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Shalekoff S, Dias BDC, Loubser S, Strehlau R, Kuhn L, Tiemessen CT. Higher CCR5 density on CD4 + T-cells in mothers and infants is associated with increased risk of in-utero HIV-1 transmission. AIDS 2024; 38:945-954. [PMID: 38329228 PMCID: PMC11064911 DOI: 10.1097/qad.0000000000003857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024]
Abstract
OBJECTIVE CCR5-tropic viruses are preferentially transmitted during perinatal HIV-1 infection. CCR5 density on CD4 + T-cells likely impacts susceptibility to HIV-1 infection. DESIGN Fifty-two mother-infant dyads were enrolled. All mothers were living with HIV-1, 27 of the infants acquired HIV-1 in utero and 25 infants remained uninfected. METHODS CCR5 density, together with frequencies of CD4 + and CD8 + T-cells expressing immune activation (CCR5, ICOS and HLA-DR) and immune checkpoint (TIGIT and PD-1) markers, were measured in whole blood from the dyads close to delivery. RESULTS Compared with mothers who did not transmit, mothers who transmitted HIV-1 had less exposure to ART during pregnancy ( P = 0.015) and higher plasma viral load close to delivery ( P = 0.0005). These mothers, additionally, had higher CCR5 density on CD4 + and CD8 + T-cells and higher frequencies of CCR5, ICOS and TIGIT-expressing CD8 + T-cells. Similarly, compared with infants without HIV-1, infants with HIV-1 had higher CCR5 density on CD4 + and CD8 + T-cells and higher frequencies of CCR5, TIGIT, and PD-1-expressing CD4 + and CD8 + T-cells as well as higher frequencies of HLA-DR-expressing CD8 + T-cells. CCR5 density on maternal CD4 + T-cells remained significantly associated with transmission after adjusting for maternal viral load and CD4 + T cell counts. Mother-infant dyads with shared high CCR5 density phenotypes had the highest risk of transmission/acquisition of infection compared with dyads with shared low-CCR5 density phenotypes. CONCLUSION This study provides strong evidence of a protective role for a combined mother-infant low CD4 + T-cell CCR5 density phenotype in in-utero transmission/acquisition of HIV-1.
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Affiliation(s)
- Sharon Shalekoff
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bianca Da Costa Dias
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shayne Loubser
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Renate Strehlau
- VIDA Nkanyezi Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Louise Kuhn
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Caroline T. Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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2
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OBrien SJ. Legacy of a magic gene- CCR5-∆32: From discovery to clinical benefit in a generation. Proc Natl Acad Sci U S A 2024; 121:e2321907121. [PMID: 38457490 PMCID: PMC10962972 DOI: 10.1073/pnas.2321907121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/22/2024] [Indexed: 03/10/2024] Open
Abstract
The discovery of the 32-bp deletion allele of the chemokine receptor gene CCR5 showed that homozygous carriers display near-complete resistance to HIV infection, irrespective of exposure. Algorithms of molecular evolutionary theory suggested that the CCR5-∆32 mutation occurred but once in the last millennium and rose by strong selective pressure relatively recently to a ~10% allele frequency in Europeans. Several lines of evidence support the hypothesis that CCR5-∆32 was selected due to its protective influence to resist Yersinia pestis, the agent of the Black Death/bubonic plague of the 14th century. Powerful anti-AIDS entry inhibitors targeting CCR5 were developed as a treatment for HIV patients, particularly those whose systems had developed resistance to powerful anti-retroviral therapies. Homozygous CCR5-∆32/∆32 stem cell transplant donors were used to produce HIV-cleared AIDS patients in at least five "cures" of HIV infection. CCR5 has also been implicated in regulating infection with Staphylococcus aureus, in recovery from stroke, and in ablation of the fatal graft versus host disease (GVHD) in cancer transplant patients. While homozygous CCR5-∆32/32 carriers block HIV infection, alternatively they display an increased risk for encephalomyelitis and death when infected with the West Nile virus.
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Affiliation(s)
- Stephen J. OBrien
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, Ft Lauderdale, FL33004
- Indiana University School of Public Health, Bloomington, IN47405
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3
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Tassaneetrithep B, Phuphuakrat A, Pasomsub E, Bhukhai K, Wongkummool W, Priengprom T, Khamaikawin W, Chaisavaneeyakorn S, Anurathapan U, Apiwattanakul N, Hongeng S. HIV-1 proviral DNA in purified peripheral blood CD34 + stem and progenitor cells in individuals with long-term HAART; paving the way to HIV gene therapy. Heliyon 2024; 10:e26613. [PMID: 38434025 PMCID: PMC10906414 DOI: 10.1016/j.heliyon.2024.e26613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 02/03/2024] [Accepted: 02/16/2024] [Indexed: 03/05/2024] Open
Abstract
Human immunodeficiency virus (HIV)-1 infection is an important public health problem worldwide. After primary HIV-1 infection, transcribed HIV-1 DNA is integrated into the host genome, serving as a reservoir of the virus and hindering a definite cure. Although highly active antiretroviral therapy suppresses active viral replication, resulting in undetectable levels of HIV RNA in the blood, a viral rebound can be detected after a few weeks of treatment interruption. This supports the concept that there is a stable HIV-1 reservoir in people living with HIV-1. Recently, a few individuals with HIV infection were reported to be probably cured by hematopoietic stem transplantation (HSCT). The underlying mechanism for this success involved transfusion of uninfected hematopoietic stem and progenitor cells (HSPCs) from CCR5-mutated donors who were naturally resistant to HIV infection. Thus, gene editing technology to provide HIV-resistant HSPC has promise in the treatment of HIV infections by HSCT. In this study, we aimed to find HIV-infected individuals likely to achieve a definite cure via gene editing HSCT. We screened for total HIV proviral DNA by Alu PCR in peripheral blood mononuclear cells (PBMCs) of 20 HIV-infected individuals with prolonged viral suppression. We assessed the amount of intact proviral DNA via a modified intact proviral DNA assay (IPDA) in purified peripheral CD34+ HSPCs. PBMCs from all 20 individuals were positive for the gag gene in Alu PCR, and peripheral CD34+ HSPCs were IPDA-negative for six individuals. Our results suggested that these six HIV-infected individuals could be candidates for further studies into the ability of gene editing HSCT to lead to a definite HIV cure.
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Affiliation(s)
- Boonrat Tassaneetrithep
- Center of Research Excellence in Immunoregulation, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | - Angsana Phuphuakrat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
| | - Ekawat Pasomsub
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
| | - Kanit Bhukhai
- Department of Physiology, Faculty of Science, Mahidol University, Thailand
| | | | - Thongkoon Priengprom
- Center of Research Excellence in Immunoregulation, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | - Wannisa Khamaikawin
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Thailand
| | | | - Usanarat Anurathapan
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
| | - Nopporn Apiwattanakul
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand
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4
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Zhang Z, Wang S, Jiang L, Wei J, Lu C, Li S, Diao Y, Fang Z, He S, Tan T, Yang Y, Zou K, Shi J, Lin J, Chen L, Bao C, Fei J, Fang H. Priority index for critical Covid-19 identifies clinically actionable targets and drugs. Commun Biol 2024; 7:189. [PMID: 38366110 PMCID: PMC10873402 DOI: 10.1038/s42003-024-05897-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 02/07/2024] [Indexed: 02/18/2024] Open
Abstract
While genome-wide studies have identified genomic loci in hosts associated with life-threatening Covid-19 (critical Covid-19), the challenge of resolving these loci hinders further identification of clinically actionable targets and drugs. Building upon our previous success, we here present a priority index solution designed to address this challenge, generating the target and drug resource that consists of two indexes: the target index and the drug index. The primary purpose of the target index is to identify clinically actionable targets by prioritising genes associated with Covid-19. We illustrate the validity of the target index by demonstrating its ability to identify pre-existing Covid-19 phase-III drug targets, with the majority of these targets being found at the leading prioritisation (leading targets). These leading targets have their evolutionary origins in Amniota ('four-leg vertebrates') and are predominantly involved in cytokine-cytokine receptor interactions and JAK-STAT signaling. The drug index highlights opportunities for repurposing clinically approved JAK-STAT inhibitors, either individually or in combination. This proposed strategic focus on the JAK-STAT pathway is supported by the active pursuit of therapeutic agents targeting this pathway in ongoing phase-II/III clinical trials for Covid-19.
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Affiliation(s)
- Zhiqiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lulu Jiang
- Translational Health Sciences, University of Bristol, Bristol, BS1 3NY, UK
| | - Jianwen Wei
- Network and Information Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chang Lu
- MRC London Institute of Medical Sciences, Imperial College London, London, W12 0HS, UK
| | - Shengli Li
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201620, China
| | - Yizhu Diao
- College of Finance and Statistics, Hunan University, Changsha, 410079, Hunan, China
| | - Zhongcheng Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuo He
- College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Tingting Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yisheng Yang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Kexin Zou
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiantao Shi
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - James Lin
- Network and Information Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liye Chen
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK.
| | - Chaohui Bao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Department of General Surgery, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, 200020, China.
| | - Jian Fei
- Department of General Surgery, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, 200020, China.
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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5
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Faivre N, Verollet C, Dumas F. The chemokine receptor CCR5: multi-faceted hook for HIV-1. Retrovirology 2024; 21:2. [PMID: 38263120 PMCID: PMC10807162 DOI: 10.1186/s12977-024-00634-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/13/2024] [Indexed: 01/25/2024] Open
Abstract
Chemokines are cytokines whose primary role is cellular activation and stimulation of leukocyte migration. They perform their various functions by interacting with G protein-coupled cell surface receptors (GPCRs) and are involved in the regulation of many biological processes such as apoptosis, proliferation, angiogenesis, hematopoiesis or organogenesis. They contribute to the maintenance of the homeostasis of lymphocytes and coordinate the function of the immune system. However, chemokines and their receptors are sometimes hijacked by some pathogens to infect the host organism. For a given chemokine receptor, there is a wide structural, organizational and conformational diversity. In this review, we describe the evidence for structural variety reported for the chemokine receptor CCR5, how this variability can be exploited by HIV-1 to infect its target cells and what therapeutic solutions are currently being developed to overcome this problem.
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Affiliation(s)
- Natacha Faivre
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Buenos Aires, Argentina
| | - Christel Verollet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Toulouse, France
- International Research Laboratory (IRP) CNRS "IM-TB/HIV", Buenos Aires, Argentina
| | - Fabrice Dumas
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France.
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6
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Beverley J, Babcock S, Carvalho G, Cowell LG, Duesing S, He Y, Hurley R, Merrell E, Scheuermann RH, Smith B. Coordinating virus research: The Virus Infectious Disease Ontology. PLoS One 2024; 19:e0285093. [PMID: 38236918 PMCID: PMC10796065 DOI: 10.1371/journal.pone.0285093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/12/2023] [Indexed: 01/22/2024] Open
Abstract
The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies-structured, controlled, vocabularies-are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects.
