Cell type–specific purifying selection of synonymous mitochondrial DNA variation
PMID: 40705423
PMCID: PMC12318227
DOI: 10.1073/pnas.2505704122
Autoren:
Caleb A. Lareau a,b,1,2, Patrick Maschmeyer c,d,1, Yajie Yin b, Jacob C. Gutierrez a,b, Ryan S. Dhindsa e,f,g, Anne-Sophie Gribling-Burrer h, Sebastian Zielinski h, Yu-Hsin Hsieh c,d, Lena Nitsch c,d,i, Veronika Dimitrova c,d, Benan Nalbant a, Frank A. Buquicchio b, Tsion Abay b,j, Robert R. Stickels b, Jacob C. Ulirsch k, Patrick Yan b, Fangyi Wang b, Zhuang Miao b,l, Katalin Sandor b, Bence Danielb, Vincent Liu b,l, Paul L. Mendez i, Petra Knaus i, Manpreet Meyer c,d,i,m, William J. Greenleaf l, Anshul Kundaje l,n, Redmond P. Smyth h,o, Mathias Munschauer h,o,p, Leif S. Ludwig c,d,2, and Ansuman T. Satpathy b,q,2
1 equal contribution (first authorship)
2 correspdonding authors
Author affiliations:
a Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
b Department of Pathology, Stanford University, Stanford, CA 94305;
c Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin 10117, Germany;
d Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin 10115, Germany;
e Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030;
f Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030;
g Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;
h Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg 97080, Germany;
i Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin 14195, Germany;
j Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115;
k Illumina AI Laboratory, San Diego, CA 92122;
l Department of Genetics, Stanford University, Stanford,CA 94305;
m Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115;
n Department of Computer Science, Stanford University, Stanford, CA 94305;
o Department of Infectious Diseases, Center for Integrative Infectious Disease Research, Heidelberg 69120, Germany;
p Department of Medicine, Heidelberg University, Heidelberg 69120, Germany;
and q Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129
Significance
We identify the cell type–specific selection of T cells with a synonymous mitochondrial DNA variant in MT-CO1, reminiscent of the purifying selection of pathogenic alleles. Mechanistically, we implicate the limited mitochondrial tRNA pool to stall effective ribosomal translation of “wobble” codons. Together, this suggests a mechanism of functional mtDNA variation that is enabled by the distinct tRNA pool. The results from a specific variant inferred from single-cell analyses provides context for patterns of mutation observed in the germline.
Abstract
While somatic variants are well-characterized drivers of tumor evolution, their influence on cellular fitness in nonmalignant contexts remains understudied. We identified a mosaic synonymous variant (m.7076A > G) in the mitochondrial DNA (mtDNA)-encoded cytochrome c-oxidase subunit 1 (MT-CO1, p.Gly391=), present at homoplasmy in 47% of immune cells from a healthy donor. Single-cell multiomics revealed strong, lineage-specific selection against the m.7076G allele in CD8+ effector memory T cells, but not other T cell subsets, mirroring patterns of purifying selection of pathogenic mtDNA alleles. The limited anticodon diversity of mitochondrial tRNAs forces m.7076G translation to rely on wobble pairing, unlike the Watson–Crick–Franklin pairing used for m.7076A. Mitochondrial ribosome profiling confirmed stalled translation of the m.7076G allele. Functional analyses demonstrated that the elevated translational and metabolic demands of short-lived effector T cells (SLECs) amplify dependence on MT-CO1, driving this selective pressure. These findings suggest that synonymous variants can alter codon syntax, impacting mitochondrial physiology in a cell type–specific manner.