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Wilson PC, Verma A, Yoshimura Y, Muto Y, Li H, Malvin NP, Dixon EE, Humphreys BD. Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease. Genome Biol 2024; 25:36. [PMID: 38287344 PMCID: PMC10823641 DOI: 10.1186/s13059-024-03173-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/12/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Mosaic loss of Y chromosome (LOY) is the most common chromosomal alteration in aging men. Here, we use single-cell RNA and ATAC sequencing to show that LOY is present in the kidney and increases with age and chronic kidney disease. RESULTS The likelihood of a cell having LOY varies depending on its location in the nephron. Cortical epithelial cell types have a greater proportion of LOY than medullary or glomerular cell types, which may reflect their proliferative history. Proximal tubule cells are the most abundant cell type in the cortex and are susceptible to hypoxic injury. A subset of these cells acquires a pro-inflammatory transcription and chromatin accessibility profile associated with expression of HAVCR1, VCAM1, and PROM1. These injured epithelial cells have the greatest proportion of LOY and their presence predicts future kidney function decline. Moreover, proximal tubule cells with LOY are more likely to harbor additional large chromosomal gains and express pro-survival pathways. Spatial transcriptomics localizes injured proximal tubule cells to a pro-fibrotic microenvironment where they adopt a secretory phenotype and likely communicate with infiltrating immune cells. CONCLUSIONS We hypothesize that LOY is an indicator of increased DNA damage and potential marker of cellular senescence that can be applied to single-cell datasets in other tissues.
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Affiliation(s)
- Parker C Wilson
- Division of Diagnostic Innovation, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Amit Verma
- Division of Diagnostic Innovation, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicole P Malvin
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Eryn E Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA
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Virolainen SJ, VonHandorf A, Viel KCMF, Weirauch MT, Kottyan LC. Gene-environment interactions and their impact on human health. Genes Immun 2023; 24:1-11. [PMID: 36585519 PMCID: PMC9801363 DOI: 10.1038/s41435-022-00192-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022]
Abstract
The molecular processes underlying human health and disease are highly complex. Often, genetic and environmental factors contribute to a given disease or phenotype in a non-additive manner, yielding a gene-environment (G × E) interaction. In this work, we broadly review current knowledge on the impact of gene-environment interactions on human health. We first explain the independent impact of genetic variation and the environment. We next detail well-established G × E interactions that impact human health involving environmental toxicants, pollution, viruses, and sex chromosome composition. We conclude with possibilities and challenges for studying G × E interactions.
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Affiliation(s)
- Samuel J Virolainen
- Division of Human Genetics, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA
- Immunology Graduate Program, University of Cincinnati College of Medicine, 3230 Eden Ave, Cincinnati, OH, 45229, USA
| | - Andrew VonHandorf
- Division of Human Genetics, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA
| | - Kenyatta C M F Viel
- Division of Human Genetics, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA
| | - Matthew T Weirauch
- Division of Human Genetics, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
- Immunology Graduate Program, University of Cincinnati College of Medicine, 3230 Eden Ave, Cincinnati, OH, 45229, USA.
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Ave, Cincinnati, OH, 45229, USA.
| | - Leah C Kottyan
- Division of Human Genetics, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
- Immunology Graduate Program, University of Cincinnati College of Medicine, 3230 Eden Ave, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Ave, Cincinnati, OH, 45229, USA.
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., MLC 15012, Cincinnati, OH, 45229, USA.
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