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Affiliation(s)
- John Beverley
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States of America
- National Center for Ontological Research, Buffalo, NY, United States of America
| | - Shane Babcock
- National Center for Ontological Research, Buffalo, NY, United States of America
- Air Force Research Laboratory, Wright Patterson Air Force Base, Riverside, OH, United States of America
| | - Gustavo Carvalho
- Department of Cognitive Science, Northwestern University, Evanston, IL, United States of America
| | - Lindsay G. Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Sebastian Duesing
- Department of Philosophy, Loyola University, Chicago, IL, United States of America
| | - Yongqun He
- Computational Medicine and Bioinformatics, University of Michigan Medical School, He Group, Ann Arbor, MI, United States of America
| | - Regina Hurley
- National Center for Ontological Research, Buffalo, NY, United States of America
- Department of Philosophy, Northwestern University, Evanston, IL, United States of America
| | - Eric Merrell
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States of America
- National Center for Ontological Research, Buffalo, NY, United States of America
| | - Richard H. Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States of America
- Department of Pathology, University of California, San Diego, CA, United States of America
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States of America
| | - Barry Smith
- Department of Philosophy, University at Buffalo, Buffalo, NY, United States of America
- National Center for Ontological Research, Buffalo, NY, United States of America
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7
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Peters U, Tomlinson I. Utilizing Human Genetics to Develop Chemoprevention for Cancer-Too Good an Opportunity to be Missed. Cancer Prev Res (Phila) 2024; 17:7-12. [PMID: 38173394 DOI: 10.1158/1940-6207.capr-22-0523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/20/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024]
Abstract
Large-scale genetic studies are reliably identifying many risk factors for disease in the general population. Several of these genetic risk factors encode potential drug targets, and genetics has already helped to introduce targeted agents for some diseases, an example being lipid-lowering drugs to reduce the incidence of cardiovascular disease. Multiple drugs have been developed to treat cancers based on somatic mutations and genomics, but in stark contrast, there seems to be a reluctance to use germline genetic data to develop drugs to prevent malignancy, despite the large numbers of people who could benefit, the potential for lowering cancer rates, and the widespread current use of non-pharmaceutical measures to reduce cancer risk factors such as tobacco, alcohol, and infectious diseases. We argue that concerted efforts for cancer prevention based on genetics, including genes influenced by common polymorphisms that modulate cancer risk, are urgently needed. There are enormous, yet underutilized, opportunities to develop novel targeted agents for chemoprevention of cancer based on human germline genetics. Such efforts are likely to require the support of a dedicated funding program by national and international agencies. See related commentary by Winham and Sherman, p. 13.
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Affiliation(s)
- Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Center and Department of Epidemiology, University of Washington, Seattle, Washington
| | - Ian Tomlinson
- Department of Oncology, University of Oxford, Oxford, United Kingdom
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8
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Laplana M, Royo JL, Real LM. Genetic Association Studies in Host-Pathogen Interaction Analysis. Methods Mol Biol 2024; 2751:19-30. [PMID: 38265707 DOI: 10.1007/978-1-0716-3617-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Studying host-pathogen interactions at a molecular level has always been technically challenging. Identifying the different biochemical and genetic pathways involved in the different stages of infection traditionally require complex molecular biology tools and often the use of costly animal models. In this chapter, we illustrate a complementary approach to address host-pathogen interactions, taking advantage of the natural interindividual genetic diversity. The application of genetic association studies allows us to identify alleles involved in infection progression or resistance. Thus, this strategy may be useful to unravel new molecular pathways underlying host-pathogen interactions. Here we present the general steps that might be followed to plan, execute, and analyze a population-based study in order to identify genetic variants affecting human exposition to pathogens.
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Affiliation(s)
- Marina Laplana
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - José Luis Royo
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología. Facultad de Medicina, Universidad de Málaga, Málaga, Spain.
| | - Luis Miguel Real
- Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología. Facultad de Medicina, Universidad de Málaga, Málaga, Spain
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario de Valme, Sevilla, Spain
- Centro de Investigación en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Instituto de Biomedicina de Sevilla, Sevilla, Spain
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9
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Rovatti PE, Muccini C, Punta M, Galli L, Mainardi I, Ponta G, Vago LAE, Castagna A. Impact of predicted HLA class I immunopeptidome on viral reservoir in a cohort of people living with HIV in Italy. HLA 2024; 103:e15298. [PMID: 37962099 DOI: 10.1111/tan.15298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 10/30/2023] [Accepted: 11/04/2023] [Indexed: 11/15/2023]
Abstract
The class I HLA genotype has been widely recognized as a factor influencing HIV disease progression in treatment-naïve subjects. However, little is known regarding its role in HIV disease course and how it influences the size of the viral reservoir once anti-retroviral therapy (ART) is started. Here, leveraging on cutting-edge bioinformatic tools, we explored the relationship between HLA class I and the HIV reservoir in a cohort of 90 people living with HIV (PLWH) undergoing ART and who achieved viral suppression. Analysis of HLA allele distribution among patients with high and low HIV reservoir allowed us to document a predominant role of HLA-B and -C genes in regulating the size of HIV reservoir. We then focused on the analysis of HIV antigen (Ag) repertoire, by investigating immunogenetic parameters such as the degree of homozygosity, HLA evolutionary distance and Ag load. In particular, we used two different bioinformatic algorithms, NetMHCpan and MixMHCpred, to predict HLA presentation of immunogenic HIV-derived peptides and identified HLA-B*57:01 and HLA-B*58:01 among the highest ranking HLAs in terms of total load, suggesting that their previously reported protective role against HIV disease progression might be linked to a more effective viral recognition and presentation to Cytotoxic T lymphocytes (CTLs). Further, we speculated that some peptide-HLA complexes, including those produced by the interaction between HLA-B*27 and the HIV Gag protein, might be particularly relevant for the efficient regulation of HIV replication and containment of the HIV reservoir. Last, we provide evidence of a possible synergistic effect between the CCR5 ∆32 mutation and Ag load in controlling HIV reservoir.
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Affiliation(s)
- Pier Edoardo Rovatti
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Camilla Muccini
- Vita-Salute San Raffaele University, Milan, Italy
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco Punta
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Galli
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | - Luca Aldo Edoardo Vago
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
- Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Antonella Castagna
- Vita-Salute San Raffaele University, Milan, Italy
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
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10
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Jain K, McCarley SC, Mukhtar G, Ferlin A, Fleming A, Morris-Rosendahl DJ, Shovlin CL. Pathogenic Variant Frequencies in Hereditary Haemorrhagic Telangiectasia Support Clinical Evidence of Protection from Myocardial Infarction. J Clin Med 2023; 13:250. [PMID: 38202257 PMCID: PMC10779873 DOI: 10.3390/jcm13010250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Hereditary haemorrhagic telangiectasia (HHT) is a vascular dysplasia inherited as an autosomal dominant trait, due to a single heterozygous loss-of-function variant, usually in ACVRL1 (encoding activin receptor-like kinase 1 [ALK1]), ENG (encoding endoglin [CD105]), or SMAD4. In a consecutive single-centre series of 37 positive clinical genetic tests performed in 2021-2023, a skewed distribution pattern was noted, with 30 of 32 variants reported only once, but ACVRL1 c.1231C>T (p.Arg411Trp) identified as the disease-causal gene in five different HHT families. In the same centre's non-overlapping 1992-2020 series where 110/134 (82.1%) HHT-causal variants were reported only once, ACVRL1 c.1231C>T (p.Arg411Trp) was identified in nine further families. In a 14-country, four-continent HHT Mutation Database where 181/250 (72.4%) HHT-causal variants were reported only once, ACVRL1 c.1231C>T (p.Arg411Trp) was reported by 12 different laboratories, the adjacent ACVRL1 c.1232G>A (p.Arg411Gln) by 14, and ACVRL1 c.1120C>T (p.Arg374Trp) by 18. Unlike the majority of HHT-causal ACVRL1 variants, these encode ALK1 protein that reaches the endothelial cell surface but fails to signal. Six variants of this type were present in the three series and were reported 6.8-25.5 (mean 8.9) times more frequently than the other ACVRL1 missense variants (all p-values < 0.0039). Noting lower rates of myocardial infarction reported in HHT, we explore potential mechanisms, including a selective paradigm relevant to ALK1's role in the initiating event of atherosclerosis, where a plausible dominant negative effect of these specific variants can be proposed. In conclusion, there is an ~9-fold excess of kinase-inactive, cell surface-expressed ACVRL1/ALK1 pathogenic missense variants in HHT. The findings support further examination of differential clinical and cellular phenotypes by HHT causal gene molecular subtypes.
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Affiliation(s)
- Kinshuk Jain
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
| | - Sarah C. McCarley
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
| | - Ghazel Mukhtar
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
| | - Anna Ferlin
- Clinical Genetics and Genomics Laboratory, Royal Brompton Hospital, Guy’s and St Thomas’ NHS Trust, London SE1 7EH, UK; (A.F.); (A.F.)
| | - Andrew Fleming
- Clinical Genetics and Genomics Laboratory, Royal Brompton Hospital, Guy’s and St Thomas’ NHS Trust, London SE1 7EH, UK; (A.F.); (A.F.)
| | - Deborah J. Morris-Rosendahl
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
- Clinical Genetics and Genomics Laboratory, Royal Brompton Hospital, Guy’s and St Thomas’ NHS Trust, London SE1 7EH, UK; (A.F.); (A.F.)
| | - Claire L. Shovlin
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
- Specialist Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London W12 0HS, UK
- Social, Genetic and Environmental Determinants of Health, NIHR Imperial Biomedical Research Centre, London W2 1NY, UK
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11
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Chen G, Calcaterra F, Ma Y, Ping X, Pontarini E, Yang D, Oriolo F, Yu Z, Cancellara A, Mikulak J, Huang Y, Della Bella S, Liu Y, Biesecker LG, Harper RL, Dalgard CL, Boehm M, Mavilio D. Derived myeloid lineage induced pluripotent stem as a platform to study human C-C chemokine receptor type 5Δ32 homozygotes. iScience 2023; 26:108331. [PMID: 38026202 PMCID: PMC10663745 DOI: 10.1016/j.isci.2023.108331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/29/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
The C-C chemokine receptor type 5 (CCR5) expressed on immune cells supports inflammatory responses by directing cells to the inflammation site. CCR5 is also a major coreceptor for macrophage tropic human immunodeficiency viruses (R5-HIV-1) and its variants can confer protection from HIV infection, making it an ideal candidate to target for therapy. We developed a stepwise protocol that differentiates induced pluripotent stem cells (iPSCs) from individuals homozygous for the CCR5Δ32 variant and healthy volunteers into myeloid lineage induced monocytes (iMono) and macrophages (iMac). By characterizing iMono and iMac against their primary counterparts, we demonstrated that CCR5Δ32 homozygous cells are endowed with similar pluripotent potential for self-renewal and differentiation as iPSC lines generated from non-variant individuals while also showing resistance to HIV infection. In conclusion, these cells are a platform to investigate CCR5 pathophysiology in HIV-positive and negative individuals and to help develop novel therapies.
