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Fedoseyeva VB, Novosadova EV, Nenasheva VV, Novosadova LV, Grivennikov IA, Tarantul VZ. Transcription of HOX Genes Is Significantly Increased during Neuronal Differentiation of iPSCs Derived from Patients with Parkinson's Disease. J Dev Biol 2023; 11:23. [PMID: 37367477 DOI: 10.3390/jdb11020023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/10/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
Parkinson's disease (PD) is the most serious movement disorder, but the actual cause of this disease is still unknown. Induced pluripotent stem cell-derived neural cultures from PD patients carry the potential for experimental modeling of underlying molecular events. We analyzed the RNA-seq data of iPSC-derived neural precursor cells (NPCs) and terminally differentiated neurons (TDNs) from healthy donors (HD) and PD patients with mutations in PARK2 published previously. The high level of transcription of HOX family protein-coding genes and lncRNA transcribed from the HOX clusters was revealed in the neural cultures from PD patients, while in HD NPCs and TDNs, the majority of these genes were not expressed or slightly transcribed. The results of this analysis were generally confirmed by qPCR. The HOX paralogs in the 3' clusters were activated more strongly than the genes of the 5' cluster. The abnormal activation of the HOX gene program upon neuronal differentiation in the cells of PD patients raises the possibility that the abnormal expression of these key regulators of neuronal development impacts PD pathology. Further research is needed to investigate this hypothesis.
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Affiliation(s)
- Viya B Fedoseyeva
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Ekaterina V Novosadova
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Valentina V Nenasheva
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Lyudmila V Novosadova
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Igor A Grivennikov
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
| | - Vyacheslav Z Tarantul
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Moscow 123182, Russia
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2
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Afzal Z, Lange JJ, Nolte C, McKinney S, Wood C, Paulson A, De Kumar B, Unruh J, Slaughter BD, Krumlauf R. Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube. Development 2023; 150:dev201259. [PMID: 37102683 PMCID: PMC10233718 DOI: 10.1242/dev.201259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
Signaling pathways regulate the patterns of Hox gene expression that underlie their functions in the specification of axial identity. Little is known about the properties of cis-regulatory elements and underlying transcriptional mechanisms that integrate graded signaling inputs to coordinately control Hox expression. Here, we optimized a single molecule fluorescent in situ hybridization (smFISH) technique with probes spanning introns to evaluate how three shared retinoic acid response element (RARE)-dependent enhancers in the Hoxb cluster regulate patterns of nascent transcription in vivo at the level of single cells in wild-type and mutant embryos. We predominately detect nascent transcription of only a single Hoxb gene in each cell, with no evidence for simultaneous co-transcriptional coupling of all or specific subsets of genes. Single and/or compound RARE mutations indicate that each enhancer differentially impacts global and local patterns of nascent transcription, suggesting that selectivity and competitive interactions between these enhancers is important to robustly maintain the proper levels and patterns of nascent Hoxb transcription. This implies that rapid and dynamic regulatory interactions potentiate transcription of genes through combined inputs from these enhancers in coordinating the retinoic acid response.
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Affiliation(s)
- Zainab Afzal
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Anatomy and Cell Biology Department, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Jeffrey J. Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christof Nolte
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christopher Wood
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Anatomy and Cell Biology Department, Kansas University Medical Center, Kansas City, KS 66160, USA
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3
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Abstract
As the first organ to form and function in all vertebrates, the heart is crucial to development. Tightly-regulated levels of retinoic acid (RA) are critical for the establishment of the regulatory networks that drive normal cardiac development. Thus, the heart is an ideal organ to investigate RA signaling, with much work remaining to be done in this area. Herein, we highlight the role of RA signaling in vertebrate heart development and provide an overview of the field's inception, its current state, and in what directions it might progress so that it may yield fruitful insight for therapeutic applications within the domain of regenerative medicine.
