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Liao C, Walters BW, DiStasio M, Lesch BJ. Human-specific epigenomic states in spermatogenesis. Comput Struct Biotechnol J 2024; 23:577-588. [PMID: 38274996 PMCID: PMC10809009 DOI: 10.1016/j.csbj.2023.12.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/23/2023] [Accepted: 12/23/2023] [Indexed: 01/27/2024] Open
Abstract
Infertility is becoming increasingly common, affecting one in six people globally. Half of these cases can be attributed to male factors, many driven by abnormalities in the process of sperm development. Emerging evidence from genome-wide association studies, genetic screening of patient cohorts, and animal models highlights an important genetic contribution to spermatogenic defects, but comprehensive identification and characterization of the genes critical for male fertility remain lacking. High divergence of gene regulation in spermatogenic cells across species poses challenges for delineating the genetic pathways required for human spermatogenesis using common model organisms. In this study, we leveraged post-translational histone modification and gene transcription data for 15,491 genes in four mammalian species (human, rhesus macaque, mouse, and opossum), to identify human-specific patterns of gene regulation during spermatogenesis. We combined H3K27me3 ChIP-seq, H3K4me3 ChIP-seq, and RNA-seq data to define epigenetic states for each gene at two stages of spermatogenesis, pachytene spermatocytes and round spermatids, in each species. We identified 239 genes that are uniquely active, poised, or dynamically regulated in human spermatogenic cells distinct from the other three species. While some of these genes have been implicated in reproductive functions, many more have not yet been associated with human infertility and may be candidates for further molecular and epidemiologic studies. Our analysis offers an example of the opportunities provided by evolutionary and epigenomic data for broadly screening candidate genes implicated in reproduction, which might lead to discoveries of novel genetic targets for diagnosis and management of male infertility and male contraception.
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Affiliation(s)
- Caiyun Liao
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
| | | | - Marcello DiStasio
- Department of Pathology, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
- Department of Opthamology & Visual Sciences, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
| | - Bluma J. Lesch
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
- Department of Genetics, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
- Yale Cancer Center, Yale School of Medicine, 333 Cedar St., New Haven, CT 06510, USA
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2
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Gu CC, Matter A, Turner A, Aggarwal P, Yang W, Sun X, Hunt SC, Lewis CE, Arnett DK, Anson B, Kattman S, Broeckel U. Transcriptional Variabilities in Human hiPSC-derived Cardiomyocytes: All Genes Are Not Equal and Their Robustness May Foretell Donor's Disease Susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.584138. [PMID: 38659937 PMCID: PMC11042381 DOI: 10.1101/2024.04.18.584138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Human induced pluripotent stem cells (hiPSCs) are frequently used to study disease-associated variations. We characterized transcriptional variability from a hiPSC-derived cardiomyocyte (hiPSC-CM) study of left ventricular hypertrophy (LVH) using donor samples from the HyperGEN study. Multiple hiPSC-CM differentiations over reprogramming events (iPSC generation) across 7 donors were used to assess variabilities from reprogramming, differentiation, and donor LVH status. Variability arising from pathological alterations was assessed using a cardiac stimulant applied to the hiPSC-CMs to trigger hypertrophic responses. We found that for most genes (73.3%~85.5%), technical variability was smaller than biological variability. Further, we identified and characterized lists of "noise" genes showing greater technical variability and "signal" genes showing greater biological variability. Together, they support a "genetic robustness" hypothesis of disease-modeling whereby cellular response to relevant stimuli in hiPSC-derived somatic cells from diseased donors tends to show more transcriptional variability. Our findings suggest that hiPSC-CMs can provide a valid model for cardiac hypertrophy and distinguish between technical and disease-relevant transcriptional changes.
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3
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Spathopoulou A, Podlesnic M, De Gaetano L, Kirsch EM, Tisch M, Finotello F, Aigner L, Günther K, Edenhofer F. Single-cell Profiling of Reprogrammed Human Neural Stem Cells Unveils High Similarity to Neural Progenitors in the Developing Central Nervous System. Stem Cell Rev Rep 2024:10.1007/s12015-024-10698-3. [PMID: 38519702 DOI: 10.1007/s12015-024-10698-3] [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] [Accepted: 02/14/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND Similar to induced pluripotent cells (iPSCs), induced neural stem cells (iNSCs) can be directly converted from human somatic cells such as dermal fibroblasts and peripheral blood monocytes. While previous studies have demonstrated the resemblance of iNSCs to neural stem cells derived from primary sources and embryonic stem cells, respectively, a comprehensive analysis of the correlation between iNSCs and their physiological counterparts remained to be investigated. METHODS Nowadays, single-cell sequencing technologies provide unique opportunities for in-depth cellular benchmarking of complex cell populations. Our study involves the comprehensive profiling of converted human iNSCs at a single-cell transcriptomic level, alongside conventional methods, like flow cytometry and immunofluorescence stainings. RESULTS Our results show that the iNSC conversion yields a homogeneous cell population expressing bona fide neural stem cell markers. Extracting transcriptomic signatures from published single cell transcriptomic atlas data and comparison to the iNSC transcriptome reveals resemblance to embryonic neuroepithelial cells of early neurodevelopmental stages observed in vivo at 5 weeks of development. CONCLUSION Our data underscore the physiological relevance of directly converted iNSCs, making them a valuable in vitro system for modeling human central nervous system development and establishing translational applications in cell therapy and compound screening.
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Affiliation(s)
- Angeliki Spathopoulou
- Department of Molecular Biology & CMBI, Genomics, Stem Cell & Regenerative Medicine Group, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Martina Podlesnic
- Department of Molecular Biology & CMBI, Genomics, Stem Cell & Regenerative Medicine Group, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Laura De Gaetano
- Department of Molecular Biology & CMBI, Genomics, Stem Cell & Regenerative Medicine Group, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Elena Marie Kirsch
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Center for Stroke Research, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Experimental Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Marcel Tisch
- Department of Molecular Biology & CMBI, Genomics, Stem Cell & Regenerative Medicine Group, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Francesca Finotello
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Ludwig Aigner
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Katharina Günther
- Department of Molecular Biology & CMBI, Genomics, Stem Cell & Regenerative Medicine Group, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Frank Edenhofer
- Department of Molecular Biology & CMBI, Genomics, Stem Cell & Regenerative Medicine Group, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.
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4
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Kim J, Kim J, Kim D, Bello AB, Kim BJ, Cha B, Lee S. Therapeutic potential of mesenchymal stem cells from human iPSC-derived teratomas for osteochondral defect regeneration. Bioeng Transl Med 2024; 9:e10629. [PMID: 38435815 PMCID: PMC10905541 DOI: 10.1002/btm2.10629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 03/05/2024] Open
Abstract
Human induced pluripotent stem cells (iPSCs) hold great promise for personalized medicine, as they can be differentiated into specific cell types, especially mesenchymal stem cells (MSCs). Therefore, our study sought to assess the feasibility of deriving MSCs from teratomas generated from human iPSCs. Teratomas serve as a model to mimic multilineage human development, thus enriching specific somatic progenitors and stem cells. Here, we discovered a small, condensed mass of MSCs within iPSC-generated teratomas. Afterward, we successfully isolated MSCs from this condensed mass, which was a byproduct of teratoma development. To evaluate the characteristics and cell behaviors of iPSC-derived MSCs (iPSC-MSCs), we conducted comprehensive assessments using qPCR, immunophenotype analysis, and cell proliferation-related assays. Remarkably, iPSC-MSCs exhibited an immunophenotype resembling that of conventional MSCs, and they displayed robust proliferative capabilities, similar to those of higher pluripotent stem cell-derived MSCs. Furthermore, iPSC-MSCs demonstrated the ability to differentiate into multiple lineages in vitro. Finally, we evaluated the therapeutic potential of iPSC-MSCs using an osteochondral defect model. Our findings demonstrated that teratomas are a promising source for the isolation of condensed MSCs. More importantly, our results suggest that iPSC-MSCs derived from teratomas possess the capacity for tissue regeneration, highlighting their promise for future therapeutic applications.
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Affiliation(s)
- Jiseong Kim
- Department of Biomedical TechnologyDongguk UniversityGoyang‐siRepublic of Korea
| | - Jin‐Su Kim
- Department of Biomedical ScienceCHA UniversitySeongnam‐siRepublic of Korea
- Biomaterials Research CenterCELLINBIO Co., Ltd.Suwon‐siGyeonggi‐doRepublic of Korea
| | - Dohyun Kim
- Department of Biomedical TechnologyDongguk UniversityGoyang‐siRepublic of Korea
| | - Alvin Bacero Bello
- Department of Biomedical TechnologyDongguk UniversityGoyang‐siRepublic of Korea
- Department of Integrative EngineeringChung‐Ang UniversitySeoulRepublic of Korea
| | - Byoung Ju Kim
- Department of Rearch & Development teamATEMsSeoulRepublic of Korea
| | - Byung‐Hyun Cha
- Division of Biomedical ConvergenceCollege of Biomedical Science, Kangwon National UniversityChuncheon‐siRepublic of Korea
| | - Soo‐Hong Lee
- Department of Biomedical TechnologyDongguk UniversityGoyang‐siRepublic of Korea
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5
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de Boer S, Laan S, Dirven R, Eikenboom J. Approaches to induce the maturation process of human induced pluripotent stem cell derived-endothelial cells to generate a robust model. PLoS One 2024; 19:e0297465. [PMID: 38394102 PMCID: PMC10889888 DOI: 10.1371/journal.pone.0297465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/05/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Endothelial cells generated from induced pluripotent stem cells (hiPSC-ECs) show the majority of endothelial cell characteristics and markers, such as cobblestone morphology and the expression of VEGF and VE-cadherin. However, these cells are failing to show a mature endothelial cell phenotype, which is represented by the low expression and production of von Willebrand Factor (VWF) leading to the round morphology of the Weibel Palade Bodies (WPBs). The aim of this study was to improve the maturation process of hiPSC-ECs and to increase the levels of VWF. METHODS hiPSC-ECs were differentiated by a standard differentiation protocol from hiPSCs generated from healthy control donors. To induce maturation, the main focus was to increase the expression and/or production of VWF by the adjustment of potential parameters influencing differentiation and maturation. We also compared alternative differentiation protocols. Cells were analyzed for the expression of endothelial cell markers, WPB structure, and the production and secretion of VWF by flow cytometry, confocal microscopy and ELISA. RESULTS The generated hiPSC-ECs have typical endothelial cell surface expression profiles, with low expression levels of non-endothelial markers as expected. Co-culture with pericytes, varying concentrations and timing of differentiation factors, applying some level of flow, and the addition of HDAC inhibitors did not substantially improve maturation of hiPSC-ECs. Transfection with the transcription factor ETV2 to induce a faster hiPSC-EC differentiation process resulted in a limited increase in VWF production, secretion, and elongation of WPB structure. Alternative differentiation protocols had limited effect. CONCLUSION hiPSCs-ECs have the potential to show a more mature endothelial phenotype with elongated WPBs after >30 days in culture. However, this comes with limitations as there are very few cells detected, and cells are deteriorating after being in culture for extended periods of time.
