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Ghosh A, Som A. Network analysis of transcriptomic data uncovers molecular signatures and the interplay of mRNAs, lncRNAs, and miRNAs in human embryonic stem cells. Differentiation 2024; 135:100738. [PMID: 38008592 DOI: 10.1016/j.diff.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 11/28/2023]
Abstract
Growing evidence has shown that besides the protein coding genes, the non-coding elements of the genome are indispensable for maintaining the property of self-renewal in human embryonic stem cells and in cell fate determination. However, the regulatory mechanisms and the landscape of interactions between the coding and non-coding elements is poorly understood. In this work, we used weighted gene co-expression network analysis (WGCNA) on transcriptomic data retrieved from RNA-seq and small RNA-seq experiments and reconstructed the core human pluripotency network (called PluriMLMiNet) consisting of 375 mRNA, 57 lncRNA and 207 miRNAs. Furthermore, we derived networks specific to the naïve and primed states of human pluripotency (called NaiveMLMiNet and PrimedMLMiNet respectively) that revealed a set of molecular markers (RPS6KA1, ZYG11A, ZNF695, ZNF273, and NLRP2 for naive state, and RAB34, TMEM178B, PTPRZ1, USP44, KIF1A and LRRN1 for primed state) which can be used to distinguish the pluripotent state from the non-pluripotent state and also to identify the intra-pluripotency states (i.e., naïve and primed state). The lncRNA DANT1 was found to be a crucial as it formed a bridge between the naive and primed state-specific networks. Analysis of the genes neighbouring DANT1 suggested its possible role as a competing endogenous RNA (ceRNA) for the induction and maintenance of human pluripotency. This was computationally validated by predicting the missing DANT1-miRNA interactions to complete the ceRNA circuit. Here we first report that DANT1 might harbour binding sites for miRNAs hsa-miR-30c-2-3p, hsa-miR-210-3p and hsa-let-7b-5p which may influence pluripotency.
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Affiliation(s)
- Arindam Ghosh
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj, 211002, India; Institute of Biomedicine, University of Eastern Finland, FI-70210, Kuopio, Finland.
| | - Anup Som
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj, 211002, India.
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Hao C, Chu S, Quan X, Zhou T, Shi J, Huang X, Wu G, Tortorella MD, Pei D. Establishing extended pluripotent stem cells from human urine cells. Cell Biosci 2023; 13:88. [PMID: 37194020 DOI: 10.1186/s13578-023-01051-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/09/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Extended pluripotent stem cells (EPSCs) can contribute to both embryonic and trophectoderm-derived extraembryonic tissues. Therefore, EPSCs have great application significance for both research and industry. However, generating EPSCs from human somatic cells remains inefficient and cumbersome. RESULTS In this study, we established a novel and robust EPSCs culture medium OCM175 with defined and optimized ingredients. Our OCM175 medium contains optimized concentration of L-selenium-methylcysteine as a source of selenium and ROCK inhibitors to maintain the single cell passaging ability of pluripotent stem cells. We also used Matrigel or the combination of laminin 511 and laminin 521(1:1) to bypass the requirement of feeder cells. With OCM175 medium, we successfully converted integration-free iPSCs from easily available human Urine-Derived Cells (hUC-iPSCs) into EPSCs (O-IPSCs). We showed that our O-IPSCs have the ability to form both intra- and extra- embryonic chimerism, and could contribute to the trophoblast ectoderm lineage and three germ layer cell lineages. CONCLUSIONS In conclusion, our novel OCM175 culture medium has defined, optimized ingredients, which enables efficient generation of EPSCs in a feeder free manner. With the robust chimeric and differentiation potential, we believe that this system provides a solid basis to improve the application of EPSCs in regenerative medicine.
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Affiliation(s)
- Chunfang Hao
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shilong Chu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
| | - Xiongzhi Quan
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
| | - Tiancheng Zhou
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
| | - Junjie Shi
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
| | - Xiaofen Huang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
| | - Guangming Wu
- Division of Basic Research, Guangzhou Laboratory, Guangzhou, 510005, China
| | - Micky Daniel Tortorella
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, 31003, China.