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4
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Paço A, Freitas R. HOX genes as transcriptional and epigenetic regulators during tumorigenesis and their value as therapeutic targets. Epigenomics 2019; 11:1539-1552. [PMID: 31556724 DOI: 10.2217/epi-2019-0090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Several HOX genes are aberrantly expressed in a wide range of cancers interfering with their development and resistance to treatment. This seems to be often caused by alterations in the methylation profiles of their promoters. The role of HOX gene products in cancer is highly 'tissue specific', relying ultimately on their ability to regulate oncogenes or tumor-suppressor genes, directly as transcriptional regulators or indirectly interfering with the levels of epigenetic regulators. Nowadays, different strategies have been tested the use of HOX genes as therapeutic targets for cancer diagnosis and treatment. Here, we trace the history of the research concerning the involvement of HOX genes in cancer, their connection with epigenetic regulation and their potential use as therapeutic targets.
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Affiliation(s)
- Ana Paço
- Laboratório de Microbiologia do Solo, Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Instituto de Investigação e Formação Avançada (IIFA), Universidade de Évora, 7006-554 Évora, Portugal
| | - Renata Freitas
- I3S - Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal.,IBMC - Institute for Molecular & Cell Biology, University of Porto, 4200-135 Porto, Portugal.,ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
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5
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Perl E, Waxman JS. Reiterative Mechanisms of Retinoic Acid Signaling during Vertebrate Heart Development. J Dev Biol 2019; 7:jdb7020011. [PMID: 31151214 PMCID: PMC6631158 DOI: 10.3390/jdb7020011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 01/07/2023] Open
Abstract
Tightly-regulated levels of retinoic acid (RA) are critical for promoting normal vertebrate development. The extensive history of research on RA has shown that its proper regulation is essential for cardiac progenitor specification and organogenesis. Here, we discuss the roles of RA signaling and its establishment of networks that drive both early and later steps of normal vertebrate heart development. We focus on studies that highlight the drastic effects alternative levels of RA have on early cardiomyocyte (CM) specification and cardiac chamber morphogenesis, consequences of improper RA synthesis and degradation, and known effectors downstream of RA. We conclude with the implications of these findings to our understanding of cardiac regeneration and the etiologies of congenital heart defects.
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Affiliation(s)
- Eliyahu Perl
- Molecular and Developmental Biology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
- The Heart Institute and Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Joshua S Waxman
- The Heart Institute and Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45267, USA.
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6
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Parker HJ, Krumlauf R. Segmental arithmetic: summing up the Hox gene regulatory network for hindbrain development in chordates. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28771970 DOI: 10.1002/wdev.286] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 06/13/2017] [Accepted: 06/15/2017] [Indexed: 11/10/2022]
Abstract
Organization and development of the early vertebrate hindbrain are controlled by a cascade of regulatory interactions that govern the process of segmentation and patterning along the anterior-posterior axis via Hox genes. These interactions can be assembled into a gene regulatory network that provides a framework to interpret experimental data, generate hypotheses, and identify gaps in our understanding of the progressive process of hindbrain segmentation. The network can be broadly separated into a series of interconnected programs that govern early signaling, segmental subdivision, secondary signaling, segmentation, and ultimately specification of segmental identity. Hox genes play crucial roles in multiple programs within this network. Furthermore, the network reveals properties and principles that are likely to be general to other complex developmental systems. Data from vertebrate and invertebrate chordate models are shedding light on the origin and diversification of the network. Comprehensive cis-regulatory analyses of vertebrate Hox gene regulation have enabled powerful cross-species gene regulatory comparisons. Such an approach in the sea lamprey has revealed that the network mediating segmental Hox expression was present in ancestral vertebrates and has been maintained across diverse vertebrate lineages. Invertebrate chordates lack hindbrain segmentation but exhibit conservation of some aspects of the network, such as a role for retinoic acid in establishing nested Hox expression domains. These comparisons lead to a model in which early vertebrates underwent an elaboration of the network between anterior-posterior patterning and Hox gene expression, leading to the gene-regulatory programs for segmental subdivision and rhombomeric segmentation. WIREs Dev Biol 2017, 6:e286. doi: 10.1002/wdev.286 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, USA.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
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7
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Stefanovic S, Zaffran S. Mechanisms of retinoic acid signaling during cardiogenesis. Mech Dev 2016; 143:9-19. [PMID: 28007475 DOI: 10.1016/j.mod.2016.12.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/29/2016] [Accepted: 12/12/2016] [Indexed: 10/20/2022]
Abstract
Substantial experimental and epidemiological data have highlighted the interplay between nutritional and genetic factors in the development of congenital heart defects. Retinoic acid (RA), a derivative of vitamin A, plays a key role during vertebrate development including the formation of the heart. Retinoids bind to RA and retinoid X receptors (RARs and RXRs) which then regulate tissue-specific genes. Here, we will focus on the roles of RA signaling and receptors in gene regulation during cardiogenesis, and the consequence of deregulated retinoid signaling on heart formation and congenital heart defects.
