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Stelloo S, Alejo-Vinogradova MT, van Gelder CAGH, Zijlmans DW, van Oostrom MJ, Valverde JM, Lamers LA, Rus T, Sobrevals Alcaraz P, Schäfers T, Furlan C, Jansen PWTC, Baltissen MPA, Sonnen KF, Burgering B, Altelaar MAFM, Vos HR, Vermeulen M. Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics. Cell Stem Cell 2024; 31:1072-1090.e8. [PMID: 38754429 DOI: 10.1016/j.stem.2024.04.017] [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: 04/24/2023] [Revised: 01/10/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Gastrulation is a critical stage in embryonic development during which the germ layers are established. Advances in sequencing technologies led to the identification of gene regulatory programs that control the emergence of the germ layers and their derivatives. However, proteome-based studies of early mammalian development are scarce. To overcome this, we utilized gastruloids and a multilayered mass spectrometry-based proteomics approach to investigate the global dynamics of (phospho) protein expression during gastruloid differentiation. Our findings revealed many proteins with temporal expression and unique expression profiles for each germ layer, which we also validated using single-cell proteomics technology. Additionally, we profiled enhancer interaction landscapes using P300 proximity labeling, which revealed numerous gastruloid-specific transcription factors and chromatin remodelers. Subsequent degron-based perturbations combined with single-cell RNA sequencing (scRNA-seq) identified a critical role for ZEB2 in mouse and human somitogenesis. Overall, this study provides a rich resource for developmental and synthetic biology communities endeavoring to understand mammalian embryogenesis.
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Affiliation(s)
- Suzan Stelloo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands.
| | - Maria Teresa Alejo-Vinogradova
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Charlotte A G H van Gelder
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Dick W Zijlmans
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Marek J van Oostrom
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Juan Manuel Valverde
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, the Netherlands; Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Lieke A Lamers
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Teja Rus
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Paula Sobrevals Alcaraz
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Tilman Schäfers
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Cristina Furlan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, the Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Marijke P A Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Katharina F Sonnen
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Boudewijn Burgering
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Maarten A F M Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, the Netherlands; Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Harmjan R Vos
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands; Division of Molecular Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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2
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Caraffi SG, van der Laan L, Rooney K, Trajkova S, Zuntini R, Relator R, Haghshenas S, Levy MA, Baldo C, Mandrile G, Lauzon C, Cordelli DM, Ivanovski I, Fetta A, Sukarova E, Brusco A, Pavinato L, Pullano V, Zollino M, McConkey H, Tartaglia M, Ferrero GB, Sadikovic B, Garavelli L. Identification of the DNA methylation signature of Mowat-Wilson syndrome. Eur J Hum Genet 2024; 32:619-629. [PMID: 38351292 PMCID: PMC11153515 DOI: 10.1038/s41431-024-01548-4] [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: 10/24/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 06/07/2024] Open
Abstract
Mowat-Wilson syndrome (MOWS) is a rare congenital disease caused by haploinsufficiency of ZEB2, encoding a transcription factor required for neurodevelopment. MOWS is characterized by intellectual disability, epilepsy, typical facial phenotype and other anomalies, such as short stature, Hirschsprung disease, brain and heart defects. Despite some recognizable features, MOWS rarity and phenotypic variability may complicate its diagnosis, particularly in the neonatal period. In order to define a novel diagnostic biomarker for MOWS, we determined the genome-wide DNA methylation profile of DNA samples from 29 individuals with confirmed clinical and molecular diagnosis. Through multidimensional scaling and hierarchical clustering analysis, we identified and validated a DNA methylation signature involving 296 differentially methylated probes as part of the broader MOWS DNA methylation profile. The prevalence of hypomethylated CpG sites agrees with the main role of ZEB2 as a transcriptional repressor, while differential methylation within the ZEB2 locus supports the previously proposed autoregulation ability. Correlation studies compared the MOWS cohort with 56 previously described DNA methylation profiles of other neurodevelopmental disorders, further validating the specificity of this biomarker. In conclusion, MOWS DNA methylation signature is highly sensitive and reproducible, providing a useful tool to facilitate diagnosis.
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Grants
- MNESYS (PE0000006) Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- 20203P8C3X Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- FOE 2020 Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- RCR-2022-23682289 Ministero della Salute (Ministry of Health, Italy)
- PNRR-MR1-2022-12376811 Ministero della Salute (Ministry of Health, Italy)
- OGI-188 Ontario Genomics Institute (OGI)
- Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
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Affiliation(s)
| | - Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Torino, 10126, Torino, Italy
| | - Roberta Zuntini
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42122, Reggio Emilia, Italy
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Chiara Baldo
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Giorgia Mandrile
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, University of Torino, 10043, Orbassano (Torino), Italy
| | - Carolyn Lauzon
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Duccio Maria Cordelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Neuropsichiatria dell'Età Pediatrica, 40139, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126, Bologna, Italy
| | - Ivan Ivanovski
- Institute of Medical Genetics, University of Zürich, Zürich, Switzerland
| | - Anna Fetta
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Neuropsichiatria dell'Età Pediatrica, 40139, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126, Bologna, Italy
| | - Elena Sukarova
- Department of Endocrinology and Genetics, University Clinic for Pediatric Diseases, Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, 1000, Skopje, Republic of North Macedonia
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Torino, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Torino, 10126, Torino, Italy
| | - Verdiana Pullano
- Department of Medical Sciences, University of Torino, Torino, Italy
- Molecular Biotechnology Center "Guido Tarone", University of Torino, 10126, Torino, Italy
| | - Marcella Zollino
- Institute of Genomic Medicine, Department of Life Sciences and Public Health, 'Sacro Cuore' Catholic University of Rome, 00168, Rome, Italy
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Bekim Sadikovic
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada.
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42122, Reggio Emilia, Italy.
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BharathwajChetty B, Sajeev A, Vishwa R, Aswani BS, Alqahtani MS, Abbas M, Kunnumakkara AB. Dynamic interplay of nuclear receptors in tumor cell plasticity and drug resistance: Shifting gears in malignant transformations and applications in cancer therapeutics. Cancer Metastasis Rev 2024; 43:321-362. [PMID: 38517618 DOI: 10.1007/s10555-024-10171-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/19/2024] [Indexed: 03/24/2024]
Abstract
Recent advances have brought forth the complex interplay between tumor cell plasticity and its consequential impact on drug resistance and tumor recurrence, both of which are critical determinants of neoplastic progression and therapeutic efficacy. Various forms of tumor cell plasticity, instrumental in facilitating neoplastic cells to develop drug resistance, include epithelial-mesenchymal transition (EMT) alternatively termed epithelial-mesenchymal plasticity, the acquisition of cancer stem cell (CSC) attributes, and transdifferentiation into diverse cell lineages. Nuclear receptors (NRs) are a superfamily of transcription factors (TFs) that play an essential role in regulating a multitude of cellular processes, including cell proliferation, differentiation, and apoptosis. NRs have been implicated to play a critical role in modulating gene expression associated with tumor cell plasticity and drug resistance. This review aims to provide a comprehensive overview of the current understanding of how NRs regulate these key aspects of cancer biology. We discuss the diverse mechanisms through which NRs influence tumor cell plasticity, including EMT, stemness, and metastasis. Further, we explore the intricate relationship between NRs and drug resistance, highlighting the impact of NR signaling on chemotherapy, radiotherapy and targeted therapies. We also discuss the emerging therapeutic strategies targeting NRs to overcome tumor cell plasticity and drug resistance. This review also provides valuable insights into the current clinical trials that involve agonists or antagonists of NRs modulating various aspects of tumor cell plasticity, thereby delineating the potential of NRs as therapeutic targets for improved cancer treatment outcomes.
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Affiliation(s)
- Bandari BharathwajChetty
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781039, Assam, India
| | - Anjana Sajeev
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781039, Assam, India
| | - Ravichandran Vishwa
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781039, Assam, India
| | - Babu Santha Aswani
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781039, Assam, India
| | - Mohammed S Alqahtani
- Radiological Sciences Department, College of Applied Medical Sciences, King Khalid University, Abha, 61421, Saudi Arabia
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, Abha, 61421, Saudi Arabia
| | - Ajaikumar B Kunnumakkara
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781039, Assam, India.
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4
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Charney RM, Prasad MS, Juan-Sing C, Patel LJ, Hernandez JC, Wu J, García-Castro MI. Mowat-Wilson syndrome factor ZEB2 controls early formation of human neural crest through BMP signaling modulation. Stem Cell Reports 2023; 18:2254-2267. [PMID: 37890485 PMCID: PMC10679662 DOI: 10.1016/j.stemcr.2023.10.002] [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: 11/21/2021] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Mowat-Wilson syndrome is caused by mutations in ZEB2, with patients exhibiting characteristics indicative of neural crest (NC) defects. We examined the contribution of ZEB2 to human NC formation using a model based on human embryonic stem cells. We found ZEB2 to be one of the earliest factors expressed in prospective human NC, and knockdown revealed a role for ZEB2 in establishing the NC state while repressing pre-placodal and non-neural ectoderm genes. Examination of ZEB2 N-terminal mutant NC cells demonstrates its requirement for the repression of enhancers in the NC gene network and proper NC cell terminal differentiation into osteoblasts and peripheral neurons and neuroglia. This ZEB2 mutation causes early misexpression of BMP signaling ligands, which can be rescued by the attenuation of BMP. Our findings suggest that ZEB2 regulates early human NC specification by modulating proper BMP signaling and further elaborate the molecular defects underlying Mowat-Wilson syndrome.
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Affiliation(s)
- Rebekah M Charney
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA, USA.
| | - Maneeshi S Prasad
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA, USA
| | - Czarina Juan-Sing
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA, USA
| | - Lipsa J Patel
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA, USA
| | - Jacqueline C Hernandez
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Martín I García-Castro
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA, USA.