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Mucci S, Isaja L, Rodríguez-Varela MS, Ferriol-Laffouillere SL, Marazita M, Videla-Richardson GA, Sevlever GE, Scassa ME, Romorini L. Acute severe hypoxia induces apoptosis of human pluripotent stem cells by a HIF-1α and P53 independent mechanism. Sci Rep 2022; 12:18803. [PMID: 36335243 PMCID: PMC9637190 DOI: 10.1038/s41598-022-23650-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 11/03/2022] [Indexed: 11/06/2022] Open
Abstract
Human embryonic and induced pluripotent stem cells are self-renewing pluripotent stem cells (hPSCs) that can differentiate into a wide range of specialized cells. Although moderate hypoxia (5% O2) improves hPSC self-renewal, pluripotency, and cell survival, the effect of acute severe hypoxia (1% O2) on hPSC viability is still not fully elucidated. In this sense, we explore the consequences of acute hypoxia on hPSC survival by culturing them under acute (maximum of 24 h) physical severe hypoxia (1% O2). After 24 h of hypoxia, we observed HIF-1α stabilization concomitant with a decrease in cell viability. We also observed an increase in the apoptotic rate (western blot analysis revealed activation of CASPASE-9, CASPASE-3, and PARP cleavage after hypoxia induction). Besides, siRNA-mediated downregulation of HIF-1α and P53 did not significantly alter hPSC apoptosis induced by hypoxia. Finally, the analysis of BCL-2 family protein expression levels disclosed a shift in the balance between pro- and anti-apoptotic proteins (evidenced by an increase in BAX/MCL-1 ratio) caused by hypoxia. We demonstrated that acute physical hypoxia reduced hPSC survival and triggered apoptosis by a HIF-1α and P53 independent mechanism.
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Affiliation(s)
- Sofía Mucci
- grid.418954.50000 0004 0620 9892Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación Para La Lucha Contra Las Enfermedades Neurológicas de La Infancia (Fleni), Ruta 9, Km 52.5, B1625XAF Belén de Escobar, Provincia de Buenos Aires Argentina
| | - Luciana Isaja
- grid.418954.50000 0004 0620 9892Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación Para La Lucha Contra Las Enfermedades Neurológicas de La Infancia (Fleni), Ruta 9, Km 52.5, B1625XAF Belén de Escobar, Provincia de Buenos Aires Argentina
| | - María Soledad Rodríguez-Varela
- grid.418954.50000 0004 0620 9892Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación Para La Lucha Contra Las Enfermedades Neurológicas de La Infancia (Fleni), Ruta 9, Km 52.5, B1625XAF Belén de Escobar, Provincia de Buenos Aires Argentina
| | - Sofía Luján Ferriol-Laffouillere
- grid.418954.50000 0004 0620 9892Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación Para La Lucha Contra Las Enfermedades Neurológicas de La Infancia (Fleni), Ruta 9, Km 52.5, B1625XAF Belén de Escobar, Provincia de Buenos Aires Argentina
| | - Mariela Marazita
- grid.418954.50000 0004 0620 9892Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación Para La Lucha Contra Las Enfermedades Neurológicas de La Infancia (Fleni), Ruta 9, Km 52.5, B1625XAF Belén de Escobar, Provincia de Buenos Aires Argentina
| | - Guillermo Agustín Videla-Richardson
- grid.418954.50000 0004 0620 9892Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación Para La Lucha Contra Las Enfermedades Neurológicas de La Infancia (Fleni), Ruta 9, Km 52.5, B1625XAF Belén de Escobar, Provincia de Buenos Aires Argentina
| | - Gustavo Emilio Sevlever
- grid.418954.50000 0004 0620 9892Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación Para La Lucha Contra Las Enfermedades Neurológicas de La Infancia (Fleni), Ruta 9, Km 52.5, B1625XAF Belén de Escobar, Provincia de Buenos Aires Argentina
| | - María Elida Scassa
- grid.418954.50000 0004 0620 9892Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación Para La Lucha Contra Las Enfermedades Neurológicas de La Infancia (Fleni), Ruta 9, Km 52.5, B1625XAF Belén de Escobar, Provincia de Buenos Aires Argentina
| | - Leonardo Romorini
- grid.418954.50000 0004 0620 9892Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación Para La Lucha Contra Las Enfermedades Neurológicas de La Infancia (Fleni), Ruta 9, Km 52.5, B1625XAF Belén de Escobar, Provincia de Buenos Aires Argentina
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