A multi-omics longitudinal aging dataset in primary human fibroblasts with mitochondrial perturbations

• Published in: Scientific data 2022-12, Vol.9 (1), p.751-19, Article 751
• Main Authors: Sturm, Gabriel, Monzel, Anna S., Karan, Kalpita R., Michelson, Jeremy, Ware, Sarah A., Cardenas, Andres, Lin, Jue, Bris, Céline, Santhanam, Balaji, Murphy, Michael P., Levine, Morgan E., Horvath, Steve, Belsky, Daniel W., Wang, Shuang, Procaccio, Vincent, Kaufman, Brett A., Hirano, Michio, Picard, Martin
• Format: Article
• Language: English
• Subjects: 631/553/1464; 631/80/509; 631/80/642/333/1465; Aging; Bioenergetics; Cell culture; Cellular Senescence; Copy number; Data Descriptor; Datasets; DNA methylation; DNA sequencing; Enzyme-linked immunosorbent assay; Epigenetics; Fibroblasts; Gene expression; Genomes; Glucocorticoids; Glycolysis; Humanities and Social Sciences; Humans; Life span; Longevity; Mitochondrial DNA; multidisciplinary; Oxidative phosphorylation; Phosphorylation; Polymerase chain reaction; Science; Science (multidisciplinary); Telomeres; Whole genome sequencing
• ISSN: 2052-4463; 2052-4463
• DOI: 10.1038/s41597-022-01852-y

Aging is a process of progressive change. To develop biological models of aging, longitudinal datasets with high temporal resolution are needed. Here we report a multi-omics longitudinal dataset for cultured primary human fibroblasts measured across their replicative lifespans. Fibroblasts were sourced from both healthy donors (n = 6) and individuals with lifespan-shortening mitochondrial disease (n = 3). The dataset includes cytological, bioenergetic, DNA methylation, gene expression, secreted proteins, mitochondrial DNA copy number and mutations, cell-free DNA, telomere length, and whole-genome sequencing data. This dataset enables the bridging of mechanistic processes of aging as outlined by the “hallmarks of aging”, with the descriptive characterization of aging such as epigenetic age clocks. Here we focus on bridging the gap for the hallmark mitochondrial metabolism. Our dataset includes measurement of healthy cells, and cells subjected to over a dozen experimental manipulations targeting oxidative phosphorylation (OxPhos), glycolysis, and glucocorticoid signaling, among others. These experiments provide opportunities to test how cellular energetics affect the biology of cellular aging. All data are publicly available at our webtool: https://columbia-picard.shinyapps.io/shinyapp-Lifespan_Study/ Measurement(s) gene expression assay • DNA Methylation • Telomere Length • Seahorse Bioenergetics • mtDNA copy number • Whole Genome Sequencing • Cytokine • cell-free DNA • mtDNA sequencing • cell-free GDF15 • cell-free IL6 Technology Type(s) Illumina HiSeq. 4000 • Illumina epic array • Real Time PCR • Seahorse XFe96 • Real Time PCR • Luminex 200 • ELISA Factor Type(s) time grown in culture Sample Characteristic - Organism Homo sapiens Sample Characteristic - Environment cell culture Sample Characteristic - Location contiguous United States of America