petersburg State University, St. Petersburg, Russia
- The Laboratory of Genogeography, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry S. Kolobkov
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Darya A. Kashatnikova
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ivan V. Redkin
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Artem N. Kuzovlev
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Andrey V. Grechko
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Lyubov E. Salnikova
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- The Laboratory of Molecular Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| |
Collapse
|
28
|
Parsons JB, Westgeest AC, Conlon BP, Fowler VG. Persistent Methicillin-Resistant Staphylococcus aureus Bacteremia: Host, Pathogen, and Treatment. Antibiotics (Basel) 2023; 12:455. [PMID: 36978320 PMCID: PMC10044482 DOI: 10.3390/antibiotics12030455] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a devastating pathogen responsible for a variety of life-threatening infections. A distinctive characteristic of this pathogen is its ability to persist in the bloodstream for several days despite seemingly appropriate antibiotics. Persistent MRSA bacteremia is common and is associated with poor clinical outcomes. The etiology of persistent MRSA bacteremia is a result of the complex interplay between the host, the pathogen, and the antibiotic used to treat the infection. In this review, we explore the factors related to each component of the host-pathogen interaction and discuss the clinical relevance of each element. Next, we discuss the treatment options and diagnostic approaches for the management of persistent MRSA bacteremia.
Collapse
Affiliation(s)
- Joshua B. Parsons
- Department of Medicine, Division of Infectious Disease, Duke University Medical Center, Durham, NC 27710, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Annette C. Westgeest
- Department of Medicine, Division of Infectious Disease, Duke University Medical Center, Durham, NC 27710, USA
- Department of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Brian P. Conlon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Vance G. Fowler
- Department of Medicine, Division of Infectious Disease, Duke University Medical Center, Durham, NC 27710, USA
- Duke Clinical Research Institute, Durham, NC 27710, USA
| |
Collapse
|
29
|
Gokul A, Arumugam T, Ramsuran V. Genetic Ethnic Differences in Human 2'-5'-Oligoadenylate Synthetase and Disease Associations: A Systematic Review. Genes (Basel) 2023; 14:527. [PMID: 36833454 PMCID: PMC9956131 DOI: 10.3390/genes14020527] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Recently, several studies have highlighted a skewed prevalence of infectious diseases within the African continent. Furthermore, a growing number of studies have demonstrated unique genetic variants found within the African genome are one of the contributing factors to the disease severity of infectious diseases within Africa. Understanding the host genetic mechanisms that offer protection against infectious diseases provides an opportunity to develop unique therapeutic interventions. Over the past two decades, several studies have linked the 2'-5'-oligoadenylate synthetase (OAS) family with a range of infectious diseases. More recently, the OAS-1 gene has also been associated with disease severity caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which led to a global pandemic. The OAS family serves as an antiviral factor through the interaction with Ribonuclease-Latent (RNase-L). This review explores the genetic variants observed within the OAS genes and the associations with various viral infections and how previously reported ethnic-specific polymorphisms drive clinical significance. This review provides an overview of OAS genetic association studies with a particular focus on viral diseases affecting individuals of African descent.
Collapse
Affiliation(s)
- Anmol Gokul
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban 4041, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban 4001, South Africa
| |
Collapse
|
30
|
Fang MZ, Jackson SS, Pfeiffer RM, Kim EY, Chen S, Hussain SK, Jacobson LP, Martinson J, Prokunina-Olsson L, Thio CL, Duggal P, Wolinsky S, O’Brien TR. No Association of IFNL4 Genotype With Opportunistic Infections and Cancers Among Men With Human Immunodeficiency Virus 1 Infection. Clin Infect Dis 2023; 76:521-527. [PMID: 36573283 PMCID: PMC10169417 DOI: 10.1093/cid/ciac447] [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: 02/03/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND IFNL4 genetic variants that are strongly associated with clearance of hepatitis C virus have been linked to risk of certain opportunistic infections (OIs) and cancers, including Kaposi sarcoma, cytomegalovirus infection, and herpes simplex virus infection. As the interferon (IFN) λ family plays a role in response to viral, bacterial, and fungal infections, IFNL4 genotype might affect risk for a wide range of OIs/cancers. METHODS We examined associations between genotype for the functional IFNL4 rs368234815 polymorphism and incidence of 16 OIs/cancers among 2310 men with human immunodeficiency virus (2038 white; 272 black) enrolled in the Multicenter AIDS Cohort Study during 1984-1990. Our primary analyses used Cox proportional hazards models adjusted for self-reported racial ancestry to estimate hazard ratios with 95% confidence intervals, comparing participants with the genotypes that generate IFN-λ4 and those with the genotype that abrogates IFN-λ4. We censored follow-up at the introduction of highly effective antiretroviral therapies. RESULTS We found no statistically significant association between IFNL4 genotype and the incidence of Kaposi sarcoma (hazard ratio, 0.92 [95% confidence interval, .76-1.11]), cytomegalovirus infection (0.94 [.71-1.24]), herpes simplex virus infection (1.37 [.68-2.93]), or any other OI/cancer. We observed consistent results using additive genetic models and after controlling for CD4 cell count through time-dependent adjustment or restriction to participants with a low CD4 cell count. CONCLUSIONS The absence of associations between IFNL4 genotype and these OIs/cancers provides evidence that this gene does not affect the risk of disease from opportunistic pathogens.
