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Wang L, Jin G, Zhou Q, Liu Y, Zhao X, Li Z, Yin N, Peng M. Induction of immortal-like and functional CAR T cells by defined factors. J Exp Med 2024; 221:e20232368. [PMID: 38530240 DOI: 10.1084/jem.20232368] [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: 12/22/2023] [Revised: 01/10/2024] [Accepted: 03/04/2024] [Indexed: 03/27/2024] Open
Abstract
Long-term antitumor efficacy of chimeric antigen receptor (CAR) T cells depends on their functional persistence in vivo. T cells with stem-like properties show better persistence, but factors conferring bona fide stemness to T cells remain to be determined. Here, we demonstrate the induction of CAR T cells into an immortal-like and functional state, termed TIF. The induction of CARTIF cells depends on the repression of two factors, BCOR and ZC3H12A, and requires antigen or CAR tonic signaling. Reprogrammed CARTIF cells possess almost infinite stemness, similar to induced pluripotent stem cells while retaining the functionality of mature T cells, resulting in superior antitumor effects. Following the elimination of target cells, CARTIF cells enter a metabolically dormant state, persisting in vivo with a saturable niche and providing memory protection. TIF represents a novel state of T cells with unprecedented stemness, which confers long-term functional persistence of CAR T cells in vivo and holds broad potential in T cell therapies.
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Affiliation(s)
- Lixia Wang
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
| | - Gang Jin
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
| | - Qiuping Zhou
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
| | - Yanyan Liu
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
| | - Xiaocui Zhao
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
| | - Zhuoyang Li
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
| | - Na Yin
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
| | - Min Peng
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory for Immunological Research on Chronic Diseases, School of Medicine, Institute for Immunology, Tsinghua University, Beijing, China
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine , Taiyuan, China
- Tsinghua-Peking Center for Life Sciences , Beijing, China
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Pazzin DB, Previato TTR, Budelon Gonçalves JI, Zanirati G, Xavier FAC, da Costa JC, Marinowic DR. Induced Pluripotent Stem Cells and Organoids in Advancing Neuropathology Research and Therapies. Cells 2024; 13:745. [PMID: 38727281 PMCID: PMC11083827 DOI: 10.3390/cells13090745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 05/13/2024] Open
Abstract
This review delves into the groundbreaking impact of induced pluripotent stem cells (iPSCs) and three-dimensional organoid models in propelling forward neuropathology research. With a focus on neurodegenerative diseases, neuromotor disorders, and related conditions, iPSCs provide a platform for personalized disease modeling, holding significant potential for regenerative therapy and drug discovery. The adaptability of iPSCs, along with associated methodologies, enables the generation of various types of neural cell differentiations and their integration into three-dimensional organoid models, effectively replicating complex tissue structures in vitro. Key advancements in organoid and iPSC generation protocols, alongside the careful selection of donor cell types, are emphasized as critical steps in harnessing these technologies to mitigate tumorigenic risks and other hurdles. Encouragingly, iPSCs show promising outcomes in regenerative therapies, as evidenced by their successful application in animal models.
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Affiliation(s)
- Douglas Bottega Pazzin
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (D.B.P.); (T.T.R.P.); (J.I.B.G.); (G.Z.); (F.A.C.X.); (J.C.d.C.)
- Graduate Program in Pediatrics and Child Health, School of Medicine, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90619-900, Brazil
| | - Thales Thor Ramos Previato
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (D.B.P.); (T.T.R.P.); (J.I.B.G.); (G.Z.); (F.A.C.X.); (J.C.d.C.)
- Graduate Program in Biomedical Gerontology, School of Medicine, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90619-900, Brazil
| | - João Ismael Budelon Gonçalves
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (D.B.P.); (T.T.R.P.); (J.I.B.G.); (G.Z.); (F.A.C.X.); (J.C.d.C.)
| | - Gabriele Zanirati
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (D.B.P.); (T.T.R.P.); (J.I.B.G.); (G.Z.); (F.A.C.X.); (J.C.d.C.)
| | - Fernando Antonio Costa Xavier
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (D.B.P.); (T.T.R.P.); (J.I.B.G.); (G.Z.); (F.A.C.X.); (J.C.d.C.)
| | - Jaderson Costa da Costa
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (D.B.P.); (T.T.R.P.); (J.I.B.G.); (G.Z.); (F.A.C.X.); (J.C.d.C.)
| | - Daniel Rodrigo Marinowic
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (D.B.P.); (T.T.R.P.); (J.I.B.G.); (G.Z.); (F.A.C.X.); (J.C.d.C.)
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3
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James C, Trevisan-Herraz M, Juan D, Rico D. Evolutionary analysis of gene ages across TADs associates chromatin topology with whole-genome duplications. Cell Rep 2024; 43:113895. [PMID: 38517894 DOI: 10.1016/j.celrep.2024.113895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/03/2023] [Accepted: 02/16/2024] [Indexed: 03/24/2024] Open
Abstract
Topologically associated domains (TADs) are interaction subnetworks of chromosomal regions in 3D genomes. TAD boundaries frequently coincide with genome breaks while boundary deletion is under negative selection, suggesting that TADs may facilitate genome rearrangements and evolution. We show that genes co-localize by evolutionary age in humans and mice, resulting in TADs having different proportions of younger and older genes. We observe a major transition in the age co-localization patterns between the genes born during vertebrate whole-genome duplications (WGDs) or before and those born afterward. We also find that genes recently duplicated in primates and rodents are more frequently essential when they are located in old-enriched TADs and interact with genes that last duplicated during the WGD. Therefore, the evolutionary relevance of recent genes may increase when located in TADs with established regulatory networks. Our data suggest that TADs could play a role in organizing ancestral functions and evolutionary novelty.
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Affiliation(s)
- Caelinn James
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Scotland's Rural College (SRUC), The Roslin Institute Building, Easter Bush, Midlothian, UK
| | - Marco Trevisan-Herraz
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - David Juan
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain; Systems Biology Department, Spanish National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Daniel Rico
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain.
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Wu Y, Wang C, Fan X, Ma Y, Liu Z, Ye X, Shen C, Wu C. The impact of induced pluripotent stem cells in animal conservation. Vet Res Commun 2024; 48:649-663. [PMID: 38228922 DOI: 10.1007/s11259-024-10294-3] [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: 11/02/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024]
Abstract
It is widely acknowledged that we are currently facing a critical tipping point with regards to global extinction, with human activities driving us perilously close to the brink of a devastating sixth mass extinction. As a promising option for safeguarding endangered species, induced pluripotent stem cells (iPSCs) hold great potential to aid in the preservation of threatened animal populations. For endangered species, such as the northern white rhinoceros (Ceratotherium simum cottoni), supply of embryos is often limited. After the death of the last male in 2019, only two females remained in the world. IPSC technology offers novel approaches and techniques for obtaining pluripotent stem cells (PSCs) from rare and endangered animal species. Successful generation of iPSCs circumvents several bottlenecks that impede the development of PSCs, including the challenges associated with establishing embryonic stem cells, limited embryo sources and immune rejection following embryo transfer. To provide more opportunities and room for growth in our work on animal welfare, in this paper we will focus on the progress made with iPSC lines derived from endangered and extinct species, exploring their potential applications and limitations in animal welfare research.
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Affiliation(s)
- Yurou Wu
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Chengwei Wang
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Xinyun Fan
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Yuxiao Ma
- Department of Biology, New York University, New York, NY, USA
| | - Zibo Liu
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Xun Ye
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Chongyang Shen
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China.
| | - Chunjie Wu
- Innovative Institute of Chinese Medicine and Pharmacy/Academy for Interdiscipline, Chengdu Univesity of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China.
- Sichuan Engineering Research Center for Endangered Medicinal Animals, Chengdu, China.
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5
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Panos LD, Bargiotas P, Arnold M, Hadjigeorgiou G, Panos GD. Revolutionizing Stroke Recovery: Unveiling the Promise of Stem Cell Therapy. Drug Des Devel Ther 2024; 18:991-1006. [PMID: 38567255 PMCID: PMC10986404 DOI: 10.2147/dddt.s460998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
Stem cells, renowned for their unique regenerative capabilities, present significant hope in treating stroke, a major cause of disability globally. This review offers a detailed analysis of stem cell applications in stroke (ischemic and hemorrhagic) recovery. It examines therapies based on autologous (patient-derived), allogeneic (donor-derived), and Granulocyte-Colony Stimulating Factor (G-CSF) based stem cells, focusing on cell types such as Mesenchymal Stem/Stromal Cells (MSCs), Bone Marrow Mononuclear Stem Cells (BMMSCs), and Neural Stem/Progenitor Cells (NSCs). The paper compiles clinical trial data to evaluate their effectiveness and safety and addresses the ethical concerns of these innovative treatments. By explaining the mechanisms of stem cell-induced neurological repair, this review underscores stem cells' potential in revolutionizing stroke rehabilitation and suggests avenues for future research.
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Affiliation(s)
- Leonidas D Panos
- Department of Neurology, Bern University Hospital Inselspital, Bern, Switzerland
- Department of Neurology, School of Medicine, University of Cyprus, Nicosia, Cyprus
| | - Panagiotis Bargiotas
- Department of Neurology, School of Medicine, University of Cyprus, Nicosia, Cyprus
| | - Marcel Arnold
- Department of Neurology, Bern University Hospital Inselspital, Bern, Switzerland
| | | | - Georgios D Panos
- Department of Ophthalmology, Queen’s Medical Centre, Nottingham University Hospitals (NUH), Nottingham, UK
- Division of Ophthalmology and Visual Sciences, School of Medicine, University of Nottingham, Nottingham, UK
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6
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Kelly RDW, Stengel KR, Chandru A, Johnson LC, Hiebert SW, Cowley SM. Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci. Genome Res 2024; 34:34-46. [PMID: 38290976 PMCID: PMC10903948 DOI: 10.1101/gr.278050.123] [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: 04/28/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024]
Abstract
Histone acetylation is a dynamic modification regulated by the opposing actions of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Deacetylation of histone tails results in chromatin tightening, and therefore, HDACs are generally regarded as transcriptional repressors. Counterintuitively, simultaneous deletion of Hdac1 and Hdac2 in embryonic stem cells (ESCs) reduces expression of the pluripotency-associated transcription factors Pou5f1, Sox2, and Nanog (PSN). By shaping global histone acetylation patterns, HDACs indirectly regulate the activity of acetyl-lysine readers, such as the transcriptional activator BRD4. Here, we use inhibitors of HDACs and BRD4 (LBH589 and JQ1, respectively) in combination with precision nuclear run-on and sequencing (PRO-seq) to examine their roles in defining the ESC transcriptome. Both LBH589 and JQ1 cause a marked reduction in the pluripotent gene network. However, although JQ1 treatment induces widespread transcriptional pausing, HDAC inhibition causes a reduction in both paused and elongating polymerase, suggesting an overall reduction in polymerase recruitment. Using enhancer RNA (eRNA) expression to measure enhancer activity, we find that LBH589-sensitive eRNAs are preferentially associated with superenhancers and PSN binding sites. These findings suggest that HDAC activity is required to maintain pluripotency by regulating the PSN enhancer network via the recruitment of RNA polymerase II.
