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Garnish SE, Martin KR, Kauppi M, Jackson VE, Ambrose R, Eng VV, Chiou S, Meng Y, Frank D, Tovey Crutchfield EC, Patel KM, Jacobsen AV, Atkin-Smith GK, Di Rago L, Doerflinger M, Horne CR, Hall C, Young SN, Cook M, Athanasopoulos V, Vinuesa CG, Lawlor KE, Wicks IP, Ebert G, Ng AP, Slade CA, Pearson JS, Samson AL, Silke J, Murphy JM, Hildebrand JM. A common human MLKL polymorphism confers resistance to negative regulation by phosphorylation. Nat Commun 2023; 14:6046. [PMID: 37770424 PMCID: PMC10539340 DOI: 10.1038/s41467-023-41724-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 09/13/2023] [Indexed: 09/30/2023] Open
Abstract
Across the globe, 2-3% of humans carry the p.Ser132Pro single nucleotide polymorphism in MLKL, the terminal effector protein of the inflammatory form of programmed cell death, necroptosis. Here we show that this substitution confers a gain in necroptotic function in human cells, with more rapid accumulation of activated MLKLS132P in biological membranes and MLKLS132P overriding pharmacological and endogenous inhibition of MLKL. In mouse cells, the equivalent Mlkl S131P mutation confers a gene dosage dependent reduction in sensitivity to TNF-induced necroptosis in both hematopoietic and non-hematopoietic cells, but enhanced sensitivity to IFN-β induced death in non-hematopoietic cells. In vivo, MlklS131P homozygosity reduces the capacity to clear Salmonella from major organs and retards recovery of hematopoietic stem cells. Thus, by dysregulating necroptosis, the S131P substitution impairs the return to homeostasis after systemic challenge. Present day carriers of the MLKL S132P polymorphism may be the key to understanding how MLKL and necroptosis modulate the progression of complex polygenic human disease.
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Affiliation(s)
- Sarah E Garnish
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - Katherine R Martin
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - Maria Kauppi
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - Victoria E Jackson
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - Rebecca Ambrose
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Vik Ven Eng
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Shene Chiou
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - Yanxiang Meng
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - Daniel Frank
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Emma C Tovey Crutchfield
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Faculty of Medicine, Dentistry and Health Sciences, Parkville, VIC, Australia
| | - Komal M Patel
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Annette V Jacobsen
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - Georgia K Atkin-Smith
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - Ladina Di Rago
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - Marcel Doerflinger
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - Christopher R Horne
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - Cathrine Hall
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Samuel N Young
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Matthew Cook
- Centre for Personalised Immunology and Canberra Clinical Genomics, Australian National University, Canberra, ACT, Australia
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Vicki Athanasopoulos
- Department of Immunology and Infection, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Carola G Vinuesa
- Centre for Personalised Immunology and Canberra Clinical Genomics, Australian National University, Canberra, ACT, Australia
- Department of Immunology and Infection, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- The Francis Crick Institute, London, UK
- University College London, London, UK
- China Australia Centre for Personalized Immunology (CACPI), Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Kate E Lawlor
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Ian P Wicks
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - Gregor Ebert
- Institute of Virology, Technical University of Munich/Helmholtz Munich, Munich, Germany
| | - Ashley P Ng
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
- Clinical Haematology Department, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, VIC, Australia
| | - Charlotte A Slade
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
- Department of Clinical Immunology & Allergy, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Jaclyn S Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - André L Samson
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - John Silke
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia
| | - Joanne M Hildebrand
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia.
- University of Melbourne, Department of Medical Biology, Parkville, VIC, Australia.
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Abondio P, Cilli E, Luiselli D. Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference. Life (Basel) 2023; 13:1360. [PMID: 37374141 DOI: 10.3390/life13061360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
A pangenome is a collection of the common and unique genomes that are present in a given species. It combines the genetic information of all the genomes sampled, resulting in a large and diverse range of genetic material. Pangenomic analysis offers several advantages compared to traditional genomic research. For example, a pangenome is not bound by the physical constraints of a single genome, so it can capture more genetic variability. Thanks to the introduction of the concept of pangenome, it is possible to use exceedingly detailed sequence data to study the evolutionary history of two different species, or how populations within a species differ genetically. In the wake of the Human Pangenome Project, this review aims at discussing the advantages of the pangenome around human genetic variation, which are then framed around how pangenomic data can inform population genetics, phylogenetics, and public health policy by providing insights into the genetic basis of diseases or determining personalized treatments, targeting the specific genetic profile of an individual. Moreover, technical limitations, ethical concerns, and legal considerations are discussed.