Collapse
Affiliation(s)
- Michelle Z Fang
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Sarah S Jackson
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Ruth M Pfeiffer
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Eun-Young Kim
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Sabrina Chen
- Information Management Services Inc., Calverton, Maryland, USA
| | - Shehnaz K Hussain
- Department of Public Health Sciences, University of California, Davis, California, USA
| | - Lisa P Jacobson
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jeremy Martinson
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Ludmila Prokunina-Olsson
- Division of Cancer Epidemiology and Genetics, Laboratory of Translational Genomics, National Cancer Institute, Bethesda, Maryland, USA
| | - Chloe L Thio
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Steven Wolinsky
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Thomas R O’Brien
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| |
Collapse
|
31
|
Gago S, Mandarano M, Floridi C, Zelante T. Host, pathogenic fungi and the microbiome: A genetic triangle in infection. Front Immunol 2023; 13:1078014. [PMID: 36733397 PMCID: PMC9887327 DOI: 10.3389/fimmu.2022.1078014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Affiliation(s)
- Sara Gago
- Manchester Fungal Infection Group, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Martina Mandarano
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Claudia Floridi
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Teresa Zelante
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy,*Correspondence: Teresa Zelante,
| |
Collapse
|
32
|
Wang D, Kumar V, Burnham KL, Mentzer AJ, Marsden B, Knight JC. COMBATdb: a database for the COVID-19 Multi-Omics Blood ATlas. Nucleic Acids Res 2023; 51:D896-D905. [PMID: 36353986 PMCID: PMC9825482 DOI: 10.1093/nar/gkac1019] [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: 08/07/2022] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 11/11/2022] Open
Abstract
Advances in our understanding of the nature of the immune response to SARS-CoV-2 infection, and how this varies within and between individuals, is important in efforts to develop targeted therapies and precision medicine approaches. Here we present a database for the COvid-19 Multi-omics Blood ATlas (COMBAT) project, COMBATdb (https://db.combat.ox.ac.uk). This enables exploration of multi-modal datasets arising from profiling of patients with different severities of illness admitted to hospital in the first phase of the pandemic in the UK prior to vaccination, compared with community cases, healthy controls, and patients with all-cause sepsis and influenza. These data include whole blood transcriptomics, plasma proteomics, epigenomics, single-cell multi-omics, immune repertoire sequencing, flow and mass cytometry, and cohort metadata. COMBATdb provides access to the processed data in a well-defined framework of samples, cell types and genes/proteins that allows exploration across the assayed modalities, with functionality including browse, search, download, calculation and visualisation via shiny apps. This advances the ability of users to leverage COMBAT datasets to understand the pathogenesis of COVID-19, and the nature of specific and shared features with other infectious diseases.
Collapse
Affiliation(s)
- Dapeng Wang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Vinod Kumar
- Kennedy Institute for Rheumatology, University of Oxford, UK
| | | | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Brian D Marsden
- Kennedy Institute for Rheumatology, University of Oxford, UK
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford, OX3 7BN, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| |
Collapse
|
33
|
Xu J, Sekiguchi T, Boonyakida J, Kato T, Park EY. Display of multiple proteins on engineered canine parvovirus-like particles expressed in cultured silkworm cells and silkworm larvae. Front Bioeng Biotechnol 2023; 11:1096363. [PMID: 36873345 PMCID: PMC9977810 DOI: 10.3389/fbioe.2023.1096363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Recent progress has been made dramatically in decorating virus-like particles (VLPs) on the surface or inside with functional molecules, such as antigens or nucleic acids. However, it is still challenging to display multiple antigens on the surface of VLP to meet the requirement as a practical vaccine candidate. Herein this study, we focus on the expression and engineering of the capsid protein VP2 of canine parvovirus for VLP display in the silkworm-expression system. The chemistry of the SpyTag/SpyCatcher (SpT/SpC) and SnoopTag/SnoopCatcher (SnT/SnC) are efficient protein covalent ligation systems to modify VP2 genetically, where SpyTag/SnoopTag are inserted into the N-terminus or two distinct loop regions (Lx and L2) of VP2. The SpC-EGFP and SnC-mCherry are employed as model proteins to evaluate their binding and display on six SnT/SnC-modified VP2 variants. From a series of protein binding assays between indicated protein partners, we showed that the VP2 variant with SpT inserted at the L2 region significantly enhanced VLP display to 80% compared to 5.4% from N-terminal SpT-fused VP2-derived VLPs. In contrast, the VP2 variant with SpT at the Lx region failed to form VLPs. Moreover, the SpT (Lx)/SnT (L2) double-engineered chimeric VP2 variants showed covalent conjugation capacity to both SpC/SnC protein partners. The orthogonal ligations between those binding partners were confirmed by both mixing purified proteins and co-infecting cultured silkworm cells or larvae with desired recombinant viruses. Our results indicate that a convenient VLP display platform was successfully developed for multiple antigen displays on demand. Further verifications can be performed to assess its capacity for displaying desirable antigens and inducing a robust immune response to targeted pathogens.
Collapse
Affiliation(s)
- Jian Xu
- Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Tomofumi Sekiguchi
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Jirayu Boonyakida
- Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Tatsuya Kato
- Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan.,Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan.,Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Enoch Y Park
- Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan.,Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan.,Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| |
Collapse
|
34
|
Barmania F, Mellet J, Holborn MA, Pepper MS. Genetic Associations with Coronavirus Susceptibility and Disease Severity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:119-140. [PMID: 37378764 DOI: 10.1007/978-3-031-28012-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19) global public health emergency, and the disease it causes is highly variable in its clinical presentation. Host genetic factors are increasingly recognised as a determinant of infection susceptibility and disease severity. Several initiatives and groups have been established to analyse and review host genetic epidemiology associated with COVID-19 outcomes. Here, we review the genetic loci associated with COVID-19 susceptibility and severity focusing on the common variants identified in genome-wide association studies.
