TY - JOUR
T1 - Stabilization of hESCs in two distinct substates along the continuum of pluripotency
AU - Dekel, Chen
AU - Morey, Robert
AU - Hanna, Jacob
AU - Laurent, Louise C.
AU - Ben-Yosef, Dalit
AU - Amir, Hadar
N1 - Funding Information: Whole Genome Sequencing, sequencing of RNA-seq and small RNA-seq libraries, and DNA methylation microarray analysis was conducted at the Institute for Genomic Medicine (IGM) Genomics Center, University of California, San Diego, La Jolla, CA. Small RNA-seq libraries were generated by Aishwarya Vuppala under the supervision of Peter De Hoff. This publication includes data generated at the UC San Diego IGM Genomics Center utilizing an Illumina NovaSeq 6000 that was purchased with funding from a National Institutes of Health SIG grant ( #S10 OD026929 ). This work used the Extreme Science and Engineering Discovery Environment ( XSEDE ) Expanse at the San Diego Super Computer through allocation MCB140074 . RM was supported by a grant from the National Institutes of Health , USA ( NIH grant T32GM008806 ). Small RNA-seq data processing was performed using the exceRpt pipeline on the Genboree Workbench developed by the Data Integration and Analysis Component (DIAC) of the Extracellular RNA Communication Consortium. The authors would also like to thank the dedicated team of embryologists, geneticists, and medical professionals at the Institution of Reproduction and IVF, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center. Additionally, we are grateful for the following funding agencies, which supported our work and enabled us to conduct this study: The Sagol fund for embryos and stem cells as part of the Sagol Network and the Israel Science Foundation Physician-Scientist Grant (Grant No. 2089/15 ). Funding Information: Whole Genome Sequencing, sequencing of RNA-seq and small RNA-seq libraries, and DNA methylation microarray analysis was conducted at the Institute for Genomic Medicine (IGM) Genomics Center, University of California, San Diego, La Jolla, CA. Small RNA-seq libraries were generated by Aishwarya Vuppala under the supervision of Peter De Hoff. This publication includes data generated at the UC San Diego IGM Genomics Center utilizing an Illumina NovaSeq 6000 that was purchased with funding from a National Institutes of Health SIG grant (#S10 OD026929). This work used the Extreme Science and Engineering Discovery Environment (XSEDE) Expanse at the San Diego Super Computer through allocation MCB140074. RM was supported by a grant from the National Institutes of Health, USA (NIH grant T32GM008806). Small RNA-seq data processing was performed using the exceRpt pipeline on the Genboree Workbench developed by the Data Integration and Analysis Component (DIAC) of the Extracellular RNA Communication Consortium. The authors would also like to thank the dedicated team of embryologists, geneticists, and medical professionals at the Institution of Reproduction and IVF, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center. Additionally, we are grateful for the following funding agencies, which supported our work and enabled us to conduct this study: The Sagol fund for embryos and stem cells as part of the Sagol Network and the Israel Science Foundation Physician-Scientist Grant (Grant No. 2089/15). C.D. and R.M. designed, conducted, analyzed, and interpreted the experiments (wet lab and dry lab, respectively) and drafted the paper. J.H. provided materials and guidance. D.B. L.L. and H.A. designed the project and experiments, interpreted the results, and drafted the paper. The authors declare no competing interests. We support inclusive, diverse, and equitable conduct of research. Publisher Copyright: © 2022 The Authors
PY - 2022/12/22
Y1 - 2022/12/22
N2 - A detailed understanding of the developmental substates of human pluripotent stem cells (hPSCs) is needed to optimize their use in cell therapy and for modeling early development. Genetic instability and risk of tumorigenicity of primed hPSCs are well documented, but a systematic isogenic comparison between substates has not been performed. We derived four hESC lines in naive human stem cell medium (NHSM) and generated isogenic pairs of NHSM and primed cultures. Through phenotypic, transcriptomic, and methylation profiling, we identified changes that arose during the transition to a primed substate. Although early NHSM cultures displayed naive characteristics, including greater proliferation and clonogenic potential compared with primed cultures, they drifted toward a more primed-like substate over time, including accumulation of genetic abnormalities. Overall, we show that transcriptomic and epigenomic profiling can be used to place human pluripotent cultures along a developmental continuum and may inform their utility for clinical and research applications.
AB - A detailed understanding of the developmental substates of human pluripotent stem cells (hPSCs) is needed to optimize their use in cell therapy and for modeling early development. Genetic instability and risk of tumorigenicity of primed hPSCs are well documented, but a systematic isogenic comparison between substates has not been performed. We derived four hESC lines in naive human stem cell medium (NHSM) and generated isogenic pairs of NHSM and primed cultures. Through phenotypic, transcriptomic, and methylation profiling, we identified changes that arose during the transition to a primed substate. Although early NHSM cultures displayed naive characteristics, including greater proliferation and clonogenic potential compared with primed cultures, they drifted toward a more primed-like substate over time, including accumulation of genetic abnormalities. Overall, we show that transcriptomic and epigenomic profiling can be used to place human pluripotent cultures along a developmental continuum and may inform their utility for clinical and research applications.
KW - Developmental biology
KW - Epigenetics
KW - Genetics
KW - Stem cell plasticity
KW - Transcriptomics
UR - https://www.scopus.com/pages/publications/85141771792
U2 - 10.1016/j.isci.2022.105469
DO - 10.1016/j.isci.2022.105469
M3 - Article
C2 - 36404921
SN - 2589-0042
VL - 25
JO - iScience
JF - iScience
IS - 12
M1 - 105469
ER -