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Li-Bao L, Díaz-Díaz C, Raiola M, Sierra R, Temiño S, Moya FJ, Rodriguez-Perales S, Santos E, Giovinazzo G, Bleckwehl T, Rada-Iglesias Á, Spitz F, Torres M. Regulation of Myc transcription by an enhancer cluster dedicated to pluripotency and early embryonic expression. Nat Commun 2024; 15:3931. [PMID: 38729993 PMCID: PMC11087473 DOI: 10.1038/s41467-024-48258-5] [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] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
MYC plays various roles in pluripotent stem cells, including the promotion of somatic cell reprogramming to pluripotency, the regulation of cell competition and the control of embryonic diapause. However, how Myc expression is regulated in this context remains unknown. The Myc gene lies within a ~ 3-megabase gene desert with multiple cis-regulatory elements. Here we use genomic rearrangements, transgenesis and targeted mutation to analyse Myc regulation in early mouse embryos and pluripotent stem cells. We identify a topologically-associated region that homes enhancers dedicated to Myc transcriptional regulation in stem cells of the pre-implantation and early post-implantation embryo. Within this region, we identify elements exclusively dedicated to Myc regulation in pluripotent cells, with distinct enhancers that sequentially activate during naive and formative pluripotency. Deletion of pluripotency-specific enhancers dampens embryonic stem cell competitive ability. These results identify a topologically defined enhancer cluster dedicated to early embryonic expression and uncover a modular mechanism for the regulation of Myc expression in different states of pluripotency.
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Affiliation(s)
- Lin Li-Bao
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro Andaluz de Biología del Desarrollo (CABD), Sevilla, Spain
| | - Covadonga Díaz-Díaz
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Morena Raiola
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Rocío Sierra
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Susana Temiño
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Francisco J Moya
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Sandra Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Elisa Santos
- Pluripotent Cell Technology Unit, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Giovanna Giovinazzo
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Pluripotent Cell Technology Unit, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Tore Bleckwehl
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Álvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria, Santander, Spain
| | - Francois Spitz
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Miguel Torres
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.
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2
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Polat S, Yazir Y, Duruksu G, Kiliç KC, Mert S, Gacar G, Öncel Duman B, Halbutoğullari ZS. Investigation of the differentiation potential of pericyte cells as an alternative source of mesenchymal stem cells. Acta Histochem 2024; 126:152145. [PMID: 38432161 DOI: 10.1016/j.acthis.2024.152145] [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: 11/03/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND The mesenchymal stem cells (MSCs) with characterized by their multipotency and capacity to differentiate into various tissue cell types, have led to their incorporation in regenerative medicine research. However, the limited numbers of MSCs in the human body and their diverse differentiation capabilities in tissues highlight the need for exploring alternative regenerative cell sources. In this study, therefore, we conducted molecular level examinations to determine whether pericytes, specialized cell communities situated near blood vessels, could serve as a substitute for human bone marrow-derived mesenchymal stem cells (hBM-MSCs). In this context, the potential application of pericytes surrounds the vessels when MSCs are insufficient for functional purposes. METHODS The pericytes utilized in this investigation were derived from the placenta and characterized at the third passage. Similarly, the hBM-MSCs were also characterized at the third passage. The pluripotent properties of the two cell types were assessed at the gene expression level. Thereafter, both pericytes and hBM-MSCs were directed towards adipogenic, osteogenic and chondrogenic differentiation. The cells in both groups were examined on days 7, 14, and, 21 and their differentiation status was compared both immunohistochemically and through gene expression analysis. RESULTS Upon comparing the pluripotency characteristics of placental pericytes and hBM-MSCs, it was discovered that there was a substantial upregulation of the pluripotency genes FoxD3, Sox2, ZPF42, UTF1, and, Lin28 in both cell types. However, no significant expression of the genes Msx1, Nr6a1, Pdx1, and, GATA6 was observed in either cell type. It was also noted that pericytes differentiate into adipogenic, osteogenic and, chondrogenic lineages similar to hBM-MSCs. DISCUSSION As a result, it has been determined that pericytes exhibit high differentiation and proliferation properties similar to those of MSCs, and therefore can be considered a suitable alternative cell source for regenerative medicine and tissue engineering research, in cases where MSCs are not available or insufficient. It is notable that pericytes have been suggested as a potential substitute in studies where MSCs are lacking.