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5
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Ninfali C, Siles L, Esteve-Codina A, Postigo A. The mesodermal and myogenic specification of hESCs depend on ZEB1 and are inhibited by ZEB2. Cell Rep 2023; 42:113222. [PMID: 37819755 DOI: 10.1016/j.celrep.2023.113222] [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: 03/12/2022] [Revised: 08/02/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
Human embryonic stem cells (hESCs) can differentiate into any cell lineage. Here, we report that ZEB1 and ZEB2 promote and inhibit mesodermal-to-myogenic specification of hESCs, respectively. Knockdown and/or overexpression experiments of ZEB1, ZEB2, or PAX7 in hESCs indicate that ZEB1 is required for hESC Nodal/Activin-mediated mesodermal specification and PAX7+ human myogenic progenitor (hMuP) generation, while ZEB2 inhibits these processes. ZEB1 downregulation induces neural markers, while ZEB2 downregulation induces mesodermal/myogenic markers. Mechanistically, ZEB1 binds to and transcriptionally activates the PAX7 promoter, while ZEB2 binds to and activates the promoter of the neural OTX2 marker. Transplanting ZEB1 or ZEB2 knocked down hMuPs into the muscles of a muscular dystrophy mouse model, showing that hMuP engraftment and generation of dystrophin-positive myofibers depend on ZEB1 and are inhibited by ZEB2. The mouse model results suggest that ZEB1 expression and/or downregulating ZEB2 in hESCs may also enhance hESC regenerative capacity for human muscular dystrophy therapy.
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Affiliation(s)
- Chiara Ninfali
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, IDIBAPS, 08036 Barcelona, Spain
| | - Laura Siles
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, IDIBAPS, 08036 Barcelona, Spain
| | | | - Antonio Postigo
- Group of Gene Regulation in Stem Cells, Cell Plasticity, Differentiation, and Cancer, IDIBAPS, 08036 Barcelona, Spain; Molecular Targets Program, J.G. Brown Center, Louisville University Healthcare Campus, Louisville, KY 40202, USA; ICREA, 08010 Barcelona, Spain.
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6
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Lucchini M, De Arcangelis V, Santoro M, Morosetti R, Broccolini A, Mirabella M. Serum-Circulating microRNAs in Sporadic Inclusion Body Myositis. Int J Mol Sci 2023; 24:11139. [PMID: 37446317 DOI: 10.3390/ijms241311139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/25/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Sporadic inclusion body myositis (s-IBM) represents a unique disease within idiopathic inflammatory myopathies with a dual myodegenerative-autoimmune physiopathology and a lack of an efficacious treatment. Circulating miRNA expression could expand our knowledge of s-IBM patho-mechanisms and provide new potential disease biomarkers. To evaluate the expression of selected pre-amplified miRNAs in the serum of s-IBM patients compared to those of a sex- and age-matched healthy control group, we enrolled 14 consecutive s-IBM patients and 8 sex- and age-matched healthy controls. By using two different normalization approaches, we found one downregulated and three upregulated miRNAs. hsa-miR-192-5p was significantly downregulated, while hsa-miR-372-3p was found to be upregulated more in the s-IBM patients compared to the level of the controls. The other two miRNAs had a very low expression levels (raw Ct data > 29). hsa-miR-192-5p and hsa-miR-372-3p were found to be significantly dysregulated in the serum of s-IBM patients. These miRNAs are involved in differentiation and regeneration processes, thus possibly reflecting pathological mechanisms in s-IBM muscles and potentially representing disease biomarkers.
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Affiliation(s)
- Matteo Lucchini
- UOC Neurologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Dipartimento di Neuroscienze, Sezione di Neurologia, Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Valeria De Arcangelis
- UOC Neurologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Massimo Santoro
- Energy and Sustainable Economic Development, Division of Health Protection Technologies ENEA-Italian National Agency for New Technologies, 00123 Rome, Italy
| | - Roberta Morosetti
- UOC Neurologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Aldobrando Broccolini
- UOC Neurologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Dipartimento di Neuroscienze, Sezione di Neurologia, Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Massimiliano Mirabella
- UOC Neurologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Dipartimento di Neuroscienze, Sezione di Neurologia, Catholic University of Sacred Heart, 00168 Rome, Italy
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7
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Birkhoff JC, Korporaal AL, Brouwer RWW, Nowosad K, Milazzo C, Mouratidou L, van den Hout MCGN, van IJcken WFJ, Huylebroeck D, Conidi A. Zeb2 DNA-Binding Sites in Neuroprogenitor Cells Reveal Autoregulation and Affirm Neurodevelopmental Defects, Including in Mowat-Wilson Syndrome. Genes (Basel) 2023; 14:genes14030629. [PMID: 36980900 PMCID: PMC10048071 DOI: 10.3390/genes14030629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Functional perturbation and action mechanism studies have shown that the transcription factor Zeb2 controls cell fate decisions, differentiation, and/or maturation in multiple cell lineages in embryos and after birth. In cultured embryonic stem cells (ESCs), Zeb2’s mRNA/protein upregulation is necessary for the exit from primed pluripotency and for entering general and neural differentiation. We edited mouse ESCs to produce Flag-V5 epitope-tagged Zeb2 protein from one endogenous allele. Using chromatin immunoprecipitation coupled with sequencing (ChIP-seq), we mapped 2432 DNA-binding sites for this tagged Zeb2 in ESC-derived neuroprogenitor cells (NPCs). A new, major binding site maps promoter-proximal to Zeb2 itself. The homozygous deletion of this site demonstrates that autoregulation of Zeb2 is necessary to elicit the appropriate Zeb2-dependent effects in ESC-to-NPC differentiation. We have also cross-referenced all the mapped Zeb2 binding sites with previously obtained transcriptome data from Zeb2 perturbations in ESC-derived NPCs, GABAergic interneurons from the ventral forebrain of mouse embryos, and stem/progenitor cells from the post-natal ventricular-subventricular zone (V-SVZ) in mouse forebrain, respectively. Despite the different characteristics of each of these neurogenic systems, we found interesting target gene overlaps. In addition, our study also contributes to explaining developmental disorders, including Mowat-Wilson syndrome caused by ZEB2 deficiency, and also other monogenic syndromes.
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Affiliation(s)
- Judith C. Birkhoff
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - Anne L. Korporaal
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - Rutger W. W. Brouwer
- Center for Biomics-Genomics, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - Karol Nowosad
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland
- The Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Claudia Milazzo
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - Lidia Mouratidou
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | | | - Wilfred F. J. van IJcken
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
- Center for Biomics-Genomics, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
- Correspondence: ; Tel.: +31-10-7043169
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8
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Cheng P, Wirka RC, Clarke LS, Zhao Q, Kundu R, Nguyen T, Nair S, Sharma D, Kim HJ, Shi H, Assimes T, Kim JB, Kundaje A, Quertermous T. ZEB2 Shapes the Epigenetic Landscape of Atherosclerosis. Circulation 2022; 145:469-485. [PMID: 34990206 PMCID: PMC8896308 DOI: 10.1161/circulationaha.121.057789] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Smooth muscle cells (SMCs) transition into a number of different phenotypes during atherosclerosis, including those that resemble fibroblasts and chondrocytes, and make up the majority of cells in the atherosclerotic plaque. To better understand the epigenetic and transcriptional mechanisms that mediate these cell state changes, and how they relate to risk for coronary artery disease (CAD), we have investigated the causality and function of transcription factors at genome-wide associated loci. METHODS We used CRISPR-Cas 9 genome and epigenome editing to identify the causal gene and cells for a complex CAD genome-wide association study signal at 2q22.3. Single-cell epigenetic and transcriptomic profiling in murine models and human coronary artery smooth muscle cells were used to understand the cellular and molecular mechanism by which this CAD risk gene exerts its function. RESULTS CRISPR-Cas 9 genome and epigenome editing showed that the complex CAD genetic signals within a genomic region at 2q22.3 lie within smooth muscle long-distance enhancers for ZEB2, a transcription factor extensively studied in the context of epithelial mesenchymal transition in development of cancer. Zeb2 regulates SMC phenotypic transition through chromatin remodeling that obviates accessibility and disrupts both Notch and transforming growth factor β signaling, thus altering the epigenetic trajectory of SMC transitions. SMC-specific loss of Zeb2 resulted in an inability of transitioning SMCs to turn off contractile programing and take on a fibroblast-like phenotype, but accelerated the formation of chondromyocytes, mirroring features of high-risk atherosclerotic plaques in human coronary arteries. CONCLUSIONS These studies identify ZEB2 as a new CAD genome-wide association study gene that affects features of plaque vulnerability through direct effects on the epigenome, providing a new therapeutic approach to target vascular disease.
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Affiliation(s)
- Paul Cheng
- Division of Cardiovascular Medicine and the Cardiovascular Institute, Stanford, CA
| | - Robert C. Wirka
- Division of Cardiology, Departments of Medicine and Cell Biology and Physiology, McAllister Heart Institute, University of North Carolina, Chapel Hill, NC
| | - Lee Shoa Clarke
- Division of Cardiovascular Medicine and the Cardiovascular Institute, Stanford, CA
| | - Quanyi Zhao
- Division of Cardiovascular Medicine and the Cardiovascular Institute, Stanford, CA
| | - Ramendra Kundu
- Division of Cardiovascular Medicine and the Cardiovascular Institute, Stanford, CA
| | - Trieu Nguyen
- Division of Cardiovascular Medicine and the Cardiovascular Institute, Stanford, CA
| | - Surag Nair
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Disha Sharma
- Division of Cardiovascular Medicine and the Cardiovascular Institute, Stanford, CA
| | - Hyun-jung Kim
- Division of Cardiovascular Medicine and the Cardiovascular Institute, Stanford, CA
| | - Huitong Shi
- Division of Cardiovascular Medicine and the Cardiovascular Institute, Stanford, CA
| | - Themistocles Assimes
- Division of Cardiovascular Medicine and the Cardiovascular Institute, Stanford, CA
| | - Juyong Brian Kim
- Division of Cardiovascular Medicine and the Cardiovascular Institute, Stanford, CA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Thomas Quertermous
- Division of Cardiovascular Medicine and the Cardiovascular Institute, Stanford, CA
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9
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McClay DR, Croce JC, Warner JF. Reprint of: Conditional specification of endomesoderm. Cells Dev 2021; 168:203731. [PMID: 34610899 DOI: 10.1016/j.cdev.2021.203731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 10/20/2022]
Abstract
Early in animal development many cells are conditionally specified based on observations that those cells can be directed toward alternate fates. The endomesoderm is so named because early specification produces cells that often have been observed to simultaneously express both early endoderm and mesoderm transcription factors. Experiments with these cells demonstrate that their progeny can directed entirely toward endoderm or mesoderm, whereas normally they establish both germ layers. This review examines the mechanisms that initiate the conditional endomesoderm state, its metastability, and the mechanisms that resolve that state into definitive endoderm and mesoderm.