Collapse
Affiliation(s)
- Fatima Barmania
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juanita Mellet
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Megan A Holborn
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Michael S Pepper
- Institute for Cellular and Molecular Medicine, Department of Immunology, SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
| |
Collapse
|
35
|
Zhou H, Astore C, Skolnick J. PHEVIR: an artificial intelligence algorithm that predicts the molecular role of pathogens in complex human diseases. Sci Rep 2022; 12:20889. [PMID: 36463386 PMCID: PMC9719543 DOI: 10.1038/s41598-022-25412-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
Infectious diseases are known to cause a wide variety of post-infection complications. However, it's been challenging to identify which diseases are most associated with a given pathogen infection. Using the recently developed LeMeDISCO approach that predicts comorbid diseases associated with a given set of putative mode of action (MOA) proteins and pathogen-human protein interactomes, we developed PHEVIR, an algorithm which predicts the corresponding human disease comorbidities of 312 viruses and 57 bacteria. These predictions provide an understanding of the molecular bases of complications and means of identifying appropriate drug targets to treat them. As an illustration of its power, PHEVIR is applied to identify putative driver pathogens and corresponding human MOA proteins for Type 2 diabetes, atherosclerosis, Alzheimer's disease, and inflammatory bowel disease. Additionally, we explore the origins of the oncogenicity/oncolyticity of certain pathogens and the relationship between heart disease and influenza. The full PHEVIR database is available at https://sites.gatech.edu/cssb/phevir/ .
Collapse
Affiliation(s)
- Hongyi Zhou
- grid.213917.f0000 0001 2097 4943Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, N.W., Atlanta, GA 30332 USA
| | - Courtney Astore
- grid.213917.f0000 0001 2097 4943Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, N.W., Atlanta, GA 30332 USA
| | - Jeffrey Skolnick
- grid.213917.f0000 0001 2097 4943Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, N.W., Atlanta, GA 30332 USA
| |
Collapse
|
36
|
Traspov AA, Minashkin MM, Poyarkov SV, Komarov AG, Shtinova IA, Speshilov GI, Karbyshev IA, Pozdniakova NV, Godkov MA. The rs17713054 and rs1800629 polymorphisms of genes LZTFL1 and TNF are associated with COVID-19 severity. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2022. [DOI: 10.24075/brsmu.2022.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Both genetic and non-genetic factors are responsible for high interindividual variability in response to SARS-CoV-2. Despite the fact that multiple genetic polymorphisms have been identified as risk factors of severe COVID-19, such polymorphisms are still insufficiently studied in the Russian population. The study was aimed to identify genetic determinants associated with severe COVID-19 in the sample of patients from the Russian Federation. The correlation of the rs17713054 polymorphism in gene LZTFL1 and rs1800629 polymorphism in gene TNF (tumor necrosis factor) with the COVID-19 severity was assessed. DNA samples obtained from 713 patients (324 males and 389 females) aged 18‒95 with COVID-19 of varying severity were analyzed. The rs1800629 polymorphism of gene TNF (OR = 1.5; p = 0.02) and rs17713054 polymorphism of gene LZTFL1 (OR = 1.60; p = 0.0043) were identified as risk factors of severe disease. The TNF polymorphism rs1800629 and LZTFL1 polymorphism rs17713054 could be considered as potential predictive biomarkers. The rs17713054 G > A polymorphism was strongly associated with severe disease. In the future the findings may provide the basis for the development of test-systems for prediction of the risk of severe viral respiratory diseases.
Collapse
Affiliation(s)
| | | | | | - AG Komarov
- State Budget Institution Of Health Of The City Of Moscow "Diagnostic Center (Center For Laboratory Research) Of The Department Of Health Of The City Of Moscow" Russian Federation, , Moscow
| | - IA Shtinova
- State Budget Institution Of Health Of The City Of Moscow "Diagnostic Center (Center For Laboratory Research) Of The Department Of Health Of The City Of Moscow" Russian Federation, , Moscow
| | - GI Speshilov
- State Budget Institution Of Health Of The City Of Moscow "Diagnostic Center (Center For Laboratory Research) Of The Department Of Health Of The City Of Moscow" Russian Federation, , Moscow
| | - IA Karbyshev
- State Budget Institution Of Health Of The City Of Moscow "Diagnostic Center (Center For Laboratory Research) Of The Department Of Health Of The City Of Moscow" Russian Federation, , Moscow
| | | | - MA Godkov
- Sklifosovsky Research Institute for Emergency Medicine, Moscow, Russia
| |
Collapse
|
37
|
Leavey K, MacKenzie RK, Faber S, Lloyd VK, Mao C, Wills MKB, Boucoiran I, Cates EC, Omar A, Marquez O, Darling EK. Lyme borreliosis in pregnancy and associations with parent and offspring health outcomes: An international cross-sectional survey. Front Med (Lausanne) 2022; 9:1022766. [PMID: 36405612 PMCID: PMC9669415 DOI: 10.3389/fmed.2022.1022766] [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: 08/18/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background Lyme disease (LD) is a complex tick-borne pathology caused by Borrelia burgdorferi sensu lato bacteria. Currently, there are limited data regarding the health outcomes of people infected during pregnancy, the potential for perinatal transmission to their fetus, and the long-term effects on these children. Therefore, the primary objective of this survey study was to investigate the impact of LD in pregnancy on both the parent and their offspring. Methods A seven-section survey was developed and administered in REDCap. Although recruitment was primarily through LD-focused organizations, participation was open to anyone over the age of 18 who had been pregnant. Participant health/symptoms were compared across those with “Diagnosed LD,” “Suspected LD,” or “No LD” at any time in their lives. The timing of LD events in the participants’ histories (tick bite, diagnosis, treatment start, etc.) were then utilized to classify the participants’ pregnancies into one of five groups: “Probable Treated LD,” “Probable Untreated LD,” “Possible Untreated LD,” “No Evidence of LD,” and “Unclear.” Results A total of 691 eligible people participated in the survey, of whom 65% had Diagnosed LD, 6% had Suspected LD, and 29% had No LD ever. Both the Diagnosed LD and Suspected LD groups indicated a high symptom burden (p < 0.01). Unfortunately, direct testing of fetal/newborn tissues for Borrelia burgdorferi only occurred following 3% of pregnancies at risk of transmission; positive/equivocal results were obtained in 14% of these cases. Pregnancies with No Evidence of LD experienced the fewest complications (p < 0.01) and were most likely to result in a live birth (p = 0.01) and limited short- and long-term offspring pathologies (p < 0.01). Within the LD-affected pregnancy groups, obtaining treatment did not decrease complications for the parent themselves but did ameliorate neonatal health status, with reduced rates of rashes, hypotonia, and respiratory distress (all p < 0.01). The impact of parent LD treatment on longer-term child outcomes was less clear. Conclusion Overall, this pioneering survey represents significant progress toward understanding the effects of LD on pregnancy and child health. A large prospective study of pregnant people with LD, combining consistent diagnostic testing, exhaustive assessment of fetal/newborn samples, and long-term offspring follow-up, is warranted.