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Affiliation(s)
- Selen Polat
- Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey
| | - Yusufhan Yazir
- Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey; Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey; Department of Histology and Embryology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey.
| | - Gökhan Duruksu
- Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey; Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey
| | - Kamil Can Kiliç
- Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey
| | - Serap Mert
- Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey; Department of Chemistry and Chemical Processing Technologies, Kocaeli University, Kocaeli, Turkey; Department of Polymer Science and Technology, Kocaeli University, Kocaeli, Turkey
| | - Gülçin Gacar
- Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey; Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey
| | - Büşra Öncel Duman
- Medical Laboratory Techniques Program, European Vocational School, Kocaeli Health and Technology University, Kocaeli, Turkey
| | - Zehra Seda Halbutoğullari
- Department of Stem Cell, Institute of Health Sciences, Kocaeli University, Kocaeli, Turkey; Center for Stem Cell and Gene Therapies Research and Practice, Kocaeli University, Kocaeli, Turkey; Department of Medical Biology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
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3
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Ishikawa M, Sugino S, Masuda Y, Tarumoto Y, Seto Y, Taniyama N, Wagai F, Yamauchi Y, Kojima Y, Kiryu H, Yusa K, Eiraku M, Mochizuki A. RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations. Commun Biol 2023; 6:1290. [PMID: 38155269 PMCID: PMC10754834 DOI: 10.1038/s42003-023-05594-4] [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: 12/08/2022] [Accepted: 11/15/2023] [Indexed: 12/30/2023] Open
Abstract
Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks with causal relationships. However, a snapshot of single-cell CRISPR data may not lead to an accurate inference, since a gene knockout can influence multi-layered downstream over time. Here, we developed RENGE, a computational method that infers gene regulatory networks using a time-series single-cell CRISPR dataset. RENGE models the propagation process of the effects elicited by a gene knockout on its regulatory network. It can distinguish between direct and indirect regulations, which allows for the inference of regulations by genes that are not knocked out. RENGE therefore outperforms current methods in the accuracy of inferring gene regulatory networks. When used on a dataset we derived from human-induced pluripotent stem cells, RENGE yielded a network consistent with multiple databases and literature. Accurate inference of gene regulatory networks by RENGE would enable the identification of key factors for various biological systems.
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Affiliation(s)
- Masato Ishikawa
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan.
| | - Seiichi Sugino
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yoshie Masuda
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yusuke Tarumoto
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yusuke Seto
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Nobuko Taniyama
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Fumi Wagai
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yuhei Yamauchi
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yasuhiro Kojima
- Laboratory of Computational Life Science, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Hisanori Kiryu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Kosuke Yusa
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Mototsugu Eiraku
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8507, Japan
| | - Atsushi Mochizuki
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
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4
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Hong L, Hong S, Zhang X. Expression and Functional Analysis of core stemness factors OSKM (OCT4, SOX2, KLF4, and MYC) in Pan-cancer. Medicine (Baltimore) 2023; 102:e36433. [PMID: 38050242 PMCID: PMC10695605 DOI: 10.1097/md.0000000000036433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/10/2023] [Indexed: 12/06/2023] Open
Abstract
The dedifferentiation process of tumorigenesis and somatic cell reprogramming has some commonness and differences, which is the key question to cancer therapeutic strategy and stem cell applications. To further explore the commonalities and variance between carcinogenesis and induced pluripotent stem cell reprogramming, we investigated the role of stemness factors OSKM (OCT4, SOX2, KLF4, and MYC) in the pan-cancer process using public clinical data. Expression of OSKM in human pan-cancer was analyzed via the Genotype Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) database based on the RNA-seq data of tissues. The correlation of expression between OSKM genes was analyzed via the Tumor Immune Evaluation Resource (TIMER) database, while the STRING tool was used to construct the protein-protein interaction network for OSKM. Prognostic impact of OSKM in pan-cancer was analyzed by Cox proportional hazards regression model. The relationships between OSKM and tumor stemness, tumor microenvironment and immune checkpoint and were performed by Sangerbox platform using Pearson correlation analysis. Our results showed that OSKM were universally expressed and significantly altered in tumors compared with adjacent normal tissues in most tumor types. In addition, correlation analysis revealed the relevance of OSKM genes to patient prognosis, cancer cell stemness, tumor microenvironment or immune checkpoint. However, there is little similarity between these genes in terms of how they function in each cancer type. This study elucidates the different roles of core stemness factors OSKM in pan-cancer, offering potential therapeutic targets for novel anti-cancer strategies and knowledge to minimize the potential carcinogenic effects during stem cell transplantation.