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Affiliation(s)
- Guibin Chen
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Calcaterra
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
- Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, 20054 Segrate, Italy
| | - Yuchi Ma
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xianfeng Ping
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - Elena Pontarini
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, London, England, UK
| | - Dan Yang
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ferdinando Oriolo
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
- Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, 20054 Segrate, Italy
| | - Zhen Yu
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Assunta Cancellara
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
- Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, 20054 Segrate, Italy
| | - Joanna Mikulak
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | - Yuting Huang
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Silvia Della Bella
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
- Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, 20054 Segrate, Italy
| | - Yangtengyu Liu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
| | - Leslie G. Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rebecca L. Harper
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University, Bethesda, MD, USA
| | - Manfred Boehm
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Domenico Mavilio
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
- Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, 20054 Segrate, Italy
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12
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van Pul L, Maurer I, Boeser-Nunnink BD, Harskamp AM, van Dort KA, Kootstra NA. A genetic variation in fucosyltransferase 8 accelerates HIV-1 disease progression indicating a role for N-glycan fucosylation. AIDS 2023; 37:1959-1969. [PMID: 37598360 PMCID: PMC10552802 DOI: 10.1097/qad.0000000000003689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/25/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
OBJECTIVES Core fucosylation by fucosyltransferase 8 (FUT8) is an important posttranslational modification that impacts components of the immune system. Genetic variations in FUT8 can alter its function and could, therefore, play a role in the antiviral immune response and pathogenesis of HIV-1. This study analysed the effect of a single nucleotide polymorphism (SNP) in FUT8 on the clinical course of HIV-1 infection. DESIGN/METHODS The effect of SNPs in FUT8 on untreated HIV-1 disease outcome were analysed in a cohort of 304 people with HIV-1 (PWH) using survival analysis. Flow-cytometry was used to determine the effect of SNP on T-cell activation, differentiation and exhaustion/senescence. T-cell function was determined by proliferation assay and by measuring intracellular cytokine production. The effect of the SNP on HIV-1 replication was determined by in-vitro HIV-1 infections. Sensitivity of HIV-1 produced in PBMC with or without the SNP to broadly neutralizing antibodies was determined using a TZM-bl based neutralization assay. RESULTS Presence of the minor allele of SNP rs4131564 was associated with accelerated disease progression. The SNP had no effect on T-cell activation and T-cell differentiation in PWH. Additionally, no differences in T-cell functionality as determined by proliferation and cytokine production was observed. HIV-1 replication and neutralization sensitivity was also unaffected by the SNP in FUT8. CONCLUSION SNP rs4131564 in FUT8 showed a major impact on HIV-1 disease course underscoring a role for N-glycan fucosylation even though no clear effect on the immune system or HIV-1 could be determined in vitro .
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Affiliation(s)
- Lisa van Pul
- Amsterdam Institute for Infection and Immunity
- Department of Experimental Immunology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Irma Maurer
- Amsterdam Institute for Infection and Immunity
- Department of Experimental Immunology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Brigitte D.M. Boeser-Nunnink
- Amsterdam Institute for Infection and Immunity
- Department of Experimental Immunology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Agnes M. Harskamp
- Amsterdam Institute for Infection and Immunity
- Department of Experimental Immunology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Karel A. van Dort
- Amsterdam Institute for Infection and Immunity
- Department of Experimental Immunology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
| | - Neeltje A. Kootstra
- Amsterdam Institute for Infection and Immunity
- Department of Experimental Immunology, Amsterdam UMC, location University of Amsterdam, Amsterdam, The Netherlands
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13
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Behrens RT, Rajashekar JK, Bruce JW, Evans EL, Hansen AM, Salazar-Quiroz N, Simons LM, Ahlquist P, Hultquist JF, Kumar P, Sherer NM. Exploiting a rodent cell block for intrinsic resistance to HIV-1 gene expression in human T cells. mBio 2023; 14:e0042023. [PMID: 37676006 PMCID: PMC10653828 DOI: 10.1128/mbio.00420-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/13/2023] [Indexed: 09/08/2023] Open
Abstract
IMPORTANCE Unlike humans, mice are unable to support HIV-1 infection. This is due, in part, to a constellation of defined minor, species-specific differences in conserved host proteins needed for viral gene expression. Here, we used precision CRISPR/Cas9 gene editing to engineer a "mousified" version of one such host protein, cyclin T1 (CCNT1), in human T cells. CCNT1 is essential for efficient HIV-1 transcription, making it an intriguing target for gene-based inactivation of virus replication. We show that isogenic cell lines engineered to encode CCNT1 bearing a single mouse-informed amino acid change (tyrosine in place of cysteine at position 261) exhibit potent, durable, and broad-spectrum resistance to HIV-1 and other pathogenic lentiviruses, and with no discernible impact on host cell biology. These results provide proof of concept for targeting CCNT1 in the context of one or more functional HIV-1 cure strategies.
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Affiliation(s)
- Ryan T. Behrens
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jyothi Krishnaswamy Rajashekar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - James W. Bruce
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Edward L. Evans
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amelia M. Hansen
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Natalia Salazar-Quiroz
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lacy M. Simons
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Paul Ahlquist
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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14
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Guo L, Liu X, Su X. The role of TEMRA cell-mediated immune senescence in the development and treatment of HIV disease. Front Immunol 2023; 14:1284293. [PMID: 37901239 PMCID: PMC10602809 DOI: 10.3389/fimmu.2023.1284293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023] Open
Abstract
Human Immunodeficiency Virus (HIV) has plagued human society for a long time since its discovery, causing a large number of patients to suffer and costing hundreds of millions of medical services every year. Scientists have found that HIV and antiretroviral therapy accelerate immune aging by inducing mitochondrial dysfunction, and that terminal effector memory T cells (TEMRA cells) are crucial in immune aging. This specific subset of effector memory T cells has terminally differentiated properties and exhibits high cytotoxicity and proinflammatory capacity. We therefore explored and described the interplay between exhaustion features, essential markers, functions, and signaling pathways from previous studies on HIV, antiretroviral therapy, immune senescence, and TEMRA cells. Their remarkable antiviral capacity is then highlighted by elucidating phenotypic changes in TEMRA cells during HIV infection, describing changes in TEMRA cells before, during, and after antiretroviral therapy and other drug treatments. Their critical role in complications and cytomegalovirus (CMV)-HIV superinfection is highlighted. These studies demonstrate that TEMRA cells play a key role in the antiviral response and immune senescence during HIV infection. Finally, we review current therapeutic strategies targeting TEMRA cells that may be clinically beneficial, highlight their potential role in HIV-1 vaccine development, and provide perspectives and predictions for related future applications.
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Affiliation(s)
- Lihui Guo
- Department of Burns and Plastic Surgery, Yanbian University Hospital, Yanji, China
- Department of Rheumatology and Immunology, The First Hospital of China Medical University, China Medical University, Shen Yang, China
| | - Xudong Liu
- Department of Rheumatology and Immunology, The First Hospital of China Medical University, China Medical University, Shen Yang, China
| | - Xin Su
- Department of Burns and Plastic Surgery, Yanbian University Hospital, Yanji, China
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15
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Pinilla M, Mazars R, Vergé R, Gorse L, Paradis M, Suire B, Santoni K, Robinson KS, Toh GA, Prouvensier L, Leon-Icaza SA, Hessel A, Péricat D, Murris M, Guet-Revillet H, Henras A, Buyck J, Ravet E, Zhong FL, Cougoule C, Planès R, Meunier E. EEF2-inactivating toxins engage the NLRP1 inflammasome and promote epithelial barrier disruption. J Exp Med 2023; 220:e20230104. [PMID: 37642996 PMCID: PMC10465324 DOI: 10.1084/jem.20230104] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/31/2023] Open
Abstract
Human airway and corneal epithelial cells, which are critically altered during chronic infections mediated by Pseudomonas aeruginosa, specifically express the inflammasome sensor NLRP1. Here, together with a companion study, we report that the NLRP1 inflammasome detects exotoxin A (EXOA), a ribotoxin released by P. aeruginosa type 2 secretion system (T2SS), during chronic infection. Mechanistically, EXOA-driven eukaryotic elongation factor 2 (EEF2) ribosylation and covalent inactivation promote ribotoxic stress and subsequent NLRP1 inflammasome activation, a process shared with other EEF2-inactivating toxins, diphtheria toxin and cholix toxin. Biochemically, irreversible EEF2 inactivation triggers ribosome stress-associated kinases ZAKα- and P38-dependent NLRP1 phosphorylation and subsequent proteasome-driven functional degradation. Finally, cystic fibrosis cells from patients exhibit exacerbated P38 activity and hypersensitivity to EXOA-induced ribotoxic stress-dependent NLRP1 inflammasome activation, a process inhibited by the use of ZAKα inhibitors. Altogether, our results show the importance of P. aeruginosa virulence factor EXOA at promoting NLRP1-dependent epithelial damage and identify ZAKα as a critical sensor of virulence-inactivated EEF2.
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Affiliation(s)
- Miriam Pinilla
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Raoul Mazars
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Romain Vergé
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Leana Gorse
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Margaux Paradis
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Bastien Suire
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Karin Santoni
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Kim Samirah Robinson
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Skin Research Institute of Singapore, Singapore, Singapore
| | - Gee Ann Toh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Skin Research Institute of Singapore, Singapore, Singapore
| | - Laure Prouvensier
- UFR Medicine and Pharmacy, INSERM U1070, University of Poitiers, Poitiers, France
| | | | - Audrey Hessel
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - David Péricat
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Marlène Murris
- Department of Pneumology, Hospital Larrey, Toulouse, France
- University Hospital of Toulouse, Toulouse, France
| | | | - Anthony Henras
- Center of Integrative Biology, University of Toulouse, CNRS, Toulouse, France
| | - Julien Buyck
- UFR Medicine and Pharmacy, INSERM U1070, University of Poitiers, Poitiers, France
| | | | - Franklin L. Zhong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Skin Research Institute of Singapore, Singapore, Singapore
| | - Céline Cougoule
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Rémi Planès
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
- Invivogen, Toulouse, France
| | - Etienne Meunier
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
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16
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Khan A, Paneerselvam N, Lawson BR. Antiretrovirals to CCR5 CRISPR/Cas9 gene editing - A paradigm shift chasing an HIV cure. Clin Immunol 2023; 255:109741. [PMID: 37611838 PMCID: PMC10631514 DOI: 10.1016/j.clim.2023.109741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/18/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023]
Abstract
The evolution of drug-resistant viral strains and anatomical and cellular reservoirs of HIV pose significant clinical challenges to antiretroviral therapy. CCR5 is a coreceptor critical for HIV host cell fusion, and a homozygous 32-bp gene deletion (∆32) leads to its loss of function. Interestingly, an allogeneic HSCT from an HIV-negative ∆32 donor to an HIV-1-infected recipient demonstrated a curative approach by rendering the recipient's blood cells resistant to viral entry. Ex vivo gene editing tools, such as CRISPR/Cas9, hold tremendous promise in generating allogeneic HSC grafts that can potentially replace allogeneic ∆32 HSCTs. Here, we review antiretroviral therapeutic challenges, clinical successes, and failures of allogeneic and allogeneic ∆32 HSCTs, and newer exciting developments within CCR5 editing using CRISPR/Cas9 in the search to cure HIV.
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Affiliation(s)
- Amber Khan
- The Scintillon Research Institute, 6868 Nancy Ridge Drive, San Diego, CA 92121, USA
| | | | - Brian R Lawson
- The Scintillon Research Institute, 6868 Nancy Ridge Drive, San Diego, CA 92121, USA.
