1
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Chen L, Li H, Liu X, Zhang N, Wang K, Shi A, Gao H, Akdis D, Saguner AM, Xu X, Osto E, Van de Veen W, Li G, Bayés-Genís A, Duru F, Song J, Li X, Hu S. PBX/Knotted 1 homeobox-2 (PKNOX2) is a novel regulator of myocardial fibrosis. Signal Transduct Target Ther 2024; 9:94. [PMID: 38644381 PMCID: PMC11033280 DOI: 10.1038/s41392-024-01804-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 02/08/2024] [Accepted: 03/13/2024] [Indexed: 04/23/2024] Open
Abstract
Much effort has been made to uncover the cellular heterogeneities of human hearts by single-nucleus RNA sequencing. However, the cardiac transcriptional regulation networks have not been systematically described because of the limitations in detecting transcription factors. In this study, we optimized a pipeline for isolating nuclei and conducting single-nucleus RNA sequencing targeted to detect a higher number of cell signal genes and an optimal number of transcription factors. With this unbiased protocol, we characterized the cellular composition of healthy human hearts and investigated the transcriptional regulation networks involved in determining the cellular identities and functions of the main cardiac cell subtypes. Particularly in fibroblasts, a novel regulator, PKNOX2, was identified as being associated with physiological fibroblast activation in healthy hearts. To validate the roles of these transcription factors in maintaining homeostasis, we used single-nucleus RNA-sequencing analysis of transplanted failing hearts focusing on fibroblast remodelling. The trajectory analysis suggested that PKNOX2 was abnormally decreased from fibroblast activation to pathological myofibroblast formation. Both gain- and loss-of-function in vitro experiments demonstrated the inhibitory role of PKNOX2 in pathological fibrosis remodelling. Moreover, fibroblast-specific overexpression and knockout of PKNOX2 in a heart failure mouse model induced by transverse aortic constriction surgery significantly improved and aggravated myocardial fibrosis, respectively. In summary, this study established a high-quality pipeline for single-nucleus RNA-sequencing analysis of heart muscle. With this optimized protocol, we described the transcriptional regulation networks of the main cardiac cell subtypes and identified PKNOX2 as a novel regulator in suppressing fibrosis and a potential therapeutic target for future translational studies.
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Affiliation(s)
- Liang Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Haotong Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Xiaorui Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Ningning Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Kui Wang
- School of Statistics and Data Science, Nankai University, Tianjin, China
| | - Anteng Shi
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Hang Gao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Deniz Akdis
- Department of Cardiology, University Heart Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Ardan M Saguner
- Department of Cardiology, University Heart Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Xinjie Xu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Elena Osto
- Department of Cardiology, University Heart Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Institute for Clinical Chemistry, University Hospital Zurich and University of Zürich, Zurich, Switzerland
| | - Willem Van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Guangyu Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Antoni Bayés-Genís
- Heart Institute, Hospital Universitari Germans Trias i Pujol, Badalona, CIBERCV, Spain
| | - Firat Duru
- Department of Cardiology, University Heart Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Jiangping Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China.
| | - Xiangjie Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China.
| | - Shengshou Hu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China.
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2
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Bobola N, Sagerström CG. TALE transcription factors: Cofactors no more. Semin Cell Dev Biol 2024; 152-153:76-84. [PMID: 36509674 DOI: 10.1016/j.semcdb.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/27/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Exd/PBX, Hth/MEIS and PREP proteins belong to the TALE (three-amino-acid loop extension) superclass of transcription factors (TFs) with an atypical homedomain (HD). Originally discovered as "cofactors" to HOX proteins, revisiting their traditional role in light of genome-wide experiments reveals a strong and reproducible pattern of HOX and TALE co-occupancy across diverse embryonic tissues. While confirming that TALE increases HOX specificity and selectivity in vivo, this wider outlook also reveals novel aspects of HOX:TALE collaboration, namely that HOX TFs generally require pre-bound TALE factors to access their functional binding sites in vivo. In contrast to the restricted expression domains of HOX TFs, TALE factors are largely ubiquitous, and PBX and PREP are expressed at the earliest developmental stages. PBX and MEIS control development of many organs and tissues and their dysregulation is associated with congenital disease and cancer. Accordingly, many instances of TALE cooperation with non HOX TFs have been documented in various systems. The model that emerges from these studies is that TALE TFs create a permissive chromatin platform that is selected by tissue-restricted TFs for binding. In turn, HOX and other tissue-restricted TFs selectively convert a ubiquitous pool of low affinity TALE binding events into high confidence, tissue-restricted binding events associated with transcriptional activation. As a result, TALE:TF complexes are associated with active chromatin and domain/lineage-specific gene activity. TALE ubiquitous expression and broad genomic occupancy, as well as the increasing examples of TALE tissue-specific partners, reveal a universal and obligatory role for TALE in the control of tissue and lineage-specific transcriptional programs, beyond their initial discovery as HOX co-factors.
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Affiliation(s)
- Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK.
| | - Charles G Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, Aurora, CO, USA.
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3
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Yang M, Tang Y, Zhu P, Lu H, Wan X, Guo Q, Xiao L, Liu C, Guo L, Liu W, Yang Y. The advances of E2A-PBX1 fusion in B-cell acute lymphoblastic Leukaemia. Ann Hematol 2023:10.1007/s00277-023-05595-7. [PMID: 38148344 DOI: 10.1007/s00277-023-05595-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/17/2023] [Indexed: 12/28/2023]
Abstract
The E2A-PBX1 gene fusion is a common translocation in B-cell acute lymphoblastic leukaemia. Patients harbouring the E2A-PBX1 fusion gene typically exhibit an intermediate prognosis. Furthermore, minimal residual disease has unsatisfactory prognostic value in E2A-PBX1 B-cell acute lymphoblastic leukaemia. However, the mechanism of E2A-PBX1 in the occurrence and progression of B-cell acute lymphoblastic leukaemia is not well understood. Here, we mainly review the roles of E2A and PBX1 in the differentiation and development of B lymphocytes, the mechanism of E2A-PBX1 gene fusion in B-cell acute lymphoblastic leukaemia, and the potential therapeutic approaches.
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Affiliation(s)
- Mengting Yang
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Yanhui Tang
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Peng Zhu
- School of Pharmacy, Wannan Medical College, Wuhu, 241000, People's Republic of China
| | - Haiquan Lu
- The Second Hospital, Centre for Reproductive Medicine, Advanced Medical Research Institute, Key Laboratory for Experimental Teratology of the Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiaohong Wan
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Qulian Guo
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Lan Xiao
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Chunyan Liu
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Ling Guo
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China
| | - Wenjun Liu
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China.
| | - You Yang
- Department of Paediatrics (Children Haematological Oncology), Birth Defects and Childhood Haematological Oncology Laboratory, Sichuan Clinical Research Centre for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Department of Paediatrics, Southwest Medical University, Luzhou, Sichuan, China.
- The Second Hospital, Centre for Reproductive Medicine, Advanced Medical Research Institute, Key Laboratory for Experimental Teratology of the Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
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4
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Kim YI, O'Rourke R, Sagerström CG. scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities. eLife 2023; 12:e87772. [PMID: 37947350 PMCID: PMC10662952 DOI: 10.7554/elife.87772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 11/09/2023] [Indexed: 11/12/2023] Open
Abstract
Rhombomeres serve to position neural progenitors in the embryonic hindbrain, thereby ensuring appropriate neural circuit formation, but the molecular identities of individual rhombomeres and the mechanism whereby they form has not been fully established. Here, we apply scMultiome analysis in zebrafish to molecularly resolve all rhombomeres for the first time. We find that rhombomeres become molecularly distinct between 10hpf (end of gastrulation) and 13hpf (early segmentation). While the embryonic hindbrain transiently contains alternating odd- versus even-type rhombomeres, our scMultiome analyses do not detect extensive odd versus even molecular characteristics in the early hindbrain. Instead, we find that each rhombomere displays a unique gene expression and chromatin profile. Prior to the appearance of distinct rhombomeres, we detect three hindbrain progenitor clusters (PHPDs) that correlate with the earliest visually observed segments in the hindbrain primordium that represent prospective rhombomere r2/r3 (possibly including r1), r4, and r5/r6, respectively. We further find that the PHPDs form in response to Fgf and RA morphogens and that individual PHPD cells co-express markers of multiple mature rhombomeres. We propose that the PHPDs contain mixed-identity progenitors and that their subdivision into individual rhombomeres requires the resolution of mixed transcription and chromatin states.
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Affiliation(s)
- Yong-Il Kim
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical SchoolAuroraUnited States
| | - Rebecca O'Rourke
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical SchoolAuroraUnited States
| | - Charles G Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical SchoolAuroraUnited States
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5
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Park YP, Roach T, Soh S, Zeumer-Spataro L, Choi SC, Ostrov DA, Yang Y, Morel L. Molecular Mechanisms of Lupus Susceptibility Allele PBX1D. J Immunol 2023; 211:727-734. [PMID: 37486226 PMCID: PMC10530199 DOI: 10.4049/jimmunol.2300362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023]
Abstract
Pre-B cell leukemia homeobox 1 (PBX1) controls chromatin accessibility to a large number of genes in various cell types. Its dominant negative splice isoform, PBX1D, which lacks the DNA and Hox-binding domains, is expressed more frequently in the CD4+ T cells from lupus-prone mice and patients with systemic lupus erythematosus than healthy control subjects. PBX1D overexpression in CD4+ T cells impaired regulatory T cell homeostasis and expanded inflammatory CD4+ T cells. In this study, we showed that PBX1 message expression is downregulated by activation in CD4+ T cells as well as in B cells. PBX1D protein was less stable than the normal isoform, PBX1B, and it is degraded through the ubiquitin-proteasome-dependent pathway. The DNA binding domain lacking in PBX1D has two putative ubiquitin binding sites, K292 and K293, that are predicted to be in direct contact with DNA. Mutation of K292-293 reduced PBX1B stability to a level similar to PBX1D and abrogated DNA binding. In addition, contrary to PBX1B, PBX1D is retained in the cytoplasm without the help of the cofactors MEIS or PREP1, indicating a different requirement for nuclear translocation. Overall, these findings suggest that multiple post-transcriptional mechanisms are responsible for PBX1D loss of function and induction of CD4+ T cell inflammatory phenotypes in systemic lupus erythematosus.