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Affiliation(s)
- Suzan de Boer
- Division of Thrombosis and Hemostasis, Department of Internal Medicine, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Sebastiaan Laan
- Division of Thrombosis and Hemostasis, Department of Internal Medicine, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Richard Dirven
- Division of Thrombosis and Hemostasis, Department of Internal Medicine, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen Eikenboom
- Division of Thrombosis and Hemostasis, Department of Internal Medicine, Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, The Netherlands
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6
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Agriesti F, Cela O, Capitanio N. "Time Is out of Joint" in Pluripotent Stem Cells: How and Why. Int J Mol Sci 2024; 25:2063. [PMID: 38396740 PMCID: PMC10889767 DOI: 10.3390/ijms25042063] [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: 01/10/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The circadian rhythm is necessary for the homeostasis and health of living organisms. Molecular clocks interconnected by transcription/translation feedback loops exist in most cells of the body. A puzzling exemption to this, otherwise, general biological hallmark is given by the cell physiology of pluripotent stem cells (PSCs) that lack circadian oscillations gradually acquired following their in vivo programmed differentiation. This process can be nicely phenocopied following in vitro commitment and reversed during the reprogramming of somatic cells to induce PSCs. The current understanding of how and why pluripotency is "time-uncoupled" is largely incomplete. A complex picture is emerging where the circadian core clockwork is negatively regulated in PSCs at the post-transcriptional/translational, epigenetic, and other-clock-interaction levels. Moreover, non-canonical functions of circadian core-work components in the balance between pluripotency identity and metabolic-driven cell reprogramming are emerging. This review selects and discusses results of relevant recent investigations providing major insights into this context.
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Affiliation(s)
- Francesca Agriesti
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy; (O.C.); (N.C.)
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7
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Sotomayor-Lugo F, Iglesias-Barrameda N, Castillo-Aleman YM, Casado-Hernandez I, Villegas-Valverde CA, Bencomo-Hernandez AA, Ventura-Carmenate Y, Rivero-Jimenez RA. The Dynamics of Histone Modifications during Mammalian Zygotic Genome Activation. Int J Mol Sci 2024; 25:1459. [PMID: 38338738 PMCID: PMC10855761 DOI: 10.3390/ijms25031459] [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: 12/29/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Mammalian fertilization initiates the reprogramming of oocytes and sperm, forming a totipotent zygote. During this intricate process, the zygotic genome undergoes a maternal-to-zygotic transition (MZT) and subsequent zygotic genome activation (ZGA), marking the initiation of transcriptional control and gene expression post-fertilization. Histone modifications are pivotal in shaping cellular identity and gene expression in many mammals. Recent advances in chromatin analysis have enabled detailed explorations of histone modifications during ZGA. This review delves into conserved and unique regulatory strategies, providing essential insights into the dynamic changes in histone modifications and their variants during ZGA in mammals. The objective is to explore recent advancements in leading mechanisms related to histone modifications governing this embryonic development phase in depth. These considerations will be useful for informing future therapeutic approaches that target epigenetic regulation in diverse biological contexts. It will also contribute to the extensive areas of evolutionary and developmental biology and possibly lay the foundation for future research and discussion on this seminal topic.
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Affiliation(s)
| | | | | | | | | | | | | | - Rene Antonio Rivero-Jimenez
- Abu Dhabi Stem Cells Center, Abu Dhabi P.O. Box 4600, United Arab Emirates; (F.S.-L.); (N.I.-B.); (Y.M.C.-A.); (I.C.-H.); (C.A.V.-V.); (A.A.B.-H.); (Y.V.-C.)
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8
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Edwards MM, Wang N, Massey DJ, Bhatele S, Egli D, Koren A. Incomplete reprogramming of DNA replication timing in induced pluripotent stem cells. Cell Rep 2024; 43:113664. [PMID: 38194345 DOI: 10.1016/j.celrep.2023.113664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/27/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024] Open
Abstract
Induced pluripotent stem cells (iPSCs) are the foundation of cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which could affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing, a process linked to both genome regulation and genome stability, is efficiently reprogrammed to the embryonic state. To answer this, we compare genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicate their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibits delayed replication at heterochromatic regions containing genes downregulated in iPSCs with incompletely reprogrammed DNA methylation. DNA replication delays are not the result of gene expression or DNA methylation aberrations and persist after cells differentiate to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and influence the quality of iPSCs.
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Affiliation(s)
- Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sakshi Bhatele
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA.
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
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9
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Tatwavedi D, Pellagatti A, Boultwood J. Recent advances in the application of induced pluripotent stem cell technology to the study of myeloid malignancies. Adv Biol Regul 2024; 91:100993. [PMID: 37827894 DOI: 10.1016/j.jbior.2023.100993] [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: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023]
Abstract
Acquired myeloid malignancies are a spectrum of clonal disorders known to be caused by sequential acquisition of genetic lesions in hematopoietic stem and progenitor cells, leading to their aberrant self-renewal and differentiation. The increasing use of induced pluripotent stem cell (iPSC) technology to study myeloid malignancies has helped usher a paradigm shift in approaches to disease modeling and drug discovery, especially when combined with gene-editing technology. The process of reprogramming allows for the capture of the diversity of genetic lesions and mutational burden found in primary patient samples into individual stable iPSC lines. Patient-derived iPSC lines, owing to their self-renewal and differentiation capacity, can thus be a homogenous source of disease relevant material that allow for the study of disease pathogenesis using various functional read-outs. Furthermore, genome editing technologies like CRISPR/Cas9 enable the study of the stepwise progression from normal to malignant hematopoiesis through the introduction of specific driver mutations, individually or in combination, to create isogenic lines for comparison. In this review, we survey the current use of iPSCs to model acquired myeloid malignancies including myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), acute myeloid leukemia and MDS/MPN overlap syndromes. The use of iPSCs has enabled the interrogation of the underlying mechanism of initiation and progression driving these diseases. It has also made drug testing, repurposing, and the discovery of novel therapies for these diseases possible in a high throughput setting.
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Affiliation(s)
- Dharamveer Tatwavedi
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Andrea Pellagatti
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jacqueline Boultwood
- Blood Cancer UK Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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10
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Zheng W, Wang L, He W, Hu X, Zhu Q, Gu L, Jiang C. Transcriptome profiles and chromatin states in mouse androgenetic haploid embryonic stem cells. Cell Prolif 2023; 56:e13436. [PMID: 36855927 PMCID: PMC10472531 DOI: 10.1111/cpr.13436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/12/2023] [Accepted: 02/17/2023] [Indexed: 03/02/2023] Open
Abstract
Haploid embryonic stem cells (haESCs) are derived from the inner cell mass of the haploid blastocyst, containing only one set of chromosomes. Extensive and accurate chromatin remodelling occurs during haESC derivation, but the intrinsic transcriptome profiles and chromatin structure of haESCs have not been fully explored. We profiled the transcriptomes, nucleosome positioning, and key histone modifications of four mouse haESC lines, and compared these profiles with those of other closely-related stem cell lines, MII oocytes, round spermatids, sperm, and mouse embryonic fibroblasts. haESCs had transcriptome profiles closer to those of naïve pluripotent stem cells. Consistent with the one X chromosome in haESCs, Xist was repressed, indicating no X chromosome inactivation. haESCs and ESCs shared a similar global chromatin structure. However, a nucleosome depletion region was identified in 2056 promoters in ESCs, which was absent in haESCs. Furthermore, three characteristic spatial relationships were formed between transcription factor motifs and nucleosomes in both haESCs and ESCs, specifically in the linker region, on the nucleosome central surface, and nucleosome borders. Furthermore, the chromatin state of 4259 enhancers was off in haESCs but active in ESCs. Functional annotation of these enhancers revealed enrichment in regulation of the cell cycle, a predominantly reported mechanism of haESC self-diploidization. Notably, the transcriptome profiles and chromatin structure of haESCs were highly preserved during passaging but different from those of differentiated cell types.
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Affiliation(s)
- Weisheng Zheng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Liping Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Wenteng He
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Xinjie Hu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Qianshu Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Liang Gu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
- Frontier Science Center for Stem Cell ResearchTongji UniversityShanghaiChina
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11
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Buckberry S, Liu X, Poppe D, Tan JP, Sun G, Chen J, Nguyen TV, de Mendoza A, Pflueger J, Frazer T, Vargas-Landín DB, Paynter JM, Smits N, Liu N, Ouyang JF, Rossello FJ, Chy HS, Rackham OJL, Laslett AL, Breen J, Faulkner GJ, Nefzger CM, Polo JM, Lister R. Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature 2023; 620:863-872. [PMID: 37587336 PMCID: PMC10447250 DOI: 10.1038/s41586-023-06424-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human embryonic stem (hES) cells differ significantly, which affects hiPS cell function1-8. These differences include epigenetic memory and aberrations that emerge during reprogramming, for which the mechanisms remain unknown. Here we characterized the persistence and emergence of these epigenetic differences by performing genome-wide DNA methylation profiling throughout primed and naive reprogramming of human somatic cells to hiPS cells. We found that reprogramming-induced epigenetic aberrations emerge midway through primed reprogramming, whereas DNA demethylation begins early in naive reprogramming. Using this knowledge, we developed a transient-naive-treatment (TNT) reprogramming strategy that emulates the embryonic epigenetic reset. We show that the epigenetic memory in hiPS cells is concentrated in cell of origin-dependent repressive chromatin marked by H3K9me3, lamin-B1 and aberrant CpH methylation. TNT reprogramming reconfigures these domains to a hES cell-like state and does not disrupt genomic imprinting. Using an isogenic system, we demonstrate that TNT reprogramming can correct the transposable element overexpression and differential gene expression seen in conventional hiPS cells, and that TNT-reprogrammed hiPS and hES cells show similar differentiation efficiencies. Moreover, TNT reprogramming enhances the differentiation of hiPS cells derived from multiple cell types. Thus, TNT reprogramming corrects epigenetic memory and aberrations, producing hiPS cells that are molecularly and functionally more similar to hES cells than conventional hiPS cells. We foresee TNT reprogramming becoming a new standard for biomedical and therapeutic applications and providing a novel system for studying epigenetic memory.
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Affiliation(s)
- Sam Buckberry
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Telethon Kids Institute, Perth, Western Australia, Australia
- John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Xiaodong Liu
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- School of Life Sciences, Westlake University, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Westlake Institute for Advanced Study, Hangzhou, China
| | - Daniel Poppe
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jia Ping Tan
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Guizhi Sun
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Joseph Chen
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Trung Viet Nguyen
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Alex de Mendoza
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Jahnvi Pflueger
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Thomas Frazer
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Dulce B Vargas-Landín
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jacob M Paynter
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Nathan Smits
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Ning Liu
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Fernando J Rossello
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Hun S Chy
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Melbourne, Victoria, Australia
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Andrew L Laslett
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Melbourne, Victoria, Australia
| | - James Breen
- John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Christian M Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia.
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, Victoria, Australia.
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia.
- Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
- The South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
| | - Ryan Lister
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia.
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
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12
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Kaneko H, Kaitsuka T, Tomizawa K. Artificial induction of circadian rhythm by combining exogenous BMAL1 expression and polycomb repressive complex 2 inhibition in human induced pluripotent stem cells. Cell Mol Life Sci 2023; 80:200. [PMID: 37421441 PMCID: PMC11072008 DOI: 10.1007/s00018-023-04847-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/10/2023]
Abstract
Understanding the physiology of human-induced pluripotent stem cells (iPSCs) is necessary for directed differentiation, mimicking embryonic development, and regenerative medicine applications. Pluripotent stem cells (PSCs) exhibit unique abilities such as self-renewal and pluripotency, but they lack some functions that are associated with normal somatic cells. One such function is the circadian oscillation of clock genes; however, whether or not PSCs demonstrate this capability remains unclear. In this study, the reason why circadian rhythm does not oscillate in human iPSCs was examined. This phenomenon may be due to the transcriptional repression of clock genes resulting from the hypermethylation of histone H3 at lysine 27 (H3K27), or it may be due to the low levels of brain and muscle ARNT-like 1 (BMAL1) protein. Therefore, BMAL1-overexpressing cells were generated and pre-treated with GSK126, an inhibitor of enhancer of zest homologue 2 (EZH2), which is a methyltransferase of H3K27 and a component of polycomb repressive complex 2. Consequently, a significant circadian rhythm following endogenous BMAL1, period 2 (PER2), and other clock gene expression was induced by these two factors, suggesting a candidate mechanism for the lack of rhythmicity of clock gene expression in iPSCs.