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8
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Adverse effect of valproic acid on an in vitro gastrulation model entails activation of retinoic acid signaling. Reprod Toxicol 2016; 66:68-83. [PMID: 27693483 DOI: 10.1016/j.reprotox.2016.09.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 09/18/2016] [Accepted: 09/26/2016] [Indexed: 02/06/2023]
Abstract
Valproic acid (VPA), an antiepileptic drug, is a teratogen that causes neural tube and axial skeletal defects, although the mechanisms are not fully understood. We previously established a gastrulation model using mouse P19C5 stem cell embryoid bodies (EBs), which exhibits axial patterning and elongation morphogenesis in vitro. Here, we investigated the effects of VPA on the EB axial morphogenesis to gain insights into its teratogenic mechanisms. Axial elongation and patterning of EBs were inhibited by VPA at therapeutic concentrations. VPA elevated expression levels of various developmental regulators, including Cdx1 and Hoxa1, known transcriptional targets of retinoic acid (RA) signaling. Co-treatment of EBs with VPA and BMS493, an RA receptor antagonist, partially rescued axial elongation as well as gene expression profiles. These results suggest that VPA requires active RA signaling to interfere with EB morphogenesis.
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9
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Jeannotte L, Gotti F, Landry-Truchon K. Hoxa5: A Key Player in Development and Disease. J Dev Biol 2016; 4:E13. [PMID: 29615582 PMCID: PMC5831783 DOI: 10.3390/jdb4020013] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/08/2016] [Accepted: 03/16/2016] [Indexed: 12/28/2022] Open
Abstract
A critical position in the developmental hierarchy is occupied by the Hox genes, which encode transcription factors. Hox genes are crucial in specifying regional identity along the embryonic axes and in regulating morphogenesis. In mouse, targeted mutations of Hox genes cause skeletal transformations and organ defects that can impair viability. Here, we present the current knowledge about the Hoxa5 gene, a paradigm for the function and the regulation of Hox genes. The phenotypic survey of Hoxa5-/- mice has unveiled its critical role in the regional specification of the skeleton and in organogenesis. Most Hoxa5-/- mice die at birth from respiratory distress due to tracheal and lung dysmorphogenesis and impaired diaphragm innervation. The severity of the phenotype establishes that Hoxa5 plays a predominant role in lung organogenesis versus other Hox genes. Hoxa5 also governs digestive tract morphogenesis, thyroid and mammary glands development, and ovary homeostasis. Deregulated Hoxa5 expression is reported in cancers, indicating Hoxa5 involvement in tumor predisposition and progression. The dynamic Hoxa5 expression profile is under the transcriptional control of multiple cis-acting sequences and trans-acting regulators. It is also modulated by epigenetic mechanisms, implicating chromatin modifications and microRNAs. Finally, lncRNAs originating from alternative splicing and distal promoters encompass the Hoxa5 locus.
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Affiliation(s)
- Lucie Jeannotte
- Centre de recherche sur le cancer de l'Université Laval; CRCHU de Québec, L'Hôtel-Dieu de Québec, QC G1R 3S3, Canada.
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, QC G1V 0A6, Canada.
| | - Florian Gotti
- Centre de recherche sur le cancer de l'Université Laval; CRCHU de Québec, L'Hôtel-Dieu de Québec, QC G1R 3S3, Canada.
