Random Mutagenesis, Clonal Events, and Embryonic or Somatic Origin Determine the MtDNA Variant Type and Load in Human Pluripotent Stem Cells

Overview

Journal Stem Cell Reports

Publisher Cell Press

Specialty Cell Biology

Date 2018 Jun 19

PMID 29910126

Citations 16

Authors

Filippo Zambelli

Joke Mertens

Dominika Dziedzicka

Johan Sterckx

Christina Markouli

Alexander Keller

Philippe Tropel

Laura Jung

Stephane Viville

Hilde Van de Velde

Mieke Geens

Sara Seneca

Karen Sermon

Claudia Spits

Affiliations

Soon will be listed here.

Abstract

In this study, we deep-sequenced the mtDNA of human embryonic and induced pluripotent stem cells (hESCs and hiPSCs) and their source cells and found that the majority of variants pre-existed in the cells used to establish the lines. Early-passage hESCs carried few and low-load heteroplasmic variants, similar to those identified in oocytes and inner cell masses. The number and heteroplasmic loads of these variants increased with prolonged cell culture. The study of 120 individual cells of early- and late-passage hESCs revealed a significant diversity in mtDNA heteroplasmic variants at the single-cell level and that the variants that increase during time in culture are always passenger to the appearance of chromosomal abnormalities. We found that early-passage hiPSCs carry much higher loads of mtDNA variants than hESCs, which single-fibroblast sequencing proved pre-existed in the source cells. Finally, we show that these variants are stably transmitted during short-term differentiation.

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References

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A . The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20(9):1297-303. PMC: 2928508. DOI: 10.1101/gr.107524.110. View

Van Landuyt L, Polyzos N, De Munck N, Blockeel C, van de Velde H, Verheyen G . A prospective randomized controlled trial investigating the effect of artificial shrinkage (collapse) on the implantation potential of vitrified blastocysts. Hum Reprod. 2015; 30(11):2509-18. DOI: 10.1093/humrep/dev218. View

Mateizel I, Spits C, De Rycke M, Liebaers I, Sermon K . Derivation, culture, and characterization of VUB hESC lines. In Vitro Cell Dev Biol Anim. 2010; 46(3-4):300-8. DOI: 10.1007/s11626-010-9284-4. View

Kang E, Wu J, Marti Gutierrez N, Koski A, Tippner-Hedges R, Agaronyan K . Mitochondrial replacement in human oocytes carrying pathogenic mitochondrial DNA mutations. Nature. 2016; 540(7632):270-275. DOI: 10.1038/nature20592. View

Boucret L, Bris C, Seegers V, Goudenege D, Desquiret-Dumas V, Domin-Bernhard M . Deep sequencing shows that oocytes are not prone to accumulate mtDNA heteroplasmic mutations during ovarian ageing. Hum Reprod. 2017; 32(10):2101-2109. DOI: 10.1093/humrep/dex268. View

Lamm N, Ben-David U, Golan-Lev T, Storchova Z, Benvenisty N, Kerem B . Genomic Instability in Human Pluripotent Stem Cells Arises from Replicative Stress and Chromosome Condensation Defects. Cell Stem Cell. 2015; 18(2):253-61. DOI: 10.1016/j.stem.2015.11.003. View

Suhr S, Chang E, Tjong J, Alcasid N, Perkins G, Goissis M . Mitochondrial rejuvenation after induced pluripotency. PLoS One. 2010; 5(11):e14095. PMC: 2991355. DOI: 10.1371/journal.pone.0014095. View

Nguyen H, Geens M, Spits C . Genetic and epigenetic instability in human pluripotent stem cells. Hum Reprod Update. 2012; 19(2):187-205. DOI: 10.1093/humupd/dms048. View

Avery S, Hirst A, Baker D, Lim C, Alagaratnam S, Skotheim R . BCL-XL mediates the strong selective advantage of a 20q11.21 amplification commonly found in human embryonic stem cell cultures. Stem Cell Reports. 2013; 1(5):379-86. PMC: 3841249. DOI: 10.1016/j.stemcr.2013.10.005. View

10.

Chambers S, Fasano C, Papapetrou E, Tomishima M, Sadelain M, Studer L . Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling. Nat Biotechnol. 2009; 27(3):275-80. PMC: 2756723. DOI: 10.1038/nbt.1529. View

11.

Van Blerkom J . Mitochondria as regulatory forces in oocytes, preimplantation embryos and stem cells. Reprod Biomed Online. 2008; 16(4):553-69. DOI: 10.1016/s1472-6483(10)60463-4. View

12.

Merkle F, Ghosh S, Kamitaki N, Mitchell J, Avior Y, Mello C . Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations. Nature. 2017; 545(7653):229-233. PMC: 5427175. DOI: 10.1038/nature22312. View

13.

Jacobs K, Mertzanidou A, Geens M, Nguyen H, Staessen C, Spits C . Low-grade chromosomal mosaicism in human somatic and embryonic stem cell populations. Nat Commun. 2014; 5:4227. DOI: 10.1038/ncomms5227. View

14.

Menten B, Pattyn F, De Preter K, Robbrecht P, Michels E, Buysse K . arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays. BMC Bioinformatics. 2005; 6:124. PMC: 1173083. DOI: 10.1186/1471-2105-6-124. View

15.

Chetty S, Pagliuca F, Honore C, Kweudjeu A, Rezania A, Melton D . A simple tool to improve pluripotent stem cell differentiation. Nat Methods. 2013; 10(6):553-6. PMC: 3694177. DOI: 10.1038/nmeth.2442. View

16.

Jung L, Tropel P, Moal Y, Teletin M, Jeandidier E, Gayon R . ONSL and OSKM cocktails act synergistically in reprogramming human somatic cells into induced pluripotent stem cells. Mol Hum Reprod. 2014; 20(6):538-49. DOI: 10.1093/molehr/gau012. View

17.

Kang E, Wang X, Tippner-Hedges R, Ma H, Folmes C, Marti Gutierrez N . Age-Related Accumulation of Somatic Mitochondrial DNA Mutations in Adult-Derived Human iPSCs. Cell Stem Cell. 2016; 18(5):625-36. DOI: 10.1016/j.stem.2016.02.005. View

18.

Jacobs K, Zambelli F, Mertzanidou A, Smolders I, Geens M, Nguyen H . Higher-Density Culture in Human Embryonic Stem Cells Results in DNA Damage and Genome Instability. Stem Cell Reports. 2016; 6(3):330-41. PMC: 4788786. DOI: 10.1016/j.stemcr.2016.01.015. View

19.

Cibulskis K, Lawrence M, Carter S, Sivachenko A, Jaffe D, Sougnez C . Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013; 31(3):213-9. PMC: 3833702. DOI: 10.1038/nbt.2514. View

20.

Sui L, Mfopou J, Geens M, Sermon K, Bouwens L . FGF signaling via MAPK is required early and improves Activin A-induced definitive endoderm formation from human embryonic stem cells. Biochem Biophys Res Commun. 2012; 426(3):380-5. DOI: 10.1016/j.bbrc.2012.08.098. View