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Affiliation(s)
- Hitomi Kaneko
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Taku Kaitsuka
- School of Pharmacy at Fukuoka, International University of Health and Welfare, Enokizu 137-1, Okawa, Fukuoka, 831-8501, Japan.
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan.
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13
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Luis J, Eastlake K, Lamb WDB, Limb GA, Jayaram H, Khaw PT. Cell-Based Therapies for Glaucoma. Transl Vis Sci Technol 2023; 12:23. [PMID: 37494052 PMCID: PMC10383000 DOI: 10.1167/tvst.12.7.23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/27/2023] Open
Abstract
Glaucomatous optic neuropathy (GON) is the major cause of irreversible visual loss worldwide and can result from a range of disease etiologies. The defining features of GON are retinal ganglion cell (RGC) degeneration and characteristic cupping of the optic nerve head (ONH) due to tissue remodeling, while intraocular pressure remains the only modifiable GON risk factor currently targeted by approved clinical treatment strategies. Efforts to understand the mechanisms that allow species such as the zebrafish to regenerate their retinal cells have greatly increased our understanding of regenerative signaling pathways. However, proper integration within the retina and projection to the brain by the newly regenerated neuronal cells remain major hurdles. Meanwhile, a range of methods for in vitro differentiation have been developed to derive retinal cells from a variety of cell sources, including embryonic and induced pluripotent stem cells. More recently, there has been growing interest in the implantation of glial cells as well as cell-derived products, including neurotrophins, microRNA, and extracellular vesicles, to provide functional support to vulnerable structures such as RGC axons and the ONH. These approaches offer the advantage of not relying upon the replacement of degenerated cells and potentially targeting earlier stages of disease pathogenesis. In order to translate these techniques into clinical practice, appropriate cell sourcing, robust differentiation protocols, and accurate implantation methods are crucial to the success of cell-based therapy in glaucoma. Translational Relevance: Cell-based therapies for glaucoma currently under active development include the induction of endogenous regeneration, implantation of exogenously derived retinal cells, and utilization of cell-derived products to provide functional support.
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Affiliation(s)
- Joshua Luis
- NIHR Biomedical Research Centre for Ophthalmology, UCL Institute of Ophthalmology & Moorfields Eye Hospital, London, UK
| | - Karen Eastlake
- NIHR Biomedical Research Centre for Ophthalmology, UCL Institute of Ophthalmology & Moorfields Eye Hospital, London, UK
| | - William D. B. Lamb
- NIHR Biomedical Research Centre for Ophthalmology, UCL Institute of Ophthalmology & Moorfields Eye Hospital, London, UK
| | - G. Astrid Limb
- NIHR Biomedical Research Centre for Ophthalmology, UCL Institute of Ophthalmology & Moorfields Eye Hospital, London, UK
| | - Hari Jayaram
- NIHR Biomedical Research Centre for Ophthalmology, UCL Institute of Ophthalmology & Moorfields Eye Hospital, London, UK
| | - Peng T. Khaw
- NIHR Biomedical Research Centre for Ophthalmology, UCL Institute of Ophthalmology & Moorfields Eye Hospital, London, UK
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14
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Edwards MM, Wang N, Massey DJ, Egli D, Koren A. Incomplete Reprogramming of DNA Replication Timing in Induced Pluripotent Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544654. [PMID: 37398435 PMCID: PMC10312660 DOI: 10.1101/2023.06.12.544654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Induced pluripotent stem cells (iPSC) are a widely used cell system and a foundation for cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which have the potential to affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing - a process linked to both genome regulation and genome stability - is efficiently reprogrammed to the embryonic state. To answer this, we profiled and compared genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicated their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibit delayed replication at heterochromatic regions containing genes downregulated in iPSC with incompletely reprogrammed DNA methylation. DNA replication delays were not the result of gene expression and DNA methylation aberrations and persisted after differentiating cells to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and lead to undesirable phenotypes in iPSCs, establishing it as an important genomic feature to consider when evaluating iPSC lines.
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Affiliation(s)
- Matthew M. Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Dashiell J. Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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15
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Watson LA, Meharena HS. From neurodevelopment to neurodegeneration: utilizing human stem cell models to gain insight into Down syndrome. Front Genet 2023; 14:1198129. [PMID: 37323671 PMCID: PMC10267712 DOI: 10.3389/fgene.2023.1198129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Down syndrome (DS), caused by triplication of chromosome 21, is the most frequent aneuploidy observed in the human population and represents the most common genetic form of intellectual disability and early-onset Alzheimer's disease (AD). Individuals with DS exhibit a wide spectrum of clinical presentation, with a number of organs implicated including the neurological, immune, musculoskeletal, cardiac, and gastrointestinal systems. Decades of DS research have illuminated our understanding of the disorder, however many of the features that limit quality of life and independence of individuals with DS, including intellectual disability and early-onset dementia, remain poorly understood. This lack of knowledge of the cellular and molecular mechanisms leading to neurological features of DS has caused significant roadblocks in developing effective therapeutic strategies to improve quality of life for individuals with DS. Recent technological advances in human stem cell culture methods, genome editing approaches, and single-cell transcriptomics have provided paradigm-shifting insights into complex neurological diseases such as DS. Here, we review novel neurological disease modeling approaches, how they have been used to study DS, and what questions might be addressed in the future using these innovative tools.
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16
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Eisen B, Binah O. Modeling Duchenne Muscular Dystrophy Cardiomyopathy with Patients' Induced Pluripotent Stem-Cell-Derived Cardiomyocytes. Int J Mol Sci 2023; 24:ijms24108657. [PMID: 37240001 DOI: 10.3390/ijms24108657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked progressive muscle degenerative disease caused by mutations in the dystrophin gene, resulting in death by the end of the third decade of life at the latest. A key aspect of the DMD clinical phenotype is dilated cardiomyopathy, affecting virtually all patients by the end of the second decade of life. Furthermore, despite respiratory complications still being the leading cause of death, with advancements in medical care in recent years, cardiac involvement has become an increasing cause of mortality. Over the years, extensive research has been conducted using different DMD animal models, including the mdx mouse. While these models present certain important similarities to human DMD patients, they also have some differences which pose a challenge to researchers. The development of somatic cell reprograming technology has enabled generation of human induced pluripotent stem cells (hiPSCs) which can be differentiated into different cell types. This technology provides a potentially endless pool of human cells for research. Furthermore, hiPSCs can be generated from patients, thus providing patient-specific cells and enabling research tailored to different mutations. DMD cardiac involvement has been shown in animal models to include changes in gene expression of different proteins, abnormal cellular Ca2+ handling, and other aberrations. To gain a better understanding of the disease mechanisms, it is imperative to validate these findings in human cells. Furthermore, with the recent advancements in gene-editing technology, hiPSCs provide a valuable platform for research and development of new therapies including the possibility of regenerative medicine. In this article, we review the DMD cardiac-related research performed so far using human hiPSCs-derived cardiomyocytes (hiPSC-CMs) carrying DMD mutations.
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Affiliation(s)
- Binyamin Eisen
- Cardiac Research Laboratory, Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Ofer Binah
- Cardiac Research Laboratory, Department of Physiology, Biophysics and Systems Biology, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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17
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Chen ACH, Lee YL, Ruan H, Huang W, Fong SW, Tian S, Lee KC, Wu GM, Tan Y, Wong TCH, Wu J, Zhang W, Cao D, Chow JFC, Liu P, Yeung WSB. Expanded Potential Stem Cells from Human Embryos Have an Open Chromatin Configuration with Enhanced Trophoblast Differentiation Ability. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204797. [PMID: 36775869 PMCID: PMC10104645 DOI: 10.1002/advs.202204797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Human expanded potential stem cells (hEPSC) have been derived from human embryonic stem cells and induced pluripotent stem cells. Here direct derivation of hEPSC from human pre-implantation embryos is reported. Like the reported hEPSC, the embryo-derived hEPSC (hEPSC-em) exhibit a transcriptome similar to morula, comparable differentiation potency, and high genome editing efficiency. Interestingly, the hEPSC-em show a unique H3 lysine-4 trimethylation (H3K4me3) open chromatin conformation; they possess a higher proportion of H3K4me3 bound broad domain (>5 kb) than the reported hEPSC, naive, and primed embryonic stem cells. The open conformation is associated with enhanced trophoblast differentiation potency with increased trophoblast gene expression upon induction of differentiation and success in derivation of trophoblast stem cells with bona fide characteristics. Hippo signaling is specifically enriched in the H3K4me3 broad domains of the hEPSC-. Knockout of the Hippo signaling gene, YAP1 abolishes the ability of the embryo-derived EPSC to form trophoblast stem cells.
