1
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Phadte P, Bishnu A, Dey P, M M, Mehrotra M, Singh P, Chakrabarty S, Majumdar R, Rekhi B, Patra M, De A, Ray P. Autophagy-mediated ID1 turnover dictates chemo-resistant fate in ovarian cancer stem cells. J Exp Clin Cancer Res 2024; 43:222. [PMID: 39123206 PMCID: PMC11316295 DOI: 10.1186/s13046-024-03147-z] [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: 03/18/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND The mechanisms enabling dynamic shifts between drug-resistant and drug-sensitive states in cancer cells are still underexplored. This study investigated the role of targeted autophagic protein degradation in regulating ovarian cancer stem cell (CSC) fate decisions and chemo-resistance. METHODS Autophagy levels were compared between CSC-enriched side population (SP) and non-SP cells (NSP) in multiple ovarian cancer cell lines using immunoblotting, immunofluorescence, and transmission electron microscopy. The impact of autophagy modulation on CSC markers and differentiation was assessed by flow cytometry, immunoblotting and qRT-PCR. In silico modeling and co-immunoprecipitation identified ID1 interacting proteins. Pharmacological and genetic approaches along with Annexin-PI assay, ChIP assay, western blotting, qRT-PCR and ICP-MS were used to evaluate effects on cisplatin sensitivity, apoptosis, SLC31A1 expression, promoter binding, and intracellular platinum accumulation in ID1 depleted backdrop. Patient-derived tumor spheroids were analyzed for autophagy and SLC31A1 levels. RESULTS Ovarian CSCs exhibited increased basal autophagy compared to non-CSCs. Further autophagy stimulation by serum-starvation and chemical modes triggered proteolysis of the stemness regulator ID1, driving the differentiation of chemo-resistant CSCs into chemo-sensitive non-CSCs. In silico modeling predicted TCF12 as a potent ID1 interactor, which was validated by co-immunoprecipitation. ID1 depletion freed TCF12 to transactivate the cisplatin influx transporter SLC31A1, increasing intracellular cisplatin levels and cytotoxicity. Patient-derived tumor spheroids exhibited a functional association between autophagy, ID1, SLC31A1, and platinum sensitivity. CONCLUSIONS This study reveals a novel autophagy-ID1-TCF12-SLC31A1 axis where targeted autophagic degradation of ID1 enables rapid remodeling of CSCs to reverse chemo-resistance. Modulating this pathway could counter drug resistance in ovarian cancer.
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Affiliation(s)
- Pratham Phadte
- Imaging Cell Signalling & Therapeutics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Aniketh Bishnu
- Imaging Cell Signalling & Therapeutics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Pranay Dey
- Molecular Functional Imaging Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Manikandan M
- Laboratory of Medicinal Chemistry and Cell Biology, Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Megha Mehrotra
- Imaging Cell Signalling & Therapeutics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Prerna Singh
- Imaging Cell Signalling & Therapeutics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Shritama Chakrabarty
- Imaging Cell Signalling & Therapeutics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
- Indian Institute of Science Education and Research, Bhopal, 462066, India
| | - Rounak Majumdar
- Imaging Cell Signalling & Therapeutics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
- Indian Institute of Science Education and Research, Kolkata, 741246, India
| | - Bharat Rekhi
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
- Department of Pathology, Tata Memorial Hospital, Mumbai, 400012, India
| | - Malay Patra
- Laboratory of Medicinal Chemistry and Cell Biology, Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India
| | - Abhijit De
- Molecular Functional Imaging Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Pritha Ray
- Imaging Cell Signalling & Therapeutics Lab, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, 410210, India.
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
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2
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Maldotti M, Lauria A, Anselmi F, Molineris I, Tamburrini A, Meng G, Polignano IL, Scrivano MG, Campestre F, Simon LM, Rapelli S, Morandi E, Incarnato D, Oliviero S. The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7. Nucleic Acids Res 2022; 50:2587-2602. [PMID: 35137201 PMCID: PMC8934626 DOI: 10.1093/nar/gkac083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/13/2022] Open
Abstract
The histone acetyltransferase p300 (also known as KAT3B) is a general transcriptional coactivator that introduces the H3K27ac mark on enhancers triggering their activation and gene transcription. Genome-wide screenings demonstrated that a large fraction of long non-coding RNAs (lncRNAs) plays a role in cellular processes and organ development although the underlying molecular mechanisms remain largely unclear (1,2). We found 122 lncRNAs that interacts directly with p300. In depth analysis of one of these, lncSmad7, is required to maintain ESC self-renewal and it interacts to the C-terminal domain of p300. lncSmad7 also contains predicted RNA-DNA Hoogsteen forming base pairing. Combined Chromatin Isolation by RNA precipitation followed by sequencing (ChIRP-seq) together with CRISPR/Cas9 mutagenesis of the target sites demonstrate that lncSmad7 binds and recruits p300 to enhancers in trans, to trigger enhancer acetylation and transcriptional activation of its target genes. Thus, these results unveil a new mechanism by which p300 is recruited to the genome.
