Extended Data Fig. 3: Supporting analyses for primary PS T cell cultures.
(a) Representative flow cytometry plot of CD4+ and CD8+ T cells. Cells from the four donors (columns) were assessed for CD45RA and CD45RO expression. The box indicates the proportion of CD45RAhi/CD45RO− cells summarized in Fig. 3d. (b) Summary of flow cytometry data from independent T cell culture comparing cells from a healthy pediatric donor to an adult donor. T cells were derived from both bone marrow mononuclear cells (BMMNCs) and peripheral blood mononuclear cells (PBMCs) for the pediatric donor. (c) Embedding of day 14T cells colored by antibody derived tags (ADTs) for CCR4 and IL2RA. (d) Dynamics of heteroplasmy for 76 heteroplasmic single nucleotide variants (SNVs) during T cell culture. m.12631T > C and m.4225A > G are highlighted. (e) Single-cell heteroplasmy of m.12631T > C and m.4225A > G, variants expanding during T cell culture, annotated in the day 14 embedding. Blue arrow indicates the subpopulation positive for the m.4225A > G variant. (f) Single-cell heteroplasmy of the PS deletion annotated on day 21 derived T cells profiled via mtscATAC-seq. (g) Single-cell heteroplasmy of m.12631T > C and m.4225A > G, variants expanding during T cell culture, annotated in the day 21 cell embedding. Blue arrow indicates the subpopulation positive for the m.4225A > G variant. (h) Day 21 embedding clustering, annotations, and per-cluster heteroplasmy quantified via a cumulative distribution function. (i) Independent validation of in vitro CD8+ T cell relative expansion (left) and overall T cell proliferation (right) defects from PT1 PBMCs. (j) Summary of cell clusters, heteroplasmy, and marker gene scores for PT1 T cells following culture. (k) Day 14 PT1 per-cluster heteroplasmy quantified via a cumulative distribution function for PT1 T cells after culture.
