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Publications

Journal Article Ahead of print

PubMed: 41839886 DOI: 10.1038/s41467-026-70399-y

Single-cell multi-omic analysis of mitochondrial mutational mosaicism and dynamics.

Nat Commun

Authors: Yu-Hsin Hsieh, Pauline Kautz, Lena Nitsch, Ambre M Giguelay, Janet Liebold, Veronika Dimitrova, Stephania Contreras Castillo, Freya Jungen, Gabor Zsurka, Genevieve Trombly, Markus Schuelke, Wolfram S Kunz, Caleb A Lareau, Leif S Ludwig

Affiliations

  • Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany.
  • Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
  • Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
  • Technische Universität Berlin, Institute of Biotechnology, Berlin, Germany.
  • Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany. Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany. Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany. Institute of Biology, Humboldt Universität zu Berlin, Berlin, Germany.
  • Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany. Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany. Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
  • Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany. Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany. Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany. Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany.
  • Institute of Experimental Epileptology and Cognition Research, University Hospital Bonn, University of Bonn, Bonn, Germany.
  • Department of Epileptology, University Hospital Bonn, University of Bonn, Bonn, Germany.
  • Charité-Universitätsmedizin Berlin, NeuroCureCluster of Excellence, Berlin, Germany.
  • Charité-Universitätsmedizin Berlin, Department of Neuropediatrics, Berlin, Germany.
  • Charité-Universitätsmedizin Berlin, NeuroCureClinical Research Center, Berlin, Germany.
  • Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
  • Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany.
  • Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
  • Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
  • Charité-Universitätsmedizin Berlin, Cluster of Excellence ImmunoPrecept, Berlin, Germany.

Abstract

Mitochondrial DNA (mtDNA) mutations occur more frequently than nuclear mutations and are associated with various diseases. While single-cell sequencing enables mtDNA variant heteroplasmy analysis, a holistic view of mtDNA mutational landscapes in individual cells has remained limited. Here, we leverage mitochondrial single-cell ATAC-seq and mtDNA-hypermutated POLG D274A knock-in HEK293 cell lines to introduce two metrics-single-cell mtDNA mutations per million base pairs (scmtMPM) and heteroplasmy-weighted mitochondrial local constraint scores (scwMSS)-to capture cellular mutational loads and somatic mosaicism. We demonstrate that individual POLG D274A cells exhibit complex mutational landscapes, with pathogenic mutations and truncating variants only present at subthreshold levels, indicative of their negative selection. In human healthy donors and mitochondriopathy patients, we identify constrained mutations in complex I, highlighting previously unrecognized mtDNA mutational landscape heterogeneity present on the single-cell level. Overall, scmtMPM and scwMSS provide a framework to investigate fundamental properties of mitochondrial genetics, disease, and somatic mosaicism.

MeSH

Cells, Mosaicism, Multiple Chronic Conditions, Dna, Mitochondrial, Heteroplasmy, Mutation