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Affiliation(s)
- Liwei Hong
- Xiamen Key Laboratory of Basic and Clinical Research on Major Obstetrical Diseases, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
- Medical College, Nanchang Institute of Technology, Nanchang, China
- Xiamen Clinical Research Center for Perinatal Medicine, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Sijie Hong
- Department of Ultrasound, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Xueqin Zhang
- Xiamen Key Laboratory of Basic and Clinical Research on Major Obstetrical Diseases, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Clinical Research Center for Perinatal Medicine, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
- Department of Obstetrics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
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5
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Ronima K R, Dey C, Thummer RP. An Insight into the Role of GLIS1 in Embryonic Development, iPSC Generation, and Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023. [PMID: 37978100 DOI: 10.1007/5584_2023_793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The curiosity to discover transcription factors to reprogram somatic cells to induced pluripotent stem cells (iPSCs) resulted in the identification of a reprogramming factor, Gli-similar transcription factor GLIS1. This proline-rich Kruppel-like zinc finger transcription factor has a role in embryonic development, iPSC generation, and cancer. The spatial and temporal expression of GLIS1 during embryonic development implicates that it can control gene expression at specific developmental stages. Moreover, GLIS1 in combination with OCT4, SOX2, and KLF4 reprogramming factors resulted in an increase in reprogramming efficiency, giving rise to primarily bona fide iPSCs. Mutations in the GLIS1 gene are associated with several types of tumors and cancers, and it shows a tissue-specific function where it acts either as an oncogene or as a tumor suppressor gene. This review gives a comprehensive overview of GLIS1 and its important role in embryonic development, cancer, and the generation of iPSCs.
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Affiliation(s)
- Ronima K R
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Chandrima Dey
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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6
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Partscht P, Schiebel E. The diverging role of CDC14B: from mitotic exit in yeast to cell fate control in humans. EMBO J 2023; 42:e114364. [PMID: 37493185 PMCID: PMC10425841 DOI: 10.15252/embj.2023114364] [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: 04/25/2023] [Revised: 05/22/2023] [Accepted: 07/07/2023] [Indexed: 07/27/2023] Open
Abstract
CDC14, originally identified as crucial mediator of mitotic exit in budding yeast, belongs to the family of dual-specificity phosphatases (DUSPs) that are present in most eukaryotes. Contradicting data have sparked a contentious discussion whether a cell cycle role is conserved in the human paralogs CDC14A and CDC14B but possibly masked due to redundancy. Subsequent studies on CDC14A and CDC14B double knockouts in human and mouse demonstrated that CDC14 activity is dispensable for mitotic progression in higher eukaryotes and instead suggested functional specialization. In this review, we provide a comprehensive overview of our current understanding of how faithful cell division is linked to phosphorylation and dephosphorylation and compare functional similarities and divergences between the mitotic phosphatases CDC14, PP2A, and PP1 from yeast and higher eukaryotes. Furthermore, we review the latest discoveries on CDC14B, which identify this nuclear phosphatase as a key regulator of gene expression and reveal its role in neuronal development. Finally, we discuss CDC14B functions in meiosis and possible implications in other developmental processes.