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17
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Santolaya JL, Schweer DS, Cardenas-Goicoechea J, Bukowski R, Santolaya-Forgas J. Bioavailability of the tumor necrosis factor alpha/regulated on activation, normal T cell expressed and secreted (RANTES) biosystem inside the gestational sac during the pre-immune stages of embryo development. J Perinat Med 2023; 51:891-895. [PMID: 37067543 DOI: 10.1515/jpm-2022-0542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/06/2023] [Indexed: 04/18/2023]
Abstract
OBJECTIVES In-vivo studies of the bioavailability of major components of the tumor necrosis factor alpha (TNFα) biosystem inside the gestational sac during embryogenesis have not been reported. We sought to determine the concentration of TNFα, soluble (s) TNFα receptors (sTNFR1, sTNFR2), and RANTES in the primate extraembryonic celomic fluid (ECF). METHODS A validated timed-pregnant baboon animal model (N: 10) for experimental research in pregnancy was used to collect paired maternal blood and ECF samples in ongoing pregnancies. The concentrations (pg/dL) of TNFα, sTNFR1, sTNFR2, and RANTES were then determined by ELISA immunoassays. RESULTS All animals delivered at term healthy newborns. The differential concentration of TNFα, sTNFR1, sTNFR2, and RANTES between the maternal plasma and the ECF could be determined with ratios for TNFα (5.4), sTNFR2 (1.85) and RANTES (3.59) that contrasted with that of sTNFR1 (0.07), which favored the gestational sac compartment. No significant correlations were noted between maternal plasma and ECF TNFR1, sTNFR2 and RANTES. There was a trend for a correlation between TNFα in maternal plasma and ECF (R=0.74; p=0.07). CONCLUSIONS We report the physiological concentrations of TNFα, sTNFR1, sTNFR2, and RANTES in extraembryonic celomic fluid during embryogenesis in primates.
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Affiliation(s)
- Jacobo L Santolaya
- Division of Pediatric Gastroenterology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David S Schweer
- Department of Obstetrics and Gynecology, University of Kentucky, Lexington, KY, USA
| | | | - Radek Bukowski
- Department of Obstetrics and Gynecology, University of Texas, Austin, TX, USA
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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.)
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19
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Espineira S, Flores-Piñas M, Chafino S, Viladés C, Negredo E, Fernández-Arroyo S, Mallolas J, Villar B, Moreno S, Vidal F, Rull A, Peraire J. Multi-omics in HIV: searching insights to understand immunological non-response in PLHIV. Front Immunol 2023; 14:1228795. [PMID: 37649488 PMCID: PMC10465175 DOI: 10.3389/fimmu.2023.1228795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023] Open
Abstract
Antiretroviral therapy (ART) induces persistent suppression of HIV-1 replication and gradual recovery of T-cell counts, and consequently, morbidity and mortality from HIV-related illnesses have been significantly reduced. However, in approximately 30% of people living with HIV (PLHIV) on ART, CD4+ T-cell counts fail to normalize despite ART and complete suppression of HIV viral load, resulting in severe immune dysfunction, which may represent an increased risk of clinical progression to AIDS and non-AIDS events as well as increased mortality. These patients are referred to as "immune inadequate responders", "immunodiscordant responders" or "immune nonresponders (INR)". The molecular mechanisms underlying poor CD4+ T-cell recovery are still unclear. In this sense, the use of omics sciences has shed light on possible factors involved in the activity and metabolic dysregulation of immune cells during the failure of CD4+ T-cell recovery in INR. Moreover, identification of key molecules by omics approaches allows for the proposal of potential biomarkers or therapeutic targets to improve CD4+ T-cell recovery and the quality of life of these patients. Hence, this review aimed to summarize the information obtained through different omics concerning the molecular factors and pathways associated with the INR phenotype to better understand the complexity of this immunological status in HIV infection.
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Affiliation(s)
- Sonia Espineira
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Marina Flores-Piñas
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
| | - Silvia Chafino
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Consuelo Viladés
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Eugenia Negredo
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Lluita contra les Infeccions, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
- Universitat de Vic - Universitat Central de Catalunya, Vic, Spain
| | - Salvador Fernández-Arroyo
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), Reus, Spain
| | - Josep Mallolas
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- HIV Unit, Hospital Clínic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Beatriz Villar
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Santiago Moreno
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Department of Infectious Diseases, University Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Universidad de Alcalá (UAH), Madrid, Spain
| | - Francesc Vidal
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Anna Rull
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Joaquim Peraire
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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20
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Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection is silent or benign in most infected individuals, but causes hypoxemic COVID-19 pneumonia in about 10% of cases. We review studies of the human genetics of life-threatening COVID-19 pneumonia, focusing on both rare and common variants. Large-scale genome-wide association studies have identified more than 20 common loci robustly associated with COVID-19 pneumonia with modest effect sizes, some implicating genes expressed in the lungs or leukocytes. The most robust association, on chromosome 3, concerns a haplotype inherited from Neanderthals. Sequencing studies focusing on rare variants with a strong effect have been particularly successful, identifying inborn errors of type I interferon (IFN) immunity in 1-5% of unvaccinated patients with critical pneumonia, and their autoimmune phenocopy, autoantibodies against type I IFN, in another 15-20% of cases. Our growing understanding of the impact of human genetic variation on immunity to SARS-CoV-2 is enabling health systems to improve protection for individuals and populations.
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Affiliation(s)
- Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France;
- Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
- Howard Hughes Medical Institute, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland;
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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21
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Trajanoska K, Bhérer C, Taliun D, Zhou S, Richards JB, Mooser V. From target discovery to clinical drug development with human genetics. Nature 2023; 620:737-745. [PMID: 37612393 DOI: 10.1038/s41586-023-06388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/29/2023] [Indexed: 08/25/2023]
Abstract
The substantial investments in human genetics and genomics made over the past three decades were anticipated to result in many innovative therapies. Here we investigate the extent to which these expectations have been met, excluding cancer treatments. In our search, we identified 40 germline genetic observations that led directly to new targets and subsequently to novel approved therapies for 36 rare and 4 common conditions. The median time between genetic target discovery and drug approval was 25 years. Most of the genetically driven therapies for rare diseases compensate for disease-causing loss-of-function mutations. The therapies approved for common conditions are all inhibitors designed to pharmacologically mimic the natural, disease-protective effects of rare loss-of-function variants. Large biobank-based genetic studies have the power to identify and validate a large number of new drug targets. Genetics can also assist in the clinical development phase of drugs-for example, by selecting individuals who are most likely to respond to investigational therapies. This approach to drug development requires investments into large, diverse cohorts of deeply phenotyped individuals with appropriate consent for genetically assisted trials. A robust framework that facilitates responsible, sustainable benefit sharing will be required to capture the full potential of human genetics and genomics and bring effective and safe innovative therapies to patients quickly.
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Affiliation(s)
- Katerina Trajanoska
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Claude Bhérer
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Daniel Taliun
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Sirui Zhou
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology and Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Vincent Mooser
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada.
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22
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Strobl J, Haniffa M. Functional heterogeneity of human skin-resident memory T cells in health and disease. Immunol Rev 2023; 316:104-119. [PMID: 37144705 PMCID: PMC10952320 DOI: 10.1111/imr.13213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/11/2023] [Accepted: 04/15/2023] [Indexed: 05/06/2023]
Abstract
The human skin is populated by a diverse pool of memory T cells, which can act rapidly in response to pathogens and cancer antigens. Tissue-resident memory T cells (TRM ) have been implicated in range of allergic, autoimmune and inflammatory skin diseases. Clonal expansion of cells with TRM properties is also known to contribute to cutaneous T-cell lymphoma. Here, we review the heterogeneous phenotypes, transcriptional programs, and effector functions of skin TRM . We summarize recent studies on TRM formation, longevity, plasticity, and retrograde migration and contextualize the findings to skin TRM and their role in maintaining skin homeostasis and altered functions in skin disease.
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Affiliation(s)
- Johanna Strobl
- Department of DermatologyMedical University of ViennaViennaAustria
- CeMM Research Center for Molecular MedicineViennaAustria
| | - Muzlifah Haniffa
- Wellcome Sanger InstituteCambridgeUK
- Department of Dermatology and NIHR Newcastle Biomedical Research CentreNewcastle Hospitals NHS Foundation TrustNewcastle upon TyneUK
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
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23
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Norasi E, Rastegar M, Hosseini SD, Aghcheli B, Tahamtan A. Prevalence of CCR5 Delta 32 Genetic Variant in the Turkmen Population of Golestan Province, Northeast of Iran. Biomed Res Int 2023; 2023:8823863. [PMID: 37388364 PMCID: PMC10307026 DOI: 10.1155/2023/8823863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/23/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023]
Abstract
The 32 bp deletion in the chemokine receptor (C-C motif) 5 gene (CCR5Δ32) is a natural loss of function polymorphism that prevents the protein from locating on the cell surface. This genetic variation acts as a double-edge sword in the pathogenesis/defense mechanism of different health conditions, such as viral infections, autoimmune diseases, and cancers. Here, we evaluated the prevalence of the CCR5Δ32 polymorphism in the Turkmen population of Golestan province, northeast of Iran. Blood samples were collected from 400 randomly selected Turkmen populations (199 women and 201 men), and genomic DNA was extracted. Characterization of CCR5Δ32 genotypes was performed by PCR using primers flanking the 32-nucleotide deletion in the CCR5 gene. The amplified DNA fragments were visualized on 2% agarose gel electrophoresis with cybergreen staining under UV light. All individuals were of Turkmen ethnicity and lived in the Golestan province, northeast of Iran. The mean age of all participants was 35.46 years, with a 20-45 year range. All the studied subjects were healthy without any severe conditions such as autoimmune disease and viral infections. All individuals had no history of HIV infection. The PCR product visualization showed that all the samples are at the 330 bp size, which means the CCR5Δ32 allele was utterly absent from the study population. The presence of the CCR5Δ32 allele among Turkmens may be attributed to the admixture with European descent people. We conclude that the CCR5Δ32 polymorphism may be absent in the Iranian Turkmen population, and further studies with a large population are needed.
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Affiliation(s)
- Elmira Norasi
- School of International, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mostafa Rastegar
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | | | - Bahman Aghcheli
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Alireza Tahamtan
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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24
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Adimulam T, Arumugam T, Gokul A, Ramsuran V. Genetic Variants within SARS-CoV-2 Human Receptor Genes May Contribute to Variable Disease Outcomes in Different Ethnicities. Int J Mol Sci 2023; 24:ijms24108711. [PMID: 37240057 DOI: 10.3390/ijms24108711] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into a global pandemic, with an alarming infectivity and mortality rate. Studies have examined genetic effects on SARS-CoV-2 disease susceptibility and severity within Eurasian populations. These studies identified contrasting effects on the severity of disease between African populations. Genetic factors can explain some of the diversity observed within SARS-CoV-2 disease susceptibility and severity. Single nucleotide polymorphisms (SNPs) within the SARS-CoV-2 receptor genes have demonstrated detrimental and protective effects across ethnic groups. For example, the TT genotype of rs2285666 (Angiotensin-converting enzyme 2 (ACE2)) is associated with the severity of SARS-CoV-2 disease, which is found at higher frequency within Asian individuals compared to African and European individuals. In this study, we examined four SARS-CoV-2 receptors, ACE2, Transmembrane serine protease 2 (TMPRSS2), Neuropilin-1 (NRP1), and Basigin (CD147). A total of 42 SNPs located within the four receptors were reviewed: ACE2 (12), TMPRSS2 (10), BSG (CD147) (5), and NRP1 (15). These SNPs may be determining factors for the decreased disease severity observed within African individuals. Furthermore, we highlight the absence of genetic studies within the African population and emphasize the importance of further research. This review provides a comprehensive summary of specific variants within the SARS-CoV-2 receptor genes, which can offer a better understanding of the pathology of the SARS-CoV-2 pandemic and identify novel potential therapeutic targets.
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Affiliation(s)
- Theolan Adimulam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Anmol Gokul
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban 4041, South Africa
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25
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Bone B, Lichterfeld M. Curating evidence for a cure of HIV-1 infection by hematopoietic stem cell transplantation. Med 2023; 4:285-287. [PMID: 37178680 PMCID: PMC11065144 DOI: 10.1016/j.medj.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023]
Abstract
A cure of HIV-1 infection has previously been described in two individuals undergoing allogeneic hematopoietic stem cell transplants from homozygous carriers of the CCR5Δ32 gene variant, which confers HIV-1 resistance. Two recent reports corroborate these earlier studies, underscoring that in HIV-1-infected persons with hematologic malignancies, these procedures may provide a realistic perspective for a cure of HIV-1 infection.