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Affiliation(s)
- Andy Chun Hang Chen
- Department of Obstetrics and Gynaecology, School of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongHong Kong
- Shenzhen Key Laboratory of Fertility RegulationReproductive Medicine CenterThe University of Hong Kong ‐ Shenzhen HospitalShenzhen518000China
- Centre for Translational Stem Cell BiologyBuilding 17 WThe Hong Kong Science and Technology ParkHong KongHong Kong
| | - Yin Lau Lee
- Department of Obstetrics and Gynaecology, School of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongHong Kong
- Shenzhen Key Laboratory of Fertility RegulationReproductive Medicine CenterThe University of Hong Kong ‐ Shenzhen HospitalShenzhen518000China
- Centre for Translational Stem Cell BiologyBuilding 17 WThe Hong Kong Science and Technology ParkHong KongHong Kong
| | - Hanzhang Ruan
- Department of Obstetrics and Gynaecology, School of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongHong Kong
| | - Wen Huang
- Department of Obstetrics and Gynaecology, School of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongHong Kong
| | - Sze Wan Fong
- Department of Obstetrics and Gynaecology, School of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongHong Kong
| | - Siyu Tian
- Department of Obstetrics and Gynaecology, School of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongHong Kong
| | - Kai Chuen Lee
- Department of Obstetrics and Gynaecology, School of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongHong Kong
- Centre for Translational Stem Cell BiologyBuilding 17 WThe Hong Kong Science and Technology ParkHong KongHong Kong
| | - Genie Minju Wu
- Department of Obstetrics and Gynaecology, School of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongHong Kong
| | - Yongqi Tan
- Department of Obstetrics and Gynaecology, School of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongHong Kong
| | - Timothy Chun Hin Wong
- Centre for Translational Stem Cell BiologyBuilding 17 WThe Hong Kong Science and Technology ParkHong KongHong Kong
| | - Jian Wu
- Centre for Translational Stem Cell BiologyBuilding 17 WThe Hong Kong Science and Technology ParkHong KongHong Kong
| | - Weiyu Zhang
- Centre for Translational Stem Cell BiologyBuilding 17 WThe Hong Kong Science and Technology ParkHong KongHong Kong
| | - Dandan Cao
- Shenzhen Key Laboratory of Fertility RegulationReproductive Medicine CenterThe University of Hong Kong ‐ Shenzhen HospitalShenzhen518000China
| | - Judy Fung Cheung Chow
- Department of Obstetrics and Gynaecology, School of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongHong Kong
| | - Pengtao Liu
- Centre for Translational Stem Cell BiologyBuilding 17 WThe Hong Kong Science and Technology ParkHong KongHong Kong
- School of Biomedical SciencesLi Ka Shing Faculty of MedicineThe University of Hong KongStem Cell and Regenerative Medicine ConsortiumHong KongHong Kong
| | - William Shu Biu Yeung
- Department of Obstetrics and Gynaecology, School of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongHong Kong
- Shenzhen Key Laboratory of Fertility RegulationReproductive Medicine CenterThe University of Hong Kong ‐ Shenzhen HospitalShenzhen518000China
- Centre for Translational Stem Cell BiologyBuilding 17 WThe Hong Kong Science and Technology ParkHong KongHong Kong
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18
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Dwivedi S, Choudhary P, Gupta A, Singh S. Therapeutical growth in oligodendroglial fate induction via transdifferentiation of stem cells for neuroregenerative therapy. Biochimie 2023; 211:35-56. [PMID: 36842627 DOI: 10.1016/j.biochi.2023.02.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/20/2022] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
The merits of stem cell therapy and research are undisputed due to their widespread usage in the treatment of neurodegenerative diseases and demyelinating disorders. Cell replacement therapy especially revolves around stem cells and their induction into different cell lineages both adult and progenitor - belonging to each germ layer, prior to transplantation or disease modeling studies. The nervous system is abundant in glial cells and among these are oligodendrocytes capable of myelinating new-born neurons and remyelination of axons with lost or damaged myelin sheath. But demyelinating diseases generate tremendous deficit between myelin loss and recovery. To compensate for this loss, analyze the defects in remyelination mechanisms as well as to trigger full recovery in such patients mesenchymal stem cells (MSCs) have been induced to transdifferentiate into oligodendrocytes. But such experiments are riddled with problems like prolonged, tenuous and complicated protocols that stretch longer than the time taken for the spread of demyelination-associated after-effects. This review delves into such protocols and the combinations of different molecules and factors that have been recruited to derive bona fide oligodendrocytes from in vitro differentiation of embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs) and MSCs with special focus on MSC-derived oligodendrocytes.
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Affiliation(s)
- Shrey Dwivedi
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, U.P., India
| | - Princy Choudhary
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, U.P., India
| | - Ayushi Gupta
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, U.P., India
| | - Sangeeta Singh
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, U.P., India.
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19
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Cheng Q, Xie H. Genome-wide analysis of bivalent histone modifications during Drosophila embryogenesis. Genesis 2022; 60:e23502. [PMID: 36125264 DOI: 10.1002/dvg.23502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/26/2022] [Accepted: 08/28/2022] [Indexed: 01/25/2023]
Abstract
In eukaryotes, histone modifications are key epigenetic regulators that are associated with distinct chromatin features. Bivalent histone modifications describe a situation where a subset of promoters have with both activating (H3K4me3) and repressive (H3K27me3) markers in pluripotent cells (e.g., ESCs). However, it remains to be understood whether bivalent histone modifications are stable throughout developmental stages. Here, by systematically analyzing ChIP-seq data of H3K4me3 and H3K27me3, we provided the first panoramic view of bivalent histone modifications in Drosophila from embryonic 0-4 to 20-24 hr. In our study, we found that bivalent histone modifications occur at other locations in the genome in addition to the promoter region. Additionally, the different genomic regions occupied by bivalent histone modifications exhibit spatiotemporal specificity at each stage. Furthermore, gene ontology and motif analysis reflected continuous and gradual changes of target genes during different developmental process. In summary, we suggest that bivalent histone modifications have potential regulatory functions throughout Drosophila embryonic stage.
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Affiliation(s)
- Qian Cheng
- School of Life Science and Technology, Southeast University, Nanjing, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province Nanjing Medical University, Nanjing, China
| | - Hao Xie
- School of Life Science and Technology, Southeast University, Nanjing, China
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20
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Bigas A, Galán Palma L, Kartha GM, Giorgetti A. Using Pluripotent Stem Cells to Understand Normal and Leukemic Hematopoietic Development. Stem Cells Transl Med 2022; 11:1123-1134. [PMID: 36398586 PMCID: PMC9672852 DOI: 10.1093/stcltm/szac071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/29/2022] [Indexed: 12/02/2023] Open
Abstract
Several decades have passed since the generation of the first embryonic stem cell (ESC) lines both in mice and in humans. Since then, stem cell biologists have tried to understand their potential biological and clinical uses for their implementation in regenerative medicine. The hematopoietic field was a pioneer in establishing the potential use for the development of blood cell products and clinical applications; however, early expectations have been truncated by the difficulty in generating bonafide hematopoietic stem cells (HSCs). Despite some progress in understanding the origin of HSCs during embryonic development, the reproduction of this process in vitro is still not possible, but the knowledge acquired in the embryo is slowly being implemented for mouse and human pluripotent stem cells (PSCs). In contrast, ESC-derived hematopoietic cells may recapitulate some leukemic transformation processes when exposed to oncogenic drivers. This would be especially useful to model prenatal leukemia development or other leukemia-predisposing syndromes, which are difficult to study. In this review, we will review the state of the art of the use of PSCs as a model for hematopoietic and leukemia development.
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Affiliation(s)
- Anna Bigas
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), CIBERONC, Barcelona, Spain
- Josep Carreras Leukemia Research Institute (IJC), Barcelona, Spain
| | - Luis Galán Palma
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), CIBERONC, Barcelona, Spain
- Josep Carreras Leukemia Research Institute (IJC), Barcelona, Spain
| | - Gayathri M Kartha
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), CIBERONC, Barcelona, Spain
- Josep Carreras Leukemia Research Institute (IJC), Barcelona, Spain
| | - Alessandra Giorgetti
- Regenerative Medicine Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), Barcelona, Spain
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, Barcelona University, Barcelona, Spain
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21
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Chu X, Wang J. Quantifying Chromosome Structural Reorganizations during Differentiation, Reprogramming, and Transdifferentiation. PHYSICAL REVIEW LETTERS 2022; 129:068102. [PMID: 36018639 DOI: 10.1103/physrevlett.129.068102] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
We developed a nonequilibrium model to study chromosome structural reorganizations within a simplified cell developmental system. From the chromosome structural perspective, we predicted that the neural progenitor cell is on the neural developmental path and very close to the transdifferentiation path from the fibroblast to the neuron cell. We identified an early bifurcation of stem cell differentiation processes and the cell-of-origin-specific reprogramming pathways. Our theoretical results are in good agreement with available experimental evidence, promoting future applications of our approach.
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Affiliation(s)
- Xiakun Chu
- Advanced Materials Thrust, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou, Guangdong 511400, China
- Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
| | - Jin Wang
- Center for Theoretical Interdisciplinary Sciences, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
- Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
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22
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Establishment and characterization of IPS-OGC-C1: a novel induced pluripotent stem cell line from healthy human ovarian granulosa cells. Hum Cell 2022; 35:1612-1620. [PMID: 35876985 DOI: 10.1007/s13577-022-00757-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/18/2022] [Indexed: 11/27/2022]
Abstract
Ovarian granulosa cell (OGC) is a critical somatic component of the ovary, which provides physical support and the microenvironment required for the developing oocyte. Human OGCs are easy to obtain and culture as a by-product of follicular aspiration performed during in vitro fertilization (IVF) procedures. Therefore, OGCs offer a potent cell source to generate induced pluripotent stem cells (iPSCs). This study established a novel OGCs-derived iPSC cell line from the follicular fluid of a healthy female donor with a Chinese Han genetic background and named it IPS-OGC-C1. IPS-OGC-C1 was verified for embryonic stem cell morphology, cell marker expression, alkaline phosphatase (AP) activity, transcriptomic profile, and pluripotency capability in developing all three embryonic germ layers in vivo and in vitro.
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23
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Kristiansen CK, Chen A, Høyland LE, Ziegler M, Sullivan GJ, Bindoff LA, Liang KX. Comparing the mitochondrial signatures in ESCs and iPSCs and their neural derivations. Cell Cycle 2022; 21:2206-2221. [PMID: 35815665 DOI: 10.1080/15384101.2022.2092185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) have distinct origins: ESCs are derived from pre-implanted embryos while iPSCs are reprogrammed somatic cells. Both have their own characteristics and lineage specificity, and both are valuable tools for studying human neurological development and disease. Thus far, few studies have analyzed how differences between stem cell types influence mitochondrial function and mitochondrial DNA (mtDNA) homeostasis during differentiation into neural and glial lineages. In this study, we compared mitochondrial function and mtDNA replication in human ESCs and iPSCs at three different stages - pluripotent, neural progenitor and astrocyte. We found that while ESCs and iPSCs have a similar mitochondrial signature, neural and astrocyte derivations manifested differences. At the neural stem cell (NSC) stage, iPSC-NSCs displayed decreased ATP production and a reduction in mitochondrial respiratory chain (MRC) complex IV expression compared to ESC-NSCs. IPSC-astrocytes showed increased mitochondrial activity including elevated ATP production, MRC complex IV expression, mtDNA copy number and mitochondrial biogenesis relative to those derived from ESCs. These findings show that while ESCs and iPSCs are similar at the pluripotent stage, differences in mitochondrial function may develop during differentiation and must be taken into account when extrapolating results from different cell types.Abbreviation: BSA: Bovine serum albumin; DCFDA: 2',7'-dichlorodihydrofluorescein diacetate; DCX: Doublecortin; EAAT-1: Excitatory amino acid transporter 1; ESCs: Embryonic stem cells; GFAP: Glial fibrillary acidic protein; GS: Glutamine synthetase; iPSCs: Induced pluripotent stem cells; LC3B: Microtubule-associated protein 1 light chain 3β; LC-MS: Liquid chromatography-mass spectrometry; mito-ROS: Mitochondrial ROS; MMP: Mitochondrial membrane potential; MRC: Mitochondrial respiratory chain; mtDNA: Mitochondrial DNA; MTDR: MitoTracker Deep Red; MTG: MitoTracker Green; NSCs: Neural stem cells; PDL: Poly-D-lysine; PFA: Paraformaldehyde; PGC-1α: PPAR-γ coactivator-1 alpha; PPAR-γ: Peroxisome proliferator-activated receptor-gamma; p-SIRT1: Phosphorylated sirtuin 1; p-ULK1: Phosphorylated unc-51 like autophagy activating kinase 1; qPCR: Quantitative PCR; RT: Room temperature; RT-qPCR: Quantitative reverse transcription PCR; SEM: Standard error of the mean; TFAM: Mitochondrial transcription factor A; TMRE: Tetramethylrhodamine ethyl ester; TOMM20: Translocase of outer mitochondrial membrane 20.