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Affiliation(s)
- Patrick Partscht
- Zentrum für Molekulare BiologieUniversität Heidelberg, DKFZ‐ZMBH AllianzHeidelbergGermany
| | - Elmar Schiebel
- Zentrum für Molekulare BiologieUniversität Heidelberg, DKFZ‐ZMBH AllianzHeidelbergGermany
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7
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Ayers KL, Eggers S, Rollo BN, Smith KR, Davidson NM, Siddall NA, Zhao L, Bowles J, Weiss K, Zanni G, Burglen L, Ben-Shachar S, Rosensaft J, Raas-Rothschild A, Jørgensen A, Schittenhelm RB, Huang C, Robevska G, van den Bergen J, Casagranda F, Cyza J, Pachernegg S, Wright DK, Bahlo M, Oshlack A, O'Brien TJ, Kwan P, Koopman P, Hime GR, Girard N, Hoffmann C, Shilon Y, Zung A, Bertini E, Milh M, Ben Rhouma B, Belguith N, Bashamboo A, McElreavey K, Banne E, Weintrob N, BenZeev B, Sinclair AH. Variants in SART3 cause a spliceosomopathy characterised by failure of testis development and neuronal defects. Nat Commun 2023; 14:3403. [PMID: 37296101 PMCID: PMC10256788 DOI: 10.1038/s41467-023-39040-0] [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: 04/03/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Squamous cell carcinoma antigen recognized by T cells 3 (SART3) is an RNA-binding protein with numerous biological functions including recycling small nuclear RNAs to the spliceosome. Here, we identify recessive variants in SART3 in nine individuals presenting with intellectual disability, global developmental delay and a subset of brain anomalies, together with gonadal dysgenesis in 46,XY individuals. Knockdown of the Drosophila orthologue of SART3 reveals a conserved role in testicular and neuronal development. Human induced pluripotent stem cells carrying patient variants in SART3 show disruption to multiple signalling pathways, upregulation of spliceosome components and demonstrate aberrant gonadal and neuronal differentiation in vitro. Collectively, these findings suggest that bi-allelic SART3 variants underlie a spliceosomopathy which we tentatively propose be termed INDYGON syndrome (Intellectual disability, Neurodevelopmental defects and Developmental delay with 46,XY GONadal dysgenesis). Our findings will enable additional diagnoses and improved outcomes for individuals born with this condition.
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Affiliation(s)
- Katie L Ayers
- The Murdoch Children's Research Institute, Melbourne, Australia.
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia.
| | - Stefanie Eggers
- The Victorian Clinical Genetics Services, Melbourne, Australia
| | - Ben N Rollo
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
| | - Katherine R Smith
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Nadia M Davidson
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- School of BioSciences, Faculty of Science, University of Melbourne, Melbourne, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Nicole A Siddall
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Liang Zhao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Josephine Bowles
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Institute of Technology, Haifa, Israel
| | - Ginevra Zanni
- Unit of Muscular and Neurodegenerative Disorders and Unit of Developmental Neurology, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lydie Burglen
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Et Laboratoire de Neurogénétique Moléculaire, Département de Génétique et Embryologie Médicale, APHP. Sorbonne Université, Hôpital Trousseau, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Shay Ben-Shachar
- Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Jenny Rosensaft
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Annick Raas-Rothschild
- Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anne Jørgensen
- Department of Growth and Reproduction, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Cheng Huang
- Monash Proteomics and Metabolomics Facility, Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | | | | | - Franca Casagranda
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Justyna Cyza