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Affiliation(s)
- David R McClay
- Department of Biology, Duke University, Durham, NC, USA.
| | - Jenifer C Croce
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche, Villefranche-sur-Mer, France.
| | - Jacob F Warner
- Department of Biology, University of North Carolina, Wilmington, NC, USA.
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10
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Birkhoff JC, Brouwer RWW, Kolovos P, Korporaal AL, Bermejo-Santos A, Boltsis I, Nowosad K, van den Hout MCGN, Grosveld FG, van IJcken WFJ, Huylebroeck D, Conidi A. Targeted chromatin conformation analysis identifies novel distal neural enhancers of ZEB2 in pluripotent stem cell differentiation. Hum Mol Genet 2021; 29:2535-2550. [PMID: 32628253 PMCID: PMC7471508 DOI: 10.1093/hmg/ddaa141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/25/2022] Open
Abstract
The transcription factor zinc finger E-box binding protein 2 (ZEB2) controls embryonic and adult cell fate decisions and cellular maturation in many stem/progenitor cell types. Defects in these processes in specific cell types underlie several aspects of Mowat–Wilson syndrome (MOWS), which is caused by ZEB2 haplo-insufficiency. Human ZEB2, like mouse Zeb2, is located on chromosome 2 downstream of a ±3.5 Mb-long gene-desert, lacking any protein-coding gene. Using temporal targeted chromatin capture (T2C), we show major chromatin structural changes based on mapping in-cis proximities between the ZEB2 promoter and this gene desert during neural differentiation of human-induced pluripotent stem cells, including at early neuroprogenitor cell (NPC)/rosette state, where ZEB2 mRNA levels increase significantly. Combining T2C with histone-3 acetylation mapping, we identified three novel candidate enhancers about 500 kb upstream of the ZEB2 transcription start site. Functional luciferase-based assays in heterologous cells and NPCs reveal co-operation between these three enhancers. This study is the first to document in-cis Regulatory Elements located in ZEB2’s gene desert. The results further show the usability of T2C for future studies of ZEB2 REs in differentiation and maturation of multiple cell types and the molecular characterization of newly identified MOWS patients that lack mutations in ZEB2 protein-coding exons.
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Affiliation(s)
- Judith C Birkhoff
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Rutger W W Brouwer
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Center for Biomics, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | - Anne L Korporaal
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Ana Bermejo-Santos
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Ilias Boltsis
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Karol Nowosad
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin 20-093, Poland
| | - Mirjam C G N van den Hout
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Center for Biomics, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Wilfred F J van IJcken
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Center for Biomics, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven B-3000, Belgium
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
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11
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Smart-RRBS for single-cell methylome and transcriptome analysis. Nat Protoc 2021; 16:4004-4030. [PMID: 34244697 PMCID: PMC8672372 DOI: 10.1038/s41596-021-00571-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 05/12/2021] [Indexed: 02/06/2023]
Abstract
The integration of DNA methylation and transcriptional state within single cells is of broad interest. Several single-cell dual- and multi-omics approaches have been reported that enable further investigation into cellular heterogeneity, including the discovery and in-depth study of rare cell populations. Such analyses will continue to provide important mechanistic insights into the regulatory consequences of epigenetic modifications. We recently reported a new method for profiling the DNA methylome and transcriptome from the same single cells in a cancer research study. Here, we present details of the protocol and provide guidance on its utility. Our Smart-RRBS (reduced representation bisulfite sequencing) protocol combines Smart-seq2 and RRBS and entails physically separating mRNA from the genomic DNA. It generates paired epigenetic promoter and RNA-expression measurements for ~24% of protein-coding genes in a typical single cell. It also works for micro-dissected tissue samples comprising hundreds of cells. The protocol, excluding flow sorting of cells and sequencing, takes ~3 d to process up to 192 samples manually. It requires basic molecular biology expertise and laboratory equipment, including a PCR workstation with UV sterilization, a DNA fluorometer and a microfluidic electrophoresis system.
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12
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McClay DR, Croce JC, Warner JF. Conditional specification of endomesoderm. Cells Dev 2021; 167:203716. [PMID: 34245941 DOI: 10.1016/j.cdev.2021.203716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 10/20/2022]
Abstract
Early in animal development many cells are conditionally specified based on observations that those cells can be directed toward alternate fates. The endomesoderm is so named because early specification produces cells that often have been observed to simultaneously express both early endoderm and mesoderm transcription factors. Experiments with these cells demonstrate that their progeny can directed entirely toward endoderm or mesoderm, whereas normally they establish both germ layers. This review examines the mechanisms that initiate the conditional endomesoderm state, its metastability, and the mechanisms that resolve that state into definitive endoderm and mesoderm.
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Affiliation(s)
- David R McClay
- Department of Biology, Duke University, Durham, NC, USA.
| | - Jenifer C Croce
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche, Villefranche-sur-Mer, France.
| | - Jacob F Warner
- Department of Biology, University of North Carolina, Wilmington, NC, USA.
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13
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ZEB2, the Mowat-Wilson Syndrome Transcription Factor: Confirmations, Novel Functions, and Continuing Surprises. Genes (Basel) 2021; 12:genes12071037. [PMID: 34356053 PMCID: PMC8304685 DOI: 10.3390/genes12071037] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/15/2022] Open
Abstract
After its publication in 1999 as a DNA-binding and SMAD-binding transcription factor (TF) that co-determines cell fate in amphibian embryos, ZEB2 was from 2003 studied by embryologists mainly by documenting the consequences of conditional, cell-type specific Zeb2 knockout (cKO) in mice. In between, it was further identified as causal gene causing Mowat-Wilson Syndrome (MOWS) and novel regulator of epithelial–mesenchymal transition (EMT). ZEB2’s functions and action mechanisms in mouse embryos were first addressed in its main sites of expression, with focus on those that helped to explain neurodevelopmental and neural crest defects seen in MOWS patients. By doing so, ZEB2 was identified in the forebrain as the first TF that determined timing of neuro-/gliogenesis, and thereby also the extent of different layers of the cortex, in a cell non-autonomous fashion, i.e., by its cell-intrinsic control within neurons of neuron-to-progenitor paracrine signaling. Transcriptomics-based phenotyping of Zeb2 mutant mouse cells have identified large sets of intact-ZEB2 dependent genes, and the cKO approaches also moved to post-natal brain development and diverse other systems in adult mice, including hematopoiesis and various cell types of the immune system. These new studies start to highlight the important adult roles of ZEB2 in cell–cell communication, including after challenge, e.g., in the infarcted heart and fibrotic liver. Such studies may further evolve towards those documenting the roles of ZEB2 in cell-based repair of injured tissue and organs, downstream of actions of diverse growth factors, which recapitulate developmental signaling principles in the injured sites. Evident questions are about ZEB2’s direct target genes, its various partners, and ZEB2 as a candidate modifier gene, e.g., in other (neuro)developmental disorders, but also the accurate transcriptional and epigenetic regulation of its mRNA expression sites and levels. Other questions start to address ZEB2’s function as a niche-controlling regulatory TF of also other cell types, in part by its modulation of growth factor responses (e.g., TGFβ/BMP, Wnt, Notch). Furthermore, growing numbers of mapped missense as well as protein non-coding mutations in MOWS patients are becoming available and inspire the design of new animal model and pluripotent stem cell-based systems. This review attempts to summarize in detail, albeit without discussing ZEB2’s role in cancer, hematopoiesis, and its emerging roles in the immune system, how intense ZEB2 research has arrived at this exciting intersection.
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14
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de Haan W, Dheedene W, Apelt K, Décombas-Deschamps S, Vinckier S, Verhulst S, Conidi A, Deffieux T, Staring MW, Vandervoort P, Caluwé E, Lox M, Mannaerts I, Takagi T, Jaekers J, Berx G, Haigh J, Topal B, Zwijsen A, Higashi Y, van Grunsven LA, van IJcken WFJ, Mulugeta E, Tanter M, Lebrin FPG, Huylebroeck D, Luttun A. Endothelial Zeb2 preserves the hepatic angioarchitecture and protects against liver fibrosis. Cardiovasc Res 2021; 118:1262-1275. [PMID: 33909875 PMCID: PMC8953454 DOI: 10.1093/cvr/cvab148] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Aims Hepatic capillaries are lined with specialized liver sinusoidal endothelial cells (LSECs) which support macromolecule passage to hepatocytes and prevent fibrosis by keeping hepatic stellate cells (HSCs) quiescent. LSEC specialization is co-determined by transcription factors. The zinc-finger E-box-binding homeobox (Zeb)2 transcription factor is enriched in LSECs. Here, we aimed to elucidate the endothelium-specific role of Zeb2 during maintenance of the liver and in liver fibrosis. Methods and results To study the role of Zeb2 in liver endothelium we generated EC-specific Zeb2 knock-out (ECKO) mice. Sequencing of liver EC RNA revealed that deficiency of Zeb2 results in prominent expression changes in angiogenesis-related genes. Accordingly, the vascular area was expanded and the presence of pillars inside ECKO liver vessels indicated that this was likely due to increased intussusceptive angiogenesis. LSEC marker expression was not profoundly affected and fenestrations were preserved upon Zeb2 deficiency. However, an increase in continuous EC markers suggested that Zeb2-deficient LSECs are more prone to dedifferentiation, a process called ‘capillarization’. Changes in the endothelial expression of ligands that may be involved in HSC quiescence together with significant changes in the expression profile of HSCs showed that Zeb2 regulates LSEC–HSC communication and HSC activation. Accordingly, upon exposure to the hepatotoxin carbon tetrachloride (CCl4), livers of ECKO mice showed increased capillarization, HSC activation, and fibrosis compared to livers from wild-type littermates. The vascular maintenance and anti-fibrotic role of endothelial Zeb2 was confirmed in mice with EC-specific overexpression of Zeb2, as the latter resulted in reduced vascularity and attenuated CCl4-induced liver fibrosis. Conclusion Endothelial Zeb2 preserves liver angioarchitecture and protects against liver fibrosis. Zeb2 and Zeb2-dependent genes in liver ECs may be exploited to design novel therapeutic strategies to attenuate hepatic fibrosis.