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Affiliation(s)
- Yuk Pheel Park
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health San Antonio, TX 78229-3900, USA
| | - Tracoyia Roach
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL32610, USA
| | - Sujung Soh
- Research Institute of Women’s Health, Sookmyung Women’s University, 100 Cheongparo 47-gil, Yongsan-Gu, Seoul 04310, South Korea, USA
| | - Leilani Zeumer-Spataro
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL32610, USA
| | - Seung-Chul Choi
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health San Antonio, TX 78229-3900, USA
| | - David A. Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL32610, USA
| | - Young Yang
- Research Institute of Women’s Health, Sookmyung Women’s University, 100 Cheongparo 47-gil, Yongsan-Gu, Seoul 04310, South Korea, USA
| | - Laurence Morel
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health San Antonio, TX 78229-3900, USA
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6
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Coulombe P, Cole G, Fentiman A, Parker JDK, Yung E, Bilenky M, Degefie L, Lac P, Ling MYM, Tam D, Humphries RK, Karsan A. Meis1 establishes the pre-hemogenic endothelial state prior to Runx1 expression. Nat Commun 2023; 14:4537. [PMID: 37500618 PMCID: PMC10374625 DOI: 10.1038/s41467-023-40283-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/20/2023] [Indexed: 07/29/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) originate from an endothelial-to-hematopoietic transition (EHT) during embryogenesis. Characterization of early hemogenic endothelial (HE) cells is required to understand what drives hemogenic specification and to accurately define cells capable of undergoing EHT. Using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), we define the early subpopulation of pre-HE cells based on both surface markers and transcriptomes. We identify the transcription factor Meis1 as an essential regulator of hemogenic cell specification in the embryo prior to Runx1 expression. Meis1 is expressed at the earliest stages of EHT and distinguishes pre-HE cells primed towards the hemogenic trajectory from the arterial endothelial cells that continue towards a vascular fate. Endothelial-specific deletion of Meis1 impairs the formation of functional Runx1-expressing HE which significantly impedes the emergence of pre-HSPC via EHT. Our findings implicate Meis1 in a critical fate-determining step for establishing EHT potential in endothelial cells.
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Affiliation(s)
- Patrick Coulombe
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Grace Cole
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Amanda Fentiman
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Jeremy D K Parker
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Eric Yung
- Terry Fox Laboratory, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Misha Bilenky
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Lemlem Degefie
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Patrick Lac
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Maggie Y M Ling
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Derek Tam
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - R Keith Humphries
- Terry Fox Laboratory, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, BC Cancer, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada.
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
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7
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Balbhim SS, Sarkar S, Vasudevan M, Ghosh SK. Three-amino acid loop extension homeodomain proteins regulate stress responses and encystation in Entamoeba. Mol Microbiol 2023. [PMID: 37424153 DOI: 10.1111/mmi.15121] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023]
Abstract
It is interesting to identify factors involved in the regulation of the encystation of Entamoeba histolytica that differentiate trophozoites into cysts. Evolutionarily conserved three amino acid loop extension (TALE) homeodomain proteins act as transcription factors and execute a variety of functions that are essential for life. A TALE homeodomain (EhHbox) protein-encoding gene has been identified in E. histolytica (Eh) that is highly upregulated during heat shock, glucose, and serum starvation. Its ortholog, EiHbox1, a putative homeobox protein in E. invadens (Ei), is also highly upregulated during the early hours of encystation, glucose starvation, and heat shock. They belong to the PBX family of TALE homeobox proteins and have conserved residues in the homeodomain that are essential for DNA binding. Both are localized in the nucleus during encystation and under different stress conditions. The electrophoretic mobility shift assay confirmed that the recombinant GST-EhHbox binds to the reported TGACAG and TGATTGAT motifs. Down-regulation of EiHbox1 by gene silencing reduced Chitin synthase, Jacob, and increased Jessie gene expression, resulting in defective cysts and decreased encystation efficiency and viability. Overall, our results suggest that the TALE homeobox family has been conserved during evolution and acts as a transcription factor to control the differentiation of Entamoeba by regulating the key encystation-induced genes.
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Affiliation(s)
- Sonar Shubham Balbhim
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Shilpa Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | | | - Sudip K Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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8
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Losa M, Barozzi I, Osterwalder M, Hermosilla-Aguayo V, Morabito A, Chacón BH, Zarrineh P, Girdziusaite A, Benazet JD, Zhu J, Mackem S, Capellini TD, Dickel D, Bobola N, Zuniga A, Visel A, Zeller R, Selleri L. A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2. Nat Commun 2023; 14:3993. [PMID: 37414772 PMCID: PMC10325989 DOI: 10.1038/s41467-023-39443-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/14/2023] [Indexed: 07/08/2023] Open
Abstract
A lingering question in developmental biology has centered on how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. Here, using the murine hindlimb as a model, we investigate the elusive mechanisms whereby PBX TALE homeoproteins, viewed primarily as HOX cofactors, attain context-specific developmental roles despite ubiquitous presence in the embryo. We first demonstrate that mesenchymal-specific loss of PBX1/2 or the transcriptional regulator HAND2 generates similar limb phenotypes. By combining tissue-specific and temporally controlled mutagenesis with multi-omics approaches, we reconstruct a gene regulatory network (GRN) at organismal-level resolution that is collaboratively directed by PBX1/2 and HAND2 interactions in subsets of posterior hindlimb mesenchymal cells. Genome-wide profiling of PBX1 binding across multiple embryonic tissues further reveals that HAND2 interacts with subsets of PBX-bound regions to regulate limb-specific GRNs. Our research elucidates fundamental principles by which promiscuous transcription factors cooperate with cofactors that display domain-restricted localization to instruct tissue-specific developmental programs.
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Affiliation(s)
- Marta Losa
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Viviana Hermosilla-Aguayo
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Angela Morabito
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Brandon H Chacón
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Peyman Zarrineh
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Ausra Girdziusaite
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Jean Denis Benazet
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Jianjian Zhu
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Diane Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK
| | - Aimée Zuniga
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, CA, 95343, USA
| | - Rolf Zeller
- Developmental Genetics, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Licia Selleri
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, San Francisco, CA, USA.
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9
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Kim YI, O’Rourke R, Sagerström CG. scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities. bioRxiv 2023:2023.01.27.525932. [PMID: 36747868 PMCID: PMC9900950 DOI: 10.1101/2023.01.27.525932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Rhombomeres serve to position neural progenitors in the embryonic hindbrain, thereby ensuring appropriate neural circuit formation, but the molecular identities of individual rhombomeres and the mechanism whereby they form have not been fully established. Here we apply scMultiome analysis in zebrafish to molecularly resolve all rhombomeres for the first time. We find that rhombomeres become molecularly distinct between 10hpf (end of gastrulation) and 13hpf (early segmentation). While the mature hindbrain consists of alternating odd- versus even-type rhombomeres, our scMultiome analyses do not detect extensive odd versus even characteristics in the early hindbrain. Instead, we find that each rhombomere displays a unique gene expression and chromatin profile. Prior to the appearance of distinct rhombomeres, we detect three hindbrain progenitor clusters (PHPDs) that correlate with the earliest visually observed segments in the hindbrain primordium and that represent prospective rhombomere r2/r3 (possibly including r1), r4 and r5/r6, respectively. We further find that the PHPDs form in response to Fgf and RA morphogens and that individual PHPD cells co-express markers of multiple mature rhombomeres. We propose that the PHPDs contain mixed-identity progenitors and that their subdivision into individual mature rhombomeres requires resolution of mixed transcription and chromatin states.
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Affiliation(s)
| | | | - Charles G. Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, 12801 E. 17th Avenue, Aurora, CO 80045
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10
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Mary L, Leclerc D, Gilot D, Belaud-Rotureau MA, Jaillard S. The TALE never ends: A comprehensive overview of the role of PBX1, a TALE transcription factor, in human developmental defects. Hum Mutat 2022; 43:1125-1148. [PMID: 35451537 DOI: 10.1002/humu.24388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/25/2022] [Accepted: 04/20/2022] [Indexed: 11/07/2022]
Abstract
PBX1 is a highly conserved atypical homeodomain transcription factor (TF) belonging to the TALE (three amino acid loop extension) family. Dimerized with other TALE proteins, it can interact with numerous partners and reach dozens of regulating sequences, suggesting its role as a pioneer factor. PBX1 is expressed throughout the embryonic stages (as early as the blastula stage) in vertebrates. In human, PBX1 germline variations are linked to syndromic renal anomalies (CAKUTHED). In this review, we summarized available data on PBX1 functions, PBX1-deficient animal models, and PBX1 germline variations in humans. Two types of genetic alterations were identified in PBX1 gene. PBX1 missense variations generate a severe phenotype including lung hypoplasia, cardiac malformations, and sexual development defects (DSDs). Conversely, truncating variants generate milder phenotypes (mainly cryptorchidism and deafness). We suggest that defects in PBX1 interactions with various partners, including proteins from the HOX (HOXA7, HOXA10, etc.), WNT (WNT9B, WNT3), and Polycomb (BMI1, EED) families are responsible for abnormal proliferation and differentiation of the embryonic mesenchyme. These alterations could explain most of the defects observed in humans. However, some phenotype variability (especially DSDs) remains poorly understood. Further studies are needed to explore the TALE family in greater depth.
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Affiliation(s)
- Laura Mary
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
| | - Delphine Leclerc
- Inserm U1242, Centre de lutte contre le cancer Eugène Marquis, Université de Rennes, Rennes, France
| | - David Gilot
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- Inserm U1242, Centre de lutte contre le cancer Eugène Marquis, Université de Rennes, Rennes, France
| | - Marc-Antoine Belaud-Rotureau
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
| | - Sylvie Jaillard
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
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11
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Abstract
Gene duplication and divergence is a major contributor to the generation of morphological diversity and the emergence of novel features in vertebrates during evolution. The availability of sequenced genomes has facilitated our understanding of the evolution of genes and regulatory elements. However, progress in understanding conservation and divergence in the function of proteins has been slow and mainly assessed by comparing protein sequences in combination with in vitro analyses. These approaches help to classify proteins into different families and sub-families, such as distinct types of transcription factors, but how protein function varies within a gene family is less well understood. Some studies have explored the functional evolution of closely related proteins and important insights have begun to emerge. In this review, we will provide a general overview of gene duplication and functional divergence and then focus on the functional evolution of HOX proteins to illustrate evolutionary changes underlying diversification and their role in animal evolution.
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Affiliation(s)
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, United States
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, United States
- *Correspondence: Robb Krumlauf,
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12
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Purushothaman D, Bianchi LF, Penkov D, Poli A, Li Q, Vermezovic J, Pramotton FM, Choudhary R, Pennacchio FA, Sommariva E, Foiani M, Gauthier N, Maiuri P, Blasi F. The transcription factor PREP1(PKNOX1) regulates nuclear stiffness, the expression of LINC complex proteins and mechanotransduction. Commun Biol 2022; 5:456. [PMID: 35550602 DOI: 10.1038/s42003-022-03406-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 04/23/2022] [Indexed: 11/16/2022] Open
Abstract
Mechanosignaling, initiated by extracellular forces and propagated through the intracellular cytoskeletal network, triggers signaling cascades employed in processes as embryogenesis, tissue maintenance and disease development. While signal transduction by transcription factors occurs downstream of cellular mechanosensing, little is known about the cell intrinsic mechanisms that can regulate mechanosignaling. Here we show that transcription factor PREP1 (PKNOX1) regulates the stiffness of the nucleus, the expression of LINC complex proteins and mechanotransduction of YAP-TAZ. PREP1 depletion upsets the nuclear membrane protein stoichiometry and renders nuclei soft. Intriguingly, these cells display fortified actomyosin network with bigger focal adhesion complexes resulting in greater traction forces at the substratum. Despite the high traction, YAP-TAZ translocation is impaired indicating disrupted mechanotransduction. Our data demonstrate mechanosignaling upstream of YAP-TAZ and suggest the existence of a transcriptional mechanism actively regulating nuclear membrane homeostasis and signal transduction through the active engagement/disengagement of the cell from the extracellular matrix. The transcription factor PREP1 binds to promoter regions of SUN1, SUN2 and LAP2 genes and promotes nuclear stiffness, and its depletion results in impaired mechanotransduction.