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Affiliation(s)
- Cecilie Katrin Kristiansen
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway.,b Neuro-SysMed, Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Anbin Chen
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway.,Neuro-SysMed, Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | | | - Mathias Ziegler
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Gareth John Sullivan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Institute of Immunology, Oslo University Hospital, Oslo, Norway.,Hybrid Technology Hub - Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
| | - Laurence A Bindoff
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway.,Neuro-SysMed, Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Kristina Xiao Liang
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway.,Neuro-SysMed, Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, Bergen, Norway
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24
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Khodeer S, Klungland A, Dahl JA. ALKBH5 regulates somatic cell reprogramming in a phase specific manner. J Cell Sci 2022; 135:275396. [PMID: 35552718 PMCID: PMC9234673 DOI: 10.1242/jcs.259824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/03/2022] [Indexed: 11/20/2022] Open
Abstract
Establishment of the pluripotency regulatory network in somatic cells by introducing four transcription factors (octamer binding transcription factor 4 (OCT4), sex determining region Y (SRY)-box 2 (SOX2), Kruppel-like factor 4 (KLF4), and cellular myelocytomatosis (c-MYC)) provides a promising tool for cell-based therapies in regenerative medicine. Nevertheless, the mechanisms at play when generating induced pluripotent stem cells from somatic cells are only partly understood. Here, we show that the RNA specific N6-methyladenosine (m6A) demethylase ALKBH5 regulates somatic cell reprogramming in a stage-specific manner through its catalytic activity. Knockdown or knockout of Alkbh5 in the early reprogramming phase impairs reprogramming efficiency by reducing the proliferation rate through arresting the cells at G2/M phase and decreasing the upregulation of epithelial markers. On the other hand, ALKBH5 overexpression at the early reprogramming phase has no significant impact on reprogramming efficiency, while overexpression at the late phase enhances reprogramming by stabilizing Nanog transcripts, resulting in upregulated Nanog expression. Our study provides mechanistic insight into the crucial dynamic role of ALKBH5 through its catalytic activity in regulating somatic cell reprogramming at the posttranscriptional level.
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Affiliation(s)
- Sherif Khodeer
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Forskningsveien 1, 0373. Oslo, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Forskningsveien 1, 0373. Oslo, Norway.,Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316. Oslo, Norway
| | - John Arne Dahl
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Forskningsveien 1, 0373. Oslo, Norway
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25
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Berrens RV, Yang A, Laumer CE, Lun ATL, Bieberich F, Law CT, Lan G, Imaz M, Bowness JS, Brockdorff N, Gaffney DJ, Marioni JC. Locus-specific expression of transposable elements in single cells with CELLO-seq. Nat Biotechnol 2022; 40:546-554. [PMID: 34782740 PMCID: PMC7614850 DOI: 10.1038/s41587-021-01093-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 09/13/2021] [Indexed: 02/07/2023]
Abstract
Transposable elements (TEs) regulate diverse biological processes, from early development to cancer. Expression of young TEs is difficult to measure with next-generation, single-cell sequencing technologies because their highly repetitive nature means that short complementary DNA reads cannot be unambiguously mapped to a specific locus. Single CELl LOng-read RNA-sequencing (CELLO-seq) combines long-read single cell RNA-sequencing with computational analyses to measure TE expression at unique loci. We used CELLO-seq to assess the widespread expression of TEs in two-cell mouse blastomeres as well as in human induced pluripotent stem cells. Across both species, old and young TEs showed evidence of locus-specific expression with simulations demonstrating that only a small number of very young elements in the mouse could not be mapped back to the reference with high confidence. Exploring the relationship between the expression of individual elements and putative regulators revealed large heterogeneity, with TEs within a class showing different patterns of correlation and suggesting distinct regulatory mechanisms.
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Affiliation(s)
- Rebecca V Berrens
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Andrian Yang
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Christopher E Laumer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Aaron T L Lun
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Genentech, South San Francisco, CA, USA
| | - Florian Bieberich
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- ETH Zürich, Basel, Switzerland
| | - Cheuk-Ting Law
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Guocheng Lan
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- School of Biomedical Sciences,Stem Cell and Regenerative Consortium, Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Maria Imaz
- Wellcome Sanger Institute, Cambridge, UK
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Joseph S Bowness
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Daniel J Gaffney
- Wellcome Sanger Institute, Cambridge, UK
- Genomics Plc, Oxford, UK
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
- Wellcome Sanger Institute, Cambridge, UK.
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26
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Endo Y, Kamei KI, Hasegawa K, Okita K, Ito H, Terada S, Inoue-Murayama M. Generation and gene expression profiles of Grevy's zebra induced Pluripotent Stem Cells. Stem Cells Dev 2022; 31:250-257. [PMID: 35316100 DOI: 10.1089/scd.2021.0253] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) can serve as a biological resource for functional and conservation research for various species. This realisation has led to the generation of iPSCs from many species, including those identified as endangered. However, the understanding of species variation in mammalian iPSCs remains largely unknown. To gain insight into species variation in iPSCs, we generated iPSCs from a new species Grevy's zebra (Equus grevyi; gz-iPSCs), which has been listed as endangered in the IUCN (International Union for Conservation of Nature) Red List. We isolated primary fibroblast cells from an individual and successfully reprogrammed them into iPSCs. The generated gz-iPSCs continued to grow under primed-type culture condition and showed pluripotency and differentiation potential. To describe the molecular characteristics of gz-iPSCs, we performed RNA sequencing analysis. The gz-iPSC transcriptome showed robust expression of pluripotency associated genes reported in human and mouse, suggesting evolutionary conservation among the species. This study provides insight into the iPSCs from a rare species and helps the understanding of the gene expression basis underlying mammalian PSCs.
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Affiliation(s)
| | - Ken-Ichiro Kamei
- Kyoto University - Yoshida Campus, 12918, Kyoto, Japan, 606-8501;
| | | | | | | | - Shiho Terada
- Kyoto University - Yoshida Campus, 12918, Kyoto, Japan;
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27
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Sabatier P, Beusch CM, Saei AA, Aoun M, Moruzzi N, Coelho A, Leijten N, Nordenskjöld M, Micke P, Maltseva D, Tonevitsky AG, Millischer V, Carlos Villaescusa J, Kadekar S, Gaetani M, Altynbekova K, Kel A, Berggren PO, Simonson O, Grinnemo KH, Holmdahl R, Rodin S, Zubarev RA. An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation. Nat Commun 2021; 12:6558. [PMID: 34772928 PMCID: PMC8590018 DOI: 10.1038/s41467-021-26879-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 10/25/2021] [Indexed: 12/21/2022] Open
Abstract
Detailed characterization of cell type transitions is essential for cell biology in general and particularly for the development of stem cell-based therapies in regenerative medicine. To systematically study such transitions, we introduce a method that simultaneously measures protein expression and thermal stability changes in cells and provide the web-based visualization tool ProteoTracker. We apply our method to study differences between human pluripotent stem cells and several cell types including their parental cell line and differentiated progeny. We detect alterations of protein properties in numerous cellular pathways and components including ribosome biogenesis and demonstrate that modulation of ribosome maturation through SBDS protein can be helpful for manipulating cell stemness in vitro. Using our integrative proteomics approach and the web-based tool, we uncover a molecular basis for the uncoupling of robust transcription from parsimonious translation in stem cells and propose a method for maintaining pluripotency in vitro.
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Affiliation(s)
- Pierre Sabatier
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Christian M Beusch
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Amir A Saei
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Mike Aoun
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Noah Moruzzi
- The Rolf Luft Research Center for Diabetes and Endocrinology, Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, 17176, Sweden
| | - Ana Coelho
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Niels Leijten
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Magnus Nordenskjöld
- Center for Molecular Medicine, Karolinska University Hospital, Stockholm, 171 76, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, 17177, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, 171 76, Sweden
| | - Patrick Micke
- Immunology, Genetics and Pathology, Rudbecklaboratoriet, Uppsala University, Uppsala, 751 85, Sweden
| | - Diana Maltseva
- Faculty of biology and biotechnology, National Research University Higher School of Economics, Myasnitskaya Street, 13/4, Moscow, 117997, Russia
| | - Alexander G Tonevitsky
- Faculty of biology and biotechnology, National Research University Higher School of Economics, Myasnitskaya Street, 13/4, Moscow, 117997, Russia
- Scientific Research Center Bioclinicum, Ugreshskaya str. 2/85, Moscow, 115088, Russia
| | - Vincent Millischer
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, 17177, Sweden
- Translational Psychiatry, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, 171 76, Sweden
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, 1090, Austria
| | - J Carlos Villaescusa
- Neurogenetic Unit, Department of Molecular Medicine and Surgery, Karolinska University Hospital, Stockholm, 171 76, Sweden
- Stem Cell R&D-TRU, Novo Nordisk A/S, Måløv, Denmark
| | - Sandeep Kadekar
- Department of Surgical Sciences, Uppsala University, Uppsala, 752 37, Sweden
| | - Massimiliano Gaetani
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
- Chemical Proteomics Core Facility, Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 171 77, Sweden
- Chemical Proteomics, Science for Life Laboratory (SciLifeLab), Stockholm, 17 177, Sweden
| | | | - Alexander Kel
- geneXplain GmbH, Am Exer 19B, 38302, Wolfenbuettel, Germany
| | - Per-Olof Berggren
- The Rolf Luft Research Center for Diabetes and Endocrinology, Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, 17176, Sweden
| | - Oscar Simonson
- Department of Surgical Sciences, Uppsala University, Uppsala, 752 37, Sweden
- Department of Cardio-thoracic Surgery and Anesthesiology, Uppsala University Hospital, Uppsala, 751 85, Sweden
| | - Karl-Henrik Grinnemo
- Department of Surgical Sciences, Uppsala University, Uppsala, 752 37, Sweden
- Department of Cardio-thoracic Surgery and Anesthesiology, Uppsala University Hospital, Uppsala, 751 85, Sweden
| | - Rikard Holmdahl
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Sergey Rodin
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden.
- Department of Surgical Sciences, Uppsala University, Uppsala, 752 37, Sweden.
- Department of Cardio-thoracic Surgery and Anesthesiology, Uppsala University Hospital, Uppsala, 751 85, Sweden.
| | - Roman A Zubarev
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden.
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, 119146, Russia.
- The National Medical Research Center for Endocrinology, Moscow, 115478, Russia.
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28
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Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells. Cell Rep 2021; 37:109909. [PMID: 34731633 DOI: 10.1016/j.celrep.2021.109909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/24/2021] [Accepted: 10/08/2021] [Indexed: 01/13/2023] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) show variable differentiation potential due to their epigenomic heterogeneity, whose extent/attributes remain unclear, except for well-studied elements/chromosomes such as imprints and the X chromosomes. Here, we show that seven hiPSC lines with variable germline potential exhibit substantial epigenomic heterogeneity, despite their uniform transcriptomes. Nearly a quarter of autosomal regions bear potentially differential chromatin modifications, with promoters/CpG islands for H3K27me3/H2AK119ub1 and evolutionarily young retrotransposons for H3K4me3. We identify 145 large autosomal blocks (≥100 kb) with differential H3K9me3 enrichment, many of which are lamina-associated domains (LADs) in somatic but not in embryonic stem cells. A majority of these epigenomic heterogeneities are independent of genetic variations. We identify an X chromosome state with chromosome-wide H3K9me3 that stably prevents X chromosome erosion. Importantly, the germline potential of female hiPSCs correlates with X chromosome inactivation. We propose that inherent genomic properties, including CpG density, transposons, and LADs, engender epigenomic heterogeneity in hiPSCs.