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Affiliation(s)
- Willeke de Haan
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Wouter Dheedene
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Katerina Apelt
- Department of Internal Medicine (Nephrology), Einthoven Laboratory for Experimental Vascular Medicine. Leiden University Medical Center, . Leiden, The Netherlands
| | - Sofiane Décombas-Deschamps
- Physics for Medicine Paris, Inserm, CNRS, ESPCI Paris, Paris Sciences et Lettres University, Paris, France
| | - Stefan Vinckier
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, KU Leuven, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Stefaan Verhulst
- Liver Cell Biology research group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Thomas Deffieux
- Physics for Medicine Paris, Inserm, CNRS, ESPCI Paris, Paris Sciences et Lettres University, Paris, France
| | - Michael W Staring
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Petra Vandervoort
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Ellen Caluwé
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Marleen Lox
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Inge Mannaerts
- Liver Cell Biology research group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tsuyoshi Takagi
- Department of Disease Model, Institute of Developmental Research, Aichi Developmental Disability Center, Aichi, Japan
| | | | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Jody Haigh
- Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.,Research Institute in Oncology and Hematology, Cancer Care Manitoba, Winnipeg, Manitoba, Canada
| | - Baki Topal
- Abdominal Surgery, UZ Leuven, Leuven, Belgium
| | - An Zwijsen
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Yujiro Higashi
- Department of Disease Model, Institute of Developmental Research, Aichi Developmental Disability Center, Aichi, Japan
| | - Leo A van Grunsven
- Liver Cell Biology research group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Wilfred F J van IJcken
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Center for Biomics-Genomics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mickael Tanter
- Physics for Medicine Paris, Inserm, CNRS, ESPCI Paris, Paris Sciences et Lettres University, Paris, France
| | - Franck P G Lebrin
- Department of Internal Medicine (Nephrology), Einthoven Laboratory for Experimental Vascular Medicine. Leiden University Medical Center, . Leiden, The Netherlands.,Physics for Medicine Paris, Inserm, CNRS, ESPCI Paris, Paris Sciences et Lettres University, Paris, France
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Aernout Luttun
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
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15
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Benito-Kwiecinski S, Giandomenico SL, Sutcliffe M, Riis ES, Freire-Pritchett P, Kelava I, Wunderlich S, Martin U, Wray GA, McDole K, Lancaster MA. An early cell shape transition drives evolutionary expansion of the human forebrain. Cell 2021; 184:2084-2102.e19. [PMID: 33765444 PMCID: PMC8054913 DOI: 10.1016/j.cell.2021.02.050] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 12/10/2020] [Accepted: 02/22/2021] [Indexed: 12/12/2022]
Abstract
The human brain has undergone rapid expansion since humans diverged from other great apes, but the mechanism of this human-specific enlargement is still unknown. Here, we use cerebral organoids derived from human, gorilla, and chimpanzee cells to study developmental mechanisms driving evolutionary brain expansion. We find that neuroepithelial differentiation is a protracted process in apes, involving a previously unrecognized transition state characterized by a change in cell shape. Furthermore, we show that human organoids are larger due to a delay in this transition, associated with differences in interkinetic nuclear migration and cell cycle length. Comparative RNA sequencing (RNA-seq) reveals differences in expression dynamics of cell morphogenesis factors, including ZEB2, a known epithelial-mesenchymal transition regulator. We show that ZEB2 promotes neuroepithelial transition, and its manipulation and downstream signaling leads to acquisition of nonhuman ape architecture in the human context and vice versa, establishing an important role for neuroepithelial cell shape in human brain expansion. Human brain organoids are expanded relative to nonhuman apes prior to neurogenesis Ape neural progenitors go through a newly identified transition morphotype state Delayed morphological transition with shorter cell cycles underlie human expansion ZEB2 is as an evolutionary regulator of this transition
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Affiliation(s)
- Silvia Benito-Kwiecinski
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stefano L Giandomenico
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Magdalena Sutcliffe
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Erlend S Riis
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
| | - Paula Freire-Pritchett
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Iva Kelava
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephanie Wunderlich
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), REBIRTH-Research Center for Translational and Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, 30625 Hannover, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), REBIRTH-Research Center for Translational and Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, 30625 Hannover, Germany
| | - Gregory A Wray
- Department of Biology, Duke University, Biological Sciences Building, 124 Science Drive, Durham, NC 27708, USA
| | - Kate McDole
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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16
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Gladka MM, Kohela A, Molenaar B, Versteeg D, Kooijman L, Monshouwer-Kloots J, Kremer V, Vos HR, Huibers MMH, Haigh JJ, Huylebroeck D, Boon RA, Giacca M, van Rooij E. Cardiomyocytes stimulate angiogenesis after ischemic injury in a ZEB2-dependent manner. Nat Commun 2021; 12:84. [PMID: 33398012 PMCID: PMC7782784 DOI: 10.1038/s41467-020-20361-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/20/2020] [Indexed: 12/25/2022] Open
Abstract
The disruption in blood supply due to myocardial infarction is a critical determinant for infarct size and subsequent deterioration in function. The identification of factors that enhance cardiac repair by the restoration of the vascular network is, therefore, of great significance. Here, we show that the transcription factor Zinc finger E-box-binding homeobox 2 (ZEB2) is increased in stressed cardiomyocytes and induces a cardioprotective cross-talk between cardiomyocytes and endothelial cells to enhance angiogenesis after ischemia. Single-cell sequencing indicates ZEB2 to be enriched in injured cardiomyocytes. Cardiomyocyte-specific deletion of ZEB2 results in impaired cardiac contractility and infarct healing post-myocardial infarction (post-MI), while cardiomyocyte-specific ZEB2 overexpression improves cardiomyocyte survival and cardiac function. We identified Thymosin β4 (TMSB4) and Prothymosin α (PTMA) as main paracrine factors released from cardiomyocytes to stimulate angiogenesis by enhancing endothelial cell migration, and whose regulation is validated in our in vivo models. Therapeutic delivery of ZEB2 to cardiomyocytes in the infarcted heart induces the expression of TMSB4 and PTMA, which enhances angiogenesis and prevents cardiac dysfunction. These findings reveal ZEB2 as a beneficial factor during ischemic injury, which may hold promise for the identification of new therapies.
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Affiliation(s)
- Monika M Gladka
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre, Utrecht, The Netherlands
| | - Arwa Kohela
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre, Utrecht, The Netherlands
| | - Bas Molenaar
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre, Utrecht, The Netherlands
| | - Danielle Versteeg
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre, Utrecht, The Netherlands
- Department of Cardiology, University Medical Center, Utrecht, The Netherlands
| | - Lieneke Kooijman
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre, Utrecht, The Netherlands
| | - Jantine Monshouwer-Kloots
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre, Utrecht, The Netherlands
| | - Veerle Kremer
- Department of Physiology, Amsterdam University Medical Center VU, Amsterdam, The Netherlands
- Department of Medical Biochemistry, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Harmjan R Vos
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center, Utrecht, The Netherlands
| | - Manon M H Huibers
- Department of Pathology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Jody J Haigh
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, Canada
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Centre, Rotterdam, The Netherlands
- Department of Development and Regeneration, University of Leuven, Leuven, Belgium
| | - Reinier A Boon
- Department of Physiology, Amsterdam University Medical Center VU, Amsterdam, The Netherlands
- Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University, Frankfurt am Main, Germany
- German Center for Cardiovascular Research (DZHK), Frankfurt am Main, Germany
| | - Mauro Giacca
- School of Cardiovascular Medicine and Sciences, King's College London, London, UK
| | - Eva van Rooij
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre, Utrecht, The Netherlands.
- Department of Cardiology, University Medical Center, Utrecht, The Netherlands.
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17
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Strategies for Cancer Immunotherapy Using Induced Pluripotency Stem Cells-Based Vaccines. Cancers (Basel) 2020; 12:cancers12123581. [PMID: 33266109 PMCID: PMC7760556 DOI: 10.3390/cancers12123581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/24/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
Despite improvements in cancer therapy, metastatic solid tumors remain largely incurable. Immunotherapy has emerged as a pioneering and promising approach for cancer therapy and management, and in particular intended for advanced tumors unresponsive to current therapeutics. In cancer immunotherapy, components of the immune system are exploited to eliminate cancer cells and treat patients. The recent clinical successes of immune checkpoint blockade and chimeric antigen receptor T cell therapies represent a turning point in cancer treatment. Despite their potential success, current approaches depend on efficient tumor antigen presentation which are often inaccessible, and most tumors turn refractory to current immunotherapy. Patient-derived induced pluripotent stem cells (iPSCs) have been shown to share several characteristics with cancer (stem) cells (CSCs), eliciting a specific anti-tumoral response when injected in rodent cancer models. Indeed, artificial cellular reprogramming has been widely compared to the biogenesis of CSCs. Here, we will discuss the state-of-the-art on the potential implication of cellular reprogramming and iPSCs for the design of patient-specific immunotherapeutic strategies, debating the similarities between iPSCs and cancer cells and introducing potential strategies that could enhance the efficiency and therapeutic potential of iPSCs-based cancer vaccines.
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18
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Hammelman J, Krismer K, Banerjee B, Gifford DK, Sherwood RI. Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay. Genome Res 2020; 30:1468-1480. [PMID: 32973041 PMCID: PMC7605270 DOI: 10.1101/gr.263228.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022]
Abstract
A key mechanism in cellular regulation is the ability of the transcriptional machinery to physically access DNA. Transcription factors interact with DNA to alter the accessibility of chromatin, which enables changes to gene expression during development or disease or as a response to environmental stimuli. However, the regulation of DNA accessibility via the recruitment of transcription factors is difficult to study in the context of the native genome because every genomic site is distinct in multiple ways. Here we introduce the multiplexed integrated accessibility assay (MIAA), an assay that measures chromatin accessibility of synthetic oligonucleotide sequence libraries integrated into a controlled genomic context with low native accessibility. We apply MIAA to measure the effects of sequence motifs on cell type-specific accessibility between mouse embryonic stem cells and embryonic stem cell-derived definitive endoderm cells, screening 7905 distinct DNA sequences. MIAA recapitulates differential accessibility patterns of 100-nt sequences derived from natively differential genomic regions, identifying E-box motifs common to epithelial-mesenchymal transition driver transcription factors in stem cell-specific accessible regions that become repressed in endoderm. We show that a single binding motif for a key regulatory transcription factor is sufficient to open chromatin, and classify sets of stem cell-specific, endoderm-specific, and shared accessibility-modifying transcription factor motifs. We also show that overexpression of two definitive endoderm transcription factors, T and Foxa2, results in changes to accessibility in DNA sequences containing their respective DNA-binding motifs and identify preferential motif arrangements that influence accessibility.