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Affiliation(s)
- Benjamin Bone
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA.
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26
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Roa-Linares VC, Escudero-Flórez M, Vicente-Manzanares M, Gallego-Gómez JC. Host Cell Targets for Unconventional Antivirals against RNA Viruses. Viruses 2023; 15:v15030776. [PMID: 36992484 PMCID: PMC10058429 DOI: 10.3390/v15030776] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/12/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
The recent COVID-19 crisis has highlighted the importance of RNA-based viruses. The most prominent members of this group are SARS-CoV-2 (coronavirus), HIV (human immunodeficiency virus), EBOV (Ebola virus), DENV (dengue virus), HCV (hepatitis C virus), ZIKV (Zika virus), CHIKV (chikungunya virus), and influenza A virus. With the exception of retroviruses which produce reverse transcriptase, the majority of RNA viruses encode RNA-dependent RNA polymerases which do not include molecular proofreading tools, underlying the high mutation capacity of these viruses as they multiply in the host cells. Together with their ability to manipulate the immune system of the host in different ways, their high mutation frequency poses a challenge to develop effective and durable vaccination and/or treatments. Consequently, the use of antiviral targeting agents, while an important part of the therapeutic strategy against infection, may lead to the selection of drug-resistant variants. The crucial role of the host cell replicative and processing machinery is essential for the replicative cycle of the viruses and has driven attention to the potential use of drugs directed to the host machinery as therapeutic alternatives to treat viral infections. In this review, we discuss small molecules with antiviral effects that target cellular factors in different steps of the infectious cycle of many RNA viruses. We emphasize the repurposing of FDA-approved drugs with broad-spectrum antiviral activity. Finally, we postulate that the ferruginol analog (18-(phthalimide-2-yl) ferruginol) is a potential host-targeted antiviral.
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Affiliation(s)
- Vicky C Roa-Linares
- Molecular and Translation Medicine Group, University of Antioquia, Medellin 050010, Colombia
| | - Manuela Escudero-Flórez
- Molecular and Translation Medicine Group, University of Antioquia, Medellin 050010, Colombia
| | - Miguel Vicente-Manzanares
- Molecular Mechanisms Program, Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca, 37007 Salamanca, Spain
| | - Juan C Gallego-Gómez
- Molecular and Translation Medicine Group, University of Antioquia, Medellin 050010, Colombia
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27
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Hsu J, Besien KV, Glesby MJ, Pahwa S, Coletti A, Warshaw MG, Petz L, Moore TB, Chen YH, Pallikkuth S, Dhummakupt A, Cortado R, Golner A, Bone F, Baldo M, Riches M, Mellors JW, Tobin NH, Browning R, Persaud D, Bryson Y. HIV-1 remission and possible cure in a woman after haplo-cord blood transplant. Cell 2023; 186:1115-1126.e8. [PMID: 36931242 PMCID: PMC10616809 DOI: 10.1016/j.cell.2023.02.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/01/2022] [Accepted: 02/17/2023] [Indexed: 03/18/2023]
Abstract
Previously, two men were cured of HIV-1 through CCR5Δ32 homozygous (CCR5Δ32/Δ32) allogeneic adult stem cell transplant. We report the first remission and possible HIV-1 cure in a mixed-race woman who received a CCR5Δ32/Δ32 haplo-cord transplant (cord blood cells combined with haploidentical stem cells from an adult) to treat acute myeloid leukemia (AML). Peripheral blood chimerism was 100% CCR5Δ32/Δ32 cord blood by week 14 post-transplant and persisted through 4.8 years of follow-up. Immune reconstitution was associated with (1) loss of detectable replication-competent HIV-1 reservoirs, (2) loss of HIV-1-specific immune responses, (3) in vitro resistance to X4 and R5 laboratory variants, including pre-transplant autologous latent reservoir isolates, and (4) 18 months of HIV-1 control with aviremia, off antiretroviral therapy, starting at 37 months post-transplant. CCR5Δ32/Δ32 haplo-cord transplant achieved remission and a possible HIV-1 cure for a person of diverse ancestry, living with HIV-1, who required a stem cell transplant for acute leukemia.
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Affiliation(s)
- Jingmei Hsu
- Department of Medicine, Division of Hematology& Oncology, Weill Cornell Medicine / New York Presbyterian Hospital, New York, NY, 10021, USA
| | - Koen Van Besien
- Department of Medicine, Division of Hematology& Oncology, Weill Cornell Medicine / New York Presbyterian Hospital, New York, NY, 10021, USA
| | - Marshall J. Glesby
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine / New York Presbyterian Hospital, New York, NY, 10021, USA
| | - Savita Pahwa
- Department of Microbiology and Immunology, Pediatrics and Medicine, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Anne Coletti
- Family Health International 360, Durham, NC, 27761, USA
| | - Meredith G Warshaw
- Center for Biostatistics in AIDS Research, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA
| | - Larry Petz
- StemCyte International Cord Blood Center, Baldwin Park, California, 91706, USA
| | - Theodore B. Moore
- Department of Pediatrics, Division of Hematology& Oncology, Ronald Reagan UCLA Medical Center, Los Angeles, CA, 90095, USA
| | - Ya Hui Chen
- Department of Pediatrics, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21025, USA
| | - Suresh Pallikkuth
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Adit Dhummakupt
- Department of Pediatrics, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21025, USA
| | - Ruth Cortado
- Department of Pediatrics, Division of Infectious Diseases, Mattel Children’s, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Amanda Golner
- Frontier Science & Technology Research Foundation, Inc, Amherst, NY, 14226, USA
| | - Frederic Bone
- Frontier Science & Technology Research Foundation, Inc, Amherst, NY, 14226, USA
| | - Maria Baldo
- Department of Medicine, Division of Hematology& Oncology, Weill Cornell Medicine / New York Presbyterian Hospital, New York, NY, 10021, USA
| | - Marcie Riches
- Center for International Blood and Marrow Transplant Research (CIBMTR), Medical College of Wisconsin Clinical Cancer Center, Milwaukee, WI, 53226, USA
| | - John W. Mellors
- Department of Medicine, Division of Infectious Diseases, University of Pittsburg School of Medicine, Pittsburgh, PA, 15261, USA
| | - Nicole H. Tobin
- Department of Pediatrics, Division of Infectious Diseases, Mattel Children’s, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Renee Browning
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA
| | - Deborah Persaud
- Department of Pediatrics, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21025, USA
| | - Yvonne Bryson
- Department of Pediatrics, Division of Infectious Diseases, Mattel Children’s, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
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Lima ÉRG, Queiroz MAF, Lima SS, Machado LFA, Cayres-Vallinoto IMV, Vallinoto ACR, Figueiredo FADPL, Guerreiro JF, Guimarães Ishak MDO, Ishak R. CCR5∆32 and SDF1 3'A: Gene Variants, Expression and Influence on Biological Markers for the Clinical Progression to AIDS among HIV-1 Virus Controllers in a Mixed Population of the Amazon Region of Brazil. Int J Mol Sci 2023; 24:ijms24054958. [PMID: 36902388 PMCID: PMC10003039 DOI: 10.3390/ijms24054958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 03/08/2023] Open
Abstract
CCR5Δ32 and SDF1-3'A polymorphisms were investigated in a cohort of viremia controllers, without the use of therapy, along with their influence on CD4+ T lymphocytes (TLs), CD8+ TLs, and plasma viral load (VL). The samples were analyzed from 32 HIV-1-infected individuals classified as viremia controllers 1 and 2 and viremia non-controllers, from both sexes, mostly heterosexuals, paired with 300 individuals from a control group. CCR5∆32 polymorphism was identified by PCR amplification of a fragment of 189 bp for the wild-type allele and 157 bp for the allele with the ∆32 deletion. SDF1-3'A polymorphism was identified by PCR, followed by enzymatic digestion (restriction fragment length polymorphism) with the Msp I enzyme. The relative quantification of gene expression was performed by real-time PCR. The distribution of allele and genotype frequencies did not show significant differences between the groups. The gene expression of CCR5 and SDF1 was not different between the profiles of AIDS progression. There was no significant correlation between the progression markers (CD4+ TL/CD8+ TL and VL) and the CCR5∆32 polymorphism carrier status. The 3'A allele variant was associated with a marked loss of CD4+ TLs and a higher plasma VL. Neither CCR5∆32 nor SDF1-3'A was associated with viremia control or the controlling phenotype.
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Affiliation(s)
- Érica Ribeiro Gomes Lima
- Virus Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Maria Alice Freitas Queiroz
- Virus Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
- Correspondence: ; Tel.: +55-91-98864-4259
| | - Sandra Souza Lima
- Virus Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | | | | | | | | | - João Farias Guerreiro
- Human and Medical Genetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | | | - Ricardo Ishak
- Virus Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
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29
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Joerin-Luque IA, Sukow NM, Bucco ID, Tessaro JG, Lopes CVG, Barbosa AAL, Beltrame MH. Ancestry, diversity, and genetics of health-related traits in African-derived communities (quilombos) from Brazil. Funct Integr Genomics 2023; 23:74. [PMID: 36867305 DOI: 10.1007/s10142-023-00999-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023]
Abstract
Brazilian quilombos are communities formed by enslaved Africans and their descendants all over the country during slavery and shortly after its abolition. Quilombos harbor a great fraction of the largely unknown genetic diversity of the African diaspora in Brazil. Thus, genetic studies in quilombos have the potential to provide important insights not only into the African roots of the Brazilian population but also into the genetic bases of complex traits and human adaptation to diverse environments. This review summarizes the main results of genetic studies performed on quilombos so far. Here, we analyzed the patterns of African, Amerindian, European, and subcontinental ancestry (within Africa) of quilombos from the five different geographic regions of Brazil. In addition, uniparental markers (from the mtDNA and the Y chromosome) studies are analyzed together to reveal demographic processes and sex-biased admixture that occurred during the formation of these unique populations. Lastly, the prevalence of known malaria-adaptive African mutations and other African-specific variants discovered in quilombos, as well as the genetic bases of health-related traits, are discussed here, together with their implication for the health of populations of African descent.
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30
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Mok C, Xiao MA, Wan YC, Zhao W, Ahmed SM, Luallen RJ, Reinke AW. High-throughput phenotyping of infection by diverse microsporidia species reveals a wild C. elegans strain with opposing resistance and susceptibility traits. PLoS Pathog 2023; 19:e1011225. [PMID: 36893187 PMCID: PMC10030041 DOI: 10.1371/journal.ppat.1011225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/21/2023] [Accepted: 02/20/2023] [Indexed: 03/10/2023] Open
Abstract
Animals are under constant selective pressure from a myriad of diverse pathogens. Microsporidia are ubiquitous animal parasites, but the influence they exert on shaping animal genomes is mostly unknown. Using multiplexed competition assays, we measured the impact of four different species of microsporidia on 22 wild isolates of Caenorhabditis elegans. This resulted in the identification and confirmation of 13 strains with significantly altered population fitness profiles under infection conditions. One of these identified strains, JU1400, is sensitive to an epidermal-infecting species by lacking tolerance to infection. JU1400 is also resistant to an intestinal-infecting species and can specifically recognize and destroy this pathogen. Genetic mapping of JU1400 demonstrates that these two opposing phenotypes are caused by separate loci. Transcriptional analysis reveals the JU1400 sensitivity to epidermal microsporidia infection results in a response pattern that shares similarity to toxin-induced responses. In contrast, we do not observe JU1400 intestinal resistance being regulated at the transcriptional level. The transcriptional response to these four microsporidia species is conserved, with C. elegans strain-specific differences in potential immune genes. Together, our results show that phenotypic differences to microsporidia infection amongst C. elegans are common and that animals can evolve species-specific genetic interactions.