Collapse
Affiliation(s)
- Katherine Leavey
- McMaster Midwifery Research Centre, McMaster University, Hamilton, ON, Canada
| | - Rachel K. MacKenzie
- McMaster Midwifery Research Centre, McMaster University, Hamilton, ON, Canada
| | | | - Vett K. Lloyd
- Department of Biology, Mount Allison University, Sackville, NB, Canada
| | - Charlotte Mao
- Dean Center for Tick Borne Illness, Spaulding Rehabilitation Hospital, Boston, MA, United States
- Invisible International, Cambridge, MA, United States
| | - Melanie K. B. Wills
- G. Magnotta Lyme Disease Research Lab, Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Isabelle Boucoiran
- Centre Hospitalier Universitaire (CHU) Sainte-Justine, Montréal, QC, Canada
- Department of Obstetrics and Gynecology, Université de Montréal, Montréal, QC, Canada
| | - Elizabeth C. Cates
- McMaster Midwifery Research Centre, McMaster University, Hamilton, ON, Canada
| | - Abeer Omar
- Trent/Fleming School of Nursing, Trent University, Peterborough, ON, Canada
| | - Olivia Marquez
- McMaster Midwifery Research Centre, McMaster University, Hamilton, ON, Canada
| | - Elizabeth K. Darling
- McMaster Midwifery Research Centre, McMaster University, Hamilton, ON, Canada
- *Correspondence: Elizabeth K. Darling,
| |
Collapse
|
38
|
Soko ND, Dlamini S, Ntsekhe M, Dandara C. The COVID-19 Pandemic and Explaining Outcomes in Africa: Could Genomic Variation Add to the Debate? OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:594-607. [PMID: 36322905 PMCID: PMC9700373 DOI: 10.1089/omi.2022.0108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, emanated from the Wuhan Province in China and rapidly spread across the globe causing extensive morbidity and mortality rate, and affecting the global economy and livelihoods. Contrary to early predictions of "body bags" across Africa, the African COVID-19 pandemic was marked by apparent low case numbers and an overall mortality rate when compared with the other geographical regions. Factors used to describe this unexpected pattern included a younger population, a swifter and more effective national health policy, limited testing capacities, and the possibility of inadequate reporting of the cases, among others. However, despite genomics contributing to interindividual variations in many diseases across the world, there are inadequate genomic and multiomics data on COVID-19 in Africa that prevent richer transdisciplinary discussions on the contribution of genomics to the spread of COVID-19 pandemic. To invite future debates on comparative studies of COVID-19 genomics and the pandemic spread around the world regions, this expert review evaluates the reported frequency distribution of genetic variants in candidate genes that are likely to affect COVID-19 infection dynamics/disease outcomes. We propose here that genomic variation should be considered among the many factors determining the COVID-19 infection and its outcomes in African populations and across the world.
Collapse
Affiliation(s)
- Nyarai D. Soko
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- UCT/South African Medical Research Council (SAMRC) Platform for Pharmacogenomics Research and Translation, Cape Town, South Africa
- Address correspondence to: Nyarai D. Soko, PhD, Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Sipho Dlamini
- Division of Infectious Diseases, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Mpiko Ntsekhe
- Division of Cardiology, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Collet Dandara
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- UCT/South African Medical Research Council (SAMRC) Platform for Pharmacogenomics Research and Translation, Cape Town, South Africa
- Address correspondence to: Collet Dandara, PhD, Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| |
Collapse
|
39
|
Onisiforou A, Spyrou GM. Systems Bioinformatics Reveals Possible Relationship between COVID-19 and the Development of Neurological Diseases and Neuropsychiatric Disorders. Viruses 2022; 14:v14102270. [PMID: 36298824 PMCID: PMC9611753 DOI: 10.3390/v14102270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
Coronavirus Disease 2019 (COVID-19) is associated with increased incidence of neurological diseases and neuropsychiatric disorders after infection, but how it contributes to their development remains under investigation. Here, we investigate the possible relationship between COVID-19 and the development of ten neurological disorders and three neuropsychiatric disorders by exploring two pathological mechanisms: (i) dysregulation of host biological processes via virus-host protein-protein interactions (PPIs), and (ii) autoreactivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epitopes with host "self" proteins via molecular mimicry. We also identify potential genetic risk factors which in combination with SARS-CoV-2 infection might lead to disease development. Our analysis indicated that neurodegenerative diseases (NDs) have a higher number of disease-associated biological processes that can be modulated by SARS-CoV-2 via virus-host PPIs than neuropsychiatric disorders. The sequence similarity analysis indicated the presence of several matching 5-mer and/or 6-mer linear motifs between SARS-CoV-2 epitopes with autoreactive epitopes found in Alzheimer's Disease (AD), Parkinson's Disease (PD), Myasthenia Gravis (MG) and Multiple Sclerosis (MS). The results include autoreactive epitopes that recognize amyloid-beta precursor protein (APP), microtubule-associated protein tau (MAPT), acetylcholine receptors, glial fibrillary acidic protein (GFAP), neurofilament light polypeptide (NfL) and major myelin proteins. Altogether, our results suggest that there might be an increased risk for the development of NDs after COVID-19 both via autoreactivity and virus-host PPIs.