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Affiliation(s)
- Jennifer Hammelman
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Konstantin Krismer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Budhaditya Banerjee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Richard I Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Hubrecht Institute, 3584 CT Utrecht, Netherlands
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19
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Menuchin-Lasowski Y, Dagan B, Conidi A, Cohen-Gulkar M, David A, Ehrlich M, Giladi PO, Clark BS, Blackshaw S, Shapira K, Huylebroeck D, Henis YI, Ashery-Padan R. Zeb2 regulates the balance between retinal interneurons and Müller glia by inhibition of BMP-Smad signaling. Dev Biol 2020; 468:80-92. [PMID: 32950463 DOI: 10.1016/j.ydbio.2020.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/24/2020] [Accepted: 09/10/2020] [Indexed: 12/27/2022]
Abstract
The interplay between signaling molecules and transcription factors during retinal development is key to controlling the correct number of retinal cell types. Zeb2 (Sip1) is a zinc-finger multidomain transcription factor that plays multiple roles in central and peripheral nervous system development. Haploinsufficiency of ZEB2 causes Mowat-Wilson syndrome, a congenital disease characterized by intellectual disability, epilepsy and Hirschsprung disease. In the developing retina, Zeb2 is required for generation of horizontal cells and the correct number of interneurons; however, its potential function in controlling gliogenic versus neurogenic decisions remains unresolved. Here we present cellular and molecular evidence of the inhibition of Müller glia cell fate by Zeb2 in late stages of retinogenesis. Unbiased transcriptomic profiling of control and Zeb2-deficient early-postnatal retina revealed that Zeb2 functions in inhibiting Id1/2/4 and Hes1 gene expression. These neural progenitor factors normally inhibit neural differentiation and promote Müller glia cell fate. Chromatin immunoprecipitation (ChIP) supported direct regulation of Id1 by Zeb2 in the postnatal retina. Reporter assays and ChIP analyses in differentiating neural progenitors provided further evidence that Zeb2 inhibits Id1 through inhibition of Smad-mediated activation of Id1 transcription. Together, the results suggest that Zeb2 promotes the timely differentiation of retinal interneurons at least in part by repressing BMP-Smad/Notch target genes that inhibit neurogenesis. These findings show that Zeb2 integrates extrinsic cues to regulate the balance between neuronal and glial cell types in the developing murine retina.
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Affiliation(s)
- Yotam Menuchin-Lasowski
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Bar Dagan
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, the Netherlands
| | - Mazal Cohen-Gulkar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ahuvit David
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Marcelo Ehrlich
- Shumins School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Pazit Oren Giladi
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Brian S Clark
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences and Department of Developmental Biology, Washington University, St. Louis, MO 63110, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Baltimore, MD 21205, USA; Department of Ophthalmology, Baltimore, MD 21205, USA; Department of Neurology, Baltimore, MD 21205, USA; Center for Human Systems Biology, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Keren Shapira
- Shumins School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, the Netherlands; Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Yoav I Henis
- Shumins School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel.
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20
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Intrinsic Balance between ZEB Family Members Is Important for Melanocyte Homeostasis and Melanoma Progression. Cancers (Basel) 2020; 12:cancers12082248. [PMID: 32796736 PMCID: PMC7465899 DOI: 10.3390/cancers12082248] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 02/07/2023] Open
Abstract
It has become clear that cellular plasticity is a main driver of cancer therapy resistance. Consequently, there is a need to mechanistically identify the factors driving this process. The transcription factors of the zinc-finger E-box-binding homeobox family, consisting of ZEB1 and ZEB2, are notorious for their roles in epithelial-to-mesenchymal transition (EMT). However, in melanoma, an intrinsic balance between ZEB1 and ZEB2 seems to determine the cellular state by modulating the expression of the master regulator of melanocyte homeostasis, microphthalmia-associated transcription factor (MITF). ZEB2 drives MITF expression and is associated with a differentiated/proliferative melanoma cell state. On the other hand, ZEB1 is correlated with low MITF expression and a more invasive, stem cell-like and therapy-resistant cell state. This intrinsic balance between ZEB1 and ZEB2 could prove to be a promising therapeutic target for melanoma patients. In this review, we will summarise what is known on the functional mechanisms of these transcription factors. Moreover, we will look specifically at their roles during melanocyte-lineage development and homeostasis. Finally, we will overview the current literature on ZEB1 and ZEB2 in the melanoma context and link this to the 'phenotype-switching' model of melanoma cellular plasticity.
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21
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Pieters T, Sanders E, Tian H, van Hengel J, van Roy F. Neural defects caused by total and Wnt1-Cre mediated ablation of p120ctn in mice. BMC DEVELOPMENTAL BIOLOGY 2020; 20:17. [PMID: 32741376 PMCID: PMC7398255 DOI: 10.1186/s12861-020-00222-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/20/2020] [Indexed: 03/11/2023]
Abstract
Background p120 catenin (p120ctn) is an important component in the cadherin-catenin cell adhesion complex because it stabilizes cadherin-mediated intercellular junctions. Outside these junctions, p120ctn is actively involved in the regulation of small GTPases of the Rho family, in actomyosin dynamics and in transcription regulation. We and others reported that loss of p120ctn in mouse embryos results in an embryonic lethal phenotype, but the exact developmental role of p120ctn during brain formation has not been reported. Results We combined floxed p120ctn mice with Del-Cre or Wnt1-Cre mice to deplete p120ctn from either all cells or specific brain and neural crest cells. Complete loss of p120ctn in mid-gestation embryos resulted in an aberrant morphology, including growth retardation, failure to switch from lordotic to fetal posture, and defective neural tube formation and neurogenesis. By expressing a wild-type p120ctn from the ROSA26 locus in p120ctn-null mouse embryonic stem cells, we could partially rescue neurogenesis. To further investigate the developmental role of p120ctn in neural tube formation, we generated conditional p120ctnfl/fl;Wnt1Cre knockout mice. p120ctn deletion in Wnt1-expressing cells resulted in neural tube closure defects (NTDs) and craniofacial abnormalities. These defects could not be correlated with misregulation of brain marker genes or cell proliferation. In contrast, we found that p120ctn is required for proper expression of the cell adhesion components N-cadherin, E-cadherin and β-catenin, and of actin-binding proteins cortactin and Shroom3 at the apical side of neural folds. This region is of critical importance for closure of neural folds. Surprisingly, the lateral side of mutant neural folds showed loss of p120ctn, but not of N-cadherin, β-catenin or cortactin. Conclusions These results indicate that p120ctn is required for neurogenesis and neurulation. Elimination of p120ctn in cells expressing Wnt1 affects neural tube closure by hampering correct formation of specific adhesion and actomyosin complexes at the apical side of neural folds. Collectively, our results demonstrate the crucial role of p120ctn during brain morphogenesis.
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Affiliation(s)
- Tim Pieters
- Molecular Cell Biology Unit, Center for Inflammation Research, VIB, Technologiepark 71, B-9052, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium.,Present address: Faculty of Medicine and Health Sciences, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Ellen Sanders
- Molecular Cell Biology Unit, Center for Inflammation Research, VIB, Technologiepark 71, B-9052, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium.,Present address: Faculty of Medicine and Health Sciences, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Huiyu Tian
- Molecular Cell Biology Unit, Center for Inflammation Research, VIB, Technologiepark 71, B-9052, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium.,Present address: Ministry of Education, College of Life Sciences, Shandong University, Jinan, People's Republic of China
| | - Jolanda van Hengel
- Molecular Cell Biology Unit, Center for Inflammation Research, VIB, Technologiepark 71, B-9052, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium.,Present address: Faculty of Medicine and Health Sciences, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Frans van Roy
- Molecular Cell Biology Unit, Center for Inflammation Research, VIB, Technologiepark 71, B-9052, Ghent, Belgium. .,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium.
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22
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Deryckere A, Stappers E, Dries R, Peyre E, van den Berghe V, Conidi A, Zampeta FI, Francis A, Bresseleers M, Stryjewska A, Vanlaer R, Maas E, Smal IV, van IJcken WFJ, Grosveld FG, Nguyen L, Huylebroeck D, Seuntjens E. Multifaceted actions of Zeb2 in postnatal neurogenesis from the ventricular-subventricular zone to the olfactory bulb. Development 2020; 147:dev184861. [PMID: 32253238 DOI: 10.1242/dev.184861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/23/2020] [Indexed: 03/01/2024]
Abstract
The transcription factor Zeb2 controls fate specification and subsequent differentiation and maturation of multiple cell types in various embryonic tissues. It binds many protein partners, including activated Smad proteins and the NuRD co-repressor complex. How Zeb2 subdomains support cell differentiation in various contexts has remained elusive. Here, we studied the role of Zeb2 and its domains in neurogenesis and neural differentiation in the young postnatal ventricular-subventricular zone (V-SVZ), in which neural stem cells generate olfactory bulb-destined interneurons. Conditional Zeb2 knockouts and separate acute loss- and gain-of-function approaches indicated that Zeb2 is essential for controlling apoptosis and neuronal differentiation of V-SVZ progenitors before and after birth, and we identified Sox6 as a potential downstream target gene of Zeb2. Zeb2 genetic inactivation impaired the differentiation potential of the V-SVZ niche in a cell-autonomous fashion. We also provide evidence that its normal function in the V-SVZ also involves non-autonomous mechanisms. Additionally, we demonstrate distinct roles for Zeb2 protein-binding domains, suggesting that Zeb2 partners co-determine neuronal output from the mouse V-SVZ in both quantitative and qualitative ways in early postnatal life.