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Affiliation(s)
- Richard D W Kelly
- Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Kristy R Stengel
- Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, Bronx, New York 10461, USA
| | - Aditya Chandru
- Cancer Research UK Beatson Institute, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Lyndsey C Johnson
- Locate Bio Limited, MediCity, Beeston, Nottingham NG90 6BH, United Kingdom
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Shaun M Cowley
- Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester LE1 9HN, United Kingdom;
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Pérez Millán MI, Cheung LYM, Mercogliano F, Camilletti MA, Chirino Felker GT, Moro LN, Miriuka S, Brinkmeier ML, Camper SA. Pituitary stem cells: past, present and future perspectives. Nat Rev Endocrinol 2024; 20:77-92. [PMID: 38102391 PMCID: PMC10964491 DOI: 10.1038/s41574-023-00922-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
Pituitary cells that express the transcription factor SOX2 are stem cells because they can self-renew and differentiate into multiple pituitary hormone-producing cell types as organoids. Wounding and physiological challenges can activate pituitary stem cells, but cell numbers are not fully restored, and the ability to mobilize stem cells decreases with increasing age. The basis of these limitations is still unknown. The regulation of stem cell quiescence and activation involves many different signalling pathways, including those mediated by WNT, Hippo and several cytokines; more research is needed to understand the interactions between these pathways. Pituitary organoids can be formed from human or mouse embryonic stem cells, or from human induced pluripotent stem cells. Human pituitary organoid transplantation is sufficient to induce corticosterone release in hypophysectomized mice, raising the possibility of therapeutic applications. Today, pituitary organoids have the potential to assess the role of individual genes and genetic variants on hormone production ex vivo, providing an important tool for the advancement of exciting frontiers in pituitary stem cell biology and pituitary organogenesis. In this article, we provide an overview of notable discoveries in pituitary stem cell function and highlight important areas for future research.
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Affiliation(s)
- María Inés Pérez Millán
- Institute of Bioscience, Biotechnology and Translational Biology (IB3-UBA), University of Buenos Aires, Buenos Aires, Argentina
| | - Leonard Y M Cheung
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Physiology and Biophysics, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Florencia Mercogliano
- Institute of Bioscience, Biotechnology and Translational Biology (IB3-UBA), University of Buenos Aires, Buenos Aires, Argentina
| | - Maria Andrea Camilletti
- Institute of Bioscience, Biotechnology and Translational Biology (IB3-UBA), University of Buenos Aires, Buenos Aires, Argentina
| | - Gonzalo T Chirino Felker
- Laboratory of Applied Research of Neurosciences (LIAN-CONICET), FLENI Sede Escobar, Buenos Aires, Argentina
| | - Lucia N Moro
- Laboratory of Applied Research of Neurosciences (LIAN-CONICET), FLENI Sede Escobar, Buenos Aires, Argentina
| | - Santiago Miriuka
- Laboratory of Applied Research of Neurosciences (LIAN-CONICET), FLENI Sede Escobar, Buenos Aires, Argentina
| | - Michelle L Brinkmeier
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sally A Camper
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA.
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8
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Gao Y, Han W, Dong R, Wei S, Chen L, Gu Z, Liu Y, Guo W, Yan F. Efficient Reprogramming of Mouse Embryonic Stem Cells into Trophoblast Stem-like Cells via Lats Kinase Inhibition. BIOLOGY 2024; 13:71. [PMID: 38392290 PMCID: PMC10886645 DOI: 10.3390/biology13020071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024]
Abstract
Mouse zygotes undergo multiple rounds of cell division, resulting in the formation of preimplantation blastocysts comprising three lineages: trophectoderm (TE), epiblast (EPI), and primitive endoderm (PrE). Cell fate determination plays a crucial role in establishing a healthy pregnancy. The initial separation of lineages gives rise to TE and inner cell mass (ICM), from which trophoblast stem cells (TSC) and embryonic stem cells (ESC) can be derived in vitro. Studying lineage differentiation is greatly facilitated by the clear functional distinction between TSC and ESC. However, transitioning between these two types of cells naturally poses challenges. In this study, we demonstrate that inhibiting LATS kinase promotes the conversion of ICM to TE and also effectively reprograms ESC into stable, self-renewing TS-like cells (TSLC). Compared to TSC, TSLC exhibits similar molecular properties, including the high expression of marker genes such as Cdx2, Eomes, and Tfap2c, as well as hypomethylation of their promoters. Importantly, TSLC not only displays the ability to differentiate into mature trophoblast cells in vitro but also participates in placenta formation in vivo. These findings highlight the efficient reprogramming of ESCs into TSLCs using a small molecular inducer, which provides a new reference for understanding the regulatory network between ESCs and TSCs.
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Affiliation(s)
- Yake Gao
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
- Reproductive Medicine Center, Wuhan Women's and Children's Medical Care Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wenrui Han
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Rui Dong
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Shu Wei
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Lu Chen
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Zhaolei Gu
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Yiming Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Wei Guo
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Fang Yan
- State Key Laboratory of Conservation and Utilization of Bio-Resources, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China
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Santa Cruz-Pavlovich FJ, Bolaños-Chang AJ, Del Rio-Murillo XI, Aranda-Preciado GA, Razura-Ruiz EM, Santos A, Navarro-Partida J. Beyond Vision: An Overview of Regenerative Medicine and Its Current Applications in Ophthalmological Care. Cells 2024; 13:179. [PMID: 38247870 PMCID: PMC10814238 DOI: 10.3390/cells13020179] [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: 12/05/2023] [Revised: 12/23/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Regenerative medicine (RM) has emerged as a promising and revolutionary solution to address a range of unmet needs in healthcare, including ophthalmology. Moreover, RM takes advantage of the body's innate ability to repair and replace pathologically affected tissues. On the other hand, despite its immense promise, RM faces challenges such as ethical concerns, host-related immune responses, and the need for additional scientific validation, among others. The primary aim of this review is to present a high-level overview of current strategies in the domain of RM (cell therapy, exosomes, scaffolds, in vivo reprogramming, organoids, and interspecies chimerism), centering around the field of ophthalmology. A search conducted on clinicaltrials.gov unveiled a total of at least 209 interventional trials related to RM within the ophthalmological field. Among these trials, there were numerous early-phase studies, including phase I, I/II, II, II/III, and III trials. Many of these studies demonstrate potential in addressing previously challenging and degenerative eye conditions, spanning from posterior segment pathologies like Age-related Macular Degeneration and Retinitis Pigmentosa to anterior structure diseases such as Dry Eye Disease and Limbal Stem Cell Deficiency. Notably, these therapeutic approaches offer tailored solutions specific to the underlying causes of each pathology, thus allowing for the hopeful possibility of bringing forth a treatment for ocular diseases that previously seemed incurable and significantly enhancing patients' quality of life. As advancements in research and technology continue to unfold, future objectives should focus on ensuring the safety and prolonged viability of transplanted cells, devising efficient delivery techniques, etc.
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Affiliation(s)
- Francisco J. Santa Cruz-Pavlovich
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64849, Mexico; (F.J.S.C.-P.); (A.J.B.-C.); (X.I.D.R.-M.); (E.M.R.-R.); (A.S.)
| | - Andres J. Bolaños-Chang
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64849, Mexico; (F.J.S.C.-P.); (A.J.B.-C.); (X.I.D.R.-M.); (E.M.R.-R.); (A.S.)
| | - Ximena I. Del Rio-Murillo
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64849, Mexico; (F.J.S.C.-P.); (A.J.B.-C.); (X.I.D.R.-M.); (E.M.R.-R.); (A.S.)
| | | | - Esmeralda M. Razura-Ruiz
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64849, Mexico; (F.J.S.C.-P.); (A.J.B.-C.); (X.I.D.R.-M.); (E.M.R.-R.); (A.S.)
| | - Arturo Santos
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64849, Mexico; (F.J.S.C.-P.); (A.J.B.-C.); (X.I.D.R.-M.); (E.M.R.-R.); (A.S.)
| | - Jose Navarro-Partida
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64849, Mexico; (F.J.S.C.-P.); (A.J.B.-C.); (X.I.D.R.-M.); (E.M.R.-R.); (A.S.)
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10
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Chowdhury MA, Zhang JJ, Rizk R, Chen WCW. Stem cell therapy for heart failure in the clinics: new perspectives in the era of precision medicine and artificial intelligence. Front Physiol 2024; 14:1344885. [PMID: 38264333 PMCID: PMC10803627 DOI: 10.3389/fphys.2023.1344885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 12/26/2023] [Indexed: 01/25/2024] Open
Abstract
Stem/progenitor cells have been widely evaluated as a promising therapeutic option for heart failure (HF). Numerous clinical trials with stem/progenitor cell-based therapy (SCT) for HF have demonstrated encouraging results, but not without limitations or discrepancies. Recent technological advancements in multiomics, bioinformatics, precision medicine, artificial intelligence (AI), and machine learning (ML) provide new approaches and insights for stem cell research and therapeutic development. Integration of these new technologies into stem/progenitor cell therapy for HF may help address: 1) the technical challenges to obtain reliable and high-quality therapeutic precursor cells, 2) the discrepancies between preclinical and clinical studies, and 3) the personalized selection of optimal therapeutic cell types/populations for individual patients in the context of precision medicine. This review summarizes the current status of SCT for HF in clinics and provides new perspectives on the development of computation-aided SCT in the era of precision medicine and AI/ML.
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Affiliation(s)
- Mohammed A. Chowdhury
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, United States
- Department of Public Health and Health Sciences, Health Sciences Ph.D. Program, School of Health Sciences, University of South Dakota, Vermillion, SD, United States
- Department of Cardiology, North Central Heart, Avera Heart Hospital, Sioux Falls, SD, United States
| | - Jing J. Zhang
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, United States
| | - Rodrigue Rizk
- Department of Computer Science, University of South Dakota, Vermillion, SD, United States
| | - William C. W. Chen
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, United States
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11
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Todorova PK, Jackson BT, Garg V, Paras KI, Brunner JS, Bridgeman AE, Chen Y, Baksh SC, Yan J, Hadjantonakis AK, Finley LWS. Amino acid intake strategies define pluripotent cell states. Nat Metab 2024; 6:127-140. [PMID: 38172382 PMCID: PMC10842923 DOI: 10.1038/s42255-023-00940-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 11/07/2023] [Indexed: 01/05/2024]
Abstract
Mammalian preimplantation development is associated with marked metabolic robustness, and embryos can develop under a wide variety of nutrient conditions, including even the complete absence of soluble amino acids. Here we show that mouse embryonic stem cells (ESCs) capture the unique metabolic state of preimplantation embryos and proliferate in the absence of several essential amino acids. Amino acid independence is enabled by constitutive uptake of exogenous protein through macropinocytosis, alongside a robust lysosomal digestive system. Following transition to more committed states, ESCs reduce digestion of extracellular protein and instead become reliant on exogenous amino acids. Accordingly, amino acid withdrawal selects for ESCs that mimic the preimplantation epiblast. More broadly, we find that all lineages of preimplantation blastocysts exhibit constitutive macropinocytic protein uptake and digestion. Taken together, these results highlight exogenous protein uptake and digestion as an intrinsic feature of preimplantation development and provide insight into the catabolic strategies that enable embryos to sustain viability before implantation.
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Affiliation(s)
- Pavlina K Todorova
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin T Jackson
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, New York, NY, USA
| | - Vidur Garg
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katrina I Paras
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Julia S Brunner
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna E Bridgeman
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanyang Chen
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sanjeethan C Baksh
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jielin Yan
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, New York, NY, USA
| | | | - Lydia W S Finley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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12
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Dhanjal DS, Singh R, Sharma V, Nepovimova E, Adam V, Kuca K, Chopra C. Advances in Genetic Reprogramming: Prospects from Developmental Biology to Regenerative Medicine. Curr Med Chem 2024; 31:1646-1690. [PMID: 37138422 DOI: 10.2174/0929867330666230503144619] [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: 11/12/2022] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 05/05/2023]
Abstract
The foundations of cell reprogramming were laid by Yamanaka and co-workers, who showed that somatic cells can be reprogrammed into pluripotent cells (induced pluripotency). Since this discovery, the field of regenerative medicine has seen advancements. For example, because they can differentiate into multiple cell types, pluripotent stem cells are considered vital components in regenerative medicine aimed at the functional restoration of damaged tissue. Despite years of research, both replacement and restoration of failed organs/ tissues have remained elusive scientific feats. However, with the inception of cell engineering and nuclear reprogramming, useful solutions have been identified to counter the need for compatible and sustainable organs. By combining the science underlying genetic engineering and nuclear reprogramming with regenerative medicine, scientists have engineered cells to make gene and stem cell therapies applicable and effective. These approaches have enabled the targeting of various pathways to reprogramme cells, i.e., make them behave in beneficial ways in a patient-specific manner. Technological advancements have clearly supported the concept and realization of regenerative medicine. Genetic engineering is used for tissue engineering and nuclear reprogramming and has led to advances in regenerative medicine. Targeted therapies and replacement of traumatized , damaged, or aged organs can be realized through genetic engineering. Furthermore, the success of these therapies has been validated through thousands of clinical trials. Scientists are currently evaluating induced tissue-specific stem cells (iTSCs), which may lead to tumour-free applications of pluripotency induction. In this review, we present state-of-the-art genetic engineering that has been used in regenerative medicine. We also focus on ways that genetic engineering and nuclear reprogramming have transformed regenerative medicine and have become unique therapeutic niches.