Collapse
|
40
|
Augusto DG, Yusufali T, Sabatino JJ, Peyser ND, Murdolo LD, Butcher X, Murray V, Pae V, Sarvadhavabhatla S, Beltran F, Gill G, Lynch K, Yun C, Maguire C, Peluso MJ, Hoh R, Henrich TJ, Deeks SG, Davidson M, Lu S, Goldberg SA, Kelly JD, Martin JN, Viera-Green CA, Spellman SR, Langton DJ, Lee S, Marcus GM, Olgin JE, Pletcher MJ, Gras S, Maiers M, Hollenbach JA. A common allele of HLA mediates asymptomatic SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2021.05.13.21257065. [PMID: 34031661 PMCID: PMC8142661 DOI: 10.1101/2021.05.13.21257065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Despite some inconsistent reporting of symptoms, studies have demonstrated that at least 20% of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will remain asymptomatic. Although most global efforts have focused on understanding factors underlying severe illness in COVID-19 (coronavirus disease of 2019), the examination of asymptomatic infection provides a unique opportunity to consider early disease and immunologic features promoting rapid viral clearance. Owing to its critical role in the immune response, we postulated that variation in the human leukocyte antigen (HLA) loci may underly processes mediating asymptomatic infection. We enrolled 29,947 individuals registered in the National Marrow Donor Program for whom high-resolution HLA genotyping data were available in the UCSF Citizen Science smartphone-based study designed to track COVID-19 symptoms and outcomes. Our discovery cohort (n=1428) was comprised of unvaccinated, self-identified subjects who reported a positive test result for SARS-CoV-2. We tested for association of five HLA loci (HLA-A, -B, -C, -DRB1, -DQB1) with disease course and identified a strong association of HLA-B*15:01 with asymptomatic infection, and reproduced this association in two independent cohorts. Suggesting that this genetic association is due to pre-existing T-cell immunity, we show that T cells from pre-pandemic individuals carrying HLA-B*15:01 were reactive to the immunodominant SARS-CoV-2 S-derived peptide NQKLIANQF, and 100% of the reactive cells displayed memory phenotype. Finally, we characterize the protein structure of HLA-B*15:01-peptide complexes, demonstrating that the NQKLIANQF peptide from SARS-CoV-2, and the highly homologous NQKLIANAF from seasonal coronaviruses OC43-CoV and HKU1-CoV, share similar ability to be stabilized and presented by HLA-B*15:01, providing the molecular basis for T-cell cross-reactivity and HLA-B*15:01-mediated pre-existing immunity.
Collapse
Affiliation(s)
- Danillo G. Augusto
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Tasneem Yusufali
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph J. Sabatino
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Noah D. Peyser
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Lawton D. Murdolo
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Xochitl Butcher
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Victoria Murray
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Vivian Pae
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sannidhi Sarvadhavabhatla
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Fiona Beltran
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gurjot Gill
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kara Lynch
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Yun
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Colin Maguire
- University of Utah, Clinical and Translational Science Institute, Salt Lake City, UT
| | - Michael J. Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Timothy J. Henrich
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michelle Davidson
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sarah A. Goldberg
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - J. Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- F.I. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Cynthia A. Viera-Green
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - Stephen R. Spellman
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - David J. Langton
- ExplantLab, The Biosphere, Newcastle Helix, Newcastle-upon-Tyne, UK
| | - Sulggi Lee
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gregory M. Marcus
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey E. Olgin
- Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mark J. Pletcher
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Division of General Internal Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | | | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
41
|
Jo HY, Kim SC, Ahn DH, Lee S, Chang SH, Jung SY, Kim YJ, Kim E, Kim JE, Kim YS, Park WY, Cho NH, Park D, Lee JH, Park HY. Establishment of the large-scale longitudinal multi-omics dataset in COVID-19 patients: data profile and biospecimen. BMB Rep 2022; 55:465-471. [PMID: 35996834 PMCID: PMC9537027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/02/2022] [Accepted: 07/29/2022] [Indexed: 03/08/2024] Open
Abstract
Understanding and monitoring virus-mediated infections has gained importance since the global outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Studies of high-throughput omics-based immune profiling of COVID-19 patients can help manage the current pandemic and future virus-mediated pandemics. Although COVID-19 is being studied since past 2 years, detailed mechanisms of the initial induction of dynamic immune responses or the molecular mechanisms that characterize disease progression remains unclear. This study involved comprehensively collected biospecimens and longitudinal multi-omics data of 300 COVID-19 patients and 120 healthy controls, including whole genome sequencing (WGS), single-cell RNA sequencing combined with T cell receptor (TCR) and B cell receptor (BCR) sequencing (scRNA(+scTCR/BCR)-seq), bulk BCR and TCR sequencing (bulk TCR/BCR-seq), and cytokine profiling. Clinical data were also collected from hospitalized COVID-19 patients, and HLA typing, laboratory characteristics, and COVID-19 viral genome sequencing were performed during the initial diagnosis. The entire set of biospecimens and multi-omics data generated in this project can be accessed by researchers from the National Biobank of Korea with prior approval. This distribution of largescale multi-omics data of COVID-19 patients can facilitate the understanding of biological crosstalk involved in COVID-19 infection and contribute to the development of potential methodologies for its diagnosis and treatment. [BMB Reports 2022; 55(9): 465-471].