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Affiliation(s)
- Mara Maldotti
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Andrea Lauria
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Francesca Anselmi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Ivan Molineris
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Annalaura Tamburrini
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Guohua Meng
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Isabelle Laurence Polignano
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Mirko Giuseppe Scrivano
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Fabiola Campestre
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Lisa Marie Simon
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Stefania Rapelli
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Edoardo Morandi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Salvatore Oliviero
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
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3
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Jiménez C, Antonelli R, Masanas M, Soriano A, Devis-Jauregui L, Camacho J, Magdaleno A, Guillén G, Hladun R, Jubierre L, Roma J, Llobet-Navas D, Sánchez de Toledo J, Moreno L, Gallego S, Segura MF. Neuronal Differentiation-Related Epigenetic Regulator ZRF1 Has Independent Prognostic Value in Neuroblastoma but Is Functionally Dispensable In Vitro. Cancers (Basel) 2021; 13:cancers13194845. [PMID: 34638328 PMCID: PMC8508520 DOI: 10.3390/cancers13194845] [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: 08/26/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 11/27/2022] Open
Abstract
Simple Summary Neuroblastoma is the most common pediatric solid tumor occurring outside the brain, and it is thought to arise from cells that acquire errors during the normal process of embryonal development. Today, we know that embryonal development is regulated by epigenetics, a mechanism that determines which genes need to be expressed in each cell type and developmental step. Epigenetic errors, therefore, are considered contributory to the appearance and progression of tumors such as neuroblastoma. Here, we aimed at finding whether ZRF1, a known epigenetic regulator, could play a significant role in the aggressiveness of neuroblastoma. Our results suggest that ZRF1 does not seem to have any relevant function in neuroblastoma cells; however, the levels of this epigenetic regulator are related to the prognostic of neuroblastoma patients and could be used to predict their progression and improve the diagnosis. Abstract Neuroblastoma is a pediatric tumor of the peripheral nervous system that accounts for up to ~15% of all cancer-related deaths in children. Recently, it has become evident that epigenetic deregulation is a relevant event in pediatric tumors such as high-risk neuroblastomas, and a determinant for processes, such as cell differentiation blockade and sustained proliferation, which promote tumor progression and resistance to current therapies. Thus, a better understanding of epigenetic factors implicated in the aggressive behavior of neuroblastoma cells is crucial for the development of better treatments. In this study, we characterized the role of ZRF1, an epigenetic activator recruited to genes involved in the maintenance of the identity of neural progenitors. We combined analysis of patient sample expression datasets with loss- and gain-of-function studies on neuroblastoma cell lines. Functional analyses revealed that ZRF1 is functionally dispensable for those cellular functions related to cell differentiation, proliferation, migration, and invasion, and does not affect the cellular response to chemotherapeutic agents. However, we found that high levels of ZRF1 mRNA expression are associated to shorter overall survival of neuroblastoma patients, even when those patients with the most common molecular alterations used as prognostic factors are removed from the analyses, thereby suggesting that ZRF1 expression could be used as an independent prognostic factor in neuroblastoma.
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Affiliation(s)
- Carlos Jiménez
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (C.J.); (R.A.); (M.M.); (A.S.); (A.M.); (G.G.); (R.H.); (L.J.); (J.R.); (J.S.d.T.); (L.M.); (S.G.)
| | - Roberta Antonelli
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (C.J.); (R.A.); (M.M.); (A.S.); (A.M.); (G.G.); (R.H.); (L.J.); (J.R.); (J.S.d.T.); (L.M.); (S.G.)
| | - Marc Masanas
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (C.J.); (R.A.); (M.M.); (A.S.); (A.M.); (G.G.); (R.H.); (L.J.); (J.R.); (J.S.d.T.); (L.M.); (S.G.)
| | - Aroa Soriano
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (C.J.); (R.A.); (M.M.); (A.S.); (A.M.); (G.G.); (R.H.); (L.J.); (J.R.); (J.S.d.T.); (L.M.); (S.G.)
| | - Laura Devis-Jauregui
- Molecular Mechanisms and Experimental Therapy in Oncology-Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Spain; (L.D.-J.); (D.L.-N.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Jessica Camacho
- Pathology Department, Vall d’Hebron University Hospital—UAB, 08035 Barcelona, Spain;
| | - Ainara Magdaleno
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (C.J.); (R.A.); (M.M.); (A.S.); (A.M.); (G.G.); (R.H.); (L.J.); (J.R.); (J.S.d.T.); (L.M.); (S.G.)
| | - Gabriela Guillén
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (C.J.); (R.A.); (M.M.); (A.S.); (A.M.); (G.G.); (R.H.); (L.J.); (J.R.); (J.S.d.T.); (L.M.); (S.G.)
- Surgery Department, Vall d’Hebron University Hospital—UAB, 08035 Barcelona, Spain
| | - Raquel Hladun
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (C.J.); (R.A.); (M.M.); (A.S.); (A.M.); (G.G.); (R.H.); (L.J.); (J.R.); (J.S.d.T.); (L.M.); (S.G.)
- Pediatric Oncology and Hematology Department, Vall d’Hebron University Hospital—UAB, 08035 Barcelona, Spain
| | - Luz Jubierre
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (C.J.); (R.A.); (M.M.); (A.S.); (A.M.); (G.G.); (R.H.); (L.J.); (J.R.); (J.S.d.T.); (L.M.); (S.G.)
| | - Josep Roma
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (C.J.); (R.A.); (M.M.); (A.S.); (A.M.); (G.G.); (R.H.); (L.J.); (J.R.); (J.S.d.T.); (L.M.); (S.G.)
| | - David Llobet-Navas
- Molecular Mechanisms and Experimental Therapy in Oncology-Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Spain; (L.D.-J.); (D.L.-N.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Josep Sánchez de Toledo
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (C.J.); (R.A.); (M.M.); (A.S.); (A.M.); (G.G.); (R.H.); (L.J.); (J.R.); (J.S.d.T.); (L.M.); (S.G.)