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Affiliation(s)
- Daljeet Singh Dhanjal
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Varun Sharma
- Head of Bioinformatic Division, NMC Genetics India Pvt. Ltd., Gurugram, India
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, 50003, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, Brno, CZ 613 00, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, Brno, CZ-612 00, Czech Republic
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, 50003, Czech Republic
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, 50005, Czech Republic
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
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13
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Kretschmer M, Fischer V, Gapp K. When Dad's Stress Gets under Kid's Skin-Impacts of Stress on Germline Cargo and Embryonic Development. Biomolecules 2023; 13:1750. [PMID: 38136621 PMCID: PMC10742275 DOI: 10.3390/biom13121750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Multiple lines of evidence suggest that paternal psychological stress contributes to an increased prevalence of neuropsychiatric and metabolic diseases in the progeny. While altered paternal care certainly plays a role in such transmitted disease risk, molecular factors in the germline might additionally be at play in humans. This is supported by findings on changes to the molecular make up of germ cells and suggests an epigenetic component in transmission. Several rodent studies demonstrate the correlation between paternal stress induced changes in epigenetic modifications and offspring phenotypic alterations, yet some intriguing cases also start to show mechanistic links in between sperm and the early embryo. In this review, we summarise efforts to understand the mechanism of intergenerational transmission from sperm to the early embryo. In particular, we highlight how stress alters epigenetic modifications in sperm and discuss the potential for these modifications to propagate modified molecular trajectories in the early embryo to give rise to aberrant phenotypes in adult offspring.
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Affiliation(s)
- Miriam Kretschmer
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Vincent Fischer
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Katharina Gapp
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
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14
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Wang X, Song C, Ye Y, Gu Y, Li X, Chen P, Leng D, Xiao J, Wu H, Xie S, Liu W, Zhao Q, Chen D, Chen X, Wu Q, Chen G, Zhang W. BRD9-mediated control of the TGF-β/Activin/Nodal pathway regulates self-renewal and differentiation of human embryonic stem cells and progression of cancer cells. Nucleic Acids Res 2023; 51:11634-11651. [PMID: 37870468 PMCID: PMC10681724 DOI: 10.1093/nar/gkad907] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
Bromodomain-containing protein 9 (BRD9) is a specific subunit of the non-canonical SWI/SNF (ncBAF) chromatin-remodeling complex, whose function in human embryonic stem cells (hESCs) remains unclear. Here, we demonstrate that impaired BRD9 function reduces the self-renewal capacity of hESCs and alters their differentiation potential. Specifically, BRD9 depletion inhibits meso-endoderm differentiation while promoting neural ectoderm differentiation. Notably, supplementation of NODAL, TGF-β, Activin A or WNT3A rescues the differentiation defects caused by BRD9 loss. Mechanistically, BRD9 forms a complex with BRD4, SMAD2/3, β-CATENIN and P300, which regulates the expression of pluripotency genes and the activity of TGF-β/Nodal/Activin and Wnt signaling pathways. This is achieved by regulating the deposition of H3K27ac on associated genes, thus maintaining and directing hESC differentiation. BRD9-mediated regulation of the TGF-β/Activin/Nodal pathway is also demonstrated in the development of pancreatic and breast cancer cells. In summary, our study highlights the crucial role of BRD9 in the regulation of hESC self-renewal and differentiation, as well as its participation in the progression of pancreatic and breast cancers.
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Affiliation(s)
- Xuepeng Wang
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR 999078, China
| | - Chengcheng Song
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Ying Ye
- Medical College of Soochow University, Suzhou 215123, China
| | - Yashi Gu
- Zhejiang University–University of Edinburgh Institute (ZJE), Zhejiang University School of Medicine, Zhejiang University, Haining 314400, China
| | - Xuemei Li
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Peixin Chen
- Medical College of Soochow University, Suzhou 215123, China
| | - Dongliang Leng
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Jing Xiao
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Hao Wu
- Medical College of Soochow University, Suzhou 215123, China
| | - Sisi Xie
- Zhejiang University–University of Edinburgh Institute (ZJE), Zhejiang University School of Medicine, Zhejiang University, Haining 314400, China
| | - Weiwei Liu
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Qi Zhao
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Di Chen
- Zhejiang University–University of Edinburgh Institute (ZJE), Zhejiang University School of Medicine, Zhejiang University, Haining 314400, China
| | - Xi Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen 518000, China
| | - Qiang Wu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR 999078, China
- The Precision Regenerative Medicine Centre, Macau University of Science and Technology, Taipa, Macao SAR 999078, China
| | - Guokai Chen
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Wensheng Zhang
- Medical College of Soochow University, Suzhou 215123, China
- Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University, Yantai 264003, China
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049, China
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15
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Cao J, Li W, Li J, Mazid MA, Li C, Jiang Y, Jia W, Wu L, Liao Z, Sun S, Song W, Fu J, Wang Y, Lu Y, Xu Y, Nie Y, Bian X, Gao C, Zhang X, Zhang L, Shang S, Li Y, Fu L, Liu H, Lai J, Wang Y, Yuan Y, Jin X, Li Y, Liu C, Lai Y, Shi X, Maxwell PH, Xu X, Liu L, Poo M, Wang X, Sun Q, Esteban MA, Liu Z. Live birth of chimeric monkey with high contribution from embryonic stem cells. Cell 2023; 186:4996-5014.e24. [PMID: 37949056 DOI: 10.1016/j.cell.2023.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 07/18/2023] [Accepted: 10/03/2023] [Indexed: 11/12/2023]
Abstract
A formal demonstration that mammalian pluripotent stem cells possess preimplantation embryonic cell-like (naive) pluripotency is the generation of chimeric animals through early embryo complementation with homologous cells. Whereas such naive pluripotency has been well demonstrated in rodents, poor chimerism has been achieved in other species including non-human primates due to the inability of the donor cells to match the developmental state of the host embryos. Here, we have systematically tested various culture conditions for establishing monkey naive embryonic stem cells and optimized the procedures for chimeric embryo culture. This approach generated an aborted fetus and a live chimeric monkey with high donor cell contribution. A stringent characterization pipeline demonstrated that donor cells efficiently (up to 90%) incorporated into various tissues (including the gonads and placenta) of the chimeric monkeys. Our results have major implications for the study of primate naive pluripotency and genetic engineering of non-human primates.
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Affiliation(s)
- Jing Cao
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wenjuan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jie Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Md Abdul Mazid
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Chunyang Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu Jiang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Wenqi Jia
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Wu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Zhaodi Liao
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiyu Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weixiang Song
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiqiang Fu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong Lu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuting Xu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanhong Nie
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinyan Bian
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Changshan Gao
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaotong Zhang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Liansheng Zhang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shenshen Shang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yunpan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lixin Fu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Hao Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Junjian Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yang Wang
- BGI-Research, Hangzhou 310030, China
| | - Yue Yuan
- BGI-Research, Hangzhou 310030, China
| | - Xin Jin
- BGI-Research, Shenzhen 518083, China; School of Medicine, South China University of Technology, Guangzhou, China
| | - Yan Li
- BGI-Research, Shenzhen 518083, China
| | | | - Yiwei Lai
- BGI-Research, Hangzhou 310030, China
| | | | - Patrick H Maxwell
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 0ST, United Kingdom
| | - Xun Xu
- BGI-Research, Hangzhou 310030, China; BGI-Research, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, China
| | | | - Muming Poo
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Qiang Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Miguel A Esteban
- BGI-Research, Hangzhou 310030, China; Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China.
| | - Zhen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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16
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Seo BJ, Na SB, Choi J, Ahn B, Habib O, Park C, Hong K, Do JT. Metabolic and cell cycle shift induced by the deletion of Dnm1l attenuates the dissolution of pluripotency in mouse embryonic stem cells. Cell Mol Life Sci 2023; 80:302. [PMID: 37747543 PMCID: PMC11073397 DOI: 10.1007/s00018-023-04962-x] [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: 04/20/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 09/26/2023]
Abstract
Mitochondria are versatile organelles that continuously change their morphology via fission and fusion. However, the detailed functions of mitochondrial dynamics-related genes in pluripotent stem cells remain largely unclear. Here, we aimed to determine the effects on energy metabolism and differentiation ability of mouse embryonic stem cells (ESCs) following deletion of the mitochondrial fission-related gene Dnml1. Resultant Dnm1l-/- ESCs maintained major pluripotency characteristics. However, Dnm1l-/- ESCs showed several phenotypic changes, including the inhibition of differentiation ability (dissolution of pluripotency). Notably, Dnm1l-/- ESCs maintained the expression of the pluripotency marker Oct4 and undifferentiated colony types upon differentiation induction. RNA sequencing analysis revealed that the most frequently differentially expressed genes were enriched in the glutathione metabolic pathway. Our data suggested that differentiation inhibition of Dnm1l-/- ESCs was primarily due to metabolic shift from glycolysis to OXPHOS, G2/M phase retardation, and high level of Nanog and 2-cell-specific gene expression.
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Affiliation(s)
- Bong Jong Seo
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Seung Bin Na
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Joonhyuk Choi
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Omer Habib
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea.
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17
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Qiu X, Liang G, Zhou W, Sen R, Atchison ML. Multiple lineage-specific epigenetic landscapes at the antigen receptor loci. AGING RESEARCH (HONG KONG, CHINA) 2023; 1:9340010. [PMID: 38770228 PMCID: PMC11103674 DOI: 10.26599/agr.2023.9340010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Antigen receptors (AgRs) expressed on B and T cells provide the adaptive immune system with ability to detect numerous foreign antigens. Epigenetic features of B cell receptor (BCR) and T cell receptor (TCR) genes were previously studied in lymphocytes, but little is known about their epigenetic features in other cells. Here, we explored histone modifications and transcription markers at the BCR and TCR loci in lymphocytes (pro-B, DP T cells, and mature CD4+ T cells), compared to embryonic stem (ES) cells and neurons. In B cells, the BCR loci exhibited active histone modifications and transcriptional markers indicative of active loci. Similar results were observed at the TCR loci in T cells. All loci were largely inactive in neurons. Surprisingly, in ES cells all AgR loci displayed a high degree of active histone modifications and markers of active transcription. Locations of these active histone modifications in ES cells were largely distinct from those in pro-B cells, and co-localized at numerous binding locations for transcription factors Oct4, Sox2, and Nanog. ES and pro-B cells also showed distinct binding patterns for the ubiquitous transcription factor YY1 and chromatin remodeler Brg1. On the contrary, there were many overlapping CCCTC-binding factor (CTCF) binding patterns when comparing ES cells, pro-B cells, and neurons. Our study identifies epigenetic features in ES cells and lymphocytes that may be related to ES cell pluripotency and lymphocyte tissue-specific activation at the AgR loci.