Collapse
Affiliation(s)
- Hye-Yeong Jo
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Sang Cheol Kim
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Do-hwan Ahn
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | | | - Se-Hyun Chang
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - So-Young Jung
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Young-Jin Kim
- Division of Genome Science, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Eugene Kim
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Jung-Eun Kim
- Division of Bio Bigdata, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Yeon-Sook Kim
- Division of Infectious Disease, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon 35015, Korea
| | - Woong-Yang Park
- Geninus Inc, Seoul 05836, Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul 08826, Korea
| | | | - Ju-Hee Lee
- Division of Healthcare and Artificial Intelligence, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| | - Hyun-Young Park
- Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea
| |
Collapse
|
42
|
Abstract
Human genetics can inform the biology and epidemiology of coronavirus disease 2019 (COVID-19) by pinpointing causal mechanisms that explain why some individuals become more severely affected by the disease upon infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Large-scale genetic association studies, encompassing both rare and common genetic variants, have used different study designs and multiple disease phenotype definitions to identify several genomic regions associated with COVID-19. Along with a multitude of follow-up studies, these findings have increased our understanding of disease aetiology and provided routes for management of COVID-19. Important emergent opportunities include the clinical translatability of genetic risk prediction, the repurposing of existing drugs, exploration of variable host effects of different viral strains, study of inter-individual variability in vaccination response and understanding the long-term consequences of SARS-CoV-2 infection. Beyond the current pandemic, these transferrable opportunities are likely to affect the study of many infectious diseases.
Collapse
Affiliation(s)
- Mari E K Niemi
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Mark J Daly
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Broad Institute, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.
- Broad Institute, Cambridge, MA, USA.
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
43
|
Assessing the Impact of SARS-CoV-2 Lineages and Mutations on Patient Survival. Viruses 2022; 14:v14091893. [PMID: 36146700 PMCID: PMC9500738 DOI: 10.3390/v14091893] [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: 08/04/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 12/29/2022] Open
Abstract
Objectives: More than two years into the COVID-19 pandemic, SARS-CoV-2 still remains a global public health problem. Successive waves of infection have produced new SARS-CoV-2 variants with new mutations for which the impact on COVID-19 severity and patient survival is uncertain. Methods: A total of 764 SARS-CoV-2 genomes, sequenced from COVID-19 patients, hospitalized from 19th February 2020 to 30 April 2021, along with their clinical data, were used for survival analysis. Results: A significant association of B.1.1.7, the alpha lineage, with patient mortality (log hazard ratio (LHR) = 0.51, C.I. = [0.14,0.88]) was found upon adjustment by all the covariates known to affect COVID-19 prognosis. Moreover, survival analysis of mutations in the SARS-CoV-2 genome revealed 27 of them were significantly associated with higher mortality of patients. Most of these mutations were located in the genes coding for the S, ORF8, and N proteins. Conclusions: This study illustrates how a combination of genomic and clinical data can provide solid evidence for the impact of viral lineage on patient survival.
Collapse
|
44
|
Caruso C, Ligotti ME, Accardi G, Aiello A, Candore G. An immunologist's guide to immunosenescence and its treatment. Expert Rev Clin Immunol 2022; 18:961-981. [PMID: 35876758 DOI: 10.1080/1744666x.2022.2106217] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION : The ageing process causes several changes in the immune system, although immune ageing is strongly influenced by individual immunological history, as well as genetic and environmental factors leading to inter-individual variability. AREAS COVERED : Here, we focused on the biological and clinical meaning of immunosenescence. Data on SARS-CoV-2 and Yellow Fever vaccine have demonstrated the clinical relevance of immunosenescence, while inconsistent results, obtained from longitudinal studies aimed at looking for immune risk phenotypes, have revealed that the immunosenescence process is highly context-dependent. Large projects have allowed the delineation of the drivers of immune system variance, including genetic and environmental factors, sex, smoking, and co-habitation. Therefore, it is difficult to identify the interventions that can be envisaged to maintain or improve immune function in older people. That suggests that drug treatment of immunosenescence should require personalized intervention. Regarding this, we discussed the role of changes in lifestyle as a potential therapeutic approach. EXPERT OPINION : Our review points out that age is only part of the problem of immunosenescence. Everyone ages differently because he/she is unique in genetics and experience of life and this applies even more to the immune system (immunobiography). Finally, the present review shows how appreciable results in the modification of immunosenescence biomarkers can be achieved with lifestyle modification.