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13
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Stafeev YS, Shevchenko EK, Boldireva MA, Penkov DN. Possible Role of Prep1 Homeodomain Transcription Factor in Cardiac Mesenchymal Stromal Cells. Mol Biol 2021. [DOI: 10.1134/s0026893321050125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Parker HJ, De Kumar B, Pushel I, Bronner ME, Krumlauf R. Analysis of lamprey meis genes reveals that conserved inputs from Hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube. Dev Biol 2021; 479:61-76. [PMID: 34310923 DOI: 10.1016/j.ydbio.2021.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/10/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022]
Abstract
Meis genes are known to play important roles in the hindbrain and neural crest cells of jawed vertebrates. To explore the roles of Meis genes in head development during evolution of vertebrates, we have identified four meis genes in the sea lamprey genome and characterized their patterns of expression and regulation, with a focus on the hindbrain and pharynx. Each of the lamprey meis genes displays temporally and spatially dynamic patterns of expression, some of which are coupled to rhombomeric domains in the developing hindbrain and select pharyngeal arches. Studies of Meis loci in mouse and zebrafish have identified enhancers that are bound by Hox and TALE (Meis and Pbx) proteins, implicating these factors in the direct regulation of Meis expression. We examined the lamprey meis loci and identified a series of cis-elements conserved between lamprey and jawed vertebrate meis genes. In transgenic reporter assays we demonstrated that these elements act as neural enhancers in lamprey embryos, directing reporter expression in appropriate domains when compared to expression of their associated endogenous meis gene. Sequence alignments reveal that these conserved elements are in similar relative positions of the meis loci and contain a series of consensus binding motifs for Hox and TALE proteins. This suggests that ancient Hox and TALE-responsive enhancers regulated expression of ancestral vertebrate meis genes in segmental domains in the hindbrain and have been retained in the meis loci during vertebrate evolution. The presence of conserved Meis, Pbx and Hox binding sites in these lamprey enhancers links Hox and TALE factors to regulation of lamprey meis genes in the developing hindbrain, indicating a deep ancestry for these regulatory interactions prior to the divergence of jawed and jawless vertebrates.
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Affiliation(s)
- Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Irina Pushel
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA; Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, 66160, USA.
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15
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Blasi F, Bruckmann C. MEIS1 in Hematopoiesis and Cancer. How MEIS1-PBX Interaction Can Be Used in Therapy. J Dev Biol 2021; 9:jdb9040044. [PMID: 34698191 PMCID: PMC8544432 DOI: 10.3390/jdb9040044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/26/2022] Open
Abstract
Recently MEIS1 emerged as a major determinant of the MLL-r leukemic phenotype. The latest and most efficient drugs effectively decrease the levels of MEIS1 in cancer cells. Together with an overview of the latest drugs developed to target MEIS1 in MLL-r leukemia, we review, in detail, the role of MEIS1 in embryonic and adult hematopoiesis and suggest how a more profound knowledge of MEIS1 biochemistry can be used to design potent and effective drugs against MLL-r leukemia. In addition, we present data showing that the interaction between MEIS1 and PBX1 can be blocked efficiently and might represent a new avenue in anti-MLL-r and anti-leukemic therapy.
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16
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Mariani L, Guo X, Menezes NA, Drozd AM, Çakal SD, Wang Q, Ferretti E. A TALE/HOX code unlocks WNT signalling response towards paraxial mesoderm. Nat Commun 2021; 12:5136. [PMID: 34446717 DOI: 10.1038/s41467-021-25370-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 08/04/2021] [Indexed: 12/02/2022] Open
Abstract
One fundamental yet unresolved question in biology remains how cells interpret the same signalling cues in a context-dependent manner resulting in lineage specification. A key step for decoding signalling cues is the establishment of a permissive chromatin environment at lineage-specific genes triggering transcriptional responses to inductive signals. For instance, bipotent neuromesodermal progenitors (NMPs) are equipped with a WNT-decoding module, which relies on TCFs/LEF activity to sustain both NMP expansion and paraxial mesoderm differentiation. However, how WNT signalling activates lineage specific genes in a temporal manner remains unclear. Here, we demonstrate that paraxial mesoderm induction relies on the TALE/HOX combinatorial activity that simultaneously represses NMP genes and activates the differentiation program. We identify the BRACHYURY-TALE/HOX code that destabilizes the nucleosomes at WNT-responsive regions and establishes the permissive chromatin landscape for de novo recruitment of the WNT-effector LEF1, unlocking the WNT-mediated transcriptional program that drives NMPs towards the paraxial mesodermal fate. Cells in the developing embryo interpret WNT signalling with context-dependence, but the mechanism decoding these cues is unclear. Here, the authors show that combinatorial TALE/HOX activity destabilizes nucleosomes at WNT-responsive regions to activate paraxial mesodermal genes.
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17
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De Kumar B, Darland DC. The Hox protein conundrum: The "specifics" of DNA binding for Hox proteins and their partners. Dev Biol 2021; 477:284-92. [PMID: 34102167 DOI: 10.1016/j.ydbio.2021.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022]
Abstract
Homeotic genes (Hox genes) are homeodomain-transcription factors involved in conferring segmental identity along the anterior-posterior body axis. Molecular characterization of HOX protein function raises some interesting questions regarding the source of the binding specificity of the HOX proteins. How do HOX proteins regulate common and unique target specificity across space and time? This review attempts to summarize and interpret findings in this area, largely focused on results from in vitro and in vivo studies in Drosophila and mouse systems. Recent studies related to HOX protein binding specificity compel us to reconsider some of our current models for transcription factor-DNA interactions. It is crucial to study transcription factor binding by incorporating components of more complex, multi-protein interactions in concert with small changes in binding motifs that can significantly impact DNA binding specificity and subsequent alterations in gene expression. To incorporate the multiple elements that can determine HOX protein binding specificity, we propose a more integrative Cooperative Binding model.
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18
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Durán Alonso MB, Vendrell V, López-Hernández I, Alonso MT, Martin DM, Giráldez F, Carramolino L, Giovinazzo G, Vázquez E, Torres M, Schimmang T. Meis2 Is Required for Inner Ear Formation and Proper Morphogenesis of the Cochlea. Front Cell Dev Biol 2021; 9:679325. [PMID: 34124068 PMCID: PMC8194062 DOI: 10.3389/fcell.2021.679325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/29/2021] [Indexed: 02/05/2023] Open
Abstract
Meis genes have been shown to control essential processes during development of the central and peripheral nervous system. Here we have explored the roles of the Meis2 gene during vertebrate inner ear induction and the formation of the cochlea. Meis2 is expressed in several tissues required for inner ear induction and in non-sensory tissue of the cochlear duct. Global inactivation of Meis2 in the mouse leads to a severely reduced size of the otic vesicle. Tissue-specific knock outs of Meis2 reveal that its expression in the hindbrain is essential for otic vesicle formation. Inactivation of Meis2 in the inner ear itself leads to an aberrant coiling of the cochlear duct. By analyzing transcriptomes obtained from Meis2 mutants and ChIPseq analysis of an otic cell line, we define candidate target genes for Meis2 which may be directly or indirectly involved in cochlear morphogenesis. Taken together, these data show that Meis2 is essential for inner ear formation and provide an entry point to unveil the network underlying proper coiling of the cochlear duct.
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Affiliation(s)
- María Beatriz Durán Alonso
- Instituto de Biología y Genética Molecular, Universidad de Valladolid y Consejo Superior de Investigaciones Científicas, Valladolid, Spain
| | - Victor Vendrell
- Instituto de Biología y Genética Molecular, Universidad de Valladolid y Consejo Superior de Investigaciones Científicas, Valladolid, Spain
| | - Iris López-Hernández
- Instituto de Biología y Genética Molecular, Universidad de Valladolid y Consejo Superior de Investigaciones Científicas, Valladolid, Spain
| | - María Teresa Alonso
- Instituto de Biología y Genética Molecular, Universidad de Valladolid y Consejo Superior de Investigaciones Científicas, Valladolid, Spain
| | - Donna M Martin
- Departments of Pediatrics and Human Genetics, University of Michigan, Ann Arbor, MI, United States
| | - Fernando Giráldez
- CEXS, Universitat Pompeu Fabra, Parc de Recerca Biomédica de Barcelona, Barcelona, Spain
| | - Laura Carramolino
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Giovanna Giovinazzo
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Enrique Vázquez
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Miguel Torres
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Thomas Schimmang
- Instituto de Biología y Genética Molecular, Universidad de Valladolid y Consejo Superior de Investigaciones Científicas, Valladolid, Spain
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19
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Delgado I, Giovinazzo G, Temiño S, Gauthier Y, Balsalobre A, Drouin J, Torres M. Control of mouse limb initiation and antero-posterior patterning by Meis transcription factors. Nat Commun 2021; 12:3086. [PMID: 34035267 PMCID: PMC8149412 DOI: 10.1038/s41467-021-23373-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 04/21/2021] [Indexed: 12/31/2022] Open
Abstract
Meis1 and Meis2 are homeodomain transcription factors that regulate organogenesis through cooperation with Hox proteins. Elimination of Meis genes after limb induction has shown their role in limb proximo-distal patterning; however, limb development in the complete absence of Meis function has not been studied. Here, we report that Meis1/2 inactivation in the lateral plate mesoderm of mouse embryos leads to limb agenesis. Meis and Tbx factors converge in this function, extensively co-binding with Tbx to genomic sites and co-regulating enhancers of Fgf10, a critical factor in limb initiation. Limbs with three deleted Meis alleles show proximal-specific skeletal hypoplasia and agenesis of posterior skeletal elements. This failure in posterior specification results from an early role of Meis factors in establishing the limb antero-posterior prepattern required for Shh activation. Our results demonstrate roles for Meis transcription factors in early limb development and identify their involvement in previously undescribed interaction networks that regulate organogenesis.
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Affiliation(s)
- Irene Delgado
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Giovanna Giovinazzo
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Susana Temiño
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Yves Gauthier
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Aurelio Balsalobre
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Jacques Drouin
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Miguel Torres
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
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20
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Abstract
The vertebrate eye is derived from the neuroepithelium, surface ectoderm, and extracellular mesenchyme. The neuroepithelium forms an optic cup in which the spatial separation of three domains is established, namely, the region of multipotent retinal progenitor cells (RPCs), the ciliary margin zone (CMZ)-which possesses both a neurogenic and nonneurogenic potential-and the optic disk (OD), the interface between the optic stalk and the neuroretina. Here, we show by genetic ablation in the developing optic cup that Meis1 and Meis2 homeobox genes function redundantly to maintain the retinal progenitor pool while they simultaneously suppress the expression of genes characteristic of CMZ and OD fates. Furthermore, we demonstrate that Meis transcription factors bind regulatory regions of RPC-, CMZ-, and OD-specific genes, thus providing a mechanistic insight into the Meis-dependent gene regulatory network. Our work uncovers the essential role of Meis1 and Meis2 as regulators of cell fate competence, which organize spatial territories in the vertebrate eye.