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, QC G1V 0A6, Canada.
| | - Kim Landry-Truchon
- Centre de recherche sur le cancer de l'Université Laval; CRCHU de Québec, L'Hôtel-Dieu de Québec, QC G1R 3S3, Canada.
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, QC G1V 0A6, Canada.
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10
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Ahn Y, Mullan HE, Krumlauf R. Long-range regulation by shared retinoic acid response elements modulates dynamic expression of posterior Hoxb genes in CNS development. Dev Biol 2014; 388:134-44. [PMID: 24525295 DOI: 10.1016/j.ydbio.2014.01.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/13/2014] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
Abstract
Retinoic acid (RA) signaling plays an important role in determining the anterior boundary of Hox gene expression in the neural tube during embryogenesis. In particular, RA signaling is implicated in a rostral expansion of the neural expression domain of 5׳ Hoxb genes (Hoxb9-Hoxb5) in mice. However, underlying mechanisms for this gene regulation have remained elusive due to the lack of RA responsive element (RARE) in the 5׳ half of the HoxB cluster. To identify cis-regulatory elements required for the rostral expansion, we developed a recombineering technology to serially label multiple genes with different reporters in a single bacterial artificial chromosome (BAC) vector containing the mouse HoxB cluster. This allowed us to simultaneously monitor the expression of multiple genes. In contrast to plasmid-based reporters, transgenic BAC reporters faithfully recapitulated endogenous gene expression patterns of the Hoxb genes including the rostral expansion. Combined inactivation of two RAREs, DE-RARE and ENE-RARE, in the BAC completely abolished the rostral expansion of the 5׳ Hoxb genes. Knock-out of endogenous DE-RARE lead to significantly reduced expression of multiple Hoxb genes and attenuated Hox gene response to exogenous RA treatment in utero. Regulatory potential of DE-RARE was further demonstrated by its ability to anteriorize 5׳ Hoxa gene expression in the neural tube when inserted into a HoxA BAC reporter. Our data demonstrate that multiple RAREs cooperate to remotely regulate 5׳ Hoxb genes during CNS development, providing a new insight into the mechanisms for gene regulation within the Hox clusters.
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Affiliation(s)
- Youngwook Ahn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Hillary E Mullan
- Stowers Institute for Medical Research, Kansas City, MO 64110, 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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11
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Kashyap V, Gudas LJ, Brenet F, Funk P, Viale A, Scandura JM. Epigenomic reorganization of the clustered Hox genes in embryonic stem cells induced by retinoic acid. J Biol Chem 2011; 286:3250-60. [PMID: 21087926 PMCID: PMC3030330 DOI: 10.1074/jbc.m110.157545] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 10/29/2010] [Indexed: 12/19/2022] Open
Abstract
Retinoic acid (RA) regulates clustered Hox gene expression during embryogenesis and is required to establish the anterior-posterior body plan. Using mutant embryonic stem cell lines deficient in the RA receptor γ (RARγ) or Hoxa1 3'-RA-responsive element, we studied the kinetics of transcriptional and epigenomic patterning responses to RA. RARγ is essential for RA-induced Hox transcriptional activation, and deletion of its binding site in the Hoxa1 enhancer attenuates transcriptional and epigenomic activation of both Hoxa and Hoxb gene clusters. The kinetics of epigenomic reorganization demonstrate that complete erasure of the polycomb repressive mark H3K27me3 is not necessary to initiate Hox transcription. RARγ is not required to establish the bivalent character of Hox clusters, but RA/RARγ signaling is necessary to erase H3K27me3 from activated Hox genes during embryonic stem cell differentiation. Highly coordinated, long range epigenetic Hox cluster reorganization is closely linked to transcriptional activation and is triggered by RARγ located at the Hoxa1 3'-RA-responsive element.