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29
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Huang R, Wang S, Zhu R, Xian S, Huang Z, Cheng L, Zhang J. Identification of Key eRNAs for Spinal Cord Injury by Integrated Multinomial Bioinformatics Analysis. Front Cell Dev Biol 2021; 9:728242. [PMID: 34708039 PMCID: PMC8542800 DOI: 10.3389/fcell.2021.728242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/25/2021] [Indexed: 12/25/2022] Open
Abstract
Background: Spinal cord injury (SCI) is a severe neurological deficit affecting both young and older people worldwide. The potential role of key enhancer RNAs (eRNAs) in SCI remains elusive, which is a prominent challenge in the trauma repair process. This study aims to investigate the roles of key eRNAs, transcription factors (TFs), signaling pathways, and small-molecule inhibitors in SCI using multi-omics bioinformatics analysis. Methods: Microarray data of peripheral blood mononuclear cell (PBMC) samples from 27 healthy volunteers and 25 chronic-phase SCI patients were retrieved from the Gene Expression Omnibus database. Differentially expressed transcription factors (DETFs), differentially expressed enhancer RNAs (DEeRNAs), and differentially expressed target genes (DETGs) were identified using the Linear Models for Microarray Data (limma) package. Fraction of immune cells was estimated using CIBERSORT algorithm. Gene Set Variation Analysis (GSVA) was applied to identify the downstream signaling pathways. The eRNA regulatory network was constructed based on the correlation results. Connectivity Map (CMap) database was used to find potential drugs for SCI patients. The cellular communication analysis was performed to explore the molecular regulation mechanism of SCI based on single-cell RNA sequencing (scRNA-seq) data. Chromatin immunoprecipitation sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data were used to validate the key regulatory mechanisms. scRNA-seq dataset was used to validate the cell subtype localization of the key eRNAs. Results: In total, 21 DETFs, 24 DEeRNAs, and 829 DETGs were identified. A regulatory network of 13 DETFs, six DEeRNAs, seven DETGs, two hallmark pathways, two immune cells, and six immune pathways was constructed. The link of Splicing factor proline and glutamine rich (SFPQ) (TF) and vesicular overexpressed in cancer prosurvival protein 1 (VOPP1) (eRNA) (R = 0.990, p < 0.001, positive), VOPP1 (eRNA) and epidermal growth factor receptor (EGFR) (target gene) (R = 0.974, p < 0.001, positive), VOPP1, and T helper (Th) cells (R = -0.987, p < 0.001, negative), and VOPP1 and hallmark coagulation (R = 0.937, p < 0.001, positive) was selected. Trichostatin A was considered the best compound target to SCI-related eRNAs (specificity = 0.471, p < 0.001). Conclusion: VOPP1, upregulated by SFPQ, strengthened the transient expression of EGFR. Th cells and coagulation were the potential downstream pathways of VOPP1. This regulatory network and potential inhibitors provide novel diagnostic biomarkers and therapeutic targets for SCI.
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Affiliation(s)
- Runzhi Huang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Siqiao Wang
- Tongji University School of Medicine, Shanghai, China
| | - Rui Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Shuyuan Xian
- Tongji University School of Medicine, Shanghai, China
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Liming Cheng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jie Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China.,Division of Spine Surgery, Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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30
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Horánszky A, Becker JL, Zana M, Ferguson-Smith AC, Dinnyés A. Epigenetic Mechanisms of ART-Related Imprinting Disorders: Lessons From iPSC and Mouse Models. Genes (Basel) 2021; 12:genes12111704. [PMID: 34828310 PMCID: PMC8620286 DOI: 10.3390/genes12111704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 12/29/2022] Open
Abstract
The rising frequency of ART-conceived births is accompanied by the need for an improved understanding of the implications of ART on gametes and embryos. Increasing evidence from mouse models and human epidemiological data suggests that ART procedures may play a role in the pathophysiology of certain imprinting disorders (IDs), including Beckwith-Wiedemann syndrome, Silver-Russell syndrome, Prader-Willi syndrome, and Angelman syndrome. The underlying molecular basis of this association, however, requires further elucidation. In this review, we discuss the epigenetic and imprinting alterations of in vivo mouse models and human iPSC models of ART. Mouse models have demonstrated aberrant regulation of imprinted genes involved with ART-related IDs. In the past decade, iPSC technology has provided a platform for patient-specific cellular models of culture-associated perturbed imprinting. However, despite ongoing efforts, a deeper understanding of the susceptibility of iPSCs to epigenetic perturbation is required if they are to be reliably used for modelling ART-associated IDs. Comparing the patterns of susceptibility of imprinted genes in mouse models and IPSCs in culture improves the current understanding of the underlying mechanisms of ART-linked IDs with implications for our understanding of the influence of environmental factors such as culture and hormone treatments on epigenetically important regions of the genome such as imprints.
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Affiliation(s)
- Alex Horánszky
- BioTalentum Ltd., H-2100 Gödöllő, Hungary; (A.H.); (M.Z.)
- Department of Physiology and Animal Health, Institute of Physiology and Animal Health, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary
| | - Jessica L. Becker
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; (J.L.B.); (A.C.F.-S.)
| | - Melinda Zana
- BioTalentum Ltd., H-2100 Gödöllő, Hungary; (A.H.); (M.Z.)
| | - Anne C. Ferguson-Smith
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; (J.L.B.); (A.C.F.-S.)
| | - András Dinnyés
- BioTalentum Ltd., H-2100 Gödöllő, Hungary; (A.H.); (M.Z.)
- Department of Physiology and Animal Health, Institute of Physiology and Animal Health, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary
- HCEMM-USZ Stem Cell Research Group, Hungarian Centre of Excellence for Molecular Medicine, H-6723 Szeged, Hungary
- Department of Cell Biology and Molecular Medicine, University of Szeged, H-6720 Szeged, Hungary
- Correspondence: ; Tel.: +36-20-510-9632; Fax: +36-28-526-151
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31
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Changes in Methylation Patterns of Tumor Suppressor Genes during Extended Human Embryonic Stem Cell Cultures. Stem Cells Int 2021; 2021:5575185. [PMID: 34552632 PMCID: PMC8452414 DOI: 10.1155/2021/5575185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 08/11/2021] [Accepted: 08/18/2021] [Indexed: 11/23/2022] Open
Abstract
While studies on embryonic stem cells have been actively conducted, little is known about the epigenetic mechanisms in human embryonic stem cells (hESCs) in extended culture systems. Here, we investigated whether CpG island (CGI) methylation patterns of 24 tumor suppressor genes could be maintained during extended hESC cultures. In total, 10 hESC lines were analyzed. For each cell line, genomic DNA was extracted from early and late passages of cell cultures. CGI methylation levels of 24 tumor suppressor genes were analyzed using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), pyrosequencing, and real-time polymerase chain reaction (PCR). Different CGI methylation patterns of CASP8, FHIT, and CHFR genes were identified in between early and late passages in some hESC lines. CGI methylation levels of CASP8 significantly increased at late passage in CHA-36, CHA-40, and CHA-42 cell lines compared to those at early passage. The CGI methylation of the FHIT gene was higher at late passage than at early passage in CHA-15, CHA-31, CHA-32, and iPS (FS)-1 cell lines but decreased at the late passage in CHA-20 and H1 cell lines. Different CGI methylation patterns were detected for the CHFR gene only in iPS (FS)-1, and the level significantly increased at late passage. Thus, our findings show that CGI methylation patterns could be altered during prolonged ESC cultures and examining these epigenetic changes is important to assess the maintenance, differentiation, and clinical usage of stem cells.
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Industrially Compatible Transfusable iPSC-Derived RBCs: Progress, Challenges and Prospective Solutions. Int J Mol Sci 2021; 22:ijms22189808. [PMID: 34575977 PMCID: PMC8472628 DOI: 10.3390/ijms22189808] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 02/06/2023] Open
Abstract
Amidst the global shortfalls in blood supply, storage limitations of donor blood and the availability of potential blood substitutes for transfusion applications, society has pivoted towards in vitro generation of red blood cells (RBCs) as a means to solve these issues. Many conventional research studies over the past few decades have found success in differentiating hematopoietic stem and progenitor cells (HSPCs) from cord blood, adult bone marrow and peripheral blood sources. More recently, techniques that involve immortalization of erythroblast sources have also gained traction in tackling this problem. However, the RBCs generated from human induced pluripotent stem cells (hiPSCs) still remain as the most favorable solution due to many of its added advantages. In this review, we focus on the breakthroughs for high-density cultures of hiPSC-derived RBCs, and highlight the major challenges and prospective solutions throughout the whole process of erythropoiesis for hiPSC-derived RBCs. Furthermore, we elaborate on the recent advances and techniques used to achieve cost-effective, high-density cultures of GMP-compliant RBCs, and on their relevant novel applications after downstream processing and purification.
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Li J, Fraenkel E. Phenotyping Neurodegeneration in Human iPSCs. Annu Rev Biomed Data Sci 2021; 4:83-100. [PMID: 34465166 DOI: 10.1146/annurev-biodatasci-092820-025214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Induced pluripotent stem cell (iPSC) technology holds promise for modeling neurodegenerative diseases. Traditional approaches for disease modeling using animal and cellular models require knowledge of disease mutations. However, many patients with neurodegenerative diseases do not have a known genetic cause. iPSCs offer a way to generate patient-specific models and study pathways of dysfunction in an in vitro setting in order to understand the causes and subtypes of neurodegeneration. Furthermore, iPSC-based models can be used to search for candidate therapeutics using high-throughput screening. Here we review how iPSC-based models are currently being used to further our understanding of neurodegenerative diseases, as well as discuss their challenges and future directions.
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Affiliation(s)
- Jonathan Li
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Ernest Fraenkel
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Li H, Gao L, Du J, Ma T, Ye Z, Li Z. To Better Generate Organoids, What Can We Learn From Teratomas? Front Cell Dev Biol 2021; 9:700482. [PMID: 34336851 PMCID: PMC8324104 DOI: 10.3389/fcell.2021.700482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
The genomic profile of animal models is not completely matched with the genomic profile of humans, and 2D cultures do not represent the cellular heterogeneity and tissue architecture found in tissues of their origin. Derived from 3D culture systems, organoids establish a crucial bridge between 2D cell cultures and in vivo animal models. Organoids have wide and promising applications in developmental research, disease modeling, drug screening, precision therapy, and regenerative medicine. However, current organoids represent only single or partial components of a tissue, which lack blood vessels, native microenvironment, communication with near tissues, and a continuous dorsal-ventral axis within 3D culture systems. Although efforts have been made to solve these problems, unfortunately, there is no ideal method. Teratoma, which has been frequently studied in pathological conditions, was recently discovered as a new in vivo model for developmental studies. In contrast to organoids, teratomas have vascularized 3D structures and regions of complex tissue-like organization. Studies have demonstrated that teratomas can be used to mimic multilineage human development, enrich specific somatic progenitor/stem cells, and even generate brain organoids. These results provide unique opportunities to promote our understanding of the vascularization and maturation of organoids. In this review, we first summarize the basic characteristics, applications, and limitations of both organoids and teratomas and further discuss the possibility that in vivo teratoma systems can be used to promote the vascularization and maturation of organoids within an in vitro 3D culture system.