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Affiliation(s)
- Astrid Deryckere
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Elke Stappers
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Ruben Dries
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Elise Peyre
- GIGA-Stem Cells and GIGA-Neurosciences, Liège University, Liège 4000, Belgium
| | - Veronique van den Berghe
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
- Department of Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, and MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - F Isabella Zampeta
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Annick Francis
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Marjolein Bresseleers
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Agata Stryjewska
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Ria Vanlaer
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Elke Maas
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven 3000, Belgium
| | - Ihor V Smal
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Wilfred F J van IJcken
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
- Center for Biomics-Genomics, Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Laurent Nguyen
- GIGA-Stem Cells and GIGA-Neurosciences, Liège University, Liège 4000, Belgium
| | - Danny Huylebroeck
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven 3000, Belgium
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
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23
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Zeb2 Regulates Myogenic Differentiation in Pluripotent Stem Cells. Int J Mol Sci 2020; 21:ijms21072525. [PMID: 32260521 PMCID: PMC7177401 DOI: 10.3390/ijms21072525] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 01/01/2023] Open
Abstract
Skeletal muscle differentiation is triggered by a unique family of myogenic basic helix-loop-helix transcription factors, including MyoD, MRF-4, Myf-5, and Myogenin. These transcription factors bind promoters and distant regulatory regions, including E-box elements, of genes whose expression is restricted to muscle cells. Other E-box binding zinc finger proteins target the same DNA response elements, however, their function in muscle development and regeneration is still unknown. Here, we show that the transcription factor zinc finger E-box-binding homeobox 2 (Zeb2, Sip-1, Zfhx1b) is present in skeletal muscle tissues. We investigate the role of Zeb2 in skeletal muscle differentiation using genetic tools and transgenic mouse embryonic stem cells, together with single-cell RNA-sequencing and in vivo muscle engraftment capability. We show that Zeb2 over-expression has a positive impact on skeletal muscle differentiation in pluripotent stem cells and adult myogenic progenitors. We therefore propose that Zeb2 is a novel myogenic regulator and a possible target for improving skeletal muscle regeneration. The non-neural roles of Zeb2 are poorly understood.
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24
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Epithelial-Mesenchymal Plasticity in Cancer Progression and Metastasis. Dev Cell 2020; 49:361-374. [PMID: 31063755 DOI: 10.1016/j.devcel.2019.04.010] [Citation(s) in RCA: 576] [Impact Index Per Article: 144.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/17/2019] [Accepted: 04/07/2019] [Indexed: 02/06/2023]
Abstract
Epithelial-to-mesenchymal transition (EMT) and its reversed process, mesenchymal-to-epithelial transition (MET), are fundamental processes in embryonic development and tissue repair but confer malignant properties to carcinoma cells, including invasive behavior, cancer stem cell activity, and greater resistance to chemotherapy and immunotherapy. Understanding the molecular and cellular basis of EMT provides fundamental insights into the etiology of cancer and may, in the long run, lead to new therapeutic strategies. Here, we discuss the regulatory mechanisms and pathological roles of epithelial-mesenchymal plasticity, with a focus on recent insights into the complexity and dynamics of this phenomenon in cancer.
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25
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Dries R, Stryjewska A, Coddens K, Okawa S, Notelaers T, Birkhoff J, Dekker M, Verfaillie CM, Del Sol A, Mulugeta E, Conidi A, Grosveld FG, Huylebroeck D. Integrative and perturbation-based analysis of the transcriptional dynamics of TGFβ/BMP system components in transition from embryonic stem cells to neural progenitors. Stem Cells 2019; 38:202-217. [PMID: 31675135 PMCID: PMC7027912 DOI: 10.1002/stem.3111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/09/2019] [Indexed: 01/05/2023]
Abstract
Cooperative actions of extrinsic signals and cell‐intrinsic transcription factors alter gene regulatory networks enabling cells to respond appropriately to environmental cues. Signaling by transforming growth factor type β (TGFβ) family ligands (eg, bone morphogenetic proteins [BMPs] and Activin/Nodal) exerts cell‐type specific and context‐dependent transcriptional changes, thereby steering cellular transitions throughout embryogenesis. Little is known about coordinated regulation and transcriptional interplay of the TGFβ system. To understand intrafamily transcriptional regulation as part of this system's actions during development, we selected 95 of its components and investigated their mRNA‐expression dynamics, gene‐gene interactions, and single‐cell expression heterogeneity in mouse embryonic stem cells transiting to neural progenitors. Interrogation at 24 hour intervals identified four types of temporal gene transcription profiles that capture all stages, that is, pluripotency, epiblast formation, and neural commitment. Then, between each stage we performed esiRNA‐based perturbation of each individual component and documented the effect on steady‐state mRNA levels of the remaining 94 components. This exposed an intricate system of multilevel regulation whereby the majority of gene‐gene interactions display a marked cell‐stage specific behavior. Furthermore, single‐cell RNA‐profiling at individual stages demonstrated the presence of detailed co‐expression modules and subpopulations showing stable co‐expression modules such as that of the core pluripotency genes at all stages. Our combinatorial experimental approach demonstrates how intrinsically complex transcriptional regulation within a given pathway is during cell fate/state transitions.
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Affiliation(s)
- Ruben Dries
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Agata Stryjewska
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Kathleen Coddens
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Satoshi Okawa
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.,Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Tineke Notelaers
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Judith Birkhoff
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mike Dekker
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.,CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.,IKERBASQUE, Basque, Foundation for Science, Bilbao, Spain
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
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26
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Fardi M, Alivand M, Baradaran B, Farshdousti Hagh M, Solali S. The crucial role of ZEB2: From development to epithelial-to-mesenchymal transition and cancer complexity. J Cell Physiol 2019; 234:14783-14799. [PMID: 30773635 DOI: 10.1002/jcp.28277] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/13/2019] [Accepted: 01/15/2019] [Indexed: 01/24/2023]
Abstract
Zinc finger E-box binding homeobox 2 (ZEB2) is a DNA-binding transcription factor, which is mainly involved in epithelial-to-mesenchymal transition (EMT). EMT is a conserved process during which mature and adherent epithelial-like state is converted into a mobile mesenchymal state. Emerging data indicate that ZEB2 plays a pivotal role in EMT-induced processes such as development, differentiation, and malignant mechanisms, for example, drug resistance, cancer stem cell-like traits, apoptosis, survival, cell cycle arrest, tumor recurrence, and metastasis. In this regard, the understanding of mentioned subjects in the development of normal and cancerous cells could be helpful in cancer complexity of diagnosis and therapy. In this study, we review recent findings about the biological properties of ZEB2 in healthy and cancerous states to find new approaches for cancer treatment.
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Affiliation(s)
- Masoumeh Fardi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Department, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Department, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Saeed Solali
- Immunology Department, Tabriz University of Medical Sciences, Tabriz, Iran
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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27
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Schuster J, Sobol M, Fatima A, Khalfallah A, Laan L, Anderlid BM, Nordgren A, Dahl N. Mowat-Wilson syndrome: Generation of two human iPS cell lines (UUIGPi004A and UUIGPi005A) from siblings with a truncating ZEB2 gene variant. Stem Cell Res 2019; 39:101518. [PMID: 31376723 DOI: 10.1016/j.scr.2019.101518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/19/2019] [Accepted: 07/25/2019] [Indexed: 12/27/2022] Open
Abstract
Mowat-Wilson syndrome (MWS) is a complex developmental syndrome caused by heterozygous mutations in the Zinc finger E-box-binding homeobox 2 gene (ZEB2). We generated the first human iPSC lines from primary fibroblasts of two siblings with MWS carrying a heterozygous ZEB2 stop mutation (c.1027C > T; p.Arg343*) using the Sendai virus reprogramming system. Both iPSC lines were free from reprogramming vector genes, expressed pluripotency markers and showed potential to differentiate into the three germ layers. Genetic analysis confirmed normal karyotypes and a preserved stop mutation. These iPSC lines will provide a useful resource to study altered neural lineage fate and neuropathophysiology in MWS.
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Affiliation(s)
- Jens Schuster
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden.
| | - Maria Sobol
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden
| | - Ambrin Fatima
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden
| | - Ayda Khalfallah
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden
| | - Loora Laan
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, and Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, and Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Niklas Dahl
- Uppsala University, Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala, Sweden.
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28
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van Mierlo G, Wester RA, Marks H. A Mass Spectrometry Survey of Chromatin-Associated Proteins in Pluripotency and Early Lineage Commitment. Proteomics 2019; 19:e1900047. [PMID: 31219242 DOI: 10.1002/pmic.201900047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/07/2019] [Indexed: 12/12/2022]
Abstract
Pluripotency can be captured in vitro in the form of Embryonic Stem Cells (ESCs). These ESCs can be either maintained in the unrestricted "naïve" state of pluripotency, adapted to developmentally more constrained "primed" pluripotency or differentiated towards each of the three germ layers. Epigenetic protein complexes and transcription factors have been shown to specify and instruct transitions from ESCs to distinct cell states. In this study, proteomic profiling of the chromatin landscape by chromatin enrichment for proteomics (ChEP) is used in mouse naive pluripotent ESCs, primed pluripotent Epiblast stem cells (EpiSCs), and cells in early stages of differentiation. A comprehensive overview of epigenetic protein complexes associated with the chromatin is provided and proteins associated with the maintenance and loss of pluripotency are identified. The data reveal major compositional alterations of epigenetic complexes during priming and differentiation of naïve pluripotent ESCs. These results contribute to the understanding of ESC differentiation and provide a framework for future studies of lineage commitment of ESCs.