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Affiliation(s)
- Xiang Qiu
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, Maryland 21224, USA
| | - Guanxiang Liang
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, Maryland 21224, USA
| | - Michael L. Atchison
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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18
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Bao M, Xie J. Geometric Confinement-Mediated Mechanical Tension Directs Patterned Differentiation of Mouse ESCs into Organized Germ Layers. ACS APPLIED MATERIALS & INTERFACES 2023; 15:34397-34406. [PMID: 37458389 DOI: 10.1021/acsami.3c03798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The self-organization of embryonic stem cells (ESCs) into organized tissues with three distinct germ layers is critical to morphogenesis and early development. While the regulation of this self-organization by soluble signals is well established, the involvement of mechanical force gradients in this process remains unclear due to the lack of a suitable platform to study this process. In this study, we developed a 3D microenvironment to examine the influence of mechanical tension gradients on ESC-patterned differentiation during morphogenesis by controlling the geometrical signals (shape and size) of ESC colonies. We found that changes in colony geometry impacted the germ layer pattern, with Cdx2-positive cells being more abundant at edges and in areas with high curvatures. The differentiation patterns were determined by geometry-mediated cell tension gradients, with an extraembryonic mesoderm-like layer forming in high-tension regions and ectodermal-like lineages at low-tension regions in the center. Suppression of cytoskeletal tension hindered ESC self-organization. These results indicate that geometric confinement-mediated mechanical tension plays a crucial role in linking multicellular organization to cell differentiation and impacting tissue patterning.
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Affiliation(s)
- Min Bao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou 325001, Zhejiang, China
| | - Jing Xie
- Institute of Biomedical Engineering, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
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19
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Aranda S, Alcaine-Colet A, Ballaré C, Blanco E, Mocavini I, Sparavier A, Vizán P, Borràs E, Sabidó E, Di Croce L. Thymine DNA glycosylase regulates cell-cycle-driven p53 transcriptional control in pluripotent cells. Mol Cell 2023:S1097-2765(23)00517-8. [PMID: 37506700 DOI: 10.1016/j.molcel.2023.07.003] [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: 01/31/2022] [Revised: 04/11/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
Cell cycle progression is linked to transcriptome dynamics and variations in the response of pluripotent cells to differentiation cues, mostly through unknown determinants. Here, we characterized the cell-cycle-associated transcriptome and proteome of mouse embryonic stem cells (mESCs) in naive ground state. We found that the thymine DNA glycosylase (TDG) is a cell-cycle-regulated co-factor of the tumor suppressor p53. Furthermore, TDG and p53 co-bind ESC-specific cis-regulatory elements and thereby control transcription of p53-dependent genes during self-renewal. We determined that the dynamic expression of TDG is required to promote the cell-cycle-associated transcriptional heterogeneity. Moreover, we demonstrated that transient depletion of TDG influences cell fate decisions during the early differentiation of mESCs. Our findings reveal an unanticipated role of TDG in promoting molecular heterogeneity during the cell cycle and highlight the central role of protein dynamics for the temporal control of cell fate during development.
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Affiliation(s)
- Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Anna Alcaine-Colet
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Cecilia Ballaré
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Ivano Mocavini
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | | | - Pedro Vizán
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Blanquerna School of Health Science, Universitat Ramon Llull, Barcelona 08025, Spain
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain.
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20
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Matsuguchi S, Hirai Y. Syntaxin4, P-cadherin, and CCAAT enhancer binding protein β as signaling elements in the novel differentiation pathway for cultured embryonic stem cells. Biochem Biophys Res Commun 2023; 672:27-35. [PMID: 37331168 DOI: 10.1016/j.bbrc.2023.06.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/15/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
Pluripotent stem cells possess the potential to differentiate into all three germ layers. However, upon removal of the stemness factors, pluripotent stem cells, such as embryonic stem cells (ESCs), exhibit EMT-like cell behavior and lose stemness signatures. This process involves the membrane translocation of the t-SNARE protein syntaxin4 (Stx4) and the expression of the intercellular adhesion molecule P-cadherin. The forced expression of either of these elements induces the emergence of such phenotypes even in the presence of stemness factors. Interestingly, extracellular Stx4, but not P-cadherin, appears to induce a significant upregulation of the gastrulation-related gene brachyury, along with a slight upregulation of the smooth muscle cell-related gene ACTA2 in ESCs. Furthermore, our findings reveal that extracellular Stx4 plays a role in preventing the elimination of CCAAT enhancer binding protein β (C/EBPβ). Notably, the forced overexpression of C/EBPβ led to the downregulation of brachyury and a significant upregulation of ACTA2 in ESCs. These observations suggest that extracellular Stx4 contributes to early mesoderm induction while simultaneously activating an element that alters the differentiation state. The fact that a single differentiation cue can elicit multiple differentiation responses may reflect the challenges associated with achieving sensitive and directed differentiation in cultured stem cells.
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Affiliation(s)
- Shuji Matsuguchi
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, 669-1330, Japan.
| | - Yohei Hirai
- Department of Biomedical Sciences, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, 669-1330, Japan.
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21
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Lynch-Sutherland CF, McDougall LI, Stockwell PA, Almomani SN, Weeks RJ, Ludgate JL, Gamage TKJB, Chatterjee A, James JL, Eccles MR, Macaulay EC. The transposable element-derived transcript of LIN28B has a placental origin and is not specific to tumours. Mol Genet Genomics 2023:10.1007/s00438-023-02033-1. [PMID: 37269361 PMCID: PMC10363060 DOI: 10.1007/s00438-023-02033-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 05/15/2023] [Indexed: 06/05/2023]
Abstract
Transposable elements (TEs) are genetic elements that have evolved as crucial regulators of human development and cancer, functioning as both genes and regulatory elements. When TEs become dysregulated in cancer cells, they can serve as alternate promoters to activate oncogenes, a process known as onco-exaptation. This study aimed to explore the expression and epigenetic regulation of onco-exaptation events in early human developmental tissues. We discovered co-expression of some TEs and oncogenes in human embryonic stem cells and first trimester and term placental tissues. Previous studies identified onco-exaptation events in various cancer types, including an AluJb SINE element-LIN28B interaction in lung cancer cells, and showed that the TE-derived LIN28B transcript is associated with poor patient prognosis in hepatocellular carcinoma. This study further characterized the AluJb-LIN28B transcript and confirmed that its expression is restricted to the placenta. Targeted DNA methylation analysis revealed differential methylation of the two LIN28B promoters between placenta and healthy somatic tissues, indicating that some TE-oncogene interactions are not cancer-specific but arise from the epigenetic reactivation of developmental TE-derived regulatory events. In conclusion, our findings provide evidence that some TE-oncogene interactions are not limited to cancer and may originate from the epigenetic reactivation of TE-derived regulatory events that are involved in early development. These insights broaden our understanding of the role of TEs in gene regulation and suggest the potential importance of targeting TEs in cancer therapy beyond their conventional use as cancer-specific markers.
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Affiliation(s)
- Chiemi F Lynch-Sutherland
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand.
| | - Lorissa I McDougall
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Peter A Stockwell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Suzan N Almomani
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Robert J Weeks
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Jackie L Ludgate
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
| | - Teena K J B Gamage
- Department of Physiology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand
| | - Joanna L James
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand
| | - Erin C Macaulay
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
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22
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Knoedler L, Knoedler S, Panayi AC, Lee CAA, Sadigh S, Huelsboemer L, Stoegner VA, Schroeter A, Kern B, Mookerjee V, Lian CG, Tullius SG, Murphy GF, Pomahac B, Kauke-Navarro M. Cellular activation pathways and interaction networks in vascularized composite allotransplantation. Front Immunol 2023; 14:1179355. [PMID: 37266446 PMCID: PMC10230044 DOI: 10.3389/fimmu.2023.1179355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Vascularized composite allotransplantation (VCA) is an evolving field of reconstructive surgery that has revolutionized the treatment of patients with devastating injuries, including those with limb losses or facial disfigurement. The transplanted units are typically comprised of different tissue types, including skin, mucosa, blood and lymphatic vasculature, muscle, and bone. It is widely accepted that the antigenicity of some VCA components, such as skin, is particularly potent in eliciting a strong recipient rejection response following transplantation. The fine line between tolerance and rejection of the graft is orchestrated by different cell types, including both donor and recipient-derived lymphocytes, macrophages, and other immune and donor-derived tissue cells (e.g., endothelium). Here, we delineate the role of different cell and tissue types during VCA rejection. Rejection of VCA grafts and the necessity of life-long multidrug immunosuppression remains one of the major challenges in this field. This review sheds light on recent developments in decoding the cellular signature of graft rejection in VCA and how these may, ultimately, influence the clinical management of VCA patients by way of novel therapies that target specific cellular processes.
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Affiliation(s)
- Leonard Knoedler
- Department of Plastic, Hand and Reconstructive Surgery, University Hospital Regensburg, Regensburg, Germany
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
| | - Samuel Knoedler
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
- Department of Surgery, Division of Plastic Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Adriana C. Panayi
- Department of Surgery, Division of Plastic Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Department of Hand, Plastic and Reconstructive Surgery, Microsurgery, Burn Center, BG Trauma Center Ludwigshafen, University of Heidelberg, Ludwigshafen, Germany
| | - Catherine A. A. Lee
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Sam Sadigh
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Lioba Huelsboemer
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
| | - Viola A. Stoegner
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
- Department of Plastic, Aesthetic, Hand and Reconstructive Surgery, Burn Center, Hannover Medical School, Hannover, Germany
| | - Andreas Schroeter
- Department of Plastic, Aesthetic, Hand and Reconstructive Surgery, Burn Center, Hannover Medical School, Hannover, Germany
- Division of Transplant Surgery, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Barbara Kern
- Department of Plastic Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Vikram Mookerjee
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
| | - Christine G. Lian
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Stefan G. Tullius
- Division of Transplant Surgery, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - George F. Murphy
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Bohdan Pomahac
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
| | - Martin Kauke-Navarro
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
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23
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Oses C, Francia MG, Verneri P, Vazquez Echegaray C, Guberman AS, Levi V. The dynamical organization of the core pluripotency transcription factors responds to differentiation cues in early S-phase. Front Cell Dev Biol 2023; 11:1125015. [PMID: 37215075 PMCID: PMC10192714 DOI: 10.3389/fcell.2023.1125015] [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: 12/15/2022] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
DNA replication in stem cells is a major challenge for pluripotency preservation and cell fate decisions. This process involves massive changes in the chromatin architecture and the reorganization of many transcription-related molecules in different spatial and temporal scales. Pluripotency is controlled by the master transcription factors (TFs) OCT4, SOX2 and NANOG that partition into condensates in the nucleus of embryonic stem cells. These condensates are proposed to play relevant roles in the regulation of gene expression and the maintenance of pluripotency. Here, we asked whether the dynamical distribution of the pluripotency TFs changes during the cell cycle, particularly during DNA replication. Since the S phase is considered to be a window of opportunity for cell fate decisions, we explored if differentiation cues in G1 phase trigger changes in the distribution of these TFs during the subsequent S phase. Our results show a spatial redistribution of TFs condensates during DNA replication which was not directly related to chromatin compaction. Additionally, fluorescence fluctuation spectroscopy revealed TF-specific, subtle changes in the landscape of TF-chromatin interactions, consistent with their particularities as key players of the pluripotency network. Moreover, we found that differentiation stimuli in the preceding G1 phase triggered a relatively fast and massive reorganization of pluripotency TFs in early-S phase. Particularly, OCT4 and SOX2 condensates dissolved whereas the lifetimes of TF-chromatin interactions increased suggesting that the reorganization of condensates is accompanied with a change in the landscape of TF-chromatin interactions. Notably, NANOG showed impaired interactions with chromatin in stimulated early-S cells in line with its role as naïve pluripotency TF. Together, these findings provide new insights into the regulation of the core pluripotency TFs during DNA replication of embryonic stem cells and highlight their different roles at early differentiation stages.
