Identification of cancer-related mutations in human pluripotent stem cells using RNA-seq analysis

Elyad Lezmi, Nissim Benvenisty

Published: 2021-08-05 DOI: 10.1038/s41596-021-00591-5

human pluripotent stem cells

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RNA-seq analysis

cancer-related mutations

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Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

ProBac-seq, a bacterial single-cell RNA sequencing methodology using droplet microfluidics and large oligonucleotide probe sets

Identification of cancer-related mutations in human pluripotent stem cells using RNA-seq analysis

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Genetic manipulation and immortalized culture of ex vivo primary human germinal center B cells

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Reproducible strategy for excisional skin-wound-healing studies in mice

CRISPR–Cas9-mediated chromosome engineering inArabidopsis thaliana

Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids

Tracking endocytosis and intracellular distribution of spherical nucleic acids with correlative single-cell imaging

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De Los Angeles, A. et al. Hallmarks of pluripotency. Nature 525, 469–478 (2015).
Tabar, V. & Studer, L. Pluripotent stem cells in regenerative medicine: challenges and recent progress. Nat. Rev. Genet. 15, 82–92 (2014).
Avior, Y., Sagi, I. & Benvenisty, N. Pluripotent stem cells in disease modelling and drug discovery. Nat. Rev. Mol. Cell Biol. 17, 170–182 (2016).
Shahbazi, M. N., Siggia, E. D. & Zernicka-Goetz, M. Self-organization of stem cells into embryos: a window on early mammalian development. Science 364, 948–951 (2019).
Weissbein, U., Benvenisty, N. & Ben-David, U. Genome maintenance in pluripotent stem cells. J. Cell Biol. 204, 153–163 (2014).
Bar, S. & Benvenisty, N. Epigenetic aberrations in human pluripotent stem cells. EMBO J. 38, 1–18 (2019).
Na, J., Baker, D., Zhang, J., Andrews, P. W. & Barbaric, I. Aneuploidy in pluripotent stem cells and implications for cancerous transformation. Protein Cell 5, 569–579 (2014).
Jo, H. Y. et al. Functional in vivo and in vitro effects of 20q11.21 genetic aberrations on hPSC differentiation. Sci. Rep. 10, 1–14 (2020).
Ben-David, U. & Benvenisty, N. The tumorigenicity of human embryonic and induced pluripotent stem cells. Nat. Rev. Cancer 11, 268–277 (2011).
Ben-David, U. et al. Aneuploidy induces profound changes in gene expression, proliferation and tumorigenicity of human pluripotent stem cells. Nat. Commun. 5, 4825 (2014).
Simonson, O. E., Domogatskaya, A., Volchkov, P. & Rodin, S. The safety of human pluripotent stem cells in clinical treatment. Ann. Med. 47, 370–380 (2015).
Gore, A. et al. Somatic coding mutations in human induced pluripotent stem cells. Nature 471, 63–67 (2011).
Merkle, F. T. et al. Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations. Nature 545, 229–233 (2017).
Avior, Y., Lezmi, E., Eggan, K. & Benvenisty, N. Cancer-related mutations identified in primed human pluripotent stem cells. Cell Stem Cell 28, 10–11 (2021).
Stirparo, G. G., Smith, A. & Guo, G. Cancer-related mutations are not enriched in naive human pluripotent stem cells. Cell Stem Cell 28, 164–169.e2 (2021).
Halliwell, J., Barbaric, I. & Andrews, P. W. Acquired genetic changes in human pluripotent stem cells: origins and consequences. Nat. Rev. Mol. Cell Biol. 21, 715–728 (2020).
Merkle, F. T. et al. Biological insights from the whole genome analysis of human embryonic stem cells. Preprint at bioRxiv https://doi.org/10.1101/2020.10.26.337352 (2020).
Trounson, A. & DeWitt, N. D. Pluripotent stem cells progressing to the clinic. Nat. Rev. Mol. Cell Biol. 17, 194–200 (2016).
Tate, J. G. et al. COSMIC: the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 47, D941–D947 (2019).
Shihab, H. A. et al. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum. Mutat. 34, 57–65 (2013).
Sherry, S. T. et al. DbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001).
Auton, A. et al. A global reference for human genetic variation. Nature 526, 68–74 (2015).
Yizhak, K. et al. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science 364, eaaw0726 (2019).
Coudray, A., Battenhouse, A. M., Bucher, P. & Iyer, V. R. Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data. PeerJ 6, (2018).
Weissbein, U., Schachter, M., Egli, D. & Benvenisty, N. Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq. Nat. Commun. 7, 12144 (2016).
Radenbaugh, A. J. et al. RADIA: RNA and DNA integrated analysis for somatic mutation detection. PLoS One 9, e111516 (2014).
DI Tommaso, P. et al. Nextflow enables reproducible computational workflows. Nat. Biotechnol. 35, 316–319 (2017).
Merkel, D. Docker: lightweight Linux containers for consistent development and deployment. Linux J. 239, 2 (2014).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Danecek, P. & McCarthy, S. A. BCFtools/csq: haplotype-aware variant consequences. Bioinformatics 33, 2037–2039 (2017).
Li, H. Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics 27, 718–719 (2011).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Brouard, J.-S., Schenkel, F., Marete, A. & Bissonnette, N. The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments. J. Anim. Sci. Biotechnol. 10, 44 (2019).
Frankish, A. et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 47, D766–D773 (2019).
Sondka, Z. et al. The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers. Nat. Rev. Cancer 18, 696–705 (2018).
Kluin, R. J. C. et al. XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data. BMC Bioinformatics 19, 366 (2018).
Collinson, A. et al. Deletion of the polycomb-group protein EZH2 leads to compromised self-renewal and differentiation defects in human embryonic stem cells article deletion of the Polycomb-group protein EZH2 leads to compromised self-renewal and differentiation defects in Hu. Cell Rep. 17, 2700–2714 (2016).
Lezmi, E. Identification of cancer-related mutations in human pluripotent stem cells utilizing RNA-seq analysis. elyadlezmi/RNA2CM https://doi.org/10.5281/zenodo.4810015 (2021).

Identification of cancer-related mutations in human pluripotent stem cells using RNA-seq analysis

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