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Affiliation(s)
- Paolo Abondio
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
| | - Elisabetta Cilli
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
| | - Donata Luiselli
- Laboratory of Ancient DNA, Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121 Ravenna, Italy
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Abondio P, Cilli E, Luiselli D. Inferring Signatures of Positive Selection in Whole-Genome Sequencing Data: An Overview of Haplotype-Based Methods. Genes (Basel) 2022; 13:genes13050926. [PMID: 35627311 PMCID: PMC9141518 DOI: 10.3390/genes13050926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
Signatures of positive selection in the genome are a characteristic mark of adaptation that can reveal an ongoing, recent, or ancient response to environmental change throughout the evolution of a population. New sources of food, climate conditions, and exposure to pathogens are only some of the possible sources of selective pressure, and the rise of advantageous genetic variants is a crucial determinant of survival and reproduction. In this context, the ability to detect these signatures of selection may pinpoint genetic variants that are responsible for a significant change in gene regulation, gene expression, or protein synthesis, structure, and function. This review focuses on statistical methods that take advantage of linkage disequilibrium and haplotype determination to reveal signatures of positive selection in whole-genome sequencing data, showing that they emerge from different descriptions of the same underlying event. Moreover, considerations are provided around the application of these statistics to different species, their suitability for ancient DNA, and the usefulness of discovering variants under selection for biomedicine and public health in an evolutionary medicine framework.
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Affiliation(s)
- Paolo Abondio
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (E.C.); (D.L.)
- Laboratory of Molecular Anthropology and Center for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
- Correspondence:
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (E.C.); (D.L.)
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121 Ravenna, Italy; (E.C.); (D.L.)
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies (FMC), Viale Adriatico 1/N, 61032 Fano, Italy
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Rowland B, Sun Q, Wang W, Miller-Fleming T, Cox N, Graff M, Faucon A, Shuey MM, Blue EE, Auer P, Li Y, Sankaran VG, Reiner AP, Raffield LM. Genetic Examination of Hematological Parameters in SARS-CoV-2 Infection and COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.02.28.22271562. [PMID: 35262092 PMCID: PMC8902884 DOI: 10.1101/2022.02.28.22271562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background People hospitalized with COVID-19 often exhibit hematological alterations, such as lower lymphocyte and platelet counts, which have been reported to associate with disease prognosis. It is unclear whether inter-individual variability in baseline hematological parameters prior to acute infection influences risk of SARS-CoV-2 infection and progression to severe COVID-19. Methods We assessed the association of blood cell counts and indices with incident SARS-CoV-2 infection and severe COVID-19 in UK Biobank and the Vanderbilt University Medical Center Synthetic Derivative (VUMC SD). Since genetically determined blood cell measures better represent cell abundance across the lifecourse, we used summary statistics from genome-wide association studies to assess the shared genetic architecture of baseline blood cell counts and indices on COVID-19 outcomes. Results We observed inconsistent associations between measured blood cell indices and both SARS-CoV-2 infection and COVID-19 hospitalization in UK Biobank and VUMC SD. In Mendelian randomization analyses using genetic summary statistics, no putative causal relationships were identified between COVID-19 related outcomes and hematological indices after adjusting for multiple testing. We observed overlapping genetic association signals between hematological parameters and COVID-19 traits. For example, we observed overlap between infection susceptibility-associated variants at PPP1R15A and red blood cell parameters, and between disease severity-associated variants at TYK2 and lymphocyte and platelet phenotypes. Conclusions We did not find convincing evidence of a relationship between baseline hematological parameters and susceptibility to SARS-CoV-2 infection or COVID-19 severity, though this relationship should be re-examined as larger and better-powered genetic analyses of SARS-CoV-2 infection and severe COVID-19 become available.
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Affiliation(s)
- Bryce Rowland
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Wanjiang Wang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Tyne Miller-Fleming
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Nancy Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Misa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Annika Faucon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Megan M. Shuey
- Department of Medicine Vanderbilt University Medical Center Nashville, TN
| | - Elizabeth E. Blue
- Department of Medical Genetics, University of Washington, Seattle, WA
| | - Paul Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
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