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Affiliation(s)
- Hongyu Li
- Department of Ophthalmology, The Chinese People's Liberation Army General Hospital, Beijing, China
| | - Lixiong Gao
- Department of Ophthalmology, The Chinese People's Liberation Army General Hospital, Beijing, China
| | - Jinlin Du
- Department of Ophthalmology, The Chinese People's Liberation Army General Hospital, Beijing, China
| | - Tianju Ma
- Department of Ophthalmology, The Chinese People's Liberation Army General Hospital, Beijing, China
| | - Zi Ye
- Department of Ophthalmology, The Chinese People's Liberation Army General Hospital, Beijing, China
| | - Zhaohui Li
- Department of Ophthalmology, The Chinese People's Liberation Army General Hospital, Beijing, China
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Wysoczynski M, Bolli R. A realistic appraisal of the use of embryonic stem cell-based therapies for cardiac repair. Eur Heart J 2021; 41:2397-2404. [PMID: 31778154 DOI: 10.1093/eurheartj/ehz787] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/06/2019] [Accepted: 10/25/2019] [Indexed: 12/22/2022] Open
Abstract
Despite the well-documented capacity of embryonic stem cells (ESCs) to differentiate into cardiomyocytes, transplantation of ESCs or ESC-derived cells is plagued by several formidable problems, including graft rejection, arrhythmias, and potential risk of teratomas. Life-long immunosuppression is a disease in itself. Transplantation of human ESC-derived cells in primates causes life-threatening arrhythmias, and the doses used to show efficacy are not clinically relevant. In contemporary clinical research, the margin of tolerance for such catastrophic effects as malignancies is zero, and although the probability of tumours can be reduced by ESC differentiation, it is unlikely to be completely eliminated, particularly when billions of cells are injected. Although ESCs and ESC-derived cells were touted as capable of long-term regeneration, these cells disappear rapidly after transplantation and there is no evidence of long-term engraftment, let alone regeneration. There is, however, mounting evidence that they act via paracrine mechanisms-just like adult cells. To date, no controlled clinical trial of ESC-derived cells in cardiovascular disease has been conducted or even initiated. In contrast, adult cells have been used in thousands of patients with heart disease, with no significant adverse effects and with results that were sufficiently encouraging to warrant Phase II and III trials. Furthermore, induced pluripotent stem cells offer pluripotency similar to ESCs without the need for lifelong immunosuppression. After two decades, the promise that ESC-derived cells would regenerate dead myocardium has not been fulfilled. The most reasonable interpretation of current data is that ESC-based therapies are not likely to have clinical application for heart disease.
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Affiliation(s)
- Marcin Wysoczynski
- Department of Medicine, Institute of Molecular Cardiology, University of Louisville, Louisville, KY, USA
| | - Roberto Bolli
- Department of Medicine, Institute of Molecular Cardiology, University of Louisville, Louisville, KY, USA
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36
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Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, Gilbert LA, Weissman JS. Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell 2021; 184:2503-2519.e17. [PMID: 33838111 PMCID: PMC8376083 DOI: 10.1016/j.cell.2021.03.025] [Citation(s) in RCA: 264] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 01/28/2021] [Accepted: 03/11/2021] [Indexed: 12/23/2022]
Abstract
A general approach for heritably altering gene expression has the potential to enable many discovery and therapeutic efforts. Here, we present CRISPRoff-a programmable epigenetic memory writer consisting of a single dead Cas9 fusion protein that establishes DNA methylation and repressive histone modifications. Transient CRISPRoff expression initiates highly specific DNA methylation and gene repression that is maintained through cell division and differentiation of stem cells to neurons. Pairing CRISPRoff with genome-wide screens and analysis of chromatin marks establishes rules for heritable gene silencing. We identify single guide RNAs (sgRNAs) capable of silencing the large majority of genes including those lacking canonical CpG islands (CGIs) and reveal a wide targeting window extending beyond annotated CGIs. The broad ability of CRISPRoff to initiate heritable gene silencing even outside of CGIs expands the canonical model of methylation-based silencing and enables diverse applications including genome-wide screens, multiplexed cell engineering, enhancer silencing, and mechanistic exploration of epigenetic inheritance.
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Affiliation(s)
- James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Jin Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | - Greg C Pommier
- Department of Urology, University of California, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - J Zachery Cogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA; Medical Scientist Training Program, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA
| | - Carmen Adriaens
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Gokul N Ramadoss
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Avi J Samelson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158
| | - Angela N Pogson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA
| | - James Y S Kim
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Amanda Chung
- Department of Urology, University of California, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA
| | | | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Bradley E Bernstein
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Volker Hovestadt
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215, USA
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Department of Urology, University of California, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA.
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge 02142, USA.
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Abstract
The ability to reprogram somatic cells into induced pluripotent stem cells (iPSCs) was developed in 2006 and represented a major breakthrough in stem cell research. A more recent milestone in biomedical research was reached in 2013 when the CRISPR/Cas9 system was used to edit the genome of mammalian cells. The coupling of both human (h)iPSCs and CRISPR/Cas9 technology offers great promise for cell therapy and regenerative medicine. However, several limitations including time and labor consumption, efficiency and efficacy of the system, and the potential off-targets effects induced by the Cas9 nuclease still need to be addressed. Here, we describe a detailed method for easily engineering genetic changes in hiPSCs, using a nucleofection-mediated protocol to deliver the CRISPR/Cas9 components into the cells, and discuss key points to be considered when designing your experiment. The clonal, genome-edited hiPSC line generated via our method can be directly used for downstream applications.
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Pichard L, Brondello JM, Becker F, Desprat R, De Ceuninck F, Pastoureau P, Noel D, Jorgensen C, Lemaitre JM. Establishment of a collection of human pluripotent stem cell lines (iPSC) from mesenchymal stem cells (MSC) from three healthy elderly donors. Stem Cell Res 2021; 53:102297. [PMID: 33780731 DOI: 10.1016/j.scr.2021.102297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 02/17/2021] [Accepted: 03/14/2021] [Indexed: 11/27/2022] Open
Abstract
The study of molecular mechanism driving osteoarticular diseases like osteoarthritis or osteoporosis is impaired by the low accessibility to mesenchymal stem cells (MSC) from healthy donors (HD) for differential multi-omics analysis. Advances in cell reprogramming have, however, provided both a new source of human cells for laboratory research and a strategy to erase epigenetic marks involved in cell identity and the development of diseases. To unravel the pathological signatures on the MSC at the origin of cellular drifts during the formation of bone and cartilage, we previously developed iPSC from MSC of osteoarthritis donors. Here we present the derivation of three iPSCs from healthy age matched donors to model the disease and further identify (epi)genomic signatures of the pathology.
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Affiliation(s)
- Lydiane Pichard
- SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France; Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France
| | - Jean-Marc Brondello
- Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France
| | - Fabienne Becker
- SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Romain Desprat
- SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Frédéric De Ceuninck
- Institut de Recherches Servier, Center for Therapeutic Innovation, Immuno-inflammatory Disease, Croissy sur Seine, France
| | - Philippe Pastoureau
- Institut de Recherches Servier, Center for Therapeutic Innovation, Immuno-inflammatory Disease, Croissy sur Seine, France
| | - Daniele Noel
- Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France
| | - Christian Jorgensen
- Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France
| | - Jean-Marc Lemaitre
- SAFE-iPSC Facility INGESTEM, Univ Montpellier, CHU de Montpellier, Montpellier, France; Institute for Regenerative Medicine and Biotherapy, INSERM UMR1183, Univ Montpellier, Montpellier, France.
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Comparative Metabolomic Profiling of Rat Embryonic and Induced Pluripotent Stem Cells. Stem Cell Rev Rep 2020; 16:1256-1265. [DOI: 10.1007/s12015-020-10052-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
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40
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"Betwixt Mine Eye and Heart a League Is Took": The Progress of Induced Pluripotent Stem-Cell-Based Models of Dystrophin-Associated Cardiomyopathy. Int J Mol Sci 2020; 21:ijms21196997. [PMID: 32977524 PMCID: PMC7582534 DOI: 10.3390/ijms21196997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022] Open
Abstract
The ultimate goal of precision disease modeling is to artificially recreate the disease of affected people in a highly controllable and adaptable external environment. This field has rapidly advanced which is evident from the application of patient-specific pluripotent stem-cell-derived precision therapies in numerous clinical trials aimed at a diverse set of diseases such as macular degeneration, heart disease, spinal cord injury, graft-versus-host disease, and muscular dystrophy. Despite the existence of semi-adequate treatments for tempering skeletal muscle degeneration in dystrophic patients, nonischemic cardiomyopathy remains one of the primary causes of death. Therefore, cardiovascular cells derived from muscular dystrophy patients' induced pluripotent stem cells are well suited to mimic dystrophin-associated cardiomyopathy and hold great promise for the development of future fully effective therapies. The purpose of this article is to convey the realities of employing precision disease models of dystrophin-associated cardiomyopathy. This is achieved by discussing, as suggested in the title echoing William Shakespeare's words, the settlements (or "leagues") made by researchers to manage the constraints ("betwixt mine eye and heart") distancing them from achieving a perfect precision disease model.
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Paniza T, Deshpande M, Wang N, O’Neil R, Zuccaro MV, Smith ME, Madireddy A, James D, Ecker J, Rosenwaks Z, Egli D, Gerhardt J. Pluripotent stem cells with low differentiation potential contain incompletely reprogrammed DNA replication. J Cell Biol 2020; 219:e201909163. [PMID: 32673399 PMCID: PMC7480103 DOI: 10.1083/jcb.201909163] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/26/2020] [Accepted: 05/13/2020] [Indexed: 12/20/2022] Open
Abstract
Reprogrammed pluripotent stem cells (PSCs) are valuable for research and potentially for cell replacement therapy. However, only a fraction of reprogrammed PSCs are developmentally competent. Genomic stability and accurate DNA synthesis are fundamental for cell development and critical for safety. We analyzed whether defects in DNA replication contribute to genomic instability and the diverse differentiation potentials of reprogrammed PSCs. Using a unique single-molecule approach, we visualized DNA replication in isogenic PSCs generated by different reprogramming approaches, either somatic cell nuclear transfer (NT-hESCs) or with defined factors (iPSCs). In PSCs with lower differentiation potential, DNA replication was incompletely reprogrammed, and genomic instability increased during replicative stress. Reprogramming of DNA replication did not correlate with DNA methylation. Instead, fewer replication origins and a higher frequency of DNA breaks in PSCs with incompletely reprogrammed DNA replication were found. Given the impact of error-free DNA synthesis on the genomic integrity and differentiation proficiency of PSCs, analyzing DNA replication may be a useful quality control tool.
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Affiliation(s)
- Theodore Paniza
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Madhura Deshpande
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Ning Wang
- Department of Pediatrics, Columbia University, New York, NY
| | - Ryan O’Neil
- Plant Molecular and Cellular Biology Laboratory, Salk Institute, La Jolla, CA
| | - Michael V. Zuccaro
- Department of Pediatrics, Columbia University, New York, NY
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | | | - Advaitha Madireddy
- Department of Pediatric Hematology/Oncology, Rutgers University, New Brunswick, NJ
| | - Daylon James
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY
| | - Joseph Ecker
- Plant Molecular and Cellular Biology Laboratory, Salk Institute, La Jolla, CA
| | - Zev Rosenwaks
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Dieter Egli
- Department of Pediatrics, Columbia University, New York, NY
| | - Jeannine Gerhardt
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY
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Gatinois V, Desprat R, Pichard L, Becker F, Goldenberg A, Balguerie X, Pellestor F, Lemaitre JM. iPSC reprogramming of fibroblasts from a patient with a Rothmund-Thomson syndrome RTS. Stem Cell Res 2020; 45:101807. [PMID: 32416578 DOI: 10.1016/j.scr.2020.101807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/21/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023] Open
Abstract
Rothmund-Thomson Syndrome (RTS) is a rare autosomal recessive disease that manifests several clinical features of accelerated aging. These findings include atrophic skin and pigment changes, alopecia, osteopenia, cataracts, and an increased incidence of cancer for patients. Mutations in RECQL4 gene are responsible for cases of RTS. RECQL4 belongs to the RECQ DNA helicase family which has been shown to participate in many aspects of DNA metabolism. To be able to study the cellular defects related to the pathology, we derived an induced pluripotent cell line from RTS patient fibroblasts, with the ability to re-differentiate into the three embryonic germ layers.