- The Murdoch Children's Research Institute, Melbourne, Australia
| | - Svenja Pachernegg
- The Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - David K Wright
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
| | - Melanie Bahlo
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Alicia Oshlack
- The Peter MacCallum Cancer Centre, Melbourne, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Terrence J O'Brien
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, Australia
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Centre, Melbourne, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Gary R Hime
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
| | - Nadine Girard
- Aix-Marseille Université, APHM. Department of Pediatric Neurology, Timone Hospital, Marseille, France
| | - Chen Hoffmann
- Radiology Department, Sheba medical Centre, Tel Aviv, Israel
| | - Yuval Shilon
- Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Amnon Zung
- Pediatrics Department, Kaplan Medical Center, Rehovot, 76100, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Hadassah Medical School, Jerusalem, Israel
| | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Disorders and Unit of Developmental Neurology, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Mathieu Milh
- Aix-Marseille Université, APHM. Department of Pediatric Neurology, Timone Hospital, Marseille, France
| | - Bochra Ben Rhouma
- Higher Institute of Nursing Sciences of Gabes, University of Gabes, Gabes, Tunisia
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| | - Neila Belguith
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Anu Bashamboo
- Institut Pasteur, Université de Paris, CNRS UMR3738, Human Developmental Genetics, 75015, Paris, France
| | - Kenneth McElreavey
- Institut Pasteur, Université de Paris, CNRS UMR3738, Human Developmental Genetics, 75015, Paris, France
| | - Ehud Banne
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
- The Rina Mor Genetic Institute, Wolfson Medical Center, Holon, 58100, Israel
| | - Naomi Weintrob
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Pediatric Endocrinology Unit, Dana-Dwek Children's Hospital, Tel Aviv Medical Center, Tel Aviv, Israel
| | | | - Andrew H Sinclair
- The Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Australia
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8
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Villarroya‐Beltri C, Martins AFB, García A, Giménez D, Zarzuela E, Novo M, del Álamo C, González‐Martínez J, Bonel‐Pérez GC, Díaz I, Guillamot M, Chiesa M, Losada A, Graña‐Castro O, Rovira M, Muñoz J, Salazar‐Roa M, Malumbres M. Mammalian CDC14 phosphatases control exit from stemness in pluripotent cells. EMBO J 2023; 42:e111251. [PMID: 36326833 PMCID: PMC9811616 DOI: 10.15252/embj.2022111251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Maintenance of stemness is tightly linked to cell cycle regulation through protein phosphorylation by cyclin-dependent kinases (CDKs). However, how this process is reversed during differentiation is unknown. We report here that exit from stemness and differentiation of pluripotent cells along the neural lineage are controlled by CDC14, a CDK-counteracting phosphatase whose function in mammals remains obscure. Lack of the two CDC14 family members, CDC14A and CDC14B, results in deficient development of the neural system in the mouse and impairs neural differentiation from embryonic stem cells (ESCs). Mechanistically, CDC14 directly dephosphorylates specific proline-directed Ser/Thr residues of undifferentiated embryonic transcription Factor 1 (UTF1) during the exit from stemness, triggering its proteasome-dependent degradation. Multiomic single-cell analysis of transcription and chromatin accessibility in differentiating ESCs suggests that increased UTF1 levels in the absence of CDC14 prevent the proper firing of bivalent promoters required for differentiation. CDC14 phosphatases are dispensable for mitotic exit, suggesting that CDC14 phosphatases have evolved to control stemness rather than cell cycle exit and establish the CDK-CDC14 axis as a critical molecular switch for linking cell cycle regulation and self-renewal.