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21
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López-Delgado AC, Delgado I, Cadenas V, Sánchez-Cabo F, Torres M. Axial skeleton anterior-posterior patterning is regulated through feedback regulation between Meis transcription factors and retinoic acid. Development 2021; 148:dev.193813. [PMID: 33298461 DOI: 10.1242/dev.193813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/20/2020] [Indexed: 11/20/2022]
Abstract
Vertebrate axial skeletal patterning is controlled by co-linear expression of Hox genes and axial level-dependent activity of HOX protein combinations. MEIS transcription factors act as co-factors of HOX proteins and profusely bind to Hox complex DNA; however, their roles in mammalian axial patterning remain unknown. Retinoic acid (RA) is known to regulate axial skeletal element identity through the transcriptional activity of its receptors; however, whether this role is related to MEIS/HOX activity remains unknown. Here, we study the role of Meis in axial skeleton formation and its relationship to the RA pathway in mice. Meis elimination in the paraxial mesoderm produces anterior homeotic transformations and rib mis-patterning associated to alterations of the hypaxial myotome. Although Raldh2 and Meis positively regulate each other, Raldh2 elimination largely recapitulates the defects associated with Meis deficiency, and Meis overexpression rescues the axial skeletal defects in Raldh2 mutants. We propose a Meis-RA-positive feedback loop, the output of which is Meis levels, that is essential to establish anterior-posterior identities and patterning of the vertebrate axial skeleton.
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Affiliation(s)
- Alejandra C López-Delgado
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28003, Spain
| | - Irene Delgado
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28003, Spain
| | - Vanessa Cadenas
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28003, Spain
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28003, Spain
| | - Miguel Torres
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28003, Spain
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22
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Ronzio M, Bernardini A, Pavesi G, Mantovani R, Dolfini D. On the NF-Y regulome as in ENCODE (2019). PLoS Comput Biol 2020; 16:e1008488. [PMID: 33370256 PMCID: PMC7793273 DOI: 10.1371/journal.pcbi.1008488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 01/08/2021] [Accepted: 11/04/2020] [Indexed: 11/19/2022] Open
Abstract
NF-Y is a trimeric Transcription Factor -TF- which binds with high selectivity to the conserved CCAAT element. Individual ChIP-seq analysis as well as ENCODE have progressively identified locations shared by other TFs. Here, we have analyzed data introduced by ENCODE over the last five years in K562, HeLa-S3 and GM12878, including several chromatin features, as well RNA-seq profiling of HeLa cells after NF-Y inactivation. We double the number of sequence-specific TFs and co-factors reported. We catalogue them in 4 classes based on co-association criteria, infer target genes categorizations, identify positional bias of binding sites and gene expression changes. Larger and novel co-associations emerge, specifically concerning subunits of repressive complexes as well as RNA-binding proteins. On the one hand, these data better define NF-Y association with single members of major classes of TFs, on the other, they suggest that it might have a wider role in the control of mRNA production. The ongoing ENCODE consortium represents a useful compendium of locations of TFs, chromatin marks, gene expression data. In previous reports, we identified modules of CCAAT-binding NF-Y with individual TFs. Here, we analyzed all 363 factors currently present: 68 with enrichment of CCAAT in their locations, 38 with overlap of peaks. New sequence-specific TFs, co-activators and co-repressors are reported. Co-association patterns correspond to specific targeted genes categorizations and gene expression changes, as assessed by RNA-seq after NF-Y inactivation. These data widen and better define a coherent model of synergy of NF-Y with selected groups of TFs and co-factors.
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Affiliation(s)
- Mirko Ronzio
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Andrea Bernardini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Giulio Pavesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
- * E-mail:
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23
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Bruckmann C, Tamburri S, De Lorenzi V, Doti N, Monti A, Mathiasen L, Cattaneo A, Ruvo M, Bachi A, Blasi F. Mapping the native interaction surfaces of PREP1 with PBX1 by cross-linking mass-spectrometry and mutagenesis. Sci Rep 2020; 10:16809. [PMID: 33033354 PMCID: PMC7545097 DOI: 10.1038/s41598-020-74032-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/25/2020] [Indexed: 02/08/2023] Open
Abstract
Both onco-suppressor PREP1 and the oncogene MEIS1 bind to PBX1. This interaction stabilizes the two proteins and allows their translocation into the nucleus and thus their transcriptional activity. Here, we have combined cross-linking mass-spectrometry and systematic mutagenesis to detail the binding geometry of the PBX1-PREP1 (and PBX1-MEIS1) complexes, under native in vivo conditions. The data confirm the existence of two distinct interaction sites within the PBC domain of PBX1 and unravel differences among the highly similar binding sites of MEIS1 and PREP1. The HR2 domain has a fundamental role in binding the PBC-B domain of PBX1 in both PREP1 and MEIS1. The HR1 domain of MEIS1, however, seem to play a less stringent role in PBX1 interaction with respect to that of PREP1. This difference is also reflected by the different binding affinity of the two proteins to PBX1. Although partial, this analysis provides for the first time some ideas on the tertiary structure of the complexes not available before. Moreover, the extensive mutagenic analysis of PREP1 identifies the role of individual hydrophobic HR1 and HR2 residues, both in vitro and in vivo.
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Affiliation(s)
- Chiara Bruckmann
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy.
| | - Simone Tamburri
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Valentina De Lorenzi
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56124, Pisa, Italy
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Lisa Mathiasen
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
| | - Angela Cattaneo
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
- Cogentech S.R.L. Benefit Corporation IT, Via Adamello 16, 20139, Milan, Italy
| | - Menotti Ruvo
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Angela Bachi
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
| | - Francesco Blasi
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy.
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VanOpstall C, Perike S, Brechka H, Gillard M, Lamperis S, Zhu B, Brown R, Bhanvadia R, Vander Griend DJ. MEIS-mediated suppression of human prostate cancer growth and metastasis through HOXB13-dependent regulation of proteoglycans. eLife 2020; 9:e53600. [PMID: 32553107 PMCID: PMC7371429 DOI: 10.7554/elife.53600] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 06/17/2020] [Indexed: 12/13/2022] Open
Abstract
The molecular roles of HOX transcriptional activity in human prostate epithelial cells remain unclear, impeding the implementation of new treatment strategies for cancer prevention and therapy. MEIS proteins are transcription factors that bind and direct HOX protein activity. MEIS proteins are putative tumor suppressors that are frequently silenced in aggressive forms of prostate cancer. Here we show that MEIS1 expression is sufficient to decrease proliferation and metastasis of prostate cancer cells in vitro and in vivo murine xenograft models. HOXB13 deletion demonstrates that the tumor-suppressive activity of MEIS1 is dependent on HOXB13. Integration of ChIP-seq and RNA-seq data revealed direct and HOXB13-dependent regulation of proteoglycans including decorin (DCN) as a mechanism of MEIS1-driven tumor suppression. These results define and underscore the importance of MEIS1-HOXB13 transcriptional regulation in suppressing prostate cancer progression and provide a mechanistic framework for the investigation of HOXB13 mutants and oncogenic cofactors when MEIS1/2 are silenced.
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Affiliation(s)
- Calvin VanOpstall
- The Committee on Cancer Biology, The University of ChicagoChicagoUnited States
| | - Srikanth Perike
- Department of Pathology, The University of Illinois at ChicagoChicagoUnited States
| | - Hannah Brechka
- The Committee on Cancer Biology, The University of ChicagoChicagoUnited States
| | - Marc Gillard
- Department of Surgery, Section of Urology, The University of ChicagoChicagoUnited States
| | - Sophia Lamperis
- Department of Pathology, The University of Illinois at ChicagoChicagoUnited States
| | - Baizhen Zhu
- Department of Surgery, Section of Urology, The University of ChicagoChicagoUnited States
| | - Ryan Brown
- Department of Pathology, The University of Illinois at ChicagoChicagoUnited States
| | - Raj Bhanvadia
- Department of Urology, UT SouthwesternDallasUnited States
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25
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Delgado I, López-Delgado AC, Roselló-Díez A, Giovinazzo G, Cadenas V, Fernández-de-Manuel L, Sánchez-Cabo F, Anderson MJ, Lewandoski M, Torres M. Proximo-distal positional information encoded by an Fgf-regulated gradient of homeodomain transcription factors in the vertebrate limb. Sci Adv 2020; 6:eaaz0742. [PMID: 32537491 PMCID: PMC7269661 DOI: 10.1126/sciadv.aaz0742] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 03/10/2020] [Indexed: 05/16/2023]
Abstract
The positional information theory proposes that a coordinate system provides information to embryonic cells about their position and orientation along a patterning axis. Cells interpret this information to produce the appropriate pattern. During development, morphogens and interpreter transcription factors provide this information. We report a gradient of Meis homeodomain transcription factors along the mouse limb bud proximo-distal (PD) axis antiparallel to and shaped by the inhibitory action of distal fibroblast growth factor (FGF). Elimination of Meis results in premature limb distalization and HoxA expression, proximalization of PD segmental borders, and phocomelia. Our results show that Meis transcription factors interpret FGF signaling to convey positional information along the limb bud PD axis. These findings establish a new model for the generation of PD identities in the vertebrate limb and provide a molecular basis for the interpretation of FGF signal gradients during axial patterning.
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Affiliation(s)
- Irene Delgado
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Alejandra C. López-Delgado
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Alberto Roselló-Díez
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Giovanna Giovinazzo
- Pluripotent Cell Technology Unit, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Vanessa Cadenas
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | | | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
| | - Matthew J. Anderson
- Cancer and Developmental Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Mark Lewandoski
- Cancer and Developmental Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Miguel Torres
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Madrid, Spain
- Corresponding author.
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Berenguer M, Meyer KF, Yin J, Duester G. Discovery of genes required for body axis and limb formation by global identification of retinoic acid-regulated epigenetic marks. PLoS Biol 2020; 18:e3000719. [PMID: 32421711 PMCID: PMC7259794 DOI: 10.1371/journal.pbio.3000719] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/29/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
Identification of target genes that mediate required functions downstream of transcription factors is hampered by the large number of genes whose expression changes when the factor is removed from a specific tissue and the numerous binding sites for the factor in the genome. Retinoic acid (RA) regulates transcription via RA receptors bound to RA response elements (RAREs) of which there are thousands in vertebrate genomes. Here, we combined chromatin immunoprecipitation sequencing (ChIP-seq) for epigenetic marks and RNA-seq on trunk tissue from wild-type and Aldh1a2-/- embryos lacking RA synthesis that exhibit body axis and forelimb defects. We identified a relatively small number of genes with altered expression when RA is missing that also have nearby RA-regulated deposition of histone H3 K27 acetylation (H3K27ac) (gene activation mark) or histone H3 K27 trimethylation (H3K27me3) (gene repression mark) associated with conserved RAREs, suggesting these genes function downstream of RA. RA-regulated epigenetic marks were identified near RA target genes already known to be required for body axis and limb formation, thus validating our approach; plus, many other candidate RA target genes were found. Nuclear receptor 2f1 (Nr2f1) and nuclear receptor 2f2 (Nr2f2) in addition to Meis homeobox 1 (Meis1) and Meis homeobox 2 (Meis2) gene family members were identified by our approach, and double knockouts of each family demonstrated previously unknown requirements for body axis and/or limb formation. A similar epigenetic approach can be used to determine the target genes for any transcriptional regulator for which a knockout is available.