- Catalan Institute of Oncology (ICO), 08908 L’Hospitalet de Llobregat, Spain
| | - Lucas Moreno
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (C.J.); (R.A.); (M.M.); (A.S.); (A.M.); (G.G.); (R.H.); (L.J.); (J.R.); (J.S.d.T.); (L.M.); (S.G.)
- Pediatric Oncology and Hematology Department, Vall d’Hebron University Hospital—UAB, 08035 Barcelona, Spain
| | - Soledad Gallego
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (C.J.); (R.A.); (M.M.); (A.S.); (A.M.); (G.G.); (R.H.); (L.J.); (J.R.); (J.S.d.T.); (L.M.); (S.G.)
- Pediatric Oncology and Hematology Department, Vall d’Hebron University Hospital—UAB, 08035 Barcelona, Spain
| | - Miguel F. Segura
- Group of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; (C.J.); (R.A.); (M.M.); (A.S.); (A.M.); (G.G.); (R.H.); (L.J.); (J.R.); (J.S.d.T.); (L.M.); (S.G.)
- Correspondence:
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4
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Long C, Li H, Li X, Yang W, Zuo Y. Nuclear Transfer Arrest Embryos Show Massive Dysregulation of Genes Involved in Transcription Pathways. Int J Mol Sci 2021; 22:ijms22158187. [PMID: 34360962 PMCID: PMC8347363 DOI: 10.3390/ijms22158187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/28/2022] Open
Abstract
Somatic cell nuclear transfer (SCNT) technology can reprogram terminally differentiated cell nuclei into a totipotent state. However, the underlying molecular barriers of SCNT embryo development remain incompletely elucidated. Here, we observed that transcription-related pathways were incompletely activated in nuclear transfer arrest (NTA) embryos compared to normal SCNT embryos and in vivo fertilized (WT) embryos, which hinders the development of SCNT embryos. We further revealed the transcription pathway associated gene regulatory networks (GRNs) and found the aberrant transcription pathways can lead to the massive dysregulation of genes in NTA embryos. The predicted target genes of transcription pathways contain a series of crucial factors in WT embryos, which play an important role in catabolic process, pluripotency regulation, epigenetic modification and signal transduction. In NTA embryos, however, these genes were varying degrees of inhibition and show a defect in synergy. Overall, our research found that the incomplete activation of transcription pathways is another potential molecular barrier for SCNT embryos besides the incomplete reprogramming of epigenetic modifications, broadening the understanding of molecular mechanism of SCNT embryonic development.
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5
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Jarrige M, Polvèche H, Carteron A, Janczarski S, Peschanski M, Auboeuf D, Martinat C. SISTEMA: A large and standardized collection of transcriptome data sets for human pluripotent stem cell research. iScience 2021; 24:102767. [PMID: 34278269 PMCID: PMC8271161 DOI: 10.1016/j.isci.2021.102767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/29/2021] [Accepted: 06/21/2021] [Indexed: 12/16/2022] Open
Abstract
Human pluripotent stem cells have ushered in an exciting new era for disease modeling, drug discovery, and cell therapy development. Continued progress toward realizing the potential of human pluripotent stem cells will be facilitated by robust data sets and complementary resources that are easily accessed and interrogated by the stem cell community. In this context, we present SISTEMA, a quality-controlled curated gene expression database, built on a valuable catalog of human pluripotent stem cell lines, and their derivatives for which transcriptomic analyses have been generated using a single experimental pipeline. SISTEMA functions as a one-step resource that will assist the stem cell community to easily evaluate the expression level for genes of interest, while comparing them across different hPSC lines, cell types, pathological conditions, or after pharmacological treatments.
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Affiliation(s)
| | | | | | - Stéphane Janczarski
- LBMC, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, 69007 Lyon, France
| | | | - Didier Auboeuf
- LBMC, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, 69007 Lyon, France
| | - Cécile Martinat
- INSERM/UEVE UMR 861, Paris Saclay Univ I-STEM, 91100 Corbeil-Essonnes, France
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6
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Teo WS, Holliday H, Karthikeyan N, Cazet AS, Roden DL, Harvey K, Konrad CV, Murali R, Varghese BA, Thankamony AP, Chan CL, McFarland A, Junankar S, Ye S, Yang J, Nikolic I, Shah JS, Baker LA, Millar EKA, Naylor MJ, Ormandy CJ, Lakhani SR, Kaplan W, Mellick AS, O'Toole SA, Swarbrick A, Nair R. Id Proteins Promote a Cancer Stem Cell Phenotype in Mouse Models of Triple Negative Breast Cancer via Negative Regulation of Robo1. Front Cell Dev Biol 2020; 8:552. [PMID: 32766238 PMCID: PMC7380117 DOI: 10.3389/fcell.2020.00552] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/10/2020] [Indexed: 01/02/2023] Open
Abstract
Breast cancers display phenotypic and functional heterogeneity and several lines of evidence support the existence of cancer stem cells (CSCs) in certain breast cancers, a minor population of cells capable of tumor initiation and metastatic dissemination. Identifying factors that regulate the CSC phenotype is therefore important for developing strategies to treat metastatic disease. The Inhibitor of Differentiation Protein 1 (Id1) and its closely related family member Inhibitor of Differentiation 3 (Id3) (collectively termed Id) are expressed by a diversity of stem cells and are required for metastatic dissemination in experimental models of breast cancer. In this study, we show that ID1 is expressed in rare neoplastic cells within ER-negative breast cancers. To address the function of Id1 expressing cells within tumors, we developed independent murine models of Triple Negative Breast Cancer (TNBC) in which a genetic reporter permitted the prospective isolation of Id1+ cells. Id1+ cells are enriched for self-renewal in tumorsphere assays in vitro and for tumor initiation in vivo. Conversely, depletion of Id1 and Id3 in the 4T1 murine model of TNBC demonstrates that Id1/3 are required for cell proliferation and self-renewal in vitro, as well as primary tumor growth and metastatic colonization of the lung in vivo. Using combined bioinformatic analysis, we have defined a novel mechanism of Id protein function via negative regulation of the Roundabout Axon Guidance Receptor Homolog 1 (Robo1) leading to activation of a Myc transcriptional programme.