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Affiliation(s)
- Guido van Mierlo
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands.,Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Roelof Alexander Wester
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525GA, The Netherlands
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29
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Diverse facets of cortical interneuron migration regulation – Implications of neuronal activity and epigenetics. Brain Res 2018; 1700:160-169. [DOI: 10.1016/j.brainres.2018.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 01/21/2023]
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30
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Skrypek N, Bruneel K, Vandewalle C, De Smedt E, Soen B, Loret N, Taminau J, Goossens S, Vandamme N, Berx G. ZEB2 stably represses RAB25 expression through epigenetic regulation by SIRT1 and DNMTs during epithelial-to-mesenchymal transition. Epigenetics Chromatin 2018; 11:70. [PMID: 30445998 PMCID: PMC6240308 DOI: 10.1186/s13072-018-0239-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/09/2018] [Indexed: 12/29/2022] Open
Abstract
Background Epithelial mesenchymal transition (EMT) is tightly regulated by a network of transcription factors (EMT-TFs). Among them is the nuclear factor ZEB2, a member of the zinc-finger E-box binding homeobox family. ZEB2 nuclear localization has been identified in several cancer types, and its overexpression is correlated with the malignant progression. ZEB2 transcriptionally represses epithelial genes, such as E-cadherin (CDH1), by directly binding to the promoter of the genes it regulates and activating mesenchymal genes by a mechanism in which there is no full agreement. Recent studies showed that EMT-TFs interact with epigenetic regulatory enzymes that alter the epigenome, thereby providing another level of control. The role of epigenetic regulation on ZEB2 function is not well understood. In this study, we aimed to characterize the epigenetic effect of ZEB2 repressive function on the regulation of a small Rab GTPase RAB25. Results Using cellular models with conditional ZEB2 expression, we show a clear transcriptional repression of RAB25 and CDH1. RAB25 contributes to the partial suppression of ZEB2-mediated cell migration. Furthermore, a highly significant reverse correlation between RAB25 and ZEB2 expression in several human cancer types could be identified. Mechanistically, ZEB2 binds specifically to E-box sequences on the RAB25 promoter. ZEB2 binding is associated with the local increase in DNA methylation requiring DNA methyltransferases as well as histone deacetylation (H3K9Ac) depending on the activity of SIRT1. Surprisingly, SIRT1 and DNMTs did not interact directly with ZEB2, and while SIRT1 inhibition decreased the stability of long-term repression, it did not prevent down-regulation of RAB25 and CDH1 by ZEB2. Conclusions ZEB2 expression is resulting in drastic changes at the chromatin level with both clear DNA hypermethylation and histone modifications. Here, we revealed that SIRT1-mediated H3K9 deacetylation helps to maintain gene repression but is not required for the direct ZEB2 repressive function. Targeting epigenetic enzymes to prevent EMT is an appealing approach to limit cancer dissemination, but inhibiting SIRT1 activity alone might have limited effect and will require drug combination to efficiently prevent EMT. Electronic supplementary material The online version of this article (10.1186/s13072-018-0239-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolas Skrypek
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kenneth Bruneel
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Cindy Vandewalle
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Eva De Smedt
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Bieke Soen
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Nele Loret
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Joachim Taminau
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Steven Goossens
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Centre for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
| | - Niels Vandamme
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Data Mining and Modeling for Biomedicine, VIB Inflammation Research Center, Ghent, Belgium.,VIB-UGent Center for Inflammation Research, Technologiepark 927, 9052, Ghent, Belgium
| | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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31
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Jin L, Chang C, Pawlik KM, Datta A, Johnson LM, Vu T, Napoli JL, Datta PK. Serine Threonine Kinase Receptor-Associated Protein Deficiency Impairs Mouse Embryonic Stem Cells Lineage Commitment Through CYP26A1-Mediated Retinoic Acid Homeostasis. Stem Cells 2018; 36:1368-1379. [PMID: 29781215 DOI: 10.1002/stem.2854] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/01/2018] [Accepted: 05/01/2018] [Indexed: 01/07/2023]
Abstract
Retinoic acid (RA) signaling is essential for the differentiation of embryonic stem cells (ESCs) and vertebrate development. RA biosynthesis and metabolism are controlled by a series of enzymes, but the molecular regulators of these enzymes remain largely obscure. In this study, we investigated the functional role of the WD-domain protein STRAP (serine threonine kinase receptor-associated protein) in the pluripotency and lineage commitment of murine ESCs. We generated Strap knockout (KO) mouse ESCs and subjected them to spontaneous differentiation. We observed that, despite the unchanged characteristics of ESCs, Strap KO ESCs exhibited defects for lineage differentiation. Signature gene expression analyses revealed that Strap deletion attenuated intracellular RA signaling in embryoid bodies (EBs), and exogenous RA significantly rescued this deficiency. Moreover, loss of Strap selectively induced Cyp26A1 expression in mouse EBs, suggesting a potential role of STRAP in RA signaling. Mechanistically, we identified putative Krüppel-like factor 9 (KLF9) binding motifs to be critical in the enhancement of non-canonical RA-induced transactivation of Cyp26A1. Increased KLF9 expression in the absence of STRAP is partially responsible for Cyp26A1 induction. Interestingly, STRAP knockdown in Xenopus embryos influenced anterior-posterior neural patterning and impaired the body axis and eye development during early Xenopus embryogenesis. Taken together, our study reveals an intrinsic role for STRAP in the regulation of RA signaling and provides new molecular insights for ESC fate determination. Stem Cells 2018;36:1368-1379.
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Affiliation(s)
- Lin Jin
- Division of Hematology and Oncology, Department of Medicine, UAB Comprehensive Cancer Center, Birmingham, Alabama, USA.,Birmingham Veterans Affairs Medical Center, Birmingham, Alabama, USA
| | - Chenbei Chang
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kevin M Pawlik
- Department of Biochemistry & Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Arunima Datta
- Division of Hematology and Oncology, Department of Medicine, UAB Comprehensive Cancer Center, Birmingham, Alabama, USA.,Birmingham Veterans Affairs Medical Center, Birmingham, Alabama, USA
| | - Larry M Johnson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Trung Vu
- Division of Hematology and Oncology, Department of Medicine, UAB Comprehensive Cancer Center, Birmingham, Alabama, USA
| | - Joseph L Napoli
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, USA
| | - Pran K Datta
- Division of Hematology and Oncology, Department of Medicine, UAB Comprehensive Cancer Center, Birmingham, Alabama, USA.,Birmingham Veterans Affairs Medical Center, Birmingham, Alabama, USA
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32
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Balcik-Ercin P, Cetin M, Yalim-Camci I, Odabas G, Tokay N, Sayan AE, Yagci T. Genome-wide analysis of endogenously expressed ZEB2 binding sites reveals inverse correlations between ZEB2 and GalNAc-transferase GALNT3 in human tumors. Cell Oncol (Dordr) 2018; 41:379-393. [PMID: 29516288 DOI: 10.1007/s13402-018-0375-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2018] [Indexed: 10/17/2022] Open
Abstract
BACKGROUND ZEB2 is a transcriptional repressor that regulates epithelial-to-mesenchymal transition (EMT) through binding to bipartite E-box motifs in gene regulatory regions. Despite the abundant presence of E-boxes within the human genome and the multiplicity of pathophysiological processes regulated during ZEB2-induced EMT, only a small fraction of ZEB2 targets has been identified so far. Hence, we explored genome-wide ZEB2 binding by chromatin immunoprecipitation-sequencing (ChIP-seq) under endogenous ZEB2 expression conditions. METHODS For ChIP-Seq we used an anti-ZEB2 monoclonal antibody, clone 6E5, in SNU398 hepatocellular carcinoma cells exhibiting a high endogenous ZEB2 expression. The ChIP-Seq targets were validated using ChIP-qPCR, whereas ZEB2-dependent expression of target genes was assessed by RT-qPCR and Western blotting in shRNA-mediated ZEB2 silenced SNU398 cells and doxycycline-induced ZEB2 overexpressing colorectal carcinoma DLD1 cells. Changes in target gene expression were also assessed using primary human tumor cDNA arrays in conjunction with RT-qPCR. Additional differential expression and correlation analyses were performed using expO and Human Protein Atlas datasets. RESULTS Over 500 ChIP-Seq positive genes were annotated, and intervals related to these genes were found to include the ZEB2 binding motif CACCTG according to TOMTOM motif analysis in the MEME Suite database. Assessment of ZEB2-dependent expression of target genes in ZEB2-silenced SNU398 cells and ZEB2-induced DLD1 cells revealed that the GALNT3 gene serves as a ZEB2 target with the highest, but inversely correlated, expression level. Remarkably, GALNT3 also exhibited the highest enrichment in the ChIP-qPCR validation assays. Through the analyses of primary tumor cDNA arrays and expO datasets a significant differential expression and a significant inverse correlation between ZEB2 and GALNT3 expression were detected in most of the tumors. We also explored ZEB2 and GALNT3 protein expression using the Human Protein Atlas dataset and, again, observed an inverse correlation in all analyzed tumor types, except malignant melanoma. In contrast to a generally negative or weak ZEB2 expression, we found that most tumor tissues exhibited a strong or moderate GALNT3 expression. CONCLUSIONS Our observation that ZEB2 negatively regulates a GalNAc-transferase (GALNT3) that is involved in O-glycosylation adds another layer of complexity to the role of ZEB2 in cancer progression and metastasis. Proteins glycosylated by GALNT3 may be exploited as novel diagnostics and/or therapeutic targets.
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Affiliation(s)
- Pelin Balcik-Ercin
- Department of Molecular Biology and Genetics, Laboratory of Molecular Oncology, Gebze Technical University, C2-Building, 41400, Gebze-Kocaeli, Turkey
| | - Metin Cetin
- Department of Molecular Biology and Genetics, Laboratory of Molecular Oncology, Gebze Technical University, C2-Building, 41400, Gebze-Kocaeli, Turkey
| | - Irem Yalim-Camci
- Department of Molecular Biology and Genetics, Laboratory of Molecular Oncology, Gebze Technical University, C2-Building, 41400, Gebze-Kocaeli, Turkey
| | - Gorkem Odabas
- Department of Molecular Biology and Genetics, Laboratory of Molecular Oncology, Gebze Technical University, C2-Building, 41400, Gebze-Kocaeli, Turkey
| | - Nurettin Tokay
- Department of Molecular Biology and Genetics, Laboratory of Molecular Oncology, Gebze Technical University, C2-Building, 41400, Gebze-Kocaeli, Turkey
| | - A Emre Sayan
- Faculty of Medicine, Cancer Sciences, University of Southampton, Somers Building, Tremona Road, Southampton, SO16 6YD, UK
| | - Tamer Yagci
- Department of Molecular Biology and Genetics, Laboratory of Molecular Oncology, Gebze Technical University, C2-Building, 41400, Gebze-Kocaeli, Turkey.
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33
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Pan P, Chen T, Zhang Y, Qi Z, Qin J, Cui G, Guo X. LIN28A inhibits lysosome‑associated membrane glycoprotein 1 protein expression in embryonic stem and bladder cancer cells. Mol Med Rep 2018; 18:399-406. [PMID: 29749495 DOI: 10.3892/mmr.2018.8965] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 03/14/2018] [Indexed: 11/06/2022] Open
Abstract
Tumor cells and embryonic stem cells (ESCs) have similar transcription mechanisms. LIN28A is an important factor in tumor cells and ESCs, it is an inhibitor of intracellular endoplasmic reticulum (ER)‑related protein translation in ESCs. The present study aimed to examine the effects of LIN28A on an ER‑related protein, lysosome‑associated membrane glycoprotein 1 (LAMP1), in human bladder cancer cells and mouse (m)ESCs, using reverse transcription‑quantitative polymerase chain reaction and western blotting to detect the expression of LAMP1 mRNA and protein, respectively, following LIN28A knockdown. LIN28A was revealed to promote the proliferation, migration and invasion in human bladder cancer cells. These data suggested similarities between ESC cells and cancer cells and may provide novel ideas for the use of induced embryonic stem cell differentiation to treat tumors.