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Affiliation(s)
- Camila Oses
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marcos Gabriel Francia
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula Verneri
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Camila Vazquez Echegaray
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alejandra Sonia Guberman
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Valeria Levi
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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24
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Ledesma AV, Mueller ML, Van Eenennaam AL. Review: Progress in producing chimeric ungulate livestock for agricultural applications. Animal 2023; 17 Suppl 1:100803. [PMID: 37567671 DOI: 10.1016/j.animal.2023.100803] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 08/13/2023] Open
Abstract
The progress made in recent years in the derivation and culture of pluripotent stem cells from farm animals opens up the possibility of creating livestock chimeras. Chimeras producing gametes exclusively derived from elite donor stem cells could pass superior genetics on to the next generation and thereby reduce the genetic lag that typically exists between the elite breeding sector and the commercial production sector, especially for industries like beef and sheep where genetics is commonly disseminated through natural service mating. Chimeras carrying germ cells generated from genome-edited or genetically engineered pluripotent stem cells could further disseminate useful genomic alterations such as climate adaptation, animal welfare improvements, the repair of deleterious genetic conditions, and/or the elimination of undesired traits such as disease susceptibility to the next generation. Despite the successful production of chimeras with germ cells generated from pluripotent donor stem cells injected into preimplantation-stage blastocysts in model species, there are no documented cases of this occurring in livestock. Here, we review the literature on the derivation of pluripotent stem cells from ungulates, and progress in the production of chimeric ungulate livestock for agricultural applications, drawing on insights from studies done in model species, and discuss future possibilities of this fast-moving and developing field. Aside from the technical aspects, the consistency of the regulatory approach taken by different jurisdictions towards chimeric ungulate livestock with germ cells generated from pluripotent stem cells and their progeny will be an important determinant of breeding industry uptake and adoption in animal agriculture.
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Affiliation(s)
- Alba V Ledesma
- Department of Animal Science, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Maci L Mueller
- Department of Animal Science, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Alison L Van Eenennaam
- Department of Animal Science, University of California, One Shields Avenue, Davis, CA 95616, USA.
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25
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RDW K, KR S, A C, LC4 J, SW H, SM C. Histone Deacetylases (HDACs) maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and non-coding loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535398. [PMID: 37066171 PMCID: PMC10104071 DOI: 10.1101/2023.04.06.535398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Histone acetylation is a dynamic modification regulated by the opposing actions of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Deacetylation of histone tails results in chromatin tightening and therefore HDACs are generally regarded as transcriptional repressors. Counterintuitively, simultaneous deletion of Hdac1 and Hdac2 in embryonic stem cells (ESC) reduced expression of pluripotent transcription factors, Oct4, Sox2 and Nanog (OSN). By shaping global histone acetylation patterns, HDACs indirectly regulate the activity of acetyl-lysine readers, such as the transcriptional activator, BRD4. We used inhibitors of HDACs and BRD4 (LBH589 and JQ1 respectively) in combination with precision nuclear run-on and sequencing (PRO-seq) to examine their roles in defining the ESC transcriptome. Both LBH589 and JQ1 caused a marked reduction in the pluripotent network. However, while JQ1 treatment induced widespread transcriptional pausing, HDAC inhibition caused a reduction in both paused and elongating polymerase, suggesting an overall reduction in polymerase recruitment. Using enhancer RNA (eRNA) expression to measure enhancer activity we found that LBH589-sensitive eRNAs were preferentially associated with super-enhancers and OSN binding sites. These findings suggest that HDAC activity is required to maintain pluripotency by regulating the OSN enhancer network via the recruitment of RNA polymerase II.
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Affiliation(s)
- Kelly RDW
- Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 9HN, UK
| | - Stengel KR
- Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue Chanin Building, Bronx, NY 10461
| | - Chandru A
- Cancer Research UK Beatson Institute, Switchback Road, Bearsden, Glasgow, G61 1BD
| | - Johnson LC4
- Locate Bio Limited, MediCity, Thane Road, Beeston, Nottingham, NG90 6BH
| | - Hiebert SW
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cowley SM
- Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 9HN, UK
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26
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Puri D, Kelkar A, Gaurishankar B, Subramanyam D. Balance between autophagy and cell death is maintained by Polycomb-mediated regulation during stem cell differentiation. FEBS J 2023; 290:1625-1644. [PMID: 36380631 DOI: 10.1111/febs.16656] [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: 05/20/2022] [Revised: 08/23/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
Autophagy is a conserved cytoprotective process, aberrations in which lead to numerous degenerative disorders. While the cytoplasmic components of autophagy have been extensively studied, the epigenetic regulation of autophagy genes, especially in stem cells, is less understood. Deciphering the epigenetic regulation of autophagy genes becomes increasingly relevant given the therapeutic benefits of small-molecule epigenetic inhibitors in novel treatment modalities. We observe that, during retinoic acid-mediated differentiation of mouse embryonic stem cells (mESCs), autophagy is induced, and identify the Polycomb group histone methyl transferase EZH2 as a regulator of this process. In mESCs, EZH2 represses several autophagy genes, including the autophagy regulator DNA damage-regulated autophagy modulator protein 1 (Dram1). EZH2 facilitates the formation of a bivalent chromatin domain at the Dram1 promoter, allowing gene expression and autophagy induction during differentiation while retaining the repressive H3K27me3 mark. EZH2 inhibition leads to loss of the bivalent domain, with consequent 'hyper-expression' of Dram1, accompanied by extensive cell death. This study shows that Polycomb group proteins help maintain a balance between autophagy and cell death during stem cell differentiation, in part, by regulating the expression of the Dram1 gene.
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Affiliation(s)
- Deepika Puri
- National Centre for Cell Science, SP Pune University, India
| | - Aparna Kelkar
- National Centre for Cell Science, SP Pune University, India
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27
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Zorzan I, Betto RM, Rossignoli G, Arboit M, Drusin A, Corridori C, Martini P, Martello G. Chemical conversion of human conventional PSCs to TSCs following transient naive gene activation. EMBO Rep 2023; 24:e55235. [PMID: 36847616 PMCID: PMC10074076 DOI: 10.15252/embr.202255235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 03/01/2023] Open
Abstract
In human embryos, naive pluripotent cells of the inner cell mass (ICM) generate epiblast, primitive endoderm and trophectoderm (TE) lineages, whence trophoblast cells derive. In vitro, naive pluripotent stem cells (PSCs) retain this potential and efficiently generate trophoblast stem cells (TSCs), while conventional PSCs form TSCs at low efficiency. Transient histone deacetylase and MEK inhibition combined with LIF stimulation is used to chemically reset conventional to naive PSCs. Here, we report that chemical resetting induces the expression of both naive and TSC markers and of placental imprinted genes. A modified chemical resetting protocol allows for the fast and efficient conversion of conventional PSCs into TSCs, entailing shutdown of pluripotency genes and full activation of the trophoblast master regulators, without induction of amnion markers. Chemical resetting generates a plastic intermediate state, characterised by co-expression of naive and TSC markers, after which cells steer towards one of the two fates in response to the signalling environment. The efficiency and rapidity of our system will be useful to study cell fate transitions and to generate models of placental disorders.
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Affiliation(s)
- Irene Zorzan
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | | | | | - Mattia Arboit
- Department of Biology, University of Padua, Padua, Italy
| | - Andrea Drusin
- Department of Biology, University of Padua, Padua, Italy
| | | | - Paolo Martini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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28
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Hao Y, Li X, Qin K, Shi Y, He Y, Zhang C, Cheng B, Zhang X, Hu G, Liang S, Tang Q, Chen X. Chemoproteomic and Transcriptomic Analysis Reveals that O-GlcNAc Regulates Mouse Embryonic Stem Cell Fate through the Pluripotency Network. Angew Chem Int Ed Engl 2023; 62:e202300500. [PMID: 36852467 DOI: 10.1002/anie.202300500] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/22/2023] [Accepted: 02/27/2023] [Indexed: 03/01/2023]
Abstract
Self-renewal and differentiation of embryonic stem cells (ESCs) are influenced by protein O-linked β-N-acetylglucosamine (O-GlcNAc) modification, but the underlying mechanism remains incompletely understood. Herein, we report the identification of 979 O-GlcNAcylated proteins and 1340 modification sites in mouse ESCs (mESCs) by using a chemoproteomics method. In addition to OCT4 and SOX2, the third core pluripotency transcription factor (PTF) NANOG was found to be modified and functionally regulated by O-GlcNAc. Upon differentiation along the neuronal lineage, the O-GlcNAc stoichiometry at 123 sites of 83 proteins-several of which were PTFs-was found to decline. Transcriptomic profiling reveals 2456 differentially expressed genes responsive to OGT inhibition during differentiation, of which 901 are target genes of core PTFs. By acting on the core PTF network, suppression of O-GlcNAcylation upregulates neuron-related genes, thus contributing to mESC fate determination.
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Affiliation(s)
- Yi Hao
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Xiang Li
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Ke Qin
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Yujie Shi
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Yanwen He
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Che Zhang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Bo Cheng
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Xiwen Zhang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Guangyu Hu
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Shuyu Liang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Qi Tang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
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29
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Takeda Y, Matsuguchi S, Nozaki S, Mihara T, Abe J, Hirai Y. Suppression of P-cadherin expression as a key regulatory element for embryonic stem cell stemness. Cell Struct Funct 2023; 48:49-57. [PMID: 36575041 PMCID: PMC10721948 DOI: 10.1247/csf.22060] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/13/2022] [Indexed: 12/28/2022] Open
Abstract
In embryonic stem (ES) cell colonies, a small subpopulation that changes cell shape and loses pluripotency often appears in two-dimensional (2D) cultures, even in the presence of a stemness factor. We have previously shown that membrane translocation of the syntaxin4, t-SNARE protein contributes to this phenomenon. Here, we show that ES cells in three-dimensional (3D) aggregates do not succumb to extruded syntaxin4 owing to suppressed expression of P-cadherin protein. While extracellular expression of syntaxin4 led to the striking upregulation of P-cadherin mRNA in both 2D and 3D-ES cells, morphological changes and appreciable expression of P-cadherin protein were detected only in 2D-ES cells. Importantly, the introduction of an expression cassette for P-cadherin practically reproduced the effects induced by extracellular syntaxin4, where the transgene product was clearly detected in 2D-, but not 3D-ES cells. An expression construct for P-cadherin-Venus harboring an in-frame insertion of the P2A sequence at the joint region gave fluorescent signals only in the cytoplasm of 2D-ES cells, demonstrating translational regulation of P-cadherin. These results provide the mechanistic insight into the uncontrollable differentiation in 2D-ES cells and shed light on the validity of the "embryoid body protocol commonly used for ES cell handling" for directional differentiation.Key words: differentiation, embryoid body, ES cells, P-cadherin, syntaxin4.
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Affiliation(s)
- Yuka Takeda
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Japan
| | - Shuji Matsuguchi
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Japan
| | - Sae Nozaki
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Japan
| | - Taisei Mihara
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Japan
| | - Junya Abe
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Japan
| | - Yohei Hirai
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Japan
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30
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Sun X, Wang D, Li W, Gao Q, Tao J, Liu H. Comprehensive analysis of nonsurrounded nucleolus and surrounded nucleolus oocytes on chromatin accessibility using ATAC-seq. Mol Reprod Dev 2023; 90:87-97. [PMID: 36598871 DOI: 10.1002/mrd.23668] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/13/2022] [Accepted: 12/25/2022] [Indexed: 01/05/2023]
Abstract
Mouse germinal vesicle (GV) oocytes are divided into surrounded nucleolus (SN) and nonsurrounded nucleolus (NSN) oocytes based on chromatin morphology. NSN oocytes spontaneously transform into SN oocytes after accumulating enough maternal transcripts. SN oocytes show transcriptional silencing. When oocyte maturation is abnormal or takes place in vitro, NSN oocytes do not go through SN stage before proceeding to MII. Nontransitive oocytes show developmental retardation, a low fertilization rate, and arrest at the two-cell embryo stage in mice. Here, chromatin-binding ribonucleic acid polymerase II (RNAP II) activity, newly synthesized RNA, and chromatin accessibility in GV oocytes were examined. In SN oocytes, RNAP II did not bind to DNA, neo-RNA was not generated in nuclei, and the phosphorylation state of RNAP II did not affect the chromatin-binding activity. The number of accessible genes in SN oocytes was remarkably lower than that in NSN oocytes. The accessibility of different functional genes was also different between the two types of oocytes. Thus, low chromatin accessibility leads to transcriptional silencing in SN oocytes.