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Affiliation(s)
| | - Lorraine J. Gudas
- From the Departments of Pharmacology and
- Medicine, Weill Cornell Medical College, New York, New York 10065 and
| | - Fabienne Brenet
- Medicine, Weill Cornell Medical College, New York, New York 10065 and
| | - Patricia Funk
- Medicine, Weill Cornell Medical College, New York, New York 10065 and
| | - Agnes Viale
- the Genomics Core Laboratory, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
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13
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Spitz F. Control of vertebrate Hox clusters by remote and global cis-acting regulatory sequences. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 689:63-78. [PMID: 20795322 DOI: 10.1007/978-1-4419-6673-5_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite apparently shared structural organisation and functional roles, vertebrate Hox genes are controlled by regulatory mechanisms rather distinct from those of the prototypic Drosophila Antennapedia (ANT-C) and Bithorax (BX-C) Complexes. If individual regulatory modules have been shown to recapitulate specific Hox expression patterns, other experimental studies underscore that vertebrate Hox clusters are controlled in many of their functions in a global manner, through distinct mechanisms. We will discuss the different models that have been proposed to account for these global regulatory modes. In this context, the studies of the regulation of the HoxD complex during limb development highlighted the role of global regulatory elements and the different mechanisms associated to transform a structural organisation into distinct temporal and spatial expression domains. We will further discuss how these mechanisms may have benefited from the structure of the vertebrate homeotic clusters and reciprocally contribute to shape their evolution towards an increased level of organisation and compaction.
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Affiliation(s)
- François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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Ribes V, Le Roux I, Rhinn M, Schuhbaur B, Dollé P. Early mouse caudal development relies on crosstalk between retinoic acid, Shh and Fgf signalling pathways. Development 2009; 136:665-76. [PMID: 19168680 DOI: 10.1242/dev.016204] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The progressive generation of embryonic trunk structures relies on the proper patterning of the caudal epiblast, which involves the integration of several signalling pathways. We have investigated the function of retinoic acid (RA) signalling during this process. We show that, in addition to posterior mesendoderm, primitive streak and node cells transiently express the RA-synthesizing enzyme Raldh2 prior to the headfold stage. RA-responsive cells (detected by the RA-activated RARE-lacZ transgene) are additionally found in the epiblast layer. Analysis of RA-deficient Raldh2(-/-) mutants reveals early caudal patterning defects, with an expansion of primitive streak and mesodermal markers at the expense of markers of the prospective neuroepithelium. As a result, many genes involved in neurogenesis and/or patterning of the embryonic spinal cord are affected in their expression. We demonstrate that RA signalling is required at late gastrulation stages for mesodermal and neural progenitors to respond to the Shh signal. Whole-embryo culture experiments indicate that the proper response of cells to Shh requires two RA-dependent mechanisms: (1) a balanced antagonism between Fgf and RA signals, and (2) a RA-mediated repression of Gli2 expression. Thus, an interplay between RA, Fgf and Shh signalling is likely to be an important mechanism underpinning the tight regulation of caudal embryonic development.
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Affiliation(s)
- Vanessa Ribes
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Inserm, U 964, Illkirch, F-67400 France
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15
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Nolte C, Rastegar M, Amores A, Bouchard M, Grote D, Maas R, Kovacs EN, Postlethwait J, Rambaldi I, Rowan S, Yan YL, Zhang F, Featherstone M. Stereospecificity and PAX6 function direct Hoxd4 neural enhancer activity along the antero-posterior axis. Dev Biol 2006; 299:582-93. [PMID: 17010333 DOI: 10.1016/j.ydbio.2006.08.061] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2006] [Revised: 08/16/2006] [Accepted: 08/25/2006] [Indexed: 12/14/2022]
Abstract
The antero-posterior (AP) and dorso-ventral (DV) patterning of the neural tube is controlled in part by HOX and PAX transcription factors, respectively. We have reported on a neural enhancer of Hoxd4 that directs expression in the CNS with the correct anterior border in the hindbrain. Comparison to the orthologous enhancer of zebrafish revealed seven conserved footprints including an obligatory retinoic acid response element (RARE), and adjacent sites D, E and F. Whereas enhancer function in the embryonic CNS is destroyed by separation of the RARE from sites D-E-F by a half turn of DNA, it is rescued by one full turn, suggesting stereospecific constraints between DNA-bound retinoid receptors and the factor(s) recognizing sites D-E-F. Alterations in the DV trajectory of the Hoxd4 anterior expression border following mutation of site D or E implicated transcriptional regulators active across the DV axis. We show that PAX6 specifically binds sites D and E in vitro, and use chromatin immunoprecipitation to demonstrate recruitment of PAX6 to the Hoxd4 neural enhancer in mouse embryos. Hoxd4 expression throughout the CNS is reduced in Pax6 mutant Sey(Neu) animals on embryonic day 8. Additionally, stage-matched zebrafish embryos having decreased pax6a and/or pax6b activity display malformed rhombomere boundaries and an anteriorized hoxd4a expression border. These results reveal an evolutionarily conserved role for Pax6 in AP-restricted expression of vertebrate Hoxd4 orthologs.