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Affiliation(s)
- Peng Pan
- Department of Pathology, Guangzhou Medical University, Guangzhou, Guangdong 510182, P.R. China
| | - Ting Chen
- Department of Pathology, Guangzhou Medical University, Guangzhou, Guangdong 510182, P.R. China
| | - Yanmin Zhang
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Shenzhen, Guangdong 518036, P.R. China
| | - Zhengyu Qi
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Shenzhen, Guangdong 518036, P.R. China
| | - Jie Qin
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Shenzhen, Guangdong 518036, P.R. China
| | - Guanghui Cui
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Shenzhen, Guangdong 518036, P.R. China
| | - Xin Guo
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Shenzhen, Guangdong 518036, P.R. China
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34
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Skrypek N, Goossens S, De Smedt E, Vandamme N, Berx G. Epithelial-to-Mesenchymal Transition: Epigenetic Reprogramming Driving Cellular Plasticity. Trends Genet 2017; 33:943-959. [PMID: 28919019 DOI: 10.1016/j.tig.2017.08.004] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 06/20/2017] [Accepted: 08/10/2017] [Indexed: 12/11/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) is a process in which epithelial cells lose their junctions and polarity to gain a motile mesenchymal phenotype. EMT is essential during embryogenesis and adult physiological processes like wound healing, but is aberrantly activated in pathological conditions like fibrosis and cancer. A series of transcription factors (EMT-inducing transcription factor; EMT-TF) regulate the induction of EMT by repressing the transcription of epithelial genes while activating mesenchymal genes through mechanisms still debated. The nuclear interaction of EMT-TFs with larger protein complexes involved in epigenetic genome modulation has attracted recent attention to explain functions of EMT-TFs during reprogramming and cellular differentiation. In this review, we discuss recent advances in understanding the interplay between epigenetic regulators and EMT transcription factors and how these findings could be used to establish new therapeutic approaches to tackle EMT-related diseases.
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Affiliation(s)
- Nicolas Skrypek
- Molecular and Cellular Oncology Laboratory, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; These authors contributed equally
| | - Steven Goossens
- Molecular and Cellular Oncology Laboratory, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Centre for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium; These authors contributed equally
| | - Eva De Smedt
- Molecular and Cellular Oncology Laboratory, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Niels Vandamme
- Molecular and Cellular Oncology Laboratory, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Inflammation Research Center (IRC), VIB, Ghent, Belgium
| | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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35
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Cao T, Xiao T, Huang G, Xu Y, Zhu JJ, Wang K, Ye W, Guan H, He J, Zheng D. CDK3, target of miR-4469, suppresses breast cancer metastasis via inhibiting Wnt/β-catenin pathway. Oncotarget 2017; 8:84917-84927. [PMID: 29156693 PMCID: PMC5689583 DOI: 10.18632/oncotarget.18171] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/08/2017] [Indexed: 12/21/2022] Open
Abstract
Cyclin-dependent kinase 3 (CDK3), a member of CDK family, is involved in G0/G1 and G1/S cell cycle transitions. Although several researchers discovered that CDK3 related to cell growth in some kinds of cancer, the functions of CDK3 during tumor development remains unclear. Here, we first found that the expression of CDK3 was higher in primary tumors of non-metastatic breast cancer compared with those in metastatic breast cancer. Overexpression of CDK3 suppressed cell migration and invasion of breast cancer cells, and decreased the metastasis in nude mice. We further identified miR-4469 was a negative regulator of CDK3 by directly targeting its 3'-untranslated region (UTR). The increase of motility induced by miR-4469 could be abolished by CDK3 overexpression. Moreover, RNA-seq analysis revealed that Wnt pathway may be inhibited by CDK3 expression, which was subsequently confirmed by western blot. Moreover, Wnt3a treatment abolished the inhibitory role of CDK3 in cell motility, suggesting that Wnt signaling is the potential downstream of CDK3. In conclusion, these results support that CDK3 which is targeted by miR-4469 suppresses breast cancer metastasis by inhibiting Wnt/β-catenin pathway.
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Affiliation(s)
- Ting Cao
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen 518060, Guangdong Province, China.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, Guangdong Province, China
| | - Tian Xiao
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen 518060, Guangdong Province, China
| | - Guanqun Huang
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen 518060, Guangdong Province, China
| | - Yafei Xu
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen 518060, Guangdong Province, China
| | - Joe Jiang Zhu
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen 518060, Guangdong Province, China
| | - Kaixin Wang
- Department of Pathology, Shenzhen Nanshan People's Hospital, Shenzhen 518052, Guangdong Province, China
| | - Wencai Ye
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, Guangdong Province, China
| | - Hong Guan
- Department of Pathology, The First Affiliated Hospital of Shenzhen University, Second People's Hospital of Shenzhen, Shenzhen 518035, Guangdong Province, China
| | - Jinsong He
- Department of Breast Surgery, The First Affiliated Hospital of Shenzhen University, Second People's Hospital of Shenzhen, Shenzhen 518035, Guangdong Province, China
| | - Duo Zheng
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen 518060, Guangdong Province, China
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36
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Pieters T, Haenebalcke L, Bruneel K, Vandamme N, Hochepied T, van Hengel J, Wirth D, Berx G, Haigh JJ, van Roy F, Goossens S. Structure-function Studies in Mouse Embryonic Stem Cells Using Recombinase-mediated Cassette Exchange. J Vis Exp 2017. [PMID: 28518103 DOI: 10.3791/55575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Gene engineering in mouse embryos or embryonic stem cells (mESCs) allows for the study of the function of a given protein. Proteins are the workhorses of the cell and often consist of multiple functional domains, which can be influenced by posttranslational modifications. The depletion of the entire protein in conditional or constitutive knock-out (KO) mice does not take into account this functional diversity and regulation. An mESC line and a derived mouse model, in which a docking site for FLPe recombination-mediated cassette exchange (RMCE) was inserted within the ROSA26 (R26) locus, was previously reported. Here, we report on a structure-function approach that allows for molecular dissection of the different functionalities of a multidomain protein. To this end, RMCE-compatible mice must be crossed with KO mice and then RMCE-compatible KO mESCs must be isolated. Next, a panel of putative rescue constructs can be introduced into the R26 locus via RMCE targeting. The candidate rescue cDNAs can be easily inserted between RMCE sites of the targeting vector using recombination cloning. Next, KO mESCs are transfected with the targeting vector in combination with an FLPe recombinase expression plasmid. RMCE reactivates the promoter-less neomycin-resistance gene in the ROSA26 docking sites and allows for the selection of the correct targeting event. In this way, high targeting efficiencies close to 100% are obtained, allowing for insertion of multiple putative rescue constructs in a semi-high throughput manner. Finally, a multitude of R26-driven rescue constructs can be tested for their ability to rescue the phenotype that was observed in parental KO mESCs. We present a proof-of-principle structure-function study in p120 catenin (p120ctn) KO mESCs using endoderm differentiation in embryoid bodies (EBs) as the phenotypic readout. This approach enables the identification of important domains, putative downstream pathways, and disease-relevant point mutations that underlie KO phenotypes for a given protein.
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Affiliation(s)
- Tim Pieters
- Department of Biomedical Molecular Biology, Ghent University; Inflammation Research Center, VIB; Center for Medical Genetics, Ghent University Hospital; Cancer Research Institute Ghent (CRIG);
| | - Lieven Haenebalcke
- Department of Biomedical Molecular Biology, Ghent University; Inflammation Research Center, VIB
| | - Kenneth Bruneel
- Department of Biomedical Molecular Biology, Ghent University; Inflammation Research Center, VIB; Cancer Research Institute Ghent (CRIG)
| | - Niels Vandamme
- Department of Biomedical Molecular Biology, Ghent University; Inflammation Research Center, VIB; Cancer Research Institute Ghent (CRIG)
| | - Tino Hochepied
- Department of Biomedical Molecular Biology, Ghent University; Inflammation Research Center, VIB
| | - Jolanda van Hengel
- Department of Basic Medical Sciences, Faculty of Medicine and Health Sciences, Ghent University
| | | | - Geert Berx
- Department of Biomedical Molecular Biology, Ghent University; Inflammation Research Center, VIB; Cancer Research Institute Ghent (CRIG)
| | - Jody J Haigh
- Mammalian Functional Genetics Laboratory, Division of Blood Cancers, Australian Centre for Blood Diseases, Department of Clinical Haematology, Monash University and Alfred Health Alfred Centre
| | - Frans van Roy
- Department of Biomedical Molecular Biology, Ghent University; Inflammation Research Center, VIB; Cancer Research Institute Ghent (CRIG)
| | - Steven Goossens
- Department of Biomedical Molecular Biology, Ghent University; Inflammation Research Center, VIB; Center for Medical Genetics, Ghent University Hospital; Cancer Research Institute Ghent (CRIG);
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Oncogenic ZEB2 activation drives sensitivity toward KDM1A inhibition in T-cell acute lymphoblastic leukemia. Blood 2017; 129:981-990. [PMID: 28069602 DOI: 10.1182/blood-2016-06-721191] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 12/22/2016] [Indexed: 01/01/2023] Open
Abstract
Elevated expression of the Zinc finger E-box binding homeobox transcription factor-2 (ZEB2) is correlated with poor prognosis and patient outcome in a variety of human cancer subtypes. Using a conditional gain-of-function mouse model, we recently demonstrated that ZEB2 is an oncogenic driver of immature T-cell acute lymphoblastic leukemia (T-ALL), a heterogenic subgroup of human leukemia characterized by a high incidence of remission failure or hematological relapse after conventional chemotherapy. Here, we identified the lysine-specific demethylase KDM1A as a novel interaction partner of ZEB2 and demonstrated that mouse and human T-ALLs with increased ZEB2 levels critically depend on KDM1A activity for survival. Therefore, targeting the ZEB2 protein complex through direct disruption of the ZEB2-KDM1A interaction or pharmacological inhibition of the KDM1A demethylase activity itself could serve as a novel therapeutic strategy for this aggressive subtype of human leukemia and possibly other ZEB2-driven malignancies.
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