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Affiliation(s)
| | - Ana Filipa B Martins
- Cell Division and Cancer groupSpanish National Cancer Research Centre (CNIO)MadridSpain
| | - Alejandro García
- Cell Division and Cancer groupSpanish National Cancer Research Centre (CNIO)MadridSpain
| | | | | | - Mónica Novo
- Cell Division and Cancer groupSpanish National Cancer Research Centre (CNIO)MadridSpain
| | - Cristina del Álamo
- Cell Division and Cancer groupSpanish National Cancer Research Centre (CNIO)MadridSpain
| | | | - Gloria C Bonel‐Pérez
- Cell Division and Cancer groupSpanish National Cancer Research Centre (CNIO)MadridSpain
| | - Irene Díaz
- Cell Division and Cancer groupSpanish National Cancer Research Centre (CNIO)MadridSpain
| | - María Guillamot
- Cell Division and Cancer groupSpanish National Cancer Research Centre (CNIO)MadridSpain
| | - Massimo Chiesa
- Cell Division and Cancer groupSpanish National Cancer Research Centre (CNIO)MadridSpain
| | - Ana Losada
- Chromosome Dynamics groupCNIOMadridSpain
| | - Osvaldo Graña‐Castro
- Bioinformatics UnitCNIOMadridSpain
- Present address:
Department of Basic Medical Sciences, Institute of Applied Molecular Medicine (IMMA‐Nemesio Díez), School of MedicineSan Pablo‐CEU University, CEU UniversitiesBoadilla del MonteSpain
| | - Meritxell Rovira
- Department of Physiological Science, School of Medicine, L'Hospitalet de LlobregatUniversity of Barcelona (UB)BarcelonaSpain
- Pancreas Regeneration: Pancreatic Progenitors and Their Niche Group, Regenerative Medicine Program, P‐CMR[C]Institut d'Investigació Biomèdica de Bellvitge—IDIBELL, L'Hospitalet de LlobregatBarcelonaSpain
| | | | - María Salazar‐Roa
- Cell Division and Cancer groupSpanish National Cancer Research Centre (CNIO)MadridSpain
- Present address:
Advanced Therapies and Cancer Group, Faculty of BiologyComplutense UniversityMadridSpain
| | - Marcos Malumbres
- Cell Division and Cancer groupSpanish National Cancer Research Centre (CNIO)MadridSpain
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9
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Kulkarni P, Leite VBP, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J, Srivastava A, Jolly MK, Onuchic JN, Uversky VN, Salgia R. Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma. BIOPHYSICS REVIEWS 2022; 3:011306. [PMID: 38505224 PMCID: PMC10903413 DOI: 10.1063/5.0080512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/17/2022] [Indexed: 03/21/2024]
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as ensembles that sample a quasi-continuum of rapidly interconverting conformations and, as such, may represent proteins at the extreme limit of the Anfinsen postulate. IDPs play important biological roles and are key components of the cellular protein interaction network (PIN). Many IDPs can interconvert between disordered and ordered states as they bind to appropriate partners. Conformational dynamics of IDPs contribute to conformational noise in the cell. Thus, the dysregulation of IDPs contributes to increased noise and "promiscuous" interactions. This leads to PIN rewiring to output an appropriate response underscoring the critical role of IDPs in cellular decision making. Nonetheless, IDPs are not easily tractable experimentally. Furthermore, in the absence of a reference conformation, discerning the energy landscape representation of the weakly funneled IDPs in terms of reaction coordinates is challenging. To understand conformational dynamics in real time and decipher how IDPs recognize multiple binding partners with high specificity, several sophisticated knowledge-based and physics-based in silico sampling techniques have been developed. Here, using specific examples, we highlight recent advances in energy landscape visualization and molecular dynamics simulations to discern conformational dynamics and discuss how the conformational preferences of IDPs modulate their function, especially in phenotypic switching. Finally, we discuss recent progress in identifying small molecules targeting IDPs underscoring the potential therapeutic value of IDPs. Understanding structure and function of IDPs can not only provide new insight on cellular decision making but may also help to refine and extend Anfinsen's structure/function paradigm.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Supriyo Bhattacharyya
- Translational Bioinformatics, Center for Informatics, Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Srisairam Achuthan
- Center for Informatics, Division of Research Informatics, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Divyoj Singh
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Jose N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005-1892, USA
| | | | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
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10
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Garcia-Domi Nguez M. Proper progression of neurogenesis relies on a defined pattern of SUMO-modified proteins. Neural Regen Res 2022; 17:1731-1732. [PMID: 35017422 PMCID: PMC8820694 DOI: 10.4103/1673-5374.332134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Mario Garcia-Domi Nguez
- Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
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