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Affiliation(s)
- Calvin Mok
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Meng A Xiao
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yin C Wan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Winnie Zhao
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shanzeh M Ahmed
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Robert J Luallen
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Aaron W Reinke
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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31
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Milne R, Patch C. Ethical Challenges Associated with Pathogen and Host Genetics in Infectious Disease. New Bioeth 2023; 29:24-36. [PMID: 35972296 DOI: 10.1080/20502877.2022.2109697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
The Covid-19 pandemic has demonstrated the potential of genomic technologies for the detection and surveillance of infectious diseases. Pathogen genomics is likely to play a major role in the future of research and clinical implementation of genomic technologies. However, unlike human genetics, the specific ethical and social challenges associated with the implementation of infectious disease genomics has received comparatively little attention. In this paper, we contribute to this literature, focusing on the potential consequences for individuals and communities of the use of these technologies. We concentrate on areas of challenges related to privacy, stigma, discrimination and the return of results in the cases of the surveillance of known pathogens, metagenomics and host genomics.
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Affiliation(s)
- Richard Milne
- Engagement and Society, Wellcome Connecting Science, Hinxton, UK.,Kavli Centre for Ethics, Science and the Public, University of Cambridge, Cambridge, UK
| | - Christine Patch
- Engagement and Society, Wellcome Connecting Science, Hinxton, UK
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32
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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33
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Fredericksen M, Fields PD, Du Pasquier L, Ricci V, Ebert D. QTL study reveals candidate genes underlying host resistance in a Red Queen model system. PLoS Genet 2023; 19:e1010570. [PMID: 36730161 PMCID: PMC9894429 DOI: 10.1371/journal.pgen.1010570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/14/2022] [Indexed: 02/03/2023] Open
Abstract
Specific interactions of host and parasite genotypes can lead to balancing selection, maintaining genetic diversity within populations. In order to understand the drivers of such specific coevolution, it is necessary to identify the molecular underpinnings of these genotypic interactions. Here, we investigate the genetic basis of resistance in the crustacean host, Daphnia magna, to attachment and subsequent infection by the bacterial parasite, Pasteuria ramosa. We discover a single locus with Mendelian segregation (3:1 ratio) with resistance being dominant, which we call the F locus. We use QTL analysis and fine mapping to localize the F locus to a 28.8-kb region in the host genome, adjacent to a known resistance supergene. We compare the 28.8-kb region in the two QTL parents to identify differences between host genotypes that are resistant versus susceptible to attachment and infection by the parasite. We identify 13 genes in the region, from which we highlight eight biological candidates for the F locus, based on presence/absence polymorphisms and differential gene expression. The top candidates include a fucosyltransferase gene that is only present in one of the two QTL parents, as well as several Cladoceran-specific genes belonging to a large family that is represented in multiple locations of the host genome. Fucosyltransferases have been linked to resistance in previous studies of Daphnia-Pasteuria and other host-parasite systems, suggesting that P. ramosa spore attachment could be mediated by changes in glycan structures on D. magna cuticle proteins. The Cladoceran-specific candidate genes suggest a resistance strategy that relies on gene duplication. Our results add a new locus to a growing genetic model of resistance in the D. magna-P. ramosa system. The identified candidate genes will be used in future functional genetic studies, with the ultimate aim to test for cycles of allele frequencies in natural populations.
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Affiliation(s)
- Maridel Fredericksen
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
- * E-mail:
| | - Peter D. Fields
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
| | - Louis Du Pasquier
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
| | - Virginie Ricci
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Basel, Switzerland
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34
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Carss KJ, Deaton AM, Del Rio-Espinola A, Diogo D, Fielden M, Kulkarni DA, Moggs J, Newham P, Nelson MR, Sistare FD, Ward LD, Yuan J. Using human genetics to improve safety assessment of therapeutics. Nat Rev Drug Discov 2023; 22:145-162. [PMID: 36261593 DOI: 10.1038/s41573-022-00561-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2022] [Indexed: 02/07/2023]
Abstract
Human genetics research has discovered thousands of proteins associated with complex and rare diseases. Genome-wide association studies (GWAS) and studies of Mendelian disease have resulted in an increased understanding of the role of gene function and regulation in human conditions. Although the application of human genetics has been explored primarily as a method to identify potential drug targets and support their relevance to disease in humans, there is increasing interest in using genetic data to identify potential safety liabilities of modulating a given target. Human genetic variants can be used as a model to anticipate the effect of lifelong modulation of therapeutic targets and identify the potential risk for on-target adverse events. This approach is particularly useful for non-clinical safety evaluation of novel therapeutics that lack pharmacologically relevant animal models and can contribute to the intrinsic safety profile of a drug target. This Review illustrates applications of human genetics to safety studies during drug discovery and development, including assessing the potential for on- and off-target associated adverse events, carcinogenicity risk assessment, and guiding translational safety study designs and monitoring strategies. A summary of available human genetic resources and recommended best practices is provided. The challenges and future perspectives of translating human genetic information to identify risks for potential drug effects in preclinical and clinical development are discussed.
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Affiliation(s)
| | - Aimee M Deaton
- Amgen, Cambridge, MA, USA.,Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Alberto Del Rio-Espinola
- Novartis Institutes for BioMedical Research, Basel, Switzerland.,GentiBio Inc., Cambridge, MA, USA
| | | | - Mark Fielden
- Amgen, Thousand Oaks, MA, USA.,Kate Therapeutics, San Diego, CA, USA
| | | | - Jonathan Moggs
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | - Frank D Sistare
- Merck & Co., West Point, PA, USA.,315 Meadowmont Ln, Chapel Hill, NC, USA
| | - Lucas D Ward
- Amgen, Cambridge, MA, USA. .,Alnylam Pharmaceuticals, Cambridge, MA, USA.
| | - Jing Yuan
- Amgen, Cambridge, MA, USA.,Pfizer, Cambridge, MA, USA
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35
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Benatar M, Goutman SA, Staats KA, Feldman EL, Weisskopf M, Talbott E, Dave KD, Thakur NM, Al-Chalabi A. A roadmap to ALS prevention: strategies and priorities. J Neurol Neurosurg Psychiatry 2023; 94:399-402. [PMID: 36690429 PMCID: PMC10176353 DOI: 10.1136/jnnp-2022-330473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/08/2023] [Indexed: 01/25/2023]
Affiliation(s)
- Michael Benatar
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Kim A Staats
- Staats Life Sciences Consulting, Los Angeles, California, USA
| | - Eva L Feldman
- Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Marc Weisskopf
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Evelyn Talbott
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Kuldip D Dave
- ALS Association, Washington, District of Columbia, USA
| | - Neil M Thakur
- ALS Association, Washington, District of Columbia, USA
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
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36
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Jasinska AJ, Apetrei C, Pandrea I. Walk on the wild side: SIV infection in African non-human primate hosts-from the field to the laboratory. Front Immunol 2023; 13:1060985. [PMID: 36713371 PMCID: PMC9878298 DOI: 10.3389/fimmu.2022.1060985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/15/2022] [Indexed: 01/15/2023] Open
Abstract
HIV emerged following cross-species transmissions of simian immunodeficiency viruses (SIVs) that naturally infect non-human primates (NHPs) from Africa. While HIV replication and CD4+ T-cell depletion lead to increased gut permeability, microbial translocation, chronic immune activation, and systemic inflammation, the natural hosts of SIVs generally avoid these deleterious consequences when infected with their species-specific SIVs and do not progress to AIDS despite persistent lifelong high viremia due to long-term coevolution with their SIV pathogens. The benign course of natural SIV infection in the natural hosts is in stark contrast to the experimental SIV infection of Asian macaques, which progresses to simian AIDS. The mechanisms of non-pathogenic SIV infections are studied mainly in African green monkeys, sooty mangabeys, and mandrills, while progressing SIV infection is experimentally modeled in macaques: rhesus macaques, pigtailed macaques, and cynomolgus macaques. Here, we focus on the distinctive features of SIV infection in natural hosts, particularly (1): the superior healing properties of the intestinal mucosa, which enable them to maintain the integrity of the gut barrier and prevent microbial translocation, thus avoiding excessive/pathologic immune activation and inflammation usually perpetrated by the leaking of the microbial products into the circulation; (2) the gut microbiome, the disruption of which is an important factor in some inflammatory diseases, yet not completely understood in the course of lentiviral infection; (3) cell population shifts resulting in target cell restriction (downregulation of CD4 or CCR5 surface molecules that bind to SIV), control of viral replication in the lymph nodes (expansion of natural killer cells), and anti-inflammatory effects in the gut (NKG2a/c+ CD8+ T cells); and (4) the genes and biological pathways that can shape genetic adaptations to viral pathogens and are associated with the non-pathogenic outcome of the natural SIV infection. Deciphering the protective mechanisms against SIV disease progression to immunodeficiency, which have been established through long-term coevolution between the natural hosts and their species-specific SIVs, may prompt the development of novel therapeutic interventions, such as drugs that can control gut inflammation, enhance gut healing capacities, or modulate the gut microbiome. These developments can go beyond HIV infection and open up large avenues for correcting gut damage, which is common in many diseases.
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Affiliation(s)
- Anna J. Jasinska
- Division of Infectious Diseases, Department of Medicine (DOM), School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Cristian Apetrei
- Division of Infectious Diseases, Department of Medicine (DOM), School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States,Department of Infectious Diseases and Immunology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ivona Pandrea
- Department of Infectious Diseases and Immunology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States,Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States,*Correspondence: Ivona Pandrea,
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37
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Schmidt JK, Kim YH, Strelchenko N, Gierczic SR, Pavelec D, Golos TG, Slukvin II. Whole genome sequencing of CCR5 CRISPR-Cas9-edited Mauritian cynomolgus macaque blastomeres reveals large-scale deletions and off-target edits. Front Genome Ed 2023; 4:1031275. [PMID: 36714391 PMCID: PMC9877282 DOI: 10.3389/fgeed.2022.1031275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/15/2022] [Indexed: 01/15/2023] Open
Abstract
Introduction: Genome editing by CRISPR-Cas9 approaches offers promise for introducing or correcting disease-associated mutations for research and clinical applications. Nonhuman primates are physiologically closer to humans than other laboratory animal models, providing ideal candidates for introducing human disease-associated mutations to develop models of human disease. The incidence of large chromosomal anomalies in CRISPR-Cas9-edited human embryos and cells warrants comprehensive genotypic investigation of editing outcomes in primate embryos. Our objective was to evaluate on- and off-target editing outcomes in CCR5 CRISPR-Cas9-targeted Mauritian cynomolgus macaque embryos. Methods: DNA isolated from individual blastomeres of two embryos, along with paternal and maternal DNA, was subjected to whole genome sequencing (WGS) analysis. Results: Large deletions were identified in macaque blastomeres at the on-target site that were not previously detected using PCR-based methods. De novo mutations were also identified at predicted CRISPR-Cas9 off-target sites. Discussion: This is the first report of WGS analysis of CRISPR-Cas9-targeted nonhuman primate embryonic cells, in which a high editing efficiency was coupled with the incidence of editing errors in cells from two embryos. These data demonstrate that comprehensive sequencing-based methods are warranted for evaluating editing outcomes in primate embryos, as well as any resultant offspring to ensure that the observed phenotype is due to the targeted edit and not due to unidentified off-target mutations.