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Affiliation(s)
- Marie Berenguer
- Development, Aging, and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Karolin F. Meyer
- Development, Aging, and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Jun Yin
- Bioinformatics Core Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Gregg Duester
- Development, Aging, and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
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Remesal L, Roger-Baynat I, Chirivella L, Maicas M, Brocal-Ruiz R, Pérez-Villalba A, Cucarella C, Casado M, Flames N. PBX1 acts as terminal selector for olfactory bulb dopaminergic neurons. Development 2020; 147:dev.186841. [PMID: 32156753 DOI: 10.1242/dev.186841] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/24/2020] [Indexed: 02/03/2023]
Abstract
Neuronal specification is a protracted process that begins with the commitment of progenitor cells and culminates with the generation of mature neurons. Many transcription factors are continuously expressed during this process but it is presently unclear how these factors modify their targets as cells transition through different stages of specification. In olfactory bulb adult neurogenesis, the transcription factor PBX1 controls neurogenesis in progenitor cells and the survival of migrating neuroblasts. Here, we show that, at later differentiation stages, PBX1 also acts as a terminal selector for the dopaminergic neuron fate. PBX1 is also required for the morphological maturation of dopaminergic neurons and to repress alternative interneuron fates, findings that expand the known repertoire of terminal-selector actions. Finally, we reveal that the temporal diversification of PBX1 functions in neuronal specification is achieved, at least in part, through the dynamic regulation of alternative splicing. In Caenorhabditis elegans, PBX/CEH-20 also acts as a dopaminergic neuron terminal selector, which suggests an ancient role for PBX factors in the regulation of terminal differentiation of dopaminergic neurons.
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Affiliation(s)
- Laura Remesal
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Isabel Roger-Baynat
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Laura Chirivella
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Miren Maicas
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Rebeca Brocal-Ruiz
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Ana Pérez-Villalba
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), and Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, 46100 Burjassot, Spain
| | - Carme Cucarella
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III (ISCIII), Metabolic Experimental Pathology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Marta Casado
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III (ISCIII), Metabolic Experimental Pathology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
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28
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Phuycharoen M, Zarrineh P, Bridoux L, Amin S, Losa M, Chen K, Bobola N, Rattray M. Uncovering tissue-specific binding features from differential deep learning. Nucleic Acids Res 2020; 48:e27. [PMID: 31974574 PMCID: PMC7049686 DOI: 10.1093/nar/gkaa009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 11/04/2019] [Accepted: 01/07/2020] [Indexed: 01/24/2023] Open
Abstract
Transcription factors (TFs) can bind DNA in a cooperative manner, enabling a mutual increase in occupancy. Through this type of interaction, alternative binding sites can be preferentially bound in different tissues to regulate tissue-specific expression programmes. Recently, deep learning models have become state-of-the-art in various pattern analysis tasks, including applications in the field of genomics. We therefore investigate the application of convolutional neural network (CNN) models to the discovery of sequence features determining cooperative and differential TF binding across tissues. We analyse ChIP-seq data from MEIS, TFs which are broadly expressed across mouse branchial arches, and HOXA2, which is expressed in the second and more posterior branchial arches. By developing models predictive of MEIS differential binding in all three tissues, we are able to accurately predict HOXA2 co-binding sites. We evaluate transfer-like and multitask approaches to regularizing the high-dimensional classification task with a larger regression dataset, allowing for the creation of deeper and more accurate models. We test the performance of perturbation and gradient-based attribution methods in identifying the HOXA2 sites from differential MEIS data. Our results show that deep regularized models significantly outperform shallow CNNs as well as k-mer methods in the discovery of tissue-specific sites bound in vivo.
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Affiliation(s)
- Mike Phuycharoen
- Department of Computer Science, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Peyman Zarrineh
- School of Health Sciences, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Laure Bridoux
- School of Medical Sciences, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Shilu Amin
- School of Medical Sciences, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Marta Losa
- Department of Orofacial Sciences and Department of Anatomy, University of California San Francisco, 513 Parnassus Avenue, HSW 740, San Francisco, CA 94143, USA
| | - Ke Chen
- Department of Computer Science, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Nicoletta Bobola
- School of Medical Sciences, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Magnus Rattray
- School of Health Sciences, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
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29
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30
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Stanney W, Ladam F, Donaldson IJ, Parsons TJ, Maehr R, Bobola N, Sagerström CG. Combinatorial action of NF-Y and TALE at embryonic enhancers defines distinct gene expression programs during zygotic genome activation in zebrafish. Dev Biol 2019; 459:161-180. [PMID: 31862379 DOI: 10.1016/j.ydbio.2019.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 01/20/2023]
Abstract
Animal embryogenesis is initiated by maternal factors, but zygotic genome activation (ZGA) shifts regulatory control to the embryo during blastula stages. ZGA is thought to be mediated by maternally provided transcription factors (TFs), but few such TFs have been identified in vertebrates. Here we report that NF-Y and TALE TFs bind zebrafish genomic elements associated with developmental control genes already at ZGA. In particular, co-regulation by NF-Y and TALE is associated with broadly acting genes involved in transcriptional control, while regulation by either NF-Y or TALE defines genes in specific developmental processes, such that NF-Y controls a cilia gene expression program while TALE controls expression of hox genes. We also demonstrate that NF-Y and TALE-occupied genomic elements function as enhancers during embryogenesis. We conclude that combinatorial use of NF-Y and TALE at developmental enhancers permits the establishment of distinct gene expression programs at zebrafish ZGA.
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Affiliation(s)
- William Stanney
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Franck Ladam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Ian J Donaldson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Teagan J Parsons
- Program in Molecular Medicine and Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - René Maehr
- Program in Molecular Medicine and Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Nicoletta Bobola
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Charles G Sagerström
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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31
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Paul S, Zhang X, He JQ. Homeobox gene Meis1 modulates cardiovascular regeneration. Semin Cell Dev Biol 2019; 100:52-61. [PMID: 31623926 DOI: 10.1016/j.semcdb.2019.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/30/2019] [Accepted: 10/04/2019] [Indexed: 12/20/2022]
Abstract
Regeneration of cardiomyocytes, endothelial cells and vascular smooth muscle cells (three major lineages of cardiac tissues) following myocardial infarction is the critical step to recover the function of the damaged heart. Myeloid ecotropic viral integration site 1 (Meis1) was first discovered in leukemic mice in 1995 and its biological function has been extensively studied in leukemia, hematopoiesis, the embryonic pattering of body axis, eye development and various genetic diseases, such as restless leg syndrome. It was found that Meis1 is highly associated with Hox genes and their cofactors to exert its regulatory effects on multiple intracellular signaling pathways. Recently with the advent of bioinformatics, biochemical methods and advanced genetic engineering tools, new function of Meis1 has been found to be involved in the cell cycle regulation of cardiomyocytes and endothelial cells. For example, inhibition of Meis1 expression increases the proliferative capacity of neonatal mouse cardiomyocytes, whereas overexpression of Meis1 results in the reduction in the length of cardiomyocyte proliferative window. Interestingly, downregulation of one of the circular RNAs, which acts downstream of Meis1 in the cardiomyocytes, promotes angiogenesis and restores the myocardial blood supply, thus reinforcing better regeneration of the damaged heart. It appears that Meis1 may play double roles in modulating proliferation and regeneration of cardiomyocytes and endothelial cells post-myocardial infarction. In this review, we propose to summarize the major findings of Meis1 in modulating fetal development and adult abnormalities, especially focusing on the recent discoveries of Meis1 in controlling the fate of cardiomyocytes and endothelial cells.
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Affiliation(s)
- Swagatika Paul
- Department of Biomedical Sciences & Pathobiology, College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Xiaonan Zhang
- Beijing Yulong Shengshi Biotechnology, Haidian District, Beijing, 100085, China
| | - Jia-Qiang He
- Department of Biomedical Sciences & Pathobiology, College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA.
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32
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Schulte D, Geerts D. MEIS transcription factors in development and disease. Development 2019; 146:146/16/dev174706. [PMID: 31416930 DOI: 10.1242/dev.174706] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 06/28/2019] [Indexed: 12/12/2022]
Abstract
MEIS transcription factors are key regulators of embryonic development and cancer. Research on MEIS genes in the embryo and in stem cell systems has revealed novel and surprising mechanisms by which these proteins control gene expression. This Primer summarizes recent findings about MEIS protein activity and regulation in development, and discusses new insights into the role of MEIS genes in disease, focusing on the pathogenesis of solid cancers.
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Affiliation(s)
- Dorothea Schulte
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, 60528 Frankfurt, Germany
| | - Dirk Geerts
- Department of Medical Biology L2-109, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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33
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Greco A, Vaipan DV, Tkachuk VA, Penkov DN. The Involvement of Cardiomyocyte-Specific Transcription Factors Meis in Adipocyte Differentiation. Mol Biol 2019. [DOI: 10.1134/s0026893319030075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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34
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Yamazaki A, Yamamoto A, Yaguchi J, Yaguchi S. cis-Regulatory analysis for later phase of anterior neuroectoderm-specific foxQ2 expression in sea urchin embryos. Genesis 2019; 57:e23302. [PMID: 31025827 DOI: 10.1002/dvg.23302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 01/31/2023]
Abstract
The specification of anterior neuroectoderm is controlled by a highly conserved molecular mechanism in bilaterians. A forkhead family gene, foxQ2, is known to be one of the pivotal regulators, which is zygotically expressed in this region during embryogenesis of a broad range of bilaterians. However, what controls the expression of this essential factor has remained unclear to date. To reveal the regulatory mechanism of foxQ2, we performed cis-regulatory analysis of two foxQ2 genes, foxQ2a and foxQ2b, in a sea urchin Hemicentrotus pulcherrimus. In sea urchin embryos, foxQ2 is initially expressed in the entire animal hemisphere and subsequently shows narrower expression restricted to the anterior pole region. In this study, as a first step to understand the foxQ2 regulation, we focused on the later restricted expression and analyzed the upstream cis-regulatory sequences of foxQ2a and foxQ2b by using the constructs fused to short half-life green fluorescent protein. Based on deletion and mutation analyses of both foxQ2, we identified each of the five regulatory sequences, which were 4-9 bp long. Neither of the regulatory sequences contains any motifs for ectopic activation or spatial repression, suggesting that later mRNA localization is regulated in situ. We also suggest that the three amino acid loop extension-class homeobox gene Meis is involved in the maintenance of foxQ2b, the expression of which is dominant during embryogenesis.