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Affiliation(s)
- Vincent Gatinois
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier France; Laboratory of Genome and Stem Cell Plasticity in Development and Aging, INSERM UMR1183, Montpellier, France; Laboratory of Cytogenetics, ChromoStem Facility, Univ Montpellier, CHU de Montpellier, Montpellier, France
| | - Romain Desprat
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier France; SAFE-iPSC Facility INGESTEM, CHU de Montpellier, Montpellier, France
| | - Lydiane Pichard
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier France; Laboratory of Genome and Stem Cell Plasticity in Development and Aging, INSERM UMR1183, Montpellier, France; SAFE-iPSC Facility INGESTEM, CHU de Montpellier, Montpellier, France
| | - Fabienne Becker
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier France; SAFE-iPSC Facility INGESTEM, CHU de Montpellier, Montpellier, France
| | - Alice Goldenberg
- Department of Medical genetics, CHU de Rouen, Univ Rouen, Inserm, Rouen U1079, France
| | | | - Franck Pellestor
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier France; Laboratory of Genome and Stem Cell Plasticity in Development and Aging, INSERM UMR1183, Montpellier, France; Laboratory of Cytogenetics, ChromoStem Facility, Univ Montpellier, CHU de Montpellier, Montpellier, France.
| | - Jean-Marc Lemaitre
- IRMB, Univ Montpellier, INSERM, CHU Montpellier, Montpellier France; SAFE-iPSC Facility INGESTEM, CHU de Montpellier, Montpellier, France.
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Generation of human pluripotent stem cell lines (iPSCs) from mesenchymal stem cells (MSCs) from three elderly patients with osteoarthritis. Stem Cell Res 2020; 44:101721. [DOI: 10.1016/j.scr.2020.101721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/17/2020] [Accepted: 01/25/2020] [Indexed: 11/20/2022] Open
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44
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Guttula PK, Gupta MK. Examining the co-expression, transcriptome clustering and variation using fuzzy cluster network of testicular stem cells and pluripotent stem cells compared with other cell types. Comput Biol Chem 2020; 85:107227. [PMID: 32044562 DOI: 10.1016/j.compbiolchem.2020.107227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 10/10/2019] [Accepted: 01/31/2020] [Indexed: 10/25/2022]
Abstract
Stem cells are crucial in the field of tissue regeneration and developmental biology. Embryonic stem cells (ESCs) which are pluripotent in nature are derived from the inner cell mass of blastocyst. The gene expression profiles of ESCs and Induced pluripotent stem cells (iPSCs) were compared to identify the differences. Spermatogonial stem cells (SSCs) are also known as Germ-line stem cells (GSCs) present in testis is having the capability of producing the sperm in their whole lifetime. Therefore can be reprogrammed into pluripotent cells called male germline pluripotent cells (gPSCs). It is very difficult to interpret the larger genomic data sets which are available in public databases without high computational facilities. In order to identify the similar groups We studied the co-expression, clustering of the transcriptome and variation of the transcriptome of the GSCs, gPSCs, ESCs and other cell types using fuzzy clustering using AutoSOME. The series matrix file with GSE ID GSE11274 was retrieved and subjected to the various normalization methods, corresponding rows and columns were clustered using p values, ensemble runs, and different running modes. Transcriptome analysis using the proposed approach intuitively and consistently characterized the variation in cell-cell significantly. Collectively, our results suggest that the GSCs and the ESCs displayed differential gene expression profiles, and the GSCs possessed the potential to acquire pluripotency based on the high expression of epigenetic factors and transcription factors. These data may provide novel insights into the reprogramming mechanism of GSCs.
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Affiliation(s)
- Praveen Kumar Guttula
- Gene Manipulation Laboratory, Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, 769008, India
| | - Mukesh Kumar Gupta
- Gene Manipulation Laboratory, Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, 769008, India.
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Thiagalingam S. Epigenetic memory in development and disease: Unraveling the mechanism. Biochim Biophys Acta Rev Cancer 2020; 1873:188349. [PMID: 31982403 DOI: 10.1016/j.bbcan.2020.188349] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 01/14/2023]
Abstract
Epigenetic memory is an essential process of life that governs the inheritance of predestined functional characteristics of normal cells and the newly acquired properties of cells affected by cancer and other diseases from parental to progeny cells. Unraveling the molecular basis of epigenetic memory dictated by protein and RNA factors in conjunction with epigenetic marks that are erased and re-established during embryogenesis/development during the formation of somatic, stem and disease cells will have far reaching implications to our understanding of embryogenesis/development and various diseases including cancer. While there has been enormous progress made, there are still gaps in knowledge which includes, the identity of unique epigenetic memory factors (EMFs) and epigenome coding enzymes/co-factors/scaffolding proteins involved in the assembly of defined "epigenetic memorysomes" and the epigenome marks that constitute collections of gene specific epigenetic memories corresponding to specific cell types and physiological conditions. A better understanding of the molecular basis for epigenetic memory will play a central role in improving diagnostics and prognostics of disease states and aid the development of targeted therapeutics of complex diseases.
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Affiliation(s)
- Sam Thiagalingam
- Department of Medicine (Biomedical Genetics Section and Cancer Center), Department of Pathology & Laboratory Medicine, Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, United States of America.
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46
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Simmnacher K, Lanfer J, Rizo T, Kaindl J, Winner B. Modeling Cell-Cell Interactions in Parkinson's Disease Using Human Stem Cell-Based Models. Front Cell Neurosci 2020; 13:571. [PMID: 32009903 PMCID: PMC6978672 DOI: 10.3389/fncel.2019.00571] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/10/2019] [Indexed: 12/27/2022] Open
Abstract
Parkinson’s disease (PD) is the most frequently occurring movement disorder, with an increasing incidence due to an aging population. For many years, the post-mortem brain was regarded as the gold standard for the analysis of the human pathology of this disease. However, modern stem cell technologies, including the analysis of patient-specific neurons and glial cells, have opened up new avenues for dissecting the pathologic mechanisms of PD. Most data on morphological changes, such as cell death or changes in neurite complexity, or functional deficits were acquired in 2D and few in 3D models. This review will examine the prerequisites for human disease modeling in PD, covering the generation of midbrain neurons, 3D organoid midbrain models, the selection of controls including genetically engineered lines, and the study of cell-cell interactions. We will present major disease phenotypes in human in vitro models of PD, focusing on those phenotypes that have been detected in genetic and sporadic PD models. An additional point covered in this review will be the use of induced pluripotent stem cell (iPSC)-derived technologies to model cell-cell interactions in PD.
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Affiliation(s)
- Katrin Simmnacher
- Department of Stem Cell Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jonas Lanfer
- Department of Stem Cell Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Tania Rizo
- Department of Stem Cell Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Johanna Kaindl
- Department of Stem Cell Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Beate Winner
- Department of Stem Cell Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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Chen K, Long Q, Xing G, Wang T, Wu Y, Li L, Qi J, Zhou Y, Ma B, Schöler HR, Nie J, Pei D, Liu X. Heterochromatin loosening by the Oct4 linker region facilitates Klf4 binding and iPSC reprogramming. EMBO J 2020; 39:e99165. [PMID: 31571238 PMCID: PMC6939195 DOI: 10.15252/embj.201899165] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 01/13/2023] Open
Abstract
The success of Yamanaka factor reprogramming of somatic cells into induced pluripotent stem cells suggests that some factor(s) must remodel the nuclei from a condensed state to a relaxed state. How factor-dependent chromatin opening occurs remains unclear. Using FRAP and ATAC-seq, we found that Oct4 acts as a pioneer factor that loosens heterochromatin and facilitates the binding of Klf4 and the expression of epithelial genes in early reprogramming, leading to enhanced mesenchymal-to-epithelial transition. A mutation in the Oct4 linker, L80A, which shows impaired interaction with the BAF complex component Brg1, is inactive in heterochromatin loosening. Oct4-L80A also blocks the binding of Klf4 and retards MET. Finally, vitamin C or Gadd45a could rescue the reprogramming deficiency of Oct4-L80A by enhancing chromatin opening and Klf4 binding. These studies reveal a cooperation between Oct4 and Klf4 at the chromatin level that facilitates MET at the cellular level and shed light into the research of multiple factors in cell fate determination.
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Affiliation(s)
- Keshi Chen
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Qi Long
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Guangsuo Xing
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
- Institute of Physical Science and Information TechnologyAnhui UniversityHefeiChina
| | - Tianyu Wang
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Yi Wu
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Linpeng Li
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Juntao Qi
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Yanshuang Zhou
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Bochao Ma
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Hans R Schöler
- Department for Cell and Developmental BiologyMax Planck Institute for Molecular BiomedicineMünsterGermany
| | - Jinfu Nie
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative BiologyJoint School of Life SciencesHefei Institute of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou Medical UniversityGuangzhouChina
- Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative MedicineInstitute for Stem Cell and RegenerationGuangzhou Institutes of Biomedicine and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesGuangzhouChina
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Blatchley MR, Gerecht S. Reconstructing the Vascular Developmental Milieu In Vitro. Trends Cell Biol 2020; 30:15-31. [DOI: 10.1016/j.tcb.2019.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 12/25/2022]
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iPSC line derived from a Bloom syndrome patient retains an increased disease-specific sister-chromatid exchange activity. Stem Cell Res 2019; 43:101696. [PMID: 31918214 DOI: 10.1016/j.scr.2019.101696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/16/2019] [Accepted: 12/24/2019] [Indexed: 11/22/2022] Open
Abstract
Bloom syndrome is characterized by severe pre- and postnatal growth deficiency, immune abnormalities, sensitivity to sunlight, insulin resistance, and a high risk for many cancers that occur at an early age. The diagnosis is established on characteristic clinical features and/or presence of biallelic pathogenic variants in the BLM gene. An increased frequency of sister-chromatid exchanges is also observed and can be useful to diagnose BS patients with weak or no clinical features. For the first time, we derived an induced pluripotent cell line from a Bloom syndrome patient retaining the specific sister-chromatid exchange feature as a unique tool to model the pathology.
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Paiva S, Joanne P, Migdal C, Soler EL, Hovhannisyan Y, Nicolas A, Agbulut O. Polyacrylamide Hydrogels with Rigidity-Independent Surface Chemistry Show Limited Long-Term Maintenance of Pluripotency of Human Induced Pluripotent Stem Cells on Soft Substrates. ACS Biomater Sci Eng 2019; 6:340-351. [DOI: 10.1021/acsbiomaterials.9b01189] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Solenne Paiva
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005 Paris, France
| | - Pierre Joanne
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005 Paris, France
| | - Camille Migdal
- Univ. Grenoble Alpes, CNRS, LTM, 38000 Grenoble, France
- Univ. Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | | | - Yeranuhi Hovhannisyan
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005 Paris, France
| | - Alice Nicolas
- Univ. Grenoble Alpes, CNRS, LTM, 38000 Grenoble, France
| | - Onnik Agbulut
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and Ageing, 75005 Paris, France
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