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Affiliation(s)
- Jenna Kropp Schmidt
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Yun Hee Kim
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Nick Strelchenko
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Sarah R. Gierczic
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Derek Pavelec
- University of Wisconsin Biotechnology Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Thaddeus G. Golos
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, United States
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, United States
| | - Igor I. Slukvin
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, United States
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38
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Jay C, Ratcliff J, Turtle L, Goulder P, Klenerman P. Exposed seronegative: Cellular immune responses to SARS-CoV-2 in the absence of seroconversion. Front Immunol 2023; 14:1092910. [PMID: 36776841 PMCID: PMC9909393 DOI: 10.3389/fimmu.2023.1092910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
The factors determining whether infection will occur following exposure to SARS-CoV-2 remain elusive. Certain SARS-CoV-2-exposed individuals mount a specific T-cell response but fail to seroconvert, representing a population that may provide further clarity on the nature of infection susceptibility and correlates of protection against SARS-CoV-2. Exposed seronegative individuals have been reported in patients exposed to the blood-borne pathogens Human Immunodeficiency virus and Hepatitis C virus and the sexually transmitted viruses Hepatitis B virus and Herpes Simplex virus. By comparing the quality of seronegative T-cell responses to SARS-CoV-2 with seronegative cellular immunity to these highly divergent viruses, common patterns emerge that offer insights on the role of cellular immunity against infection. For both SARS-CoV-2 and Hepatitis C, T-cell responses in exposed seronegatives are consistently higher than in unexposed individuals, but lower than in infected, seropositive patients. Durability of T-cell responses to Hepatitis C is dependent upon repeated exposure to antigen - single exposures do not generate long-lived memory T-cells. Finally, exposure to SARS-CoV-2 induces varying degrees of immune activation, suggesting that exposed seronegative individuals represent points on a spectrum rather than a discrete group. Together, these findings paint a complex landscape of the nature of infection but provide clues as to what may be protective early on in SARS-CoV-2 disease course. Further research on this phenomenon, particularly through cohort studies, is warranted.
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Affiliation(s)
- Cecilia Jay
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jeremy Ratcliff
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Lance Turtle
- National Institute for Health and Care Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, United Kingdom
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Morales V, González A, Cabello-Verrugio C. Upregulation of CCL5/RANTES Gene Expression in the Diaphragm of Mice with Cholestatic Liver Disease. Adv Exp Med Biol 2023; 1408:201-218. [PMID: 37093429 DOI: 10.1007/978-3-031-26163-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Chronic liver diseases are a group of pathologies affecting the liver with high prevalence worldwide. Among them, cholestatic chronic liver diseases (CCLD) are characterized by alterations in liver function and increased plasma bile acids. Secondary to liver disease, under cholestasis, is developed sarcopenia, a skeletal muscle dysfunction with decreased muscle mass, strength, and physical function. CCL5/RANTES is a chemokine involved in the immune and inflammatory response. Indeed, CCL5 is a myokine because it is produced by skeletal muscle. Several studies show that bile acids induce CCL5/RANTES expression in liver cells. However, it is unknown if the expression of CCL5/RANTES is changed in the skeletal muscle of mice with cholestatic liver disease. We used a murine model of cholestasis-induced sarcopenia by intake of hepatotoxin 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC diet), in which we detected the mRNA levels for ccl5. We determined that mice fed the DDC diet presented high levels of serum bile acids and developed typical features of sarcopenia. Under these conditions, we detected the ccl5 gene expression in diaphragm muscle showing elevated mRNA levels compared to mice fed with a standard diet (chow diet). Our results collectively suggest an increased ccl5 gene expression in the diaphragm muscle concomitantly with elevated serum bile acids and the development of sarcopenia.
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Affiliation(s)
- Vania Morales
- Laboratory of Muscle Pathology, Fragility and Aging, Faculty of Life Sciences, Universidad Andres Bello, Santiago, 8370146, Chile
- Millennium Institute on Immunology and Immunotherapy, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
- Center for the Development of Nanoscience and Nanotechnology (CEDENNA), Universidad de Santiago de Chile, Santiago, Chile
| | - Andrea González
- Laboratory of Muscle Pathology, Fragility and Aging, Faculty of Life Sciences, Universidad Andres Bello, Santiago, 8370146, Chile
- Millennium Institute on Immunology and Immunotherapy, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
- Center for the Development of Nanoscience and Nanotechnology (CEDENNA), Universidad de Santiago de Chile, Santiago, Chile
| | - Claudio Cabello-Verrugio
- Laboratory of Muscle Pathology, Fragility and Aging, Faculty of Life Sciences, Universidad Andres Bello, Santiago, 8370146, Chile.
- Millennium Institute on Immunology and Immunotherapy, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.
- Center for the Development of Nanoscience and Nanotechnology (CEDENNA), Universidad de Santiago de Chile, Santiago, Chile.
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40
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Papageorgiou L, Papakonstantinou E, Diakou I, Pierouli K, Dragoumani K, Bacopoulou F, Chrousos GP, Eliopoulos E, Vlachakis D. Semantic and Population Analysis of the Genetic Targets Related to COVID-19 and Its Association with Genes and Diseases. Adv Exp Med Biol 2023; 1423:59-78. [PMID: 37525033 DOI: 10.1007/978-3-031-31978-5_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
SARS-CoV-2 is a coronavirus responsible for one of the most serious, modern worldwide pandemics, with lasting and multifaceted effects. By late 2021, SARS-CoV-2 has infected more than 180 million people and has killed more than 3 million. The virus gains entrance to human cells through binding to ACE2 via its surface spike protein and causes a complex disease of the respiratory system, termed COVID-19. Vaccination efforts are being made to hinder the viral spread, and therapeutics are currently under development. Toward this goal, scientific attention is shifting toward variants and SNPs that affect factors of the disease such as susceptibility and severity. This genomic grammar, tightly related to the dark part of our genome, can be explored through the use of modern methods such as natural language processing. We present a semantic analysis of SARS-CoV-2-related publications, which yielded a repertoire of SNPs, genes, and disease ontologies. Population data from the 1000 Genomes Project were subsequently integrated into the pipeline. Data mining approaches of this scale have the potential to elucidate the complex interaction between COVID-19 pathogenesis and host genetic variation; the resulting knowledge can facilitate the management of high-risk groups and aid the efforts toward precision medicine.
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Affiliation(s)
- Louis Papageorgiou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Flora Bacopoulou
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - George P Chrousos
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece.
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece.
- Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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Sears CL, Li JZ, Singh U. Turning the page: a welcome from the new leadership of the Journal of Infectious Diseases. J Infect Dis 2022; 227:1-3. [PMID: 36576495 DOI: 10.1093/infdis/jiac400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 12/29/2022] Open
Affiliation(s)
- Cynthia L Sears
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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Jai J, Shirleen D, Hanbali C, Wijaya P, Anginan TB, Husada W, Pratama MY. Multiplexed shRNA-miRs as a candidate for anti HIV-1 therapy: strategies, challenges, and future potential. J Genet Eng Biotechnol 2022; 20:172. [PMID: 36576612 PMCID: PMC9797628 DOI: 10.1186/s43141-022-00451-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 12/04/2022] [Indexed: 12/29/2022]
Abstract
The spread of HIV is on the rise and has become a global issue, especially for underdeveloped and developing countries. This is due to the fact that HIV majorly occurs asymptomatically and is implausible for early diagnosis. Recent advances in research and science have enabled the investigation of a new potential treatment involving gene-based therapy, known as RNA interference (RNAi) that will direct gene silencing and further compensate for natural variants and viral mutants. Several types of small regulatory RNA are discussed in this present study, including microRNA (miRNA), small interfering RNA (siRNA), and short hairpin RNA (shRNA).This paper examines the mechanism of RNAi as a viable HIV therapy, using a minimum of four shRNAs to target both dispensable host components (CCR5) and viral genes (Gag, Env, Tat, Pol I, Pol II and Vif). Moreover, a multiplexed mechanism of shRNAs and miRNA is known to be effective in preventing viral escape due to mutation as the miRNA develops a general polycistronic platform for the expression of a large amount of shRNA-miRs. Several administration methods as well as the advantages of this RNAi treatment are also discussed in this study. The administration methods include (1) ex vivo delivery with the help of viral vectors, nanoparticles, and electroporation, (2) nonspecific in vivo delivery using non-viral carriers including liposomes, dendrimers and aptamers, as well as (3) targeted delivery that uses antibodies, modified nanoparticles, nucleic acid aptamers, and tissue-specific serotypes of AAV. Moreover, the advantages of this treatment are related to the effectiveness in silencing the HIV gene, which is more compatible compared to other gene therapy treatments, such as ZFN, TALEN, and CRISPR/Cas9.
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Affiliation(s)
- Jyotsna Jai
- grid.504251.70000 0004 7706 8927Department of Biotechnology, Indonesia International Institute for Life-Sciences (i3L), Jakarta, Indonesia
| | - Deborah Shirleen
- grid.504251.70000 0004 7706 8927Department of Biotechnology, Indonesia International Institute for Life-Sciences (i3L), Jakarta, Indonesia
| | - Christian Hanbali
- grid.504251.70000 0004 7706 8927Department of Biomedicine, Indonesia International Institute for Life-Sciences (i3L), Jakarta, Indonesia
| | - Pamela Wijaya
- grid.504251.70000 0004 7706 8927Department of Biomedicine, Indonesia International Institute for Life-Sciences (i3L), Jakarta, Indonesia
| | - Theresia Brigita Anginan
- grid.504251.70000 0004 7706 8927Department of Biomedicine, Indonesia International Institute for Life-Sciences (i3L), Jakarta, Indonesia
| | - William Husada
- grid.504251.70000 0004 7706 8927Department of Biotechnology, Indonesia International Institute for Life-Sciences (i3L), Jakarta, Indonesia
| | - Muhammad Yogi Pratama
- grid.504251.70000 0004 7706 8927Department of Biomedicine, Indonesia International Institute for Life-Sciences (i3L), Jakarta, Indonesia ,grid.240324.30000 0001 2109 4251Division of Vascular Surgery, Department of Surgery, New York University Medical Center, New York, USA
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Abisi HK, Otieno LE, Irungu E, Onyambu FG, Chepchirchir A, Anzala O, Wamalwa DC, Nduati RW, McKinnon L, Kimani J, Mulinge MM. Net charge and position 22 of the V3 loop are associated with HIV-1 tropism in recently infected female sex workers in Nairobi, Kenya. Medicine (Baltimore) 2022; 101:e32024. [PMID: 36626483 PMCID: PMC9750520 DOI: 10.1097/md.0000000000032024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection affects around 37 million people worldwide, and in Kenya, key populations especially female sex workers (FSW), are thought to play a substantial role in the wider, mostly heterosexual HIV-1 transmission structure. Notably, HIV tropism has been found to correlate with HIV-1 transmission and disease progression in HIV-infected patients. In this study, recently infected FSWs from Nairobi, Kenya, were assessed for HIV tropism and the factors related to it. We used a cross-sectional study design to analyze 76 HIV-1 positive plasma samples obtained from FSWs enrolled in sex worker outreach program clinics in Nairobi between November 2020 and April 2021. The effects of clinical, demographic, and viral genetic characteristics were determined using multivariable logistic regression. HIV-1 subtype A1 accounted for 89.5% of all cases, with a prevalence of CXCR4-tropic viruses of 26.3%. WebPSSMR5X4 and Geno2Pheno [G2P:10-15% false positive rate] showed high concordance of 88%. Subjects infected with CXCR4-tropic viruses had statistically significant lower baseline CD4+T-cell counts than those infected with CCR5-tropic viruses (P = .044). Using multivariable logistic regression and adjusting for potential confounders, we found that net charge, the amino acid at position 22 of the V3 loop, and the geographic location of the subject were associated with tropism. A unit increase in V3 loop's net-charge increased the odds of a virus being CXCR4-tropic by 2.4 times (OR = 2.40, 95%CI = 1.35-5.00, P = .007). Second, amino acid threonine at position 22 of V3 loop increased the odds of a strain being X4 by 55.7 times compared to the alanine which occurred in CCR5-tropic strains (OR = 55.7, 95%CI = 4.04-84.1, P < .003). The Kawangware sex worker outreach program clinic was associated with CXCR4-tropic strains (P = .034), but there was there was no evidence of a distinct CXCR4-tropic transmission cluster. In conclusion, this study revealed a high concordance of WebPSSMR5X4 and Geno2Pheno in predicting HIV tropism. The most striking finding was that amino acid position 22 of the V3 loop is linked to tropism in HIV-1 subtype A1. Additional studies with a large dataset are warranted to confirm our findings.