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Affiliation(s)
- Atsuko Yamazaki
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Akane Yamamoto
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Junko Yaguchi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Shunsuke Yaguchi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
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35
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Dard A, Jia Y, Reboulet J, Bleicher F, Lavau C, Merabet S. The human HOXA9 protein uses paralog-specific residues of the homeodomain to interact with TALE-class cofactors. Sci Rep 2019; 9:5664. [PMID: 30952900 DOI: 10.1038/s41598-019-42096-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/22/2019] [Indexed: 12/15/2022] Open
Abstract
HOX proteins interact with PBX and MEIS cofactors, which belong to the TALE-class of homeodomain (HD)-containing transcription factors. Although the formation of HOX-PBX complexes depends on a unique conserved HOX motif called hexapeptide (HX), the additional presence of MEIS induces a remodeling of the interaction, leading to a global dispensability of the HX motif for trimeric complex formation in the large majority of HOX proteins. In addition, it was shown that the anterior HOXB3 and central HOXA7 and HOXC8 proteins could use different alternative TALE interaction motifs, with or without the HX motif, depending on the DNA-binding site and cell context. Here we dissected the molecular interaction properties of the human posterior HOXA9 protein with its TALE cofactors, PBX1 and MEIS1. Analysis was performed on different DNA-binding sites in vitro and by doing Bimolecular Fluorescence Complementation (BiFC) in different cell lines. Notably, we observed that the HOXA9-TALE interaction relies consistently on the redundant activity of the HX motif and two paralog-specific residues of the HOXA9 HD. Together with previous work, our results show that HOX proteins interact with their generic TALE cofactors through various modalities, ranging from unique and context-independent to versatile and context-dependent TALE binding interfaces.
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Abstract
Pbx genes encode transcription factors that belong to the TALE (three-amino-acid loop extension) superclass of homeodomain proteins. We have witnessed a surge in information about the roles of this gene family as leading actors in the transcriptional control of development. PBX proteins represent a clear example of how transcription factors can regulate developmental processes by combinatorial properties, acting within multimeric complexes to implement activation or repression of transcription depending on their interaction partners. Here, we revisit long-emphasized functions of PBX transcription factors as cofactors for HOX proteins, major architects of the body plan. We further discuss new knowledge on roles of PBX proteins in different developmental contexts as upstream regulators of Hox genes-as factors that interact with non-HOX proteins and can work independently of HOX-as well as potential pioneer factors. Committed to building a perfect body, PBX proteins govern regulatory networks that direct essential morphogenetic processes and organogenesis in vertebrate development. Perturbations of PBX-dependent networks can cause human congenital disease and cancer.
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Affiliation(s)
- Licia Selleri
- Program in Craniofacial Biology, University of California at San Francisco, San Francisco, California 94143, USA.,Institute of Human Genetics, University of California at San Francisco, San Francisco, California 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143, USA.,Department of Orofacial Sciences, University of California at San Francisco, San Francisco, California 94143, USA.,Department of Anatomy, University of California at San Francisco, San Francisco, California 94143, USA
| | - Vincenzo Zappavigna
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Elisabetta Ferretti
- The Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
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37
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Sanz-Navarro M, Delgado I, Torres M, Mustonen T, Michon F, Rice DP. Dental Epithelial Stem Cells Express the Developmental Regulator Meis1. Front Physiol 2019; 10:249. [PMID: 30914971 PMCID: PMC6423187 DOI: 10.3389/fphys.2019.00249] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 02/25/2019] [Indexed: 11/13/2022] Open
Abstract
MEIS1 is a key developmental regulator of several organs and participates in stem cell maintenance in different niches. However, despite the murine continuously growing incisor being a well described model for the study of adult stem cells, Meis1 has not been investigated in a dental context. Here, we uncover that Meis1 expression in the tooth is confined to the epithelial compartment. Its expression arises during morphogenesis and becomes restricted to the mouse incisor epithelial stem cell niche, the labial cervical loop. Meis1 is specifically expressed by Sox2+ stem cells, which give rise to all dental epithelial cell lineages. Also, we have found that Meis1 in the incisor is coexpressed with potential binding partner Pbx1 during both embryonic and adult stages. Interestingly, Meis2 is present in different areas of the forming tooth and it is not expressed by dental epithelial stem cells, suggesting different roles for these two largely homologous genes. Additionally, we have established the expression patterns of Meis1 and Meis2 during tongue, hair, salivary gland and palate formation. Finally, analysis of Meis1-null allele mice indicated that, similarly, to SOX2, MEIS1 is not essential for tooth initiation, but might have a role during adult incisor renewal.
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Affiliation(s)
- Maria Sanz-Navarro
- Helsinki Institute of Life Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Orthodontics, Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Irene Delgado
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Miguel Torres
- Departamento de Desarrollo y Reparación Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Tuija Mustonen
- Orthodontics, Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Frederic Michon
- Helsinki Institute of Life Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,The Institute for Neurosciences of Montpellier, Inserm UMR1051, University of Montpellier, Saint Eloi Hospital, Montpellier, France
| | - David P Rice
- Orthodontics, Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland.,Orthodontics, Oral and Maxillofacial Diseases, Helsinki University Hospital, Helsinki, Finland
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38
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Johng D, Torga G, Ewing CM, Jin K, Norris JD, McDonnell DP, Isaacs WB. HOXB13 interaction with MEIS1 modifies proliferation and gene expression in prostate cancer. Prostate 2019; 79:414-424. [PMID: 30560549 DOI: 10.1002/pros.23747] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/02/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND The recurrent p.Gly84Glu germline mutation (G84E) in HOXB13 is consistently associated with prostate cancer (PCa), although the mechanisms underlying such linkage remain elusive. The majority of the PCa-associated HOXB13 mutations identified are localized to two conserved domains in HOXB13 that have been shown to mediate the interaction with MEIS cofactors belonging to the TALE family of homeodomain transcription factors. In this study, we sought to interrogate the biochemical and functional interactions between HOXB13 and MEIS in prostatic cells with a goal of defining how the HOXB13-MEIS complex impacts PCa pathobiology and define the extent to which the oncogenic activity of G84E is related to its effect on HOXB13-MEIS interaction/function. METHODS HOXB13 and MEIS paralog expression in prostate epithelial cells and PCa cell lines was characterized by qPCR and immunoblot analyses. HOXB13 and MEIS1 co-expression in human prostate tissue was confirmed by IHC, followed by co-IP mapping of HOXB13-MEIS1 interactions. Proliferation of the PCa cell line LAPC4 following shRNA-mediated knockdown of each gene or both genes was assessed using DNA- and metabolic-based assays. Transcriptional targets of HOXB13 and MEIS1 were identified by gene expression profiling and qPCR. Finally, protein stability of HOXB13 in the context of MEIS1 was determined using pulse-chase assays. RESULTS HOXB13 and MEIS1 are co-expressed and interact in prostate cells. Both of the putative MEIS interacting domains (MID) within HOXB13 were shown to be capable of mediating the interaction between HOXB13 and MEIS1 independently and such interactions were not influenced by the G84E mutation. The inhibitory effect of either HOXB13 or MEIS1 knockdown on cellular proliferation was augmented by knockdown of both genes, and MEIS1 knockdown abolished HOXB13-driven regulation of BCHE and TNFSF10 mRNA expression. Notably, we demonstrated that MEIS1 stabilized the HOXB13 protein in LAPC4 cells. CONCLUSIONS Our study provides evidence for functional HOXB13-MEIS1 interactions in PCa. MEIS1 may contribute to the cancer-promoting actions of HOXB13 in cellular proliferation and gene regulation by prolonging HOXB13 half-life. Our data demonstrates that G84E is not a loss-of-function mutation that interferes with HOXB13 stability or ability to interact with MEIS1.
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Affiliation(s)
- Dorhyun Johng
- Brady Urological Institute, Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Gonzalo Torga
- Brady Urological Institute, Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Charles M Ewing
- Brady Urological Institute, Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Kideok Jin
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York
| | - John D Norris
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - Donald P McDonnell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - William B Isaacs
- Brady Urological Institute, Johns Hopkins University, School of Medicine, Baltimore, Maryland
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39
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Völkel S, Stielow B, Finkernagel F, Berger D, Stiewe T, Nist A, Suske G. Transcription factor Sp2 potentiates binding of the TALE homeoproteins Pbx1:Prep1 and the histone-fold domain protein Nf-y to composite genomic sites. J Biol Chem 2018; 293:19250-19262. [PMID: 30337366 DOI: 10.1074/jbc.ra118.005341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/17/2018] [Indexed: 11/06/2022] Open
Abstract
Different transcription factors operate together at promoters and enhancers to regulate gene expression. Transcription factors either bind directly to their target DNA or are tethered to it by other proteins. The transcription factor Sp2 serves as a paradigm for indirect genomic binding. It does not require its DNA-binding domain for genomic DNA binding and occupies target promoters independently of whether they contain a cognate DNA-binding motif. Hence, Sp2 is strikingly different from its closely related paralogs Sp1 and Sp3, but how Sp2 recognizes its targets is unknown. Here, we sought to gain more detailed insights into the genomic targeting mechanism of Sp2. ChIP-exo sequencing in mouse embryonic fibroblasts revealed genomic binding of Sp2 to a composite motif where a recognition sequence for TALE homeoproteins and a recognition sequence for the trimeric histone-fold domain protein nuclear transcription factor Y (Nf-y) are separated by 11 bp. We identified a complex consisting of the TALE homeobox protein Prep1, its partner PBX homeobox 1 (Pbx1), and Nf-y as the major partners in Sp2-promoter interactions. We found that the Pbx1:Prep1 complex together with Nf-y recruits Sp2 to co-occupied regulatory elements. In turn, Sp2 potentiates binding of Pbx1:Prep1 and Nf-y. We also found that the Sp-box, a short sequence motif close to the Sp2 N terminus, is crucial for Sp2's cofactor function. Our findings reveal a mechanism by which the DNA binding-independent activity of Sp2 potentiates genomic loading of Pbx1:Prep1 and Nf-y to composite motifs present in many promoters of highly expressed genes.
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Affiliation(s)
- Sara Völkel
- From the Institute of Molecular Biology and Tumor Research (IMT) and
| | - Bastian Stielow
- From the Institute of Molecular Biology and Tumor Research (IMT) and
| | | | - Dana Berger
- From the Institute of Molecular Biology and Tumor Research (IMT) and
| | - Thorsten Stiewe
- the Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps-University of Marburg, 35043 Marburg, Germany
| | - Andrea Nist
- the Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps-University of Marburg, 35043 Marburg, Germany
| | - Guntram Suske
- From the Institute of Molecular Biology and Tumor Research (IMT) and
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40
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Catoire H, Sarayloo F, Mourabit Amari K, Apuzzo S, Grant A, Rochefort D, Xiong L, Montplaisir J, Earley CJ, Turecki G, Dion PA, Rouleau GA. A direct interaction between two Restless Legs Syndrome predisposing genes: MEIS1 and SKOR1. Sci Rep 2018; 8:12173. [PMID: 30111810 PMCID: PMC6093889 DOI: 10.1038/s41598-018-30665-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/16/2018] [Indexed: 12/03/2022] Open
Abstract
Restless Legs syndrome (RLS) is a common sleep disorder for which the genetic contribution remains poorly explained. In 2007, the first large scale genome wide association study (GWAS) identified three genomic regions associated with RLS. MEIS1, BTBD9 and MAP2K5/SKOR1 are the only known genes located within these loci and their association with RLS was subsequently confirmed in a number of follow up GWAS. Following this finding, our group reported the MEIS1 risk haplotype to be associated with its decreased expression at the mRNA and protein levels. Here we report the effect of the risk variants of the three other genes strongly associated with RLS. While these variants had no effect on the mRNA levels of the genes harboring them, we find that the homeobox transcription factor MEIS1 positively regulates the expression of the transcription co-repressor SKOR1. This regulation appears mediated through the binding of MEIS1 at two specific sites located in the SKOR1 promoter region and is modified by an RLS associated SNP in the promoter region of the gene. Our findings directly link MEIS1 and SKOR1, two significantly associated genes with RLS and also prioritize SKOR1 over MAP2K5 in the RLS associated intergenic region of MAP2K5/SKOR1 found by GWAS.
