Fig 2: Experimental replication and technical variation across multi-modal measurements. (A) Timecourse of the number of days between each passage for each phase of the study. (B) Growth curves of donors repeated at different phases of the study. Color indicates phase of study and shape indicates cell line donor. (C–H) Variation in technical replicates for (C) telomere length, (D) mtDNA copy number, (E) cell-free DNA, (F) IL6 as measured by ELISA, (G) DNAmAge as estimated by three epigenetic clocks and there PC-adjusted calibrations, and (H) average RNAseq-based transcript levels across all expressed genes. (I) Principal component analysis of all expressed genes for the full 354 sample RNAseq dataset. Technical replicates are highlighted in blue (n = 7). (J) Coefficient of variations in transcript per million (TPM) across the 7 RNAseq technical replicates for each mapped gene. The majority of genes have CVs <5%, and 99% of genes have CVs <10%. (K) Mean sequencing coverage for whole genome sequencing (n = 94 samples).

Fig 3: OxPhos defects trigger hypersecretion of metabokines and age-related cytokines.a Cytokine dynamics across the lifespan measured on two multiplexes (Luminex) arrays. Cytokine levels are normalized to the number of cells at the time of sampling, shown as Log2 median-centered for each cytokine; samples with undetectable values are shown as gray cells. Columns represent repeated measures (n = 6–8) along the lifespan of each control and SURF1 donor (n = 3 per group). b Comparison of maximum cytokine concentration reached in each of the SURF1 and healthy control donors, showing general upregulation of most metabokines and cytokines. The value for TGF-α is heavily influenced by a single very high value in Donor 3. c Cell-free media GDF15 concentration time course as measured on the Cytokine array. Inset compares early release between 20 and 80 days. d Media IL-6 levels across the cellular lifespan by enzyme-linked immunosorbent assay (ELISA), normalized to the number of cells at the time of sampling. e Media GDF15 levels across the cellular lifespan measured by ELISA, normalized to the number of cells at the time of sampling. Samples with non-detectable values (N.D.) are shown as zero values. f Cell-free mitochondrial DNA (cf-mtDNA) dynamics across the cellular lifespan using qPCR, normalized to the number of cells at the time of sampling. n = 3 per group, 6–13 timepoints per condition. Data are means ± SEM. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001, mixed effects model (fixed effect of Control/SURF1/Oligo group and days grown, random effects of donor or cell line). Abbreviations: CCL7 C-C motif chemokine ligand 7, IL-8 interleukin 8, CHI3L1 chitinase-3-like protein 1, MMP7 Matrix metallopeptidase 7, IL-6 Interleukin 6, IGFBP-rp1 Insulin-like growth factor binding protein 7, TNF-RII tumor necrosis factor receptor superfamily member 1B, TGF-α tumor growth factor alpha, IFN-γ interferon-gamma, TNFRSF9 TNF receptor superfamily member 9, GDF-15 growth differentiation factor 15, TNF-β tumor necrosis factor beta, Fas Fas cell surface death receptor, CCL3 C-C motif chemokine ligand 7, FSTL1 Follistatin like 1, CCL23 C-C motif chemokine ligand 23, TIMP-1 tissue inhibitor of metallopeptidase 1, CD163 CD163 antigen, Lumican keratan sulfate proteoglycan Lumican, IL-18 interleukin-18, CXCL16 C-X-C motif chemokine ligand 16, Fetuin A alpha 2-HS glycoprotein, ALCAM activated leukocyte cell adhesion molecule, TNF-RI TNF receptor superfamily member 1A, PCSK9 proprotein convertase subtilisin/kexin type 9, TFPI tissue factor pathway inhibitor.