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Affiliation(s)
- Hellen K Abisi
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | - Leon E Otieno
- Molecular Medicine and Infectious Diseases Laboratory, University of Nairobi, Nairobi, Kenya
| | - Erastus Irungu
- Partners for Health and Development in Africa (PHDA), Nairobi, Kenya
| | - Frank G Onyambu
- School of Health Sciences, Meru University of Science and Technology, Meru, Kenya
| | | | - Omu Anzala
- Kenya AIDS Vaccine Initiative - Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Dalton C Wamalwa
- Department of Paediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Ruth W Nduati
- Department of Paediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Lyle McKinnon
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Manitoba, MB, Canada
| | - Joshua Kimani
- Partners for Health and Development in Africa (PHDA), Nairobi, Kenya
| | - Martin M Mulinge
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
- Kenya AIDS Vaccine Initiative - Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
- * Correspondence: Martin M Mulinge, University of Nairobi, Chiromo Campus - Nairobi 30197-00100, Kenya (e-mail: )
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Qiu HY, Ji RJ, Zhang Y. Current advances of CRISPR-Cas technology in cell therapy. Cell Insight 2022; 1:100067. [PMID: 37193354 PMCID: PMC10120314 DOI: 10.1016/j.cellin.2022.100067] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 05/18/2023]
Abstract
CRISPR-Cas is a versatile genome editing technology that has been broadly applied in both basic research and translation medicine. Ever since its discovery, the bacterial derived endonucleases have been engineered to a collection of robust genome-editing tools for introducing frameshift mutations or base conversions at site-specific loci. Since the initiation of first-in-human trial in 2016, CRISPR-Cas has been tested in 57 cell therapy trials, 38 of which focusing on engineered CAR-T cells and TCR-T cells for cancer malignancies, 15 trials of engineered hematopoietic stem cells treating hemoglobinopathies, leukemia and AIDS, and 4 trials of engineered iPSCs for diabetes and cancer. Here, we aim to review the recent breakthroughs of CRISPR technology and highlight their applications in cell therapy.
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Affiliation(s)
- Hou-Yuan Qiu
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Rui-Jin Ji
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Ying Zhang
- Department of Rheumatology and Immunology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
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45
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Abstract
Since the identification of sickle cell trait as a heritable form of resistance to malaria, candidate gene studies, linkage analysis paired with sequencing, and genome-wide association (GWA) studies have revealed many examples of genetic resistance and susceptibility to infectious diseases. GWA studies enabled the identification of many common variants associated with small shifts in susceptibility to infectious diseases. This is exemplified by multiple loci associated with leprosy, malaria, HIV, tuberculosis, and coronavirus disease 2019 (COVID-19), which illuminate genetic architecture and implicate pathways underlying pathophysiology. Despite these successes, most of the heritability of infectious diseases remains to be explained. As the field advances, current limitations may be overcome by applying methodological innovations such as cellular GWA studies and phenome-wide association (PheWA) studies as well as by improving methodological rigor with more precise case definitions, deeper phenotyping, increased cohort diversity, and functional validation of candidate loci in the laboratory or human challenge studies.
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Affiliation(s)
- Kyle D Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA;
| | - Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA; .,Duke University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA; .,Duke University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA.,Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, North Carolina, USA
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46
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Çerçi B, Uzay IA, Kara MK, Dinçer P. Clinical trials and promising preclinical applications of CRISPR/Cas gene editing. Life Sci 2022; 312:121204. [PMID: 36403643 DOI: 10.1016/j.lfs.2022.121204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/03/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Treatment of genetic disorders by genomic manipulation has been the unreachable goal of researchers for many decades. Although our understanding of the genetic basis of genetic diseases has advanced tremendously in the last few decades, the tools developed for genomic editing were not efficient and practical for their use in the clinical setting until now. The recent advancements in the research of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) systems offered an easy and efficient way to edit the genome and accelerated the research on their potential use in the treatment of genetic disorders. In this review, we summarize the clinical trials that evaluate the CRISPR/Cas systems for treating different genetic diseases and highlight promising preclinical research on CRISPR/Cas mediated treatment of a great diversity of genetic disorders. Ultimately, we discuss the future of CRISPR/Cas mediated genome editing in genetic diseases.
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Affiliation(s)
- Barış Çerçi
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey.
| | - Ihsan Alp Uzay
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | | | - Pervin Dinçer
- Department of Medical Biology, Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
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Weiser B, Shi B, Kemal K, Burger H, Minkoff H, Shi Q, Gao W, Robison E, Holman S, Schroeder T, Gormley A, Anastos K, Ramirez C. Long-term antiretroviral therapy mitigates mortality and morbidity independent of HIV tropism: 18 years follow-up in a women's cohort. AIDS 2022; 36:1979-1986. [PMID: 35848576 PMCID: PMC9617757 DOI: 10.1097/qad.0000000000003337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE CXCR4 (X4)-tropic HIV-1 was found previously to herald CD4 + cell depletion and disease progression in individuals who were antiretroviral-naive or took combination antiretroviral therapy (cART) for less than 5 years. We updated this finding by investigating whether the deleterious effect of X4-tropic strains is mitigated by long-term cART. DESIGN We examined morbidity and mortality in relation to HIV-1 tropism and cART in 529 participants followed up to 18 years in the Women's Interagency HIV Study; 91% were women of color. METHODS Plasma-derived HIV-1 tropism was determined genotypically. RESULTS We categorized participants according to the number of visits reported on cART after initiation. Group 1: three or less visits, 74% of these participants reporting no cART; group 2: at least four visits and less than 70% of visits on cART; group 3: at least 70% of visits on cART. AIDS mortality rates for participants in each group with X4 virus compared with those with R5 virus exclusively were, respectively: 62 vs. 40% ( P = 0.0088); 23% vs. 22% [nonsignificant (NS)]; 7% vs. 14% (NS). Kaplan-Meier curves showed accelerated progression to AIDS death or AIDS-defining illness in participants with three or less cART visits and X4 viruses ( P = 0.0028) but no difference in progression rates stratified by tropism in other groups. Logistic regression found that HIV-1 suppression for at least 10 semiannual visits (≥5 years total) mitigated X4 tropism's deleterious effect on mortality, controlling for maximal viral load, and CD4 + nadir. CONCLUSION Long-term cART markedly mitigated the deleterious effect of X4 viruses on AIDS morbidity and mortality. Mitigation was correlated with duration of viral suppression, supporting HIV-1 suppression as a crucial goal.
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Affiliation(s)
- Barbara Weiser
- Department of Medicine, University of California, Davis School of Medicine, Sacramento
- Department of Medicine, Veterans Affairs Northern California Healthcare System, Sacramento Medical Center, Mather, CA
| | - Binshan Shi
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences
| | - Kimdar Kemal
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Harold Burger
- Department of Medicine, University of California, Davis School of Medicine, Sacramento
- Department of Medicine, Veterans Affairs Northern California Healthcare System, Sacramento Medical Center, Mather, CA
| | - Howard Minkoff
- Department of Obstetrics/Gynecology, State University of New York Health Science Center at Brooklyn
| | - Qiuhu Shi
- Department of Statistics, School of Health Sciences and Practice, New York Medical College, Valhalla
| | - Wei Gao
- Department of Medicine, Albert Einstein College of Medicine and Montefiore Health Systems, Bronx
| | - Esther Robison
- Department of Medicine, Albert Einstein College of Medicine and Montefiore Health Systems, Bronx
| | - Susan Holman
- Department of Medicine, State University of New York Health Science Center at Brooklyn, NY
| | - Tamara Schroeder
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Alissa Gormley
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine and Montefiore Health Systems, Bronx
| | - Christina Ramirez
- Department of Biostatistics, University of California, Los Angeles, Fielding School of Public Health, Los Angeles, CA, USA
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Khalid M, Murphy D, Shoai M, Nesson George-william J, Al-ebini Y. Geographical distribution of host's specific SARS-CoV-2 mutations in the early phase of the COVID-19 pandemic. Gene 2022. [DOI: 10.1016/j.gene.2022.147020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
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49
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Ellwanger JH, Secchi M, Aliberti J, Vangelista L. Editorial: CCR5: A receptor at the center stage in infection. Front Immunol 2022; 13:1054430. [DOI: 10.3389/fimmu.2022.1054430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022] Open
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50
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Valenzuela-fernández A, Cabrera-rodríguez R, Casado C, Pérez-yanes S, Pernas M, García-luis J, Marfil S, Olivares I, Estévez-herrera J, Trujillo-gonzález R, Blanco J, Lopez-galindez C. Contribution of the HIV-1 Envelope Glycoprotein to AIDS Pathogenesis and Clinical Progression. Biomedicines 2022; 10:2172. [PMID: 36140273 PMCID: PMC9495913 DOI: 10.3390/biomedicines10092172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/21/2022] [Accepted: 08/27/2022] [Indexed: 11/29/2022] Open
Abstract
In the absence of antiviral therapy, HIV-1 infection progresses to a wide spectrum of clinical manifestations that are the result of an entangled contribution of host, immune and viral factors. The contribution of these factors is not completely established. Several investigations have described the involvement of the immune system in the viral control. In addition, distinct HLA-B alleles, HLA-B27, -B57-58, were associated with infection control. The combination of these elements and antiviral host restriction factors results in different clinical outcomes. The role of the viral proteins in HIV-1 infection has been, however, less investigated. We will review contributions dedicated to the pathogenesis of HIV-1 infection focusing on studies identifying the function of the viral envelope glycoprotein (Env) in the clinical progression because of its essential role in the initial events of the virus life-cycle. Some analysis showed that inefficient viral Envs were dominant in non-progressor individuals. These poorly-functional viral proteins resulted in lower cellular activation, viral replication and minor viral loads. This limited viral antigenic production allows a better immune response and a lower immune exhaustion. Thus, the properties of HIV-1 Env are significant in the clinical outcome of the HIV-1 infection and AIDS pathogenesis.
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