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Affiliation(s)
- Christof Nolte
- McGill Cancer Centre, McGill University, 3655 Promenade Sir-William-Osler, Montreal, QC, Canada H3G 1Y6
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16
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Wallden B, Emond M, Swift ME, Disis ML, Swisshelm K. Antimetastatic gene expression profiles mediated by retinoic acid receptor beta 2 in MDA-MB-435 breast cancer cells. BMC Cancer 2005; 5:140. [PMID: 16255778 PMCID: PMC1283145 DOI: 10.1186/1471-2407-5-140] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2005] [Accepted: 10/28/2005] [Indexed: 01/04/2023] Open
Abstract
Background The retinoic acid receptor beta 2 (RARβ2) gene modulates proliferation and survival of cultured human breast cancer cells. Previously we showed that ectopic expression of RARβ2 in a mouse xenograft model prevented metastasis, even in the absence of the ligand, all-trans retinoic acid. We investigated both cultured cells and xenograft tumors in order to delineate the gene expression profiles responsible for an antimetastatic phenotype. Methods RNA from MDA-MB-435 human breast cancer cells transduced with RARβ2 or empty retroviral vector (LXSN) was analyzed using Agilent Human 1A Oligo microarrays. The one hundred probes with the greatest differential intensity (p < 0.004, jointly) were determined by selecting the top median log ratios from eight-paired microarrays. Validation of differences in expression was done using Northern blot analysis and quantitative RT-PCR (qRT-PCR). We determined expression of selected genes in xenograft tumors. Results RARβ2 cells exhibit gene profiles with overrepresentation of genes from Xq28 (p = 2 × 10-8), a cytogenetic region that contains a large portion of the cancer/testis antigen gene family. Other functions or factors impacted by the presence of exogenous RARβ2 include mediators of the immune response and transcriptional regulatory mechanisms. Thirteen of fifteen (87%) of the genes evaluated in xenograft tumors were consistent with differences we found in the cell cultures (p = 0.007). Conclusion Antimetastatic RARβ2 signalling, direct or indirect, results in an elevation of expression for genes such as tumor-cell antigens (CTAG1 and CTAG2), those involved in innate immune response (e.g., RIG-I/DDX58), and tumor suppressor functions (e.g., TYRP1). Genes whose expression is diminished by RARβ2 signalling include cell adhesion functions (e.g, CD164) nutritional or metabolic processes (e.g., FABP6), and the transcription factor, JUN.
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MESH Headings
- Animals
- Blotting, Northern
- Blotting, Western
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Cell Adhesion
- Cell Line, Tumor
- Chromosomes, Human, X
- Gene Expression Profiling/methods
- Gene Expression Regulation
- Gene Expression Regulation, Neoplastic
- Genetic Vectors
- Genotype
- Humans
- Interferons/metabolism
- Ligands
- Mice
- Models, Statistical
- Neoplasm Metastasis
- Neoplasm Transplantation
- Nucleic Acid Hybridization
- Phenotype
- Proto-Oncogene Proteins c-jun/metabolism
- RNA/metabolism
- Receptors, Retinoic Acid/biosynthesis
- Receptors, Retinoic Acid/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Signal Transduction
- Transcription, Genetic
- Tretinoin/metabolism
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Affiliation(s)
- Brett Wallden
- Department of Pathology, Box 357470, University of Washington, Seattle, WA, USA
| | - Mary Emond
- Department of Biostatistics, Box 357232, University of Washington, Seattle, WA, