Synonymous mitochondrial DNA variation impairs CD8 T cell fate via codon affinity [PBMC scATAC]

Somatic variation contributes to biological heterogeneity by modulating the cellular proclivity to differentiate, expand, adapt, or die. While large-scale sequencing efforts have revealed the foundational role of somatic variants to drive human tumor evolution, our understanding of the contribution of somatic variation to modulate cellular fitness in non-malignant contexts remains understudied. Here, we identify a somatic synonymous variant (m.7076A>G) in the mitochondrial DNA (mtDNA) encoded cytochrome c-oxidase subunit 1 gene (COX1), which was present at homoplasmy in 47% of immune cells from a healthy donor. Using single-cell multi-omics, we discover highly specific selection against the m.7076G mutant allele in the CD8+ effector memory T cell compartment in vivo, reminiscent of selection observed for pathogenic mtDNA alleles and indicative of lineage-specific metabolic vulnerabilities. Due to the limited transfer RNA (tRNA) pool in mitochondria, the m.7076G mutant allele requires wobble-dependent translation whereas the wildtype m.7076A allele can translate via Watson-Crick-Franklin (WCF) base-pairing. Mitochondrial ribosome profiling revealed that the synonymous m.7076G mutant allele altered codon-anticodon affinity by 33% at the wobble position, stalling translation at the glycine residue within COX1 encoded at m.7076. Leveraging population-based sequencing analyses, we identify evidence of synonymous somatic variants in tumor genomes and dozens of germline variants associated with complex diseases, suggesting broad functional effects of synonymous variation altering codon affinity across the mitochondrial genome. Together, these results provide a new ontogeny for mitochondrial genetic variation and elucidate a framework whereby somatic variation can impact cell state transitions in a lineage-specific manner.