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Affiliation(s)
- Xiaofan Sun
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Dayu Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Weijian Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Qian Gao
- Laboratory Animal Center, College of Veterinary Medicine, Nanjing Agriculture University, Nanjing, China
| | - Jingli Tao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Honglin Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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31
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Sramkó B, Földes A, Kádár K, Varga G, Zsembery Á, Pircs K. The Wisdom in Teeth: Neuronal Differentiation of Dental Pulp Cells. Cell Reprogram 2023; 25:32-44. [PMID: 36719998 PMCID: PMC9963504 DOI: 10.1089/cell.2022.0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Mesenchymal stem/stromal cells (MSCs) are found in almost all postnatal organs. Under appropriate environmental cues, multipotency enables MSCs to serve as progenitors for several lineage-specific, differentiated cell types. In vitro expansion and differentiation of MSCs give the opportunity to obtain hardly available somatic cells, such as neurons. The neurogenic potential of MSCs makes them a promising, autologous source to restore damaged tissue and as such, they have received much attention in the field of regenerative medicine. Several stem cell pool candidates have been studied thus far, but only a few of them showed neurogenic differentiation potential. Due to their embryonic ontology, stem cells residing in the stroma of the dental pulp chamber are an exciting source for in vitro neural cell differentiation. In this study, we review the key properties of dental pulp stem cells (DPSCs), with a particular focus on their neurogenic potential. Moreover, we summarize the various presently available methods used for neural differentiation of human DPSCs also emphasizing the difficulties in reproducibly high production of such cells. We postulate that because DPSCs are stem cells with very close ontology to neurogenic lineages, they may serve as excellent targets for neuronal differentiation in vitro and even for direct reprogramming.
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Affiliation(s)
- Bendegúz Sramkó
- HCEMM-SU Neurobiology and Neurodegenerative Diseases Research Group, Budapest, Hungary.,Institute of Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Anna Földes
- Department of Oral Biology, Faculty of Dentistry, Semmelweis University, Budapest, Hungary
| | - Kristóf Kádár
- Department of Oral Biology, Faculty of Dentistry, Semmelweis University, Budapest, Hungary
| | - Gábor Varga
- Department of Oral Biology, Faculty of Dentistry, Semmelweis University, Budapest, Hungary
| | - Ákos Zsembery
- Department of Oral Biology, Faculty of Dentistry, Semmelweis University, Budapest, Hungary
| | - Karolina Pircs
- HCEMM-SU Neurobiology and Neurodegenerative Diseases Research Group, Budapest, Hungary.,Institute of Translational Medicine, Semmelweis University, Budapest, Hungary.,Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, Lund, Sweden
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32
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Kang C, McElroy M, Voulgarakis NK. Emergent Criticality in Coupled Boolean Networks. ENTROPY (BASEL, SWITZERLAND) 2023; 25:e25020235. [PMID: 36832602 PMCID: PMC9955248 DOI: 10.3390/e25020235] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 06/01/2023]
Abstract
Early embryonic development involves forming all specialized cells from a fluid-like mass of identical stem cells. The differentiation process consists of a series of symmetry-breaking events, starting from a high-symmetry state (stem cells) to a low-symmetry state (specialized cells). This scenario closely resembles phase transitions in statistical mechanics. To theoretically study this hypothesis, we model embryonic stem cell (ESC) populations through a coupled Boolean network (BN) model. The interaction is applied using a multilayer Ising model that considers paracrine and autocrine signaling, along with external interventions. It is demonstrated that cell-to-cell variability can be interpreted as a mixture of steady-state probability distributions. Simulations have revealed that such models can undergo a series of first- and second-order phase transitions as a function of the system parameters that describe gene expression noise and interaction strengths. These phase transitions result in spontaneous symmetry-breaking events that generate new types of cells characterized by various steady-state distributions. Coupled BNs have also been shown to self-organize in states that allow spontaneous cell differentiation.
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Affiliation(s)
- Chris Kang
- Department of Mathematics and Statistics, Washington State University, Pullman, WA 99164, USA
| | - Madelynn McElroy
- Department of Mathematics and Statistics, Washington State University, Pullman, WA 99164, USA
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Nikolaos K. Voulgarakis
- Department of Mathematics and Statistics, Washington State University, Pullman, WA 99164, USA
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33
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Sarmah H, Sawada A, Hwang Y, Miura A, Shimamura Y, Tanaka J, Yamada K, Mori M. Towards human organ generation using interspecies blastocyst complementation: Challenges and perspectives for therapy. Front Cell Dev Biol 2023; 11:1070560. [PMID: 36743411 PMCID: PMC9893295 DOI: 10.3389/fcell.2023.1070560] [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: 10/15/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
Millions of people suffer from end-stage refractory diseases. The ideal treatment option for terminally ill patients is organ transplantation. However, donor organs are in absolute shortage, and sadly, most patients die while waiting for a donor organ. To date, no technology has achieved long-term sustainable patient-derived organ generation. In this regard, emerging technologies of chimeric human organ production via blastocyst complementation (BC) holds great promise. To take human organ generation via BC and transplantation to the next step, we reviewed current emerging organ generation technologies and the associated efficiency of chimera formation in human cells from the standpoint of developmental biology.
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Affiliation(s)
- Hemanta Sarmah
- Department of Medicine, Columbia Center for Human Development, Columbia University Medical Center, New York, NY, United States
| | - Anri Sawada
- Department of Medicine, Columbia Center for Human Development, Columbia University Medical Center, New York, NY, United States
| | - Youngmin Hwang
- Department of Medicine, Columbia Center for Human Development, Columbia University Medical Center, New York, NY, United States
| | - Akihiro Miura
- Department of Medicine, Columbia Center for Human Development, Columbia University Medical Center, New York, NY, United States
| | - Yuko Shimamura
- Department of Medicine, Columbia Center for Human Development, Columbia University Medical Center, New York, NY, United States
| | - Junichi Tanaka
- Department of Medicine, Columbia Center for Human Development, Columbia University Medical Center, New York, NY, United States
| | - Kazuhiko Yamada
- Department of Surgery, Johns Hopkins University, Baltimore, MD, United States
| | - Munemasa Mori
- Department of Medicine, Columbia Center for Human Development, Columbia University Medical Center, New York, NY, United States
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34
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Iannone C, Kainov Y, Zhuravskaya A, Hamid F, Nojima T, Makeyev EV. PTBP1-activated co-transcriptional splicing controls epigenetic status of pluripotent stem cells. Mol Cell 2023; 83:203-218.e9. [PMID: 36626906 DOI: 10.1016/j.molcel.2022.12.014] [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: 04/01/2022] [Revised: 11/15/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023]
Abstract
Many spliceosomal introns are excised from nascent transcripts emerging from RNA polymerase II (RNA Pol II). The extent of cell-type-specific regulation and possible functions of such co-transcriptional events remain poorly understood. We examined the role of the RNA-binding protein PTBP1 in this process using an acute depletion approach followed by the analysis of chromatin- and RNA Pol II-associated transcripts. We show that PTBP1 activates the co-transcriptional excision of hundreds of introns, a surprising effect given that this protein is known to promote intron retention. Importantly, some co-transcriptionally activated introns fail to complete their splicing without PTBP1. In a striking example, retention of a PTBP1-dependent intron triggers nonsense-mediated decay of transcripts encoding DNA methyltransferase DNMT3B. We provide evidence that this regulation facilitates the natural decline in DNMT3B levels in developing neurons and protects differentiation-specific genes from ectopic methylation. Thus, PTBP1-activated co-transcriptional splicing is a widespread phenomenon mediating epigenetic control of cellular identity.
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Affiliation(s)
- Camilla Iannone
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Yaroslav Kainov
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Anna Zhuravskaya
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Fursham Hamid
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Takayuki Nojima
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK.
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35
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Geng Z, Guo H, Li Y, Liu Y, Zhao Y. Stem cell-derived extracellular vesicles: A novel and potential remedy for primary ovarian insufficiency. Front Cell Dev Biol 2023; 11:1090997. [PMID: 36875770 PMCID: PMC9977284 DOI: 10.3389/fcell.2023.1090997] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Primary ovarian insufficiency (POI) is an essential cause of young female fertility loss. At present, there are many treatments for primary ovarian insufficiency, but due to the complexity of the pathogenesis of primary ovarian insufficiency, the efficacy still could not be satisfactory. Stem cell transplantation is a feasible intervention protocol for primary ovarian insufficiency. However, its wide application in the clinic is limited by some defects such as tumorigenic and controversial ethical issues. Stem cell-derived extracellular vesicles (EVs) represent an important mode of intercellular communication attracting increasing interest. It is well documented that stem cell-derived extracellular vesicles for primary ovarian insufficiency with exciting therapeutic effects. Studies have found that stem cell-derived extracellular vesicles could improve ovarian reserve, increase the growth of follicles, reduce follicle atresia, and restore hormone levels of FSH and E2. Its mechanisms include inhibiting ovarian granulosa cells (GCs) apoptosis, reactive oxygen species, and inflammatory response and promoting granulosa cells proliferation and angiogenesis. Thus, stem cell-derived extracellular vesicles are a promising and potential method for primary ovarian insufficiency patients. However, stem cell-derived extracellular vesicles are still a long way from clinical translation. This review will provide an overview of the role and the mechanisms of stem cell-derived extracellular vesicles in primary ovarian insufficiency, and further elaborate on the current challenges. It may suggest new directions for future research.
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Affiliation(s)
- Zixiang Geng
- Shi's Center of Orthopedics and Traumatology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Traumatology and Orthopedics, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Hailing Guo
- Shi's Center of Orthopedics and Traumatology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Traumatology and Orthopedics, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yifei Li
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ying Liu
- Department of Dermatology, Shanghai Songjiang District Central Hospital, Shanghai, China
| | - Yongfang Zhao
- Shi's Center of Orthopedics and Traumatology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Traumatology and Orthopedics, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
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36
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Yu L, Ballard E, Pinzon Arteaga CA, Wu J. Derivation and Primordial Germ Cell Induction of Intermediate Pluripotent Stem Cells. Methods Mol Biol 2023; 2677:269-280. [PMID: 37464248 DOI: 10.1007/978-1-0716-3259-8_16] [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] [Indexed: 07/20/2023]
Abstract
Dynamic pluripotent stem cell (PSC) states are in vitro adaptations of the pluripotency continuum in vivo. Previous studies have generated a number of PSCs with distinct properties. By modulating the FGF, TGF-β, and WNT pathways, we have derived intermediate PSCs (FTW-PSCs) that are permissive for direct primordial germ cell-like cell (PGC-LC) induction in vitro. Here, we describe the method for derivation and maintenance of mouse and human FTW-PSCs, as well as PGC-LC induction from FTW-PSCs.
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Affiliation(s)
- Leqian Yu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Emily Ballard
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Carlos A Pinzon Arteaga
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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37
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Jiang J, Qiu T, Yang C, Yuan Y, Qin L, Zhang P. Atypical cell cycle profile of mouse embryonic stem cell is regulated by classic oncogenic and tumor suppressive genes in vitro. Heliyon 2022; 8:e11979. [PMID: 36578422 PMCID: PMC9791322 DOI: 10.1016/j.heliyon.2022.e11979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/17/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Embryonic stem cells (ESCs) exhibit an unusual cell cycle profile containing a short G1 phase. Whether this feature is required to maintain pluripotency is a matter of debate. Here, we report that the short G1 phase is a consequence of MEK1/2 kinase-mediated promotion of G1/S transition, but not necessarily coupled with pluripotency maintenance. We find that compared to primed ESCs, naïve ESCs exhibit a significantly longer G1 phase due to the inhibition of MEK1/2 kinases. MEK1/2 inhibition increases intracellular level of reactive oxygen species (ROS), leading to the stabilization of p53 protein. The genetic ablation of p53 largely converts the cell cycle profile of naïve ESCs to that of primed ESCs. These results demonstrate that pluripotency and proliferation are separable cellular events, and the short G1 phase of primed ESCs is a manifestation of the intricate interplay between classical oncogenes MEK1/2 and tumor suppressor gene TP53 to promote G1/S transition.