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Affiliation(s)
- Helene Catoire
- McGill University, Montreal Neurological Institute, Montréal, QC, H3A 1A1, Canada
| | - Faezeh Sarayloo
- McGill University, Montreal Neurological Institute, Montréal, QC, H3A 1A1, Canada.,McGill University, Department of Human Genetics, Montréal, QC, H3A 1A1, Canada
| | - Karim Mourabit Amari
- Centre Hospitalier de l'Université de Montréal Research Center, Montréal, QC, H2L 2W5, Canada
| | - Sergio Apuzzo
- Centre Hospitalier de l'Université de Montréal Research Center, Montréal, QC, H2L 2W5, Canada
| | - Alanna Grant
- McGill University, Montreal Neurological Institute, Montréal, QC, H3A 1A1, Canada.,McGill University, Department of Human Genetics, Montréal, QC, H3A 1A1, Canada
| | - Daniel Rochefort
- McGill University, Montreal Neurological Institute, Montréal, QC, H3A 1A1, Canada
| | - Lan Xiong
- McGill University, Montreal Neurological Institute, Montréal, QC, H3A 1A1, Canada.,McGill University, Department of Neurology and Neurosurgery, Montréal, QC, H3A 2B4, Canada
| | - Jacques Montplaisir
- Université de Montréal, Département de psychiatrie, Laboratoire de neurogénétique, Centre de recherche, Institut universitaire en santé mentale de Montréal, Montréal, QC, H1N 3V2, Canada
| | - Christopher J Earley
- Johns Hopkins University, Department of Neurology, Hopkins Bayview Medical Center, Baltimore, MD, 21224, USA
| | - Gustavo Turecki
- McGill University, Department of Psychiatry, McGill Group for Suicide Studies, Douglas Institute, Montréal, QC, H4H 1R3, Canada
| | - Patrick A Dion
- McGill University, Montreal Neurological Institute, Montréal, QC, H3A 1A1, Canada.,McGill University, Department of Neurology and Neurosurgery, Montréal, QC, H3A 2B4, Canada
| | - Guy A Rouleau
- McGill University, Montreal Neurological Institute, Montréal, QC, H3A 1A1, Canada. .,McGill University, Department of Neurology and Neurosurgery, Montréal, QC, H3A 2B4, Canada.
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41
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Ladam F, Stanney W, Donaldson IJ, Yildiz O, Bobola N, Sagerström CG. TALE factors use two distinct functional modes to control an essential zebrafish gene expression program. eLife 2018; 7:36144. [PMID: 29911973 PMCID: PMC6023610 DOI: 10.7554/elife.36144] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/08/2018] [Indexed: 12/21/2022] Open
Abstract
TALE factors are broadly expressed embryonically and known to function in complexes with transcription factors (TFs) like Hox proteins at gastrula/segmentation stages, but it is unclear if such generally expressed factors act by the same mechanism throughout embryogenesis. We identify a TALE-dependent gene regulatory network (GRN) required for anterior development and detect TALE occupancy associated with this GRN throughout embryogenesis. At blastula stages, we uncover a novel functional mode for TALE factors, where they occupy genomic DECA motifs with nearby NF-Y sites. We demonstrate that TALE and NF-Y form complexes and regulate chromatin state at genes of this GRN. At segmentation stages, GRN-associated TALE occupancy expands to include HEXA motifs near PBX:HOX sites. Hence, TALE factors control a key GRN, but utilize distinct DNA motifs and protein partners at different stages – a strategy that may also explain their oncogenic potential and may be employed by other broadly expressed TFs.
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Affiliation(s)
- Franck Ladam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - William Stanney
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Ian J Donaldson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Ozge Yildiz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Nicoletta Bobola
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Charles G Sagerström
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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42
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Guerra A, Germano RF, Stone O, Arnaout R, Guenther S, Ahuja S, Uribe V, Vanhollebeke B, Stainier DY, Reischauer S. Distinct myocardial lineages break atrial symmetry during cardiogenesis in zebrafish. eLife 2018; 7:32833. [PMID: 29762122 PMCID: PMC5953537 DOI: 10.7554/elife.32833] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 04/04/2018] [Indexed: 02/06/2023] Open
Abstract
The ultimate formation of a four-chambered heart allowing the separation of the pulmonary and systemic circuits was key for the evolutionary success of tetrapods. Complex processes of cell diversification and tissue morphogenesis allow the left and right cardiac compartments to become distinct but remain poorly understood. Here, we describe an unexpected laterality in the single zebrafish atrium analogous to that of the two atria in amniotes, including mammals. This laterality appears to derive from an embryonic antero-posterior asymmetry revealed by the expression of the transcription factor gene meis2b. In adult zebrafish hearts, meis2b expression is restricted to the left side of the atrium where it controls the expression of pitx2c, a regulator of left atrial identity in mammals. Altogether, our studies suggest that the multi-chambered atrium in amniotes arose from a molecular blueprint present before the evolutionary emergence of cardiac septation and provide insights into the establishment of atrial asymmetry.
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Affiliation(s)
- Almary Guerra
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Raoul Fv Germano
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Laboratory of Neurovascular Signaling, Department of Molecular Biology, ULB Neuroscience Institute, Université libre de Bruxelles, Bruxelles, Belgium
| | - Oliver Stone
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Rima Arnaout
- Division of Cardiology, Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Stefan Guenther
- ECCPS Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Suchit Ahuja
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Verónica Uribe
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Benoit Vanhollebeke
- Laboratory of Neurovascular Signaling, Department of Molecular Biology, ULB Neuroscience Institute, Université libre de Bruxelles, Bruxelles, Belgium
| | - Didier Yr Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Sven Reischauer
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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43
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Losa M, Risolino M, Li B, Hart J, Quintana L, Grishina I, Yang H, Choi IF, Lewicki P, Khan S, Aho R, Feenstra J, Vincent CT, Brown AMC, Ferretti E, Williams T, Selleri L. Face morphogenesis is promoted by Pbx-dependent EMT via regulation of Snail1 during frontonasal prominence fusion. Development 2018; 145:dev157628. [PMID: 29437830 PMCID: PMC5868993 DOI: 10.1242/dev.157628] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 01/24/2018] [Indexed: 12/17/2022]
Abstract
Human cleft lip with or without cleft palate (CL/P) is a common craniofacial abnormality caused by impaired fusion of the facial prominences. We have previously reported that, in the mouse embryo, epithelial apoptosis mediates fusion at the seam where the prominences coalesce. Here, we show that apoptosis alone is not sufficient to remove the epithelial layers. We observed morphological changes in the seam epithelia, intermingling of cells of epithelial descent into the mesenchyme and molecular signatures of epithelial-mesenchymal transition (EMT). Utilizing mouse lines with cephalic epithelium-specific Pbx loss exhibiting CL/P, we demonstrate that these cellular behaviors are Pbx dependent, as is the transcriptional regulation of the EMT driver Snail1. Furthermore, in the embryo, the majority of epithelial cells expressing high levels of Snail1 do not undergo apoptosis. Pbx1 loss- and gain-of-function in a tractable epithelial culture system revealed that Pbx1 is both necessary and sufficient for EMT induction. This study establishes that Pbx-dependent EMT programs mediate murine upper lip/primary palate morphogenesis and fusion via regulation of Snail1. Of note, the EMT signatures observed in the embryo are mirrored in the epithelial culture system.
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Affiliation(s)
- Marta Losa
- Program in Craniofacial Biology, Institute of Human Genetics, Eli and Edyth Broad Center of Regeneration Medicine & Stem Cell Research, Departments of Orofacial Sciences and Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 710, San Francisco, CA 94143, USA
| | - Maurizio Risolino
- Program in Craniofacial Biology, Institute of Human Genetics, Eli and Edyth Broad Center of Regeneration Medicine & Stem Cell Research, Departments of Orofacial Sciences and Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 710, San Francisco, CA 94143, USA
| | - Bingsi Li
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - James Hart
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Laura Quintana
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Irina Grishina
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Hui Yang
- Departments of Craniofacial Biology and Cell and Developmental Biology, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Irene F Choi
- Departments of Craniofacial Biology and Cell and Developmental Biology, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Patrick Lewicki
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Sameer Khan
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Robert Aho
- Program in Craniofacial Biology, Institute of Human Genetics, Eli and Edyth Broad Center of Regeneration Medicine & Stem Cell Research, Departments of Orofacial Sciences and Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 710, San Francisco, CA 94143, USA
| | - Jennifer Feenstra
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
- Karolinska Institute, Department of Physiology and Pharmacology, Nanna svartz väg 2, 17177 Stockholm, Sweden
| | - C Theresa Vincent
- Karolinska Institute, Department of Physiology and Pharmacology, Nanna svartz väg 2, 17177 Stockholm, Sweden
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Anthony M C Brown
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Elisabetta Ferretti
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
| | - Trevor Williams
- Departments of Craniofacial Biology and Cell and Developmental Biology, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Licia Selleri
- Program in Craniofacial Biology, Institute of Human Genetics, Eli and Edyth Broad Center of Regeneration Medicine & Stem Cell Research, Departments of Orofacial Sciences and Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 710, San Francisco, CA 94143, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, W-512, New York, NY 10065, USA
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Dard A, Reboulet J, Jia Y, Bleicher F, Duffraisse M, Vanaker JM, Forcet C, Merabet S. Human HOX Proteins Use Diverse and Context-Dependent Motifs to Interact with TALE Class Cofactors. Cell Rep 2018. [DOI: 10.1016/j.celrep.2018.02.070] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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45
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Palmigiano A, Santaniello F, Cerutti A, Penkov D, Purushothaman D, Makhija E, Luzi L, di Fagagna FD, Pelicci PG, Shivashankar V, Dellino GI, Blasi F. PREP1 tumor suppressor protects the late-replicating DNA by controlling its replication timing and symmetry. Sci Rep 2018; 8:3198. [PMID: 29453404 PMCID: PMC5816642 DOI: 10.1038/s41598-018-21363-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/01/2018] [Indexed: 12/15/2022] Open
Abstract
The synthesis of middle-to-late-replicating DNA can be affected independently of the rest of the genome by down-regulating the tumor suppressor PREP1 (PKNOX1). Indeed, DNA combing shows that PREP1 down-regulation affects DNA replication rate, increases the number of simultaneously firing origins and the asymmetry of DNA replication, leading to DNA damage. Genome-wide analysis of replication timing by Repli-seq shows that, upon PREP1 down-regulation, 25% of the genome is replicated earlier in the S-phase. The targeted DNA sequences correspond to Lamin-Associated Domains (LADs), and include late-replicating (LRRs) and temporal transition regions (TTRs). Notably, the distribution of PREP1 DNA binding sites and of its target genes indicates that DNA replication defects are independent of the overall PREP1 transcriptional activity. Finally, PREP1 down-regulation causes a substantial decrease in Lamin B1 levels. This suggests that DNA is released from the nuclear lamina earlier than in the control cells and is available for replication, thus explaining timing defects and DNA damage.This is the first evidence that the replication timing of a specific fraction of the human genome is affected by PREP1 tumor suppressor. This previously unknown function might significantly contribute to the genomic instability observed in human tumors.