Collapse
Affiliation(s)
- Calogero Caruso
- Laboratorio di Immunopatologia e Immunosenescenza, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, Palermo, Italy
| | - Mattia Emanuela Ligotti
- Laboratorio di Immunopatologia e Immunosenescenza, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, Palermo, Italy
| | - Giulia Accardi
- Laboratorio di Immunopatologia e Immunosenescenza, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, Palermo, Italy
| | - Anna Aiello
- Laboratorio di Immunopatologia e Immunosenescenza, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, Palermo, Italy
| | - Giuseppina Candore
- Laboratorio di Immunopatologia e Immunosenescenza, Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata, Università di Palermo, Palermo, Italy
| |
Collapse
|
45
|
Mørup SB, Nazaryan-Petersen L, Gabrielaite M, Reekie J, Marquart HV, Hartling HJ, Marvig RL, Katzenstein TL, Masmas TN, Lundgren J, Murray DD, Helleberg M, Borgwardt L. Added Value of Reanalysis of Whole Exome- and Whole Genome Sequencing Data From Patients Suspected of Primary Immune Deficiency Using an Extended Gene Panel and Structural Variation Calling. Front Immunol 2022; 13:906328. [PMID: 35874679 PMCID: PMC9302041 DOI: 10.3389/fimmu.2022.906328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background Knowledge of the genetic variation underlying Primary Immune Deficiency (PID) is increasing. Reanalysis of genome-wide sequencing data from undiagnosed patients with suspected PID may improve the diagnostic rate. Methods We included patients monitored at the Department of Infectious Diseases or the Child and Adolescent Department, Rigshospitalet, Denmark, for a suspected PID, who had been analysed previously using a targeted PID gene panel (457 PID-related genes) on whole exome- (WES) or whole genome sequencing (WGS) data. A literature review was performed to extend the PID gene panel used for reanalysis of single nucleotide variation (SNV) and small indels. Structural variant (SV) calling was added on WGS data. Results Genetic data from 94 patients (86 adults) including 36 WES and 58 WGS was reanalysed a median of 23 months after the initial analysis. The extended gene panel included 208 additional PID-related genes. Genetic reanalysis led to a small increase in the proportion of patients with new suspicious PID related variants of uncertain significance (VUS). The proportion of patients with a causal genetic diagnosis was constant. In total, five patients (5%, including three WES and two WGS) had a new suspicious PID VUS identified due to reanalysis. Among these, two patients had a variant added due to the expansion of the PID gene panel, and three patients had a variant reclassified to a VUS in a gene included in the initial PID gene panel. The total proportion of patients with PID related VUS, likely pathogenic, and pathogenic variants increased from 43 (46%) to 47 (50%), as one patient had a VUS detected in both initial- and reanalysis. In addition, we detected new suspicious SNVs and SVs of uncertain significance in PID candidate genes with unknown inheritance and/or as heterozygous variants in genes with autosomal recessive inheritance in 8 patients. Conclusion These data indicate a possible diagnostic gain of reassessing WES/WGS data from patients with suspected PID. Reasons for the possible gain included improved knowledge of genotype-phenotype correlation, expanding the gene panel, and adding SV analyses. Future studies of genotype-phenotype correlations may provide additional knowledge on the impact of the new suspicious VUSs.
Collapse
Affiliation(s)
- Sara Bohnstedt Mørup
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lusine Nazaryan-Petersen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Migle Gabrielaite
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Joanne Reekie
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Hanne V. Marquart
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Hans Jakob Hartling
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rasmus L. Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Terese L. Katzenstein
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Tania N. Masmas
- The Child and Adolescent Department, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jens Lundgren
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Daniel D. Murray
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marie Helleberg
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Line Borgwardt
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| |
Collapse
|
46
|
Redin C, Thorball CW, Fellay J. Host genomics of SARS-CoV-2 infection. Eur J Hum Genet 2022; 30:908-914. [PMID: 35768520 PMCID: PMC9244159 DOI: 10.1038/s41431-022-01136-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/02/2022] [Accepted: 06/13/2022] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 infected a large fraction of humans in the past 2 years. The clinical presentation of acute infection varies greatly between individuals, ranging from asymptomatic or mild to life-threatening COVID-19 pneumonia with multi-organ complications. Demographic and comorbid factors explain part of this variability, yet it became clear early in the pandemic that human genetic variation also plays a role in the stark differences observed amongst SARS-CoV-2 infected individuals. Using tools and approaches successfully developed for human genomic studies in the previous decade, large international collaborations embarked in the exploration of the genetic determinants of multiple outcomes of SARS-CoV-2 infection, with a special emphasis on disease severity. Genome-wide association studies identified multiple common genetic variants associated with COVID-19 pneumonia, most of which in regions encoding genes with known or suspected immune function. However, the downstream, functional work required to understand the precise causal variants at each locus has only begun. The interrogation of rare genetic variants using targeted, exome, or genome sequencing approaches has shown that defects in genes involved in type I interferon response explain some of the most severe cases. By highlighting genes and pathways involved in SARS-CoV-2 pathogenesis and host-virus interactions, human genomic studies not only revealed novel preventive and therapeutic targets, but also paved the way for more individualized disease management.
Collapse
Affiliation(s)
- Claire Redin
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Christian W Thorball
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland. .,School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| |
Collapse
|
47
|
Epigenomic analysis reveals a dynamic and context-specific macrophage enhancer landscape associated with innate immune activation and tolerance. Genome Biol 2022; 23:136. [PMID: 35751107 PMCID: PMC9229144 DOI: 10.1186/s13059-022-02702-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 06/09/2022] [Indexed: 11/21/2022] Open
Abstract
Background Chromatin states and enhancers associate gene expression, cell identity and disease. Here, we systematically delineate the acute innate immune response to endotoxin in terms of human macrophage enhancer activity and contrast with endotoxin tolerance, profiling the coding and non-coding transcriptome, chromatin accessibility and epigenetic modifications. Results We describe the spectrum of enhancers under acute and tolerance conditions and the regulatory networks between these enhancers and biological processes including gene expression, splicing regulation, transcription factor binding and enhancer RNA signatures. We demonstrate that the vast majority of differentially regulated enhancers on acute stimulation are subject to tolerance and that expression quantitative trait loci, disease-risk variants and eRNAs are enriched in these regulatory regions and related to context-specific gene expression. We find enrichment for context-specific eQTL involving endotoxin response and specific infections and delineate specific differential regions informative for GWAS variants in inflammatory bowel disease and multiple sclerosis, together with a context-specific enhancer involving a bacterial infection eQTL for KLF4. We show enrichment in differential enhancers for tolerance involving transcription factors NFκB-p65, STATs and IRFs and prioritize putative causal genes directly linking genetic variants and disease risk enhancers. We further delineate similarities and differences in epigenetic landscape between stem cell-derived macrophages and primary cells and characterize the context-specific enhancer activities for key innate immune response genes KLF4, SLAMF1 and IL2RA. Conclusions Our study demonstrates the importance of context-specific macrophage enhancers in gene regulation and utility for interpreting disease associations, providing a roadmap to link genetic variants with molecular and cellular functions. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02702-1.