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Affiliation(s)
- Jinfeng Jiang
- Departments of Pediatrics and Obstetrics & Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China,Frontiers Science Center for Disease-related Molecular Network, West China Hospital
| | - Tong Qiu
- Departments of Pediatrics and Obstetrics & Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China,Frontiers Science Center for Disease-related Molecular Network, West China Hospital
| | - Chao Yang
- Departments of Pediatrics and Obstetrics & Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China,Frontiers Science Center for Disease-related Molecular Network, West China Hospital
| | - Yuan Yuan
- Division of Bioinformatics, Sichuan Cunde Therapeutics, Chengdu 610093, China
| | - Ling Qin
- Department of Gastroenterology, First Affiliated Hospital of Chengdu Medical College,Corresponding authors.
| | - Peixuan Zhang
- Departments of Pediatrics and Obstetrics & Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China,Corresponding authors.
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38
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Hu S, Metcalf E, Mahat DB, Chan L, Sohal N, Chakraborty M, Hamilton M, Singh A, Singh A, Lees JA, Sharp PA, Garg S. Transcription factor antagonism regulates heterogeneity in embryonic stem cell states. Mol Cell 2022; 82:4410-4427.e12. [PMID: 36356583 PMCID: PMC9722640 DOI: 10.1016/j.molcel.2022.10.022] [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: 04/15/2022] [Revised: 05/19/2022] [Accepted: 10/20/2022] [Indexed: 11/10/2022]
Abstract
Gene expression heterogeneity underlies cell states and contributes to developmental robustness. While heterogeneity can arise from stochastic transcriptional processes, the extent to which it is regulated is unclear. Here, we characterize the regulatory program underlying heterogeneity in murine embryonic stem cell (mESC) states. We identify differentially active and transcribed enhancers (DATEs) across states. DATEs regulate differentially expressed genes and are distinguished by co-binding of transcription factors Klf4 and Zfp281. In contrast to other factors that interact in a positive feedback network stabilizing mESC cell-type identity, Klf4 and Zfp281 drive opposing transcriptional and chromatin programs. Abrogation of factor binding to DATEs dampens variation in gene expression, and factor loss alters kinetics of switching between states. These results show antagonism between factors at enhancers results in gene expression heterogeneity and formation of cell states, with implications for the generation of diverse cell types during development.
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Affiliation(s)
- Sofia Hu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Emily Metcalf
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dig Bijay Mahat
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lynette Chan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Noor Sohal
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Meenakshi Chakraborty
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maxwell Hamilton
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arundeep Singh
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
| | - Jacqueline A Lees
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Phillip A Sharp
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Salil Garg
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Laboratory Medicine, Yale Stem Cell Center and Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT 06510, USA.
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39
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Rajabi H, Mortazavi D, Konyalilar N, Aksoy GT, Erkan S, Korkunc SK, Kayalar O, Bayram H, Rahbarghazi R. Forthcoming complications in recovered COVID-19 patients with COPD and asthma; possible therapeutic opportunities. Cell Commun Signal 2022; 20:173. [PMID: 36320055 PMCID: PMC9623941 DOI: 10.1186/s12964-022-00982-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/01/2022] [Indexed: 11/21/2022] Open
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been growing swiftly worldwide. Patients with background chronic pulmonary inflammations such as asthma or chronic obstructive pulmonary diseases (COPD) are likely to be infected with this virus. Of note, there is an argument that COVID-19 can remain with serious complications like fibrosis or other pathological changes in the pulmonary tissue of patients with chronic diseases. Along with conventional medications, regenerative medicine, and cell-based therapy could be alternative approaches to compensate for organ loss or restore injured sites using different stem cell types. Owing to unique differentiation capacity and paracrine activity, these cells can accelerate the healing procedure. In this review article, we have tried to scrutinize different reports related to the harmful effects of SARS-CoV-2 on patients with asthma and COPD, as well as the possible therapeutic effects of stem cells in the alleviation of post-COVID-19 complications. Video abstract.
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Affiliation(s)
- Hadi Rajabi
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey
| | - Deniz Mortazavi
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey
| | - Nur Konyalilar
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey
| | - Gizem Tuse Aksoy
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey
| | - Sinem Erkan
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey
| | - Seval Kubra Korkunc
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey
| | - Ozgecan Kayalar
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey
| | - Hasan Bayram
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey.
- Department of Pulmonary Medicine, School of Medicine, Koç University, Istanbul, Turkey.
| | - Reza Rahbarghazi
- Stem Cell Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran.
- Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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40
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Liu XM, Mao Y, Wang S, Zhou J, Qian SB. METTL3 modulates chromatin and transcription dynamics during cell fate transition. Cell Mol Life Sci 2022; 79:559. [PMID: 36266520 DOI: 10.1007/s00018-022-04590-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/26/2022]
Abstract
Transcriptional programming plays a key role in determining the cell state. Timely reconfiguration of chromatin structure and attenuation of pluripotent genes are required for efficient embryonic stem cell (ESC) differentiation. Here, we identify METTL3, a core N6-methyladenosine (m6A) catalyzing enzyme, as a crucial modulator of dynamic transcription and chromatin accessibility upon ESC-derived cardiac differentiation. Genome-wide analysis of chromatin-associated RNAs revealed that depletion of METTL3 failed to dramatically attenuate the transcription of pluripotent genes, as well as activate nascent cardiomyocyte-specific transcripts upon differentiation. Consistently, ATAC-seq analysis showed that loss of METTL3 markedly attenuated the dynamic alteration of chromatin accessibility at both promoters and gene bodies, resulting in reduced sensitivity of ESC chromatin structure to cardiac differentiation signal. Furthermore, we found that METTL3 negatively regulated the histone modifications H3K4me3 and H3K36me3, which are involved in METTL3-modulated dynamic chromatin architecture during cell state transition. Unexpectedly, using chromatin-associated m6A sequencing, we found that nuclear m6A underwent a dramatic increase upon differentiation, which correlates with the decrease of chromatin accessibility. Collectively, our findings reveal that METTL3 and nuclear m6A epitranscriptome couple with chromatin state to ensure transcriptional regulation of cell fate transition.
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Affiliation(s)
- Xiao-Min Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China.
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14853, USA
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Shen Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China
| | - Jun Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14853, USA.
- Field of Genetics, Genomics, and Development, Cornell University, Ithaca, NY, 14853, USA.
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Marikawa Y. Toward better assessments of developmental toxicity using stem cell-based in vitro embryogenesis models. Birth Defects Res 2022; 114:972-982. [PMID: 35102709 PMCID: PMC9339025 DOI: 10.1002/bdr2.1984] [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: 12/29/2021] [Accepted: 01/18/2022] [Indexed: 12/30/2022]
Abstract
In the past few decades, pluripotent stem cells have been explored as nonanimal alternatives to assess the developmental toxicity of chemicals. To date, numerous versions of stem cell-based assays have been reported that are allegedly effective. Nonetheless, none of the assays has become the gold standard in developmental toxicity assessment. Why? This article discusses several issues in the hope of facilitating the refinement of stem cell assays and their acceptance as the cornerstone in predictive developmental toxicology. Each stem cell assay is built on a limited representation of embryogenesis, so that multiple assays are needed to detect the diverse effects of various chemicals. To validate and compare the strengths and weaknesses of individual assays, standardized lists of reference chemicals should be established. Reference lists should consist of exposures defined by toxicokinetic data, namely maternal plasma concentrations that cause embryonic death or malformations, and also by the effects on the molecular machineries that control embryogenesis. Although not entirely replacing human or animal tests, carefully selected stem cell assays should serve as practical and ethical alternatives to proactively identify chemical exposures that disturb embryogenesis. To achieve this goal, unprecedented levels of coordination and conviction are required among research and regulatory communities.
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Affiliation(s)
- Yusuke Marikawa
- Department of Anatomy, Biochemistry and PhysiologyInstitute for Biogenesis Research, University of Hawaii John A. Burns School of MedicineHonoluluHawaiiUSA
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42
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Xu Y, Yang X. Autophagy and pluripotency: self-eating your way to eternal youth. Trends Cell Biol 2022; 32:868-882. [PMID: 35490141 PMCID: PMC10433133 DOI: 10.1016/j.tcb.2022.04.001] [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: 01/17/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 01/18/2023]
Abstract
Pluripotent stem cells (PSCs) can self-renew indefinitely in culture while retaining the potential to differentiate into virtually all normal cell types in the adult animal. Due to these remarkable properties, PSCs not only provide a superb system to investigate mammalian development and model diseases, but also hold promise for regenerative therapies. Autophagy is a self-digestive process that targets proteins, organelles, and other cellular contents for lysosomal degradation. Here, we review recent literature on the mechanistic role of different types of autophagy in embryonic development, embryonic stem cells (ESCs), and induced PSCs (iPSCs), focusing on their remodeling functions on protein, metabolism, and epigenetics. We present a perspective on unsolved issues and propose that autophagy is a promising target to modulate acquisition, maintenance, and directed differentiation of PSCs.
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Affiliation(s)
- Yi Xu
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.
| | - Xiaolu Yang
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
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Liu K, Li X, Li Z, Cao J, Li X, Xu Y, Liu L, Zhao T. Evaluating mitophagy in embryonic stem cells by using fluorescence-based imaging. Front Cell Dev Biol 2022; 10:910464. [PMID: 36187486 PMCID: PMC9520453 DOI: 10.3389/fcell.2022.910464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/30/2022] [Indexed: 12/09/2022] Open
Abstract
Embryonic stem cells (ESCs), which are characterized by the capacity for self-renewal and pluripotency, hold great promise for regenerative medicine. Increasing evidence points to the essential role of mitophagy in pluripotency regulation. Our recent work showed that PINK1/OPTN take part in guarding ESC mitochondrial homeostasis and pluripotency. Evaluating mitophagy in ESCs is important for exploring the relationships between mitochondrial homeostasis and pluripotency. ESCs are smaller in size than adult somatic cells and the mitophagosomes in ESCs are difficult to observe. Many methods have been employed—for example, detecting colocalization of LC3-II and mitochondria—to evaluate mitophagy in ESCs. However, it is important to define an objective way to detect mitophagy in ESCs. Here, we evaluated two commonly used fluorescence-based imaging methods to detect mitophagy in ESCs. By using autophagy- or mitophagy-defective ESC lines, we showed that the mito-Keima (mt-Keima) system is a suitable and effective way for detecting and quantifying mitophagy in ESCs. Our study provides evidence that mt-Keima is an effective tool to study mitophagy function in ESCs.
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Affiliation(s)
- Kun Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Xing Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Li
- Department of Gastroenterology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jiani Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Xiaoyan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Youqing Xu
- Department of Gastroenterology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Tongbiao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- *Correspondence: Tongbiao Zhao,
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44
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Dubois A, Vincenti L, Chervova A, Greenberg MVC, Vandormael-Pournin S, Bourc'his D, Cohen-Tannoudji M, Navarro P. H3K9 tri-methylation at Nanog times differentiation commitment and enables the acquisition of primitive endoderm fate. Development 2022; 149:276335. [PMID: 35976266 PMCID: PMC9482333 DOI: 10.1242/dev.201074] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022]
Abstract
Mouse embryonic stem cells have an inherent propensity to explore gene regulatory states associated with either self-renewal or differentiation. This property depends on ERK, which downregulates pluripotency genes such as Nanog. Here, we aimed at identifying repressive histone modifications that would mark Nanog for inactivation in response to ERK activity. We found that the transcription factor ZFP57, which binds methylated DNA to nucleate heterochromatin, is recruited upstream of Nanog, within a region enriched for histone H3 lysine 9 tri-methylation (H3K9me3). Whereas before differentiation H3K9me3 at Nanog depends on ERK, in somatic cells it becomes independent of ERK. Moreover, the loss of H3K9me3 at Nanog, induced by deleting the region or by knocking out DNA methyltransferases or Zfp57, is associated with reduced heterogeneity of NANOG, delayed commitment into differentiation and impaired ability to acquire a primitive endoderm fate. Hence, a network axis centred on DNA methylation, ZFP57 and H3K9me3 links Nanog regulation to ERK activity for the timely establishment of new cell identities. We suggest that establishment of irreversible H3K9me3 at specific master regulators allows the acquisition of particular cell fates during differentiation. Summary: A regulatory axis integrating ERK, ZFP57, DNA and H3K9 methylation underlies the transition of Nanog expression from heterogeneous and dynamic to irreversibly silenced, enabling differentiation commitment and primitive endoderm specification.
