Segregation of mitochondrial DNA heteroplasmy through a developmental genetic bottleneck in human embryos

Abstract

Mitochondrial DNA (mtDNA) mutations cause inherited diseases and are implicated in the pathogenesis of common late-onset disorders, but how they arise is not clear1,2. Here we show that mtDNA mutations are present in primordial germ cells (PGCs) within healthy female human embryos. Isolated PGCs have a profound reduction in mtDNA content, with discrete mitochondria containing ~5 mtDNA molecules. Single-cell deep mtDNA sequencing of in vivo human female PGCs showed rare variants reaching higher heteroplasmy levels in late PGCs, consistent with the observed genetic bottleneck. We also saw the signature of selection against non-synonymous protein-coding, tRNA gene and D-loop variants, concomitant with a progressive upregulation of genes involving mtDNA replication and transcription, and linked to a transition from glycolytic to oxidative metabolism. The associated metabolic shift would expose deleterious mutations to selection during early germ cell development, preventing the relentless accumulation of mtDNA mutations in the human population predicted by Muller’s ratchet. Mutations escaping this mechanism will show shifts in heteroplasmy levels within one human generation, explaining the extreme phenotypic variation seen in human pedigrees with inherited mtDNA disorders.

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Fig. 1: Isolation of a pure population of human primordial germ cells (PGCs).
Fig. 2: Mitochondrial DNA variants in human primordial germ cells.
Fig. 3: Morphology and deep sequencing of single human primordial germ cells in vivo.
Fig. 4: Transcriptome analysis of human primordial germ cells.
Fig. 5: Mitochondrial DNA analysis of somatic cells in vivo and mechanisms of selection.

Change history

  • 19 April 2018

    In the version of this Letter originally published, an author error led to the affiliations for Brendan Payne, Jonathan Coxhead and Gavin Hudson being incorrect. The correct affiliations are: Brendan Payne: 3Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK. 6Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK; this is a new affiliation 6 and subsequent existing affiliations have been renumbered. Jonathan Coxhead: 11Genomic Core Facility, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK; this is a new affiliation 11 and subsequent existing affiliations have been renumbered. Gavin Hudson: 3Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK. In addition, in Fig. 2d, the numbers on the x-axis of the left plot were incorrectly labelled as negative; they should have been positive. These errors have now been corrected in all online versions of the Letter.

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Acknowledgements

P.F.C. is a Wellcome Trust Senior Fellow in Clinical Science (101876/Z/13/Z), and a UK NIHR Senior Investigator, who receives support from the Medical Research Council Mitochondrial Biology Unit (MC_UP_1501/2), the Medical Research Council (UK) Centre for Translational Muscle Disease research (G0601943) and the National Institute for Health Research (NIHR) Biomedical Research Centre based at Cambridge University Hospitals NHS Foundation Trust and the University of Cambridge. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health. W.W.C.T. is supported by a Croucher Foundation studentship, and M.A.S. by a Wellcome Investigator Award.

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V.I.F. developed methods and isolated the in vivo human and mouse PGCs, and performed the microscopy; S.D. performed RNA-seq bioinformatic analysis; A.P. and W.W.C.T. carried out the real-time PCR assays; W.W.C.T. performed the RNA-seq experiments and N.I. derived and isolated the hESCs, hPGCLCs and in vitro somatic cells; W.W. performed additional informatic and statistical analysis; A.C. and L.N. isolated the human inner cell mass and trophectoderm cells, overseen by D.I. and Y.K. J.C. carried out the library preparation and deep sequencing; M.C. helped with the human tissue dissection; H.S. helped with the super-resolution microscopy; B.P. performed the technical validation of the deep sequencing protocol; M.S. provided the BVSC mouse; G.H. advised on the NGS data analysis; M.A.S. supervised the RNA-seq experiments and real-time PCR expression assays and advised on the project; P.F.C. supervised the project, designed experiments, analysed the data and wrote the paper. All authors contributed to the manuscript.

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Correspondence to Patrick F. Chinnery.

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Floros, V.I., Pyle, A., Dietmann, S. et al. Segregation of mitochondrial DNA heteroplasmy through a developmental genetic bottleneck in human embryos. Nat Cell Biol 20, 144–151 (2018). https://doi.org/10.1038/s41556-017-0017-8

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