Collapse
|
48
|
López-Rodríguez R, Del Pozo-Valero M, Corton M, Minguez P, Ruiz-Hornillos J, Pérez-Tomás ME, Barreda-Sánchez M, Mancebo E, Villaverde C, Núñez-Moreno G, Romero R, Paz-Artal E, Guillén-Navarro E, Almoguera B, Ayuso C. Presence of rare potential pathogenic variants in subjects under 65 years old with very severe or fatal COVID-19. Sci Rep 2022; 12:10369. [PMID: 35725860 PMCID: PMC9208539 DOI: 10.1038/s41598-022-14035-x] [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: 12/30/2021] [Accepted: 05/31/2022] [Indexed: 02/06/2023] Open
Abstract
Rare variants affecting host defense against pathogens could be involved in COVID-19 severity and may help explain fatal outcomes in young and middle-aged patients. Our aim was to report the presence of rare genetic variants in certain genes, by using whole exome sequencing, in a selected group of COVID-19 patients under 65 years who required intubation or resulting in death (n = 44). To this end, different etiopathogenic mechanisms were explored using gene prioritization-based analysis in which genes involved in immune response, immunodeficiencies or blood coagulation were studied. We detected 44 different variants of interest, in 29 different patients (66%). Some of these variants were previously described as pathogenic and were located in genes mainly involved in immune response. A network analysis, including the 42 genes with candidate variants, showed three main components, consisting of 25 highly interconnected genes related to immune response and two additional networks composed by genes enriched in carbohydrate metabolism and in DNA metabolism and repair processes. In conclusion, we have detected candidate variants that may potentially influence COVID-19 outcome in our cohort of patients. Further studies are needed to confirm the ultimate role of the genetic variants described in the present study on COVID-19 severity.
Collapse
Affiliation(s)
- Rosario López-Rodríguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Department of Pharmaceutical and Health Sciences, Faculty of Pharmacy, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - Marta Del Pozo-Valero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Marta Corton
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Pablo Minguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Javier Ruiz-Hornillos
- Allergy Unit, Hospital Infanta Elena, Valdemoro, Madrid, Spain.,Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Faculty of Medicine, Universidad Francisco de Vitoria, Pozuelo de Alarcón, Madrid, Spain
| | - María Elena Pérez-Tomás
- Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca (IMIB-Arrixaca), Murcia, Spain
| | - María Barreda-Sánchez
- Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca (IMIB-Arrixaca), Murcia, Spain.,Health Sciences Faculty, Universidad Católica San Antonio de Murcia (UCAM), Murcia, Spain
| | - Esther Mancebo
- Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain.,Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Cristina Villaverde
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Gonzalo Núñez-Moreno
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Raquel Romero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | | | - Estela Paz-Artal
- Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain.,Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain.,Department of Immunology, Ophthalmology and ENT, Universidad Complutense de Madrid, Madrid, Spain.,Center for Biomedical Network Research on Infectious Diseases (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Encarna Guillén-Navarro
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca (IMIB-Arrixaca), Murcia, Spain.,Medical Genetics Section, Pediatric Department, Virgen de la Arrixaca University Clinical Hospital, Faculty of Medicine, University of Murcia (UMU), Murcia, Spain
| | - Berta Almoguera
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain. .,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain.
| |
Collapse
|
49
|
Scudeller L. Infectious diseases and inborn errors of immunity. Clin Microbiol Infect 2022; 28:1409-1410. [PMID: 35654314 DOI: 10.1016/j.cmi.2022.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 11/20/2022]
Affiliation(s)
- Luigia Scudeller
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Reseach and Innovation Unit, Bologna, Italy.
| |
Collapse
|
50
|
Opportunities and challenges for the use of common controls in sequencing studies. Nat Rev Genet 2022; 23:665-679. [PMID: 35581355 DOI: 10.1038/s41576-022-00487-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2022] [Indexed: 01/02/2023]
Abstract
Genome-wide association studies using large-scale genome and exome sequencing data have become increasingly valuable in identifying associations between genetic variants and disease, transforming basic research and translational medicine. However, this progress has not been equally shared across all people and conditions, in part due to limited resources. Leveraging publicly available sequencing data as external common controls, rather than sequencing new controls for every study, can better allocate resources by augmenting control sample sizes or providing controls where none existed. However, common control studies must be carefully planned and executed as even small differences in sample ascertainment and processing can result in substantial bias. Here, we discuss challenges and opportunities for the robust use of common controls in high-throughput sequencing studies, including study design, quality control and statistical approaches. Thoughtful generation and use of large and valuable genetic sequencing data sets will enable investigation of a broader and more representative set of conditions, environments and genetic ancestries than otherwise possible.
Collapse
|