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Affiliation(s)
- Agnès Dubois
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
| | - Loris Vincenti
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
| | - Almira Chervova
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
| | - Maxim V. C. Greenberg
- Department of Genetics and Developmental Biology, Institut Curie, PSL Research University, INSERM, CNRS 2 , 75005 Paris , France
- Université Paris Cité, CNRS, Institut Jacques Monod 3 , F-75013 Paris , France
| | - Sandrine Vandormael-Pournin
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
| | - Déborah Bourc'his
- Department of Genetics and Developmental Biology, Institut Curie, PSL Research University, INSERM, CNRS 2 , 75005 Paris , France
| | - Michel Cohen-Tannoudji
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
| | - Pablo Navarro
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
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45
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Roodgar M, Suchy FP, Nguyen LH, Bajpai VK, Sinha R, Vilches-Moure JG, Van Bortle K, Bhadury J, Metwally A, Jiang L, Jian R, Chiang R, Oikonomopoulos A, Wu JC, Weissman IL, Mankowski JL, Holmes S, Loh KM, Nakauchi H, VandeVoort CA, Snyder MP. Chimpanzee and pig-tailed macaque iPSCs: Improved culture and generation of primate cross-species embryos. Cell Rep 2022; 40:111264. [PMID: 36044843 PMCID: PMC10075238 DOI: 10.1016/j.celrep.2022.111264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/06/2022] [Accepted: 08/04/2022] [Indexed: 12/26/2022] Open
Abstract
As our closest living relatives, non-human primates uniquely enable explorations of human health, disease, development, and evolution. Considerable effort has thus been devoted to generating induced pluripotent stem cells (iPSCs) from multiple non-human primate species. Here, we establish improved culture methods for chimpanzee (Pan troglodytes) and pig-tailed macaque (Macaca nemestrina) iPSCs. Such iPSCs spontaneously differentiate in conventional culture conditions, but can be readily propagated by inhibiting endogenous WNT signaling. As a unique functional test of these iPSCs, we injected them into the pre-implantation embryos of another non-human species, rhesus macaques (Macaca mulatta). Ectopic expression of gene BCL2 enhances the survival and proliferation of chimpanzee and pig-tailed macaque iPSCs within the pre-implantation embryo, although the identity and long-term contribution of the transplanted cells warrants further investigation. In summary, we disclose transcriptomic and proteomic data, cell lines, and cell culture resources that may be broadly enabling for non-human primate iPSCs research.
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Affiliation(s)
- Morteza Roodgar
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Fabian P Suchy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lan H Nguyen
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Vivek K Bajpai
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jose G Vilches-Moure
- Department of Comparative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Kevin Van Bortle
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Joydeep Bhadury
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Biomedicine, Sahlgrenska University Hospital, University of Gothenburg, SE 413 45 Gothenburg, Sweden
| | - Ahmed Metwally
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Rosaria Chiang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Angelos Oikonomopoulos
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph L Mankowski
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Kyle M Loh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hiromitsu Nakauchi
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Catherine A VandeVoort
- California National Primate Research Center and Department of Obstetrics and Gynecology, University of California, Davis, Davis, CA, USA.
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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46
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Khateb M, Perovanovic J, Ko KD, Jiang K, Feng X, Acevedo-Luna N, Chal J, Ciuffoli V, Genzor P, Simone J, Haase AD, Pourquié O, Dell'Orso S, Sartorelli V. Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution. Cell Rep 2022; 40:111219. [PMID: 35977485 DOI: 10.1016/j.celrep.2022.111219] [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: 03/31/2022] [Revised: 06/11/2022] [Accepted: 07/25/2022] [Indexed: 11/03/2022] Open
Abstract
Embryonic stem cells (ESCs) can adopt lineage-specific gene-expression programs by stepwise exposure to defined factors, resulting in the generation of functional cell types. Bulk and single-cell-based assays were employed to catalog gene expression, histone modifications, chromatin conformation, and accessibility transitions in ESC populations and individual cells acquiring a presomitic mesoderm fate and undergoing further specification toward myogenic and neurogenic lineages. These assays identified cis-regulatory regions and transcription factors presiding over gene-expression programs occurring at defined ESC transitions and revealed the presence of heterogeneous cell populations within discrete ESC developmental stages. The datasets were employed to identify previously unappreciated genomic elements directing the initial activation of Pax7 and myogenic and neurogenic gene-expression programs. This study provides a resource for the discovery of genomic and transcriptional features of pluripotent, mesoderm-induced ESCs and ESC-derived cell lineages.
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Affiliation(s)
- Mamduh Khateb
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Jelena Perovanovic
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Kyung Dae Ko
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Kan Jiang
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD, USA
| | - Xuesong Feng
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Natalia Acevedo-Luna
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Jérome Chal
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Boston, MA, USA
| | - Veronica Ciuffoli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Pavol Genzor
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - James Simone
- FlowCytometry Section, NIAMS, NIH, Bethesda, MD, USA
| | - Astrid D Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Boston, MA, USA
| | | | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA.
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47
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Wang X, Wu Q. The Divergent Pluripotent States in Mouse and Human Cells. Genes (Basel) 2022; 13:genes13081459. [PMID: 36011370 PMCID: PMC9408542 DOI: 10.3390/genes13081459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022] Open
Abstract
Pluripotent stem cells (PSCs), which can self-renew and give rise to all cell types in all three germ layers, have great potential in regenerative medicine. Recent studies have shown that PSCs can have three distinct but interrelated pluripotent states: naive, formative, and primed. The PSCs of each state are derived from different stages of the early developing embryo and can be maintained in culture by different molecular mechanisms. In this review, we summarize the current understanding on features of the three pluripotent states and review the underlying molecular mechanisms of maintaining their identities. Lastly, we discuss the interrelation and transition among these pluripotency states. We believe that comprehending the divergence of pluripotent states is essential to fully harness the great potential of stem cells in regenerative medicine.
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Affiliation(s)
| | - Qiang Wu
- Correspondence: ; Tel.: +853-8897-2708
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48
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Perera M, Nissen SB, Proks M, Pozzi S, Monteiro RS, Trusina A, Brickman JM. Transcriptional heterogeneity and cell cycle regulation as central determinants of primitive endoderm priming. eLife 2022; 11:78967. [PMID: 35969041 PMCID: PMC9417417 DOI: 10.7554/elife.78967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
During embryonic development cells acquire identity as they proliferate, implying that an intrinsic facet of cell fate choice requires coupling lineage decisions to cell division. How is the cell cycle regulated to promote or suppress heterogeneity and differentiation? We explore this question combining time lapse imaging with single-cell RNA-seq in the contexts of self-renewal, priming, and differentiation of mouse embryonic stem cells (ESCs) towards the Primitive Endoderm (PrE) lineage. Since ESCs are derived from the inner cell mass (ICM) of the mammalian blastocyst, ESCs in standard culture conditions are transcriptionally heterogeneous containing dynamically interconverting subfractions primed for either of the two ICM lineages, Epiblast and PrE. Here, we find that differential regulation of cell cycle can tip the balance between these primed populations, such that naïve ESC culture promotes Epiblast-like expansion and PrE differentiation stimulates the selective survival and proliferation of PrE-primed cells. In endoderm differentiation, this change is accompanied by a counter-intuitive increase in G1 length, also observed in vivo. While fibroblast growth factor/extracellular signal-regulated kinase (FGF/ERK) signalling is a key regulator of ESC differentiation and PrE specification, we find it is not just responsible for ESCs heterogeneity, but also the inheritance of similar cell cycles between sisters and cousins. Taken together, our results indicate a tight relationship between transcriptional heterogeneity and cell cycle regulation in lineage specification, with primed cell populations providing a pool of flexible cell types that can be expanded in a lineage-specific fashion while allowing plasticity during early determination.
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Affiliation(s)
- Marta Perera
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Martin Proks
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sara Pozzi
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rita Soares Monteiro
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joshua M Brickman
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
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Borges G, Criqui M, Harrington L. Tieing together loose ends: telomere instability in cancer and aging. Mol Oncol 2022; 16:3380-3396. [PMID: 35920280 PMCID: PMC9490142 DOI: 10.1002/1878-0261.13299] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/27/2022] [Accepted: 08/02/2022] [Indexed: 11/29/2022] Open
Abstract
Telomere maintenance is essential for maintaining genome integrity in both normal and cancer cells. Without functional telomeres, chromosomes lose their protective structure and undergo fusion and breakage events that drive further genome instability, including cell arrest or death. One means by which this loss can be overcome in stem cells and cancer cells is via re‐addition of G‐rich telomeric repeats by the telomerase reverse transcriptase (TERT). During aging of somatic tissues, however, insufficient telomerase expression leads to a proliferative arrest called replicative senescence, which is triggered when telomeres reach a critically short threshold that induces a DNA damage response. Cancer cells express telomerase but do not entirely escape telomere instability as they often possess short telomeres; hence there is often selection for genetic alterations in the TERT promoter that result in increased telomerase expression. In this review, we discuss our current understanding of the consequences of telomere instability in cancer and aging, and outline the opportunities and challenges that lie ahead in exploiting the reliance of cells on telomere maintenance for preserving genome stability.
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Affiliation(s)
- Gustavo Borges
- University of Montreal, Molecular Biology Programme, Institute for Research in Immunology and Cancer, 2950 chemin Polytechnique, Montreal, Quebec, Canada H3T 1J4
| | - Mélanie Criqui
- University of Montreal, Molecular Biology Programme, Institute for Research in Immunology and Cancer, 2950 chemin Polytechnique, Montreal, Quebec, Canada H3T 1J4
| | - Lea Harrington
- University of Montreal, Molecular Biology Programme, Institute for Research in Immunology and Cancer, 2950 chemin Polytechnique, Montreal, Quebec, Canada H3T 1J4.,Departments of Medicine and Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3T 1J4
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Zhang B, Feng J. Mouse embryonic stem cells require multiple amino acids. Exp Biol Med (Maywood) 2022; 247:1379-1387. [PMID: 35611795 PMCID: PMC9442457 DOI: 10.1177/15353702221096059] [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: 01/17/2022] [Accepted: 04/05/2022] [Indexed: 02/03/2023] Open
Abstract
Previous studies suggest that mouse embryonic stem cells (mESCs) have a unique requirement for threonine when cultured in serum and leukemia inhibitory factor (LIF). Here, we replicated the experiments and found that the growth of mESCs (E14 and AB2.2) in serum/LIF was significantly attenuated by the individual absence of multiple amino acids. When mESCs were maintained in naïve pluripotency by the MEK inhibitor, GSK3 inhibitor (2i), and LIF, their growth was significantly affected by the lack of any one of the nine essential amino acids or some non-essential amino acids. There was no unique requirement for threonine in both culture conditions. This study shows that, like many other cells, mESCs do not have any special requirements for amino acids.
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Affiliation(s)
- Boyang Zhang
- Department of Physiology and Biophysics, The State
University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Jian Feng
- Department of Physiology and Biophysics, The State
University of New York at Buffalo, Buffalo, NY 14203, USA
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