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Affiliation(s)
- Angela Palmigiano
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milan, 20138, Italy
| | - Francesco Santaniello
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139, Milan, Italy
| | - Aurora Cerutti
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Oncogenomics Department, Netherland Cancer Institute (NKI), Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Dmitry Penkov
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Lomonosov Moscow State University, Leninskiye Gori 1, 119991, Moscow, Russia
| | - Divya Purushothaman
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
| | - Ekta Makhija
- Mechano-Biology Institute, National University of Singapore, Singapore, Singapore
| | - Lucilla Luzi
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139, Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy
| | - Viveswara Shivashankar
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy
- Mechano-Biology Institute, National University of Singapore, Singapore, Singapore
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, 20139, Milan, Italy.
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy.
| | - Francesco Blasi
- IFOM (Foundation FIRC Institute of Molecular Oncology), via Adamello 16, 20139, Milan, Italy.
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Wang M, Fones L, Cave JW. Conserved Upstream Regulatory Regions in Mammalian Tyrosine Hydroxylase. Mol Neurobiol 2018; 55:7340-51. [PMID: 29404959 DOI: 10.1007/s12035-018-0936-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 01/25/2018] [Indexed: 10/18/2022]
Abstract
Tyrosine hydroxylase (Th) encodes the rate-limiting enzyme in catecholamine biosynthesis, and the regulation of its transcription is critical for the specification and maintenance of catecholaminergic neuron phenotypes. For many genes, regulatory genomic DNA sequences that are upstream of the proximal promoter control expression levels as well as region-specific expression patterns. The regulatory architecture of the genomic DNA upstream of the Th proximal promoter, however, is poorly understood. In this study, we examined the 11 kb upstream nucleotide sequence of Th from nine mammalian species and identified five highly conserved regions. Using cultured human cells and mouse olfactory bulb tissue, chromatin immunoprecipitation (ChIP) assays show that these conserved regions recruit transcription factors that are established regulators of Th transcription (such as NURR1, PITX3, FOXA2, MEIS2, and PAX6). This analysis also identified a conserved binding site for CTCF, and functional studies in cultured human cells and ChIP assays with mouse tissue show that CTCF is a novel regulator of Th transcription in the forebrain. Together, the findings in this study provide key insights into the upstream regulatory genomic architecture and regulatory mechanisms controlling mammalian Th gene transcription.
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47
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McCulley DJ, Wienhold MD, Hines EA, Hacker TA, Rogers A, Pewowaruk RJ, Zewdu R, Chesler NC, Selleri L, Sun X. PBX transcription factors drive pulmonary vascular adaptation to birth. J Clin Invest 2017; 128:655-667. [PMID: 29251627 DOI: 10.1172/jci93395] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 11/07/2017] [Indexed: 01/14/2023] Open
Abstract
A critical event in the adaptation to extrauterine life is relaxation of the pulmonary vasculature at birth, allowing for a rapid increase in pulmonary blood flow that is essential for efficient gas exchange. Failure of this transition leads to pulmonary hypertension (PH), a major cause of newborn mortality associated with preterm birth, infection, hypoxia, and malformations including congenital diaphragmatic hernia (CDH). While individual vasoconstrictor and dilator genes have been identified, the coordination of their expression is not well understood. Here, we found that lung mesenchyme-specific deletion of CDH-implicated genes encoding pre-B cell leukemia transcription factors (Pbx) led to lethal PH in mice shortly after birth. Loss of Pbx genes resulted in the misexpression of both vasoconstrictors and vasodilators in multiple pathways that converge to increase phosphorylation of myosin in vascular smooth muscle (VSM) cells, causing persistent constriction. While targeting endothelin and angiotensin, which are upstream regulators that promote VSM contraction, was not effective, treatment with the Rho-kinase inhibitor Y-27632 reduced vessel constriction and PH in Pbx-mutant mice. These results demonstrate a lung-intrinsic, herniation-independent cause of PH in CDH. More broadly, our findings indicate that neonatal PH can result from perturbation of multiple pathways and suggest that targeting the downstream common effectors may be a more effective treatment for neonatal PH.
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Affiliation(s)
| | | | | | | | | | - Ryan J Pewowaruk
- Department of Biomedical Engineering, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Rediet Zewdu
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, USA
| | - Naomi C Chesler
- Department of Pediatrics.,Department of Biomedical Engineering, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Licia Selleri
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, USA.,Program in Craniofacial Biology, Institute of Human Genetics, Departments of Orofacial Sciences and Anatomy, UCSF, San Francisco, California, USA
| | - Xin Sun
- Laboratory of Genetics.,Department of Pediatrics, UCSD, San Diego, California, USA
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Slavotinek A, Risolino M, Losa M, Cho MT, Monaghan KG, Schneidman-Duhovny D, Parisotto S, Herkert JC, Stegmann APA, Miller K, Shur N, Chui J, Muller E, DeBrosse S, Szot JO, Chapman G, Pachter NS, Winlaw DS, Mendelsohn BA, Dalton J, Sarafoglou K, Karachunski PI, Lewis JM, Pedro H, Dunwoodie SL, Selleri L, Shieh J. De novo, deleterious sequence variants that alter the transcriptional activity of the homeoprotein PBX1 are associated with intellectual disability and pleiotropic developmental defects. Hum Mol Genet 2017; 26:4849-4860. [PMID: 29036646 PMCID: PMC6455034 DOI: 10.1093/hmg/ddx363] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/25/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022] Open
Abstract
We present eight patients with de novo, deleterious sequence variants in the PBX1 gene. PBX1 encodes a three amino acid loop extension (TALE) homeodomain transcription factor that forms multimeric complexes with TALE and HOX proteins to regulate target gene transcription during development. As previously reported, Pbx1 homozygous mutant mice (Pbx1-/-) develop malformations and hypoplasia or aplasia of multiple organs, including the craniofacial skeleton, ear, branchial arches, heart, lungs, diaphragm, gut, kidneys, and gonads. Clinical findings similar to those in Pbx mutant mice were observed in all patients with varying expressivity and severity, including external ear anomalies, abnormal branchial arch derivatives, heart malformations, diaphragmatic hernia, renal hypoplasia and ambiguous genitalia. All patients but one had developmental delays. Previously reported patients with congenital anomalies affecting the kidney and urinary tract exhibited deletions and loss of function variants in PBX1. The sequence variants in our cases included missense substitutions adjacent to the PBX1 homeodomain (p.Arg184Pro, p.Met224Lys, and p.Arg227Pro) or within the homeodomain (p.Arg234Pro, and p.Arg235Gln), whereas p.Ser262Glnfs*2, and p.Arg288* yielded truncated PBX1 proteins. Functional studies on five PBX1 sequence variants revealed perturbation of intrinsic, PBX-dependent transactivation ability and altered nuclear translocation, suggesting abnormal interactions between mutant PBX1 proteins and wild-type TALE or HOX cofactors. It is likely that the mutations directly affect the transcription of PBX1 target genes to impact embryonic development. We conclude that deleterious sequence variants in PBX1 cause intellectual disability and pleiotropic malformations resembling those in Pbx1 mutant mice, arguing for strong conservation of gene function between these two species.
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Affiliation(s)
- Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Maurizio Risolino
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Marta Losa
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Biochemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sarah Parisotto
- Division of Genetics, Department of Pediatrics, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Johanna C Herkert
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Kathryn Miller
- Department of Pediatrics, Albany Medical Center, Albany, NY, USA
| | - Natasha Shur
- Department of Pediatrics, Albany Medical Center, Albany, NY, USA
| | - Jacqueline Chui
- Clinical Genetics, Stanford Children’s Health at CPMC, San Francisco, CA, USA
| | - Eric Muller
- Clinical Genetics, Stanford Children’s Health at CPMC, San Francisco, CA, USA
| | - Suzanne DeBrosse
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Justin O Szot
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- University of New South Wales, Sydney, NSW, Australia
| | - Gavin Chapman
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- University of New South Wales, Sydney, NSW, Australia
| | - Nicholas S Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, Australia
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
| | - David S Winlaw
- University of Sydney, Medical School, Sydney, NSW, Australia
- Heart Centre for Children, Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Bryce A Mendelsohn
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Joline Dalton
- Paul and Shelia Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, USA
| | - Kyriakie Sarafoglou
- Department of Pediatrics, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA
| | | | - Jane M Lewis
- Department of Urology, University of Minnesota Masonic Children's Hospital, Minneapolis, MN, USA
| | - Helio Pedro
- Division of Genetics, Department of Pediatrics, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Sally L Dunwoodie
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- University of New South Wales, Sydney, NSW, Australia
| | - Licia Selleri
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
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49
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Maroni G, Tkachuk VA, Egorov A, Morelli MJ, Luongo R, Levantini E, Blasi F, Magli MC, Penkov D. Prep1 prevents premature adipogenesis of mesenchymal progenitors. Sci Rep 2017; 7:15573. [PMID: 29138456 DOI: 10.1038/s41598-017-15828-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/31/2017] [Indexed: 11/09/2022] Open
Abstract
Transcriptional regulators are crucial in adipocyte differentiation. We now show that the homeodomain-containing transcription factor Prep1 is a repressor of adipogenic differentiation since its down-regulation (DR) in both ex vivo bone marrow-derived mesenchymal stromal cells (MSC) and in vitro 3T3-L1 preadipocytes significantly increases their adipogenic differentiation ability. Prep1 acts at a stage preceding the activation of the differentiation machinery because its DR makes cells more prone to adipogenic differentiation even in the absence of the adipogenic inducers. Prep1 DR expands the DNA binding landscape of C/EBPβ (CCAAT enhancer binding protein β) without affecting its expression or activation. The data indicate that Prep1 normally acts by restricting DNA binding of transcription factors to adipogenic enhancers, in particular C/EBPβ.
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50
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Abstract
Bobola previews work from the Schulte laboratory showing that the atypical homeodomain protein MEIS2 facilitates chromatin accessibility of transcriptionally inactive genes in neuronal differentiation. How transcription factors (TFs) control enhancer and promoter functions to effect changes in gene expression is an important question. In this issue, Hau et al. (2017. J. Cell Biol.https://doi.org/10.1083/jcb.201701154) show that the TALE TF MEIS recruits the histone modifier PARP1/ARTD1 at promoters to decompact chromatin and activate transcription.
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Affiliation(s)
- Nicoletta Bobola
- Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, England, UK
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