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Affiliation(s)
- Wee S. Teo
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | - Holly Holliday
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | - Nitheesh Karthikeyan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Aurélie S. Cazet
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | - Daniel L. Roden
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | - Kate Harvey
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | | | - Reshma Murali
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Binitha Anu Varghese
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Archana P. Thankamony
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
- Manipal Academy of Higher Education, Manipal, India
| | - Chia-Ling Chan
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | - Andrea McFarland
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Simon Junankar
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | - Sunny Ye
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Jessica Yang
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Iva Nikolic
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | - Jaynish S. Shah
- Gene & Stem Cell Therapy Program, Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Laura A. Baker
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | - Ewan K. A. Millar
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Department of Anatomical Pathology, NSW Health Pathology, St George Hospital, Kogarah, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Kensington, NSW, Australia
- School of Medicine, Western Sydney University, Penrith, NSW, Australia
| | - Matthew J. Naylor
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Discipline of Physiology & Bosch Institute, University of Sydney, Sydney, NSW, Australia
| | - Christopher J. Ormandy
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, School of Medicine and Pathology Queensland, Royal Brisbane & Women's Hospital, The University of Queensland, Herston, QLD, Australia
| | - Warren Kaplan
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Peter Wills Bioinformatics Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Albert S. Mellick
- UNSW Medicine, University of NSW, Kensington, NSW, Australia
- Medical Oncology Group, Ingham Institute for Applied Medical Research, South Western Sydney Clinical School UNSW & CONCERT Translational Cancer Research Centre, Liverpool, NSW, Australia
| | - Sandra A. O'Toole
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Alexander Swarbrick
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | - Radhika Nair
- Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
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7
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Rao C, Malaguti M, Mason JO, Lowell S. The transcription factor E2A drives neural differentiation in pluripotent cells. Development 2020; 147:dev184093. [PMID: 32487737 PMCID: PMC7328008 DOI: 10.1242/dev.184093] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 05/26/2020] [Indexed: 12/21/2022]
Abstract
The intrinsic mechanisms that link extracellular signalling to the onset of neural differentiation are not well understood. In pluripotent mouse cells, BMP blocks entry into the neural lineage via transcriptional upregulation of inhibitor of differentiation (Id) factors. We have previously identified the major binding partner of Id proteins in pluripotent cells as the basic helix-loop-helix (bHLH) transcription factor (TF) E2A. Id1 can prevent E2A from forming heterodimers with bHLH TFs or from forming homodimers. Here, we show that overexpression of a forced E2A homodimer is sufficient to drive robust neural commitment in pluripotent cells, even under non-permissive conditions. Conversely, we find that E2A null cells display a defect in their neural differentiation capacity. E2A acts as an upstream activator of neural lineage genes, including Sox1 and Foxd4, and as a repressor of Nodal signalling. Our results suggest a crucial role for E2A in establishing neural lineage commitment in pluripotent cells.
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Affiliation(s)
- Chandrika Rao
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Mattias Malaguti
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - John O Mason
- Centre for Discovery Brain Sciences, University of Edinburgh, 15 George Square, Edinburgh EH8 9XD, UK
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Sally Lowell
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
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8
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Malaguti M, Migueles RP, Blin G, Lin CY, Lowell S. Id1 Stabilizes Epiblast Identity by Sensing Delays in Nodal Activation and Adjusting the Timing of Differentiation. Dev Cell 2019; 50:462-477.e5. [PMID: 31204172 PMCID: PMC6706657 DOI: 10.1016/j.devcel.2019.05.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/04/2019] [Accepted: 05/13/2019] [Indexed: 12/11/2022]
Abstract
Controlling responsiveness to prevailing signals is critical for robust transitions between cell states during development. For example, fibroblast growth factor (FGF) drives naive pluripotent cells into extraembryonic lineages before implantation but sustains pluripotency in primed cells of the post-implantation epiblast. Nanog supports pluripotency in naive cells, while Nodal supports pluripotency in primed cells, but the handover from Nanog to Nodal does not proceed seamlessly, opening up the risk of aberrant differentiation if FGF is activated before Nodal. Here, we report that Id1 acts as a sensor to detect delays in Nodal activation after the downregulation of Nanog. Id1 then suppresses FGF activity to delay differentiation. Accordingly, Id1 is not required for naive or primed pluripotency but rather stabilizes epiblast identity during the transition between these states. These findings help explain how development proceeds robustly in the face of imprecise signals and highlight the importance of mechanisms that stabilize cell identity during developmental transitions.
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Affiliation(s)
- Mattias Malaguti
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, the University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Rosa Portero Migueles
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, the University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Guillaume Blin
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, the University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Chia-Yi Lin
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, the University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Sally Lowell
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, the University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK.
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9
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Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70. PLoS One 2019; 14:e0217098. [PMID: 31091298 PMCID: PMC6519820 DOI: 10.1371/journal.pone.0217098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/03/2019] [Indexed: 11/28/2022] Open
Abstract
The J-domain protein Zuotin is a multi-domain eukaryotic Hsp70 co-chaperone. Though it is primarily ribosome-associated, positioned at the exit of the 60S subunit tunnel where it promotes folding of nascent polypeptide chains, Zuotin also has off-ribosome functions. Domains of Zuotin needed for 60S association and interaction with Hsp70 are conserved in eukaryotes. However, whether the 4-helix bundle (4HB) domain is conserved remains an open question. We undertook evolutionary and structural approaches to clarify this issue. We found that the 4HB segment of human Zuotin also forms a bundle of 4 helices. The positive charge of Helix I, which in Saccharomyces cerevisiae is responsible for interaction with the 40S subunit, is particularly conserved. However, the C-termini of fungal and human 4HBs are not similar. In fungi the C-terminal segment forms a plug that folds back into the bundle; in S. cerevisiae it plays an important role in bundle stability and, off the ribosome, in transcriptional activation. In human, C-terminal helix IV of the 4HB is extended, protruding from the bundle. This extension serves as a linker to the regulatory SANT domains, which are present in animals, plants and protists, but not fungi. Further analysis of Zuotin sequences revealed that the plug likely arose as a result of genomic rearrangement upon SANT domain loss early in the fungal lineage. In the lineage leading to S. cerevisiae, the 4HB was subjected to positive selection with the plug becoming increasingly hydrophobic. Eventually, these hydrophobic plug residues were coopted for a novel regulatory function—activation of a recently emerged transcription factor, Pdr1. Our data suggests that Zuotin evolved off-ribosome functions twice—once involving SANT domains, then later in fungi, after SANT domain loss, by coopting the hydrophobic plug. Zuotin serves as an example of complex intertwining of molecular chaperone function and cell regulation.
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10
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Li Y, Li H, Zhang L, Xiong S, Wen S, Xia X, Zhou X. Growth/differentiation 5 promotes the differentiation of retinal stem cells into neurons via Atoh8. J Cell Physiol 2019; 234:21307-21315. [PMID: 31066042 DOI: 10.1002/jcp.28735] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/28/2019] [Accepted: 04/10/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Yanxiu Li
- Department of Ophthalmology, The Xiangya Hospital Central South University Changsha Hunan China
| | - Haibo Li
- Department of Ophthalmology, The Xiangya Hospital Central South University Changsha Hunan China
| | - LuSi Zhang
- The School of Life Sciences Central South University Changsha Hunan China
| | - Siqi Xiong
- Department of Ophthalmology, The Xiangya Hospital Central South University Changsha Hunan China
| | - ShiJin Wen
- Department of Ophthalmology, The Xiangya Hospital Central South University Changsha Hunan China
| | - Xiaobo Xia
- Department of Ophthalmology, The Xiangya Hospital Central South University Changsha Hunan China
| | - Xia Zhou
- Department of Ophthalmology, The Xiangya Hospital Central South University Changsha Hunan China
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11
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Inhibitor of Differentiation-3 and Estrogenic Endocrine Disruptors: Implications for Susceptibility to Obesity and Metabolic Disorders. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6821601. [PMID: 29507860 PMCID: PMC5817379 DOI: 10.1155/2018/6821601] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 11/07/2017] [Accepted: 11/23/2017] [Indexed: 12/28/2022]
Abstract
The rising global incidence of obesity cannot be fully explained within the context of traditional risk factors such as an unhealthy diet, physical inactivity, aging, or genetics. Adipose tissue is an endocrine as well as a metabolic organ that may be susceptible to disruption by environmental estrogenic chemicals. Since some of the endocrine disruptors are lipophilic chemicals with long half-lives, they tend to bioaccumulate in the adipose tissue of exposed populations. Elevated exposure to these chemicals may predispose susceptible individuals to weight gain by increasing the number and size of fat cells. Genetic studies have demonstrated that the transcriptional regulator inhibitor of differentiation-3 (ID3) promotes high fat diet-induced obesity in vivo. We have shown previously that PCB153 and natural estrogen 17β-estradiol increase ID3 expression. Based on our findings, we postulate that ID3 is a molecular target of estrogenic endocrine disruptors (EEDs) in the adipose tissue and a better understanding of this relationship may help to explain how EEDs can lead to the transcriptional programming of deviant fat cells. This review will discuss the current understanding of ID3 in excess fat accumulation and the potential for EEDs to influence susceptibility to obesity or metabolic disorders via ID3 signaling.
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12
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Two chaperones locked in an embrace: structure and function of the ribosome-associated complex RAC. Nat Struct Mol Biol 2017; 24:611-619. [PMID: 28771464 DOI: 10.1038/nsmb.3435] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/14/2017] [Indexed: 12/26/2022]
Abstract
Chaperones, which assist protein folding are essential components of every living cell. The yeast ribosome-associated complex (RAC) is a chaperone that is highly conserved in eukaryotic cells. The RAC consists of the J protein Zuo1 and the unconventional Hsp70 homolog Ssz1. The RAC heterodimer stimulates the ATPase activity of the ribosome-bound Hsp70 homolog Ssb, which interacts with nascent polypeptide chains to facilitate de novo protein folding. In addition, the RAC-Ssb system is required to maintain the fidelity of protein translation. Recent work reveals important details of the unique structures of RAC and Ssb and identifies how the chaperones interact with the ribosome. The new findings start to uncover how the exceptional chaperone triad cooperates in protein folding and maintenance of translational fidelity and its connection to extraribosomal functions.
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13
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Yang J, Tanaka Y, Seay M, Li Z, Jin J, Garmire LX, Zhu X, Taylor A, Li W, Euskirchen G, Halene S, Kluger Y, Snyder MP, Park IH, Pan X, Weissman SM. Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors. Nucleic Acids Res 2017; 45:1281-1296. [PMID: 28003475 PMCID: PMC5388401 DOI: 10.1093/nar/gkw1214] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/23/2016] [Indexed: 12/18/2022] Open
Abstract
Molecular changes underlying stem cell differentiation are of fundamental interest. scRNA-seq on murine hematopoietic stem cells (HSC) and their progeny MPP1 separated the cells into 3 main clusters with distinct features: active, quiescent, and an un-characterized cluster. Induction of anemia resulted in mobilization of the quiescent to the active cluster and of the early to later stage of cell cycle, with marked increase in expression of certain transcription factors (TFs) while maintaining expression of interferon response genes. Cells with surface markers of long term HSC increased the expression of a group of TFs expressed highly in normal cycling MPP1 cells. However, at least Id1 and Hes1 were significantly activated in both HSC and MPP1 cells in anemic mice. Lineage-specific genes were differently expressed between cells, and correlated with the cell cycle stages with a specific augmentation of erythroid related genes in the G2/M phase. Most lineage specific TFs were stochastically expressed in the early precursor cells, but a few, such as Klf1, were detected only at very low levels in few precursor cells. The activation of these factors may correlate with stages of differentiation. This study reveals effects of cell cycle progression on the expression of lineage specific genes in precursor cells, and suggests that hematopoietic stress changes the balance of renewal and differentiation in these homeostatic cells.
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Affiliation(s)
- Jennifer Yang
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Yoshiaki Tanaka
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Montrell Seay
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Zhen Li
- Department of Neurobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jiaqi Jin
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Lana Xia Garmire
- Epidemiology Program, University of Hawaii Cancer Center, HI, USA
| | - Xun Zhu
- Epidemiology Program, University of Hawaii Cancer Center, HI, USA
| | - Ashley Taylor
- Hematology, Yale Comprehensive Cancer Center and Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Weidong Li
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,JiangXi Key Laboratory of Systems Biomedicine, Jiujiang University, Jiangxi, PR China
| | - Ghia Euskirchen
- Department of Genetics, Stanford University, Palo, Alto, CA, USA
| | - Stephanie Halene
- Hematology, Yale Comprehensive Cancer Center and Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Yuval Kluger
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Palo, Alto, CA, USA
| | - In-Hyun Park
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Xinghua Pan
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Guangdong Key Laboratory of Biochip Technology, Southern Medical University, Guangzhou, Guangdong, PR China
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14
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Song XQ, Su LN, Wei HP, Liu YH, Yin HF, Li JH, Zhu DX, Zhang AL. The effect of Id1gene silencing on the neural differentiation of MSCs. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1286234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Xiao-qing Song
- Department of Biology, Basic Medical College, Hebei North University, Zhangjiakou, China
| | - Li-ning Su
- Department of Biology, Basic Medical College, Hebei North University, Zhangjiakou, China
| | - Hui-ping Wei
- Department of Biology, Basic Medical College, Hebei North University, Zhangjiakou, China
| | - Ying-hui Liu
- Department of Agriculture Science, Agriculture and Forestry College of Hebei North University, Zhangjiakou, China
| | - Hai-feng Yin
- Department of Biology, Basic Medical College, Hebei North University, Zhangjiakou, China
| | - Ji-hong Li
- Department of Biology, Basic Medical College, Hebei North University, Zhangjiakou, China
| | - Deng-xiang Zhu
- Department of Biology, Basic Medical College, Hebei North University, Zhangjiakou, China
| | - Ai-lan Zhang
- Department of Biology, Basic Medical College, Hebei North University, Zhangjiakou, China
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15
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Abstract
Inhibitors of DNA binding and cell differentiation (Id) proteins are members of the large family of the helix-loop-helix (HLH) transcription factors, but they lack any DNA-binding motif. During development, the Id proteins play a key role in the regulation of cell-cycle progression and cell differentiation by modulating different cell-cycle regulators both by direct and indirect mechanisms. Several Id-protein interacting partners have been identified thus far, which belong to structurally and functionally unrelated families, including, among others, the class I and II bHLH transcription factors, the retinoblastoma protein and related pocket proteins, the paired-box transcription factors, and the S5a subunit of the 26 S proteasome. Although the HLH domain of the Id proteins is involved in most of their protein-protein interaction events, additional motifs located in their N-terminal and C-terminal regions are required for the recognition of diverse protein partners. The ability of the Id proteins to interact with structurally different proteins is likely to arise from their conformational flexibility: indeed, these proteins contain intrinsically disordered regions that, in the case of the HLH region, undergo folding upon self- or heteroassociation. Besides their crucial role for cell-fate determination and cell-cycle progression during development, other important cellular events have been related to the Id-protein expression in a number of pathologies. Dysregulated Id-protein expression has been associated with tumor growth, vascularization, invasiveness, metastasis, chemoresistance and stemness, as well as with various developmental defects and diseases. Herein we provide an overview on the structural properties, mode of action, biological function and therapeutic potential of these regulatory proteins.
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Affiliation(s)
- Cornelia Roschger
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, Salzburg, 5020, Austria
| | - Chiara Cabrele
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, Salzburg, 5020, Austria.
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16
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Roschger C, Cabrele C. The Id-protein family in developmental and cancer-associated pathways. Cell Commun Signal 2017; 15:7. [PMID: 28122577 PMCID: PMC5267474 DOI: 10.1186/s12964-016-0161-y] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/29/2016] [Indexed: 01/15/2023] Open
Abstract
Inhibitors of DNA binding and cell differentiation (Id) proteins are members of the large family of the helix-loop-helix (HLH) transcription factors, but they lack any DNA-binding motif. During development, the Id proteins play a key role in the regulation of cell-cycle progression and cell differentiation by modulating different cell-cycle regulators both by direct and indirect mechanisms. Several Id-protein interacting partners have been identified thus far, which belong to structurally and functionally unrelated families, including, among others, the class I and II bHLH transcription factors, the retinoblastoma protein and related pocket proteins, the paired-box transcription factors, and the S5a subunit of the 26 S proteasome. Although the HLH domain of the Id proteins is involved in most of their protein-protein interaction events, additional motifs located in their N-terminal and C-terminal regions are required for the recognition of diverse protein partners. The ability of the Id proteins to interact with structurally different proteins is likely to arise from their conformational flexibility: indeed, these proteins contain intrinsically disordered regions that, in the case of the HLH region, undergo folding upon self- or heteroassociation. Besides their crucial role for cell-fate determination and cell-cycle progression during development, other important cellular events have been related to the Id-protein expression in a number of pathologies. Dysregulated Id-protein expression has been associated with tumor growth, vascularization, invasiveness, metastasis, chemoresistance and stemness, as well as with various developmental defects and diseases. Herein we provide an overview on the structural properties, mode of action, biological function and therapeutic potential of these regulatory proteins.
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Affiliation(s)
- Cornelia Roschger
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, Salzburg, 5020, Austria
| | - Chiara Cabrele
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, Salzburg, 5020, Austria.
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17
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Kaymak A, Richly H. Zrf1 controls mesoderm lineage genes and cardiomyocyte differentiation. Cell Cycle 2016; 15:3306-3317. [PMID: 27754813 DOI: 10.1080/15384101.2016.1245246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In the present study we addressed the function of the transcriptional activator Zrf1 in the generation of the 3 germ layers during in vitro development. Currently, Zrf1 is rather regarded as a factor that drives the expression of neuronal genes. Here, we have employed mouse embryonic stem cells and P19 cells to understand the role of Zrf1 in the generation of mesoderm-derived tissues like adipocytes, cartilage and heart. Our data shows that Zrf1 is essential for the transcriptional activation of genes that give rise to mesoderm and in particular heart development. In both, the mESC and P19 systems, we provide evidence that Zrf1 contributes to the generation of functional cardiomyocytes. We further demonstrate that Zrf1 binds to the transcription start sites (TSSs) of heart tissue-specific genes from the first and second heart field where it drives their temporal expression during differentiation. Taken together, we have identified Zrf1 as a novel regulator of the mesodermal lineage that might facilitate spatiotemporal expression of genes.
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Affiliation(s)
- Aysegül Kaymak
- a Laboratory of Molecular Epigenetics, Institute of Molecular Biology (IMB) , Mainz , Germany.,b Faculty of Biology, Johannes Gutenberg University , Mainz , Germany
| | - Holger Richly
- a Laboratory of Molecular Epigenetics, Institute of Molecular Biology (IMB) , Mainz , Germany
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18
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Guzmán-López JA, Abraham-Juárez MJ, Lozano-Sotomayor P, de Folter S, Simpson J. Arabidopsis thaliana gonidialess A/Zuotin related factors (GlsA/ZRF) are essential for maintenance of meristem integrity. PLANT MOLECULAR BIOLOGY 2016; 91:37-51. [PMID: 26826012 DOI: 10.1007/s11103-016-0439-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/12/2016] [Indexed: 06/05/2023]
Abstract
Observation of a differential expression pattern, including strong expression in meristematic tissue of an Agave tequilana GlsA/ZRF ortholog suggested an important role for this gene during bulbil formation and developmental changes in this species. In order to better understand this role, the two GlsA/ZFR orthologs present in the genome of Arabidopsis thaliana were functionally characterized by analyzing expression patterns, double mutant phenotypes, promoter-GUS fusions and expression of hormone related or meristem marker genes. Patterns of expression for A. thaliana show that GlsA/ZFR genes are strongly expressed in SAMs and RAMs in mature plants and developing embryos and double mutants showed multiple changes in morphology related to both SAM and RAM tissues. Typical double mutants showed stunted growth of aerial and root tissue, formation of multiple ectopic meristems and effects on cotyledons, leaves and flowers. The KNOX genes STM and BP were overexpressed in double mutants whereas CLV3, WUSCHEL and AS1 were repressed and lack of AtGlsA expression was also associated with changes in localization of auxin and cytokinin. These results suggest that GlsA/ZFR is an essential component of the machinery that maintains the integrity of SAM and RAM tissue and underline the potential to identify new genes or gene functions based on observations in non-model plants.
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Affiliation(s)
- José Alfredo Guzmán-López
- Department of Plant Genetic Engineering, CINVESTAV Unidad Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, Apdo. Postal 629, 36821, Irapuato, Guanajuato, Mexico
| | - María Jazmín Abraham-Juárez
- Department of Plant Genetic Engineering, CINVESTAV Unidad Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, Apdo. Postal 629, 36821, Irapuato, Guanajuato, Mexico
- Plant Gene Expression Center, USDA-ARS, UC Berkeley, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Paulina Lozano-Sotomayor
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), CINVESTAV Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, Apdo. Postal 629, 36821, Irapuato, Guanajuato, Mexico
| | - Stefan de Folter
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), CINVESTAV Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, Apdo. Postal 629, 36821, Irapuato, Guanajuato, Mexico
| | - June Simpson
- Department of Plant Genetic Engineering, CINVESTAV Unidad Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, Apdo. Postal 629, 36821, Irapuato, Guanajuato, Mexico.
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19
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Aloia L, Demajo S, Di Croce L. ZRF1: a novel epigenetic regulator of stem cell identity and cancer. Cell Cycle 2015; 14:510-5. [PMID: 25665097 DOI: 10.4161/15384101.2014.988022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Zuotin-related factor 1, ZRF1, has recently been identified as an epigenetic regulator of gene transcription in stem cells and cancer. During differentiation of human teratocarcinoma cells, ZRF1 promotes transcriptional induction of developmental genes that are repressed by Polycomb complexes. Importantly, ZRF1 has recently been shown to be required for both neural differentiation of embryonic stem cells (ESCs) and for maintenance of neural progenitor cell (NPC) identity. Moreover, a dual role has now emerged for ZRF1 in cancer: on the one hand, ZRF1 plays a crucial role in oncogene-induced senescence (OIS) by activating the INK4/ARF locus, thus working as a tumor suppressor; on the other hand, ZRF1 promotes leukemogenesis in acute myeloid leukemia (AML) in a Polycomb-independent fashion. Therefore, increasing evidence points to ZRF1 as a novel target for therapy of neurodegenerative diseases and cancer.
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Key Words
- AML, acute myeloid leukemia
- ChIP, chromatin immunoprecipitation
- ESC, embryonic stem cells
- H2Aub1, mono-ubiquitinated histone H2A
- HDAC, histone deacetylase
- NPC, neural progenitor cells
- OIS, oncogene-induced senescence
- PRC1, polycomb repressive complex 1
- PRC2, polycomb repressive complex 2
- RA, retinoic acid
- RARa, retinoic acid receptor a
- UBD, ubiquitin binding domain
- ZRF1
- cancer
- cell fate
- development
- differentiation
- epigenetics
- polycomb
- retinoic acid
- senescence
- stem cell
- transcription
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Affiliation(s)
- Luigi Aloia
- a Centre for Genomic Regulation (CRG) ; Barcelona , Spain
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20
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Histone modifications controlling native and induced neural stem cell identity. Curr Opin Genet Dev 2015; 34:95-101. [DOI: 10.1016/j.gde.2015.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/31/2015] [Accepted: 08/11/2015] [Indexed: 12/31/2022]
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Diotel N, Beil T, Strähle U, Rastegar S. Differential expression of id genes and their potential regulator znf238 in zebrafish adult neural progenitor cells and neurons suggests distinct functions in adult neurogenesis. Gene Expr Patterns 2015; 19:1-13. [PMID: 26107416 DOI: 10.1016/j.gep.2015.05.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 12/18/2022]
Abstract
Teleost fish display a remarkable ability to generate new neurons and to repair brain lesions during adulthood. They are, therefore, a very popular model to investigate the molecular mechanisms of constitutive and induced neurogenesis in adult vertebrates. In this study, we investigated the expression patterns of inhibitor of DNA binding (id) genes and of their potential transcriptional repressor, znf238, in the whole brain of adult zebrafish. We show that while id1 is exclusively expressed in ventricular cells in the whole brain, id2a, id3 and id4 genes are expressed in broader areas. Interestingly, znf238 was also detected in these regions, its expression overlapping with id2a, id3 and id4 expression. Further detailed characterization of the id-expressing cells demonstrated that (a) id1 is expressed in type 1 and type 2 neural progenitors as previously published, (b) id2a in type 1, 2 and 3 neural progenitors, (c) id3 in type 3 neural progenitors and (d) id4 in postmitotic neurons. Our data provide a detailed map of id and znf238 expression in the brain of adult zebrafish, supplying a framework for studies of id genes function during adult neurogenesis and brain regeneration in the zebrafish.
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Affiliation(s)
- Nicolas Diotel
- Karlsruhe Institute of Technology, Campus Nord, Institute of Toxicology and Genetics, Karlsruhe, Germany; Inserm, UMR 1188 Diabète athérothrombose Thérapies Réunion Océan Indien (DéTROI), Plateforme CYROI, Sainte-Clotilde, F-97490, France; Université de La Réunion, UMR 1188, Sainte-Clotilde, F-97490, France.
| | - Tanja Beil
- Karlsruhe Institute of Technology, Campus Nord, Institute of Toxicology and Genetics, Karlsruhe, Germany
| | - Uwe Strähle
- Karlsruhe Institute of Technology, Campus Nord, Institute of Toxicology and Genetics, Karlsruhe, Germany
| | - Sepand Rastegar
- Karlsruhe Institute of Technology, Campus Nord, Institute of Toxicology and Genetics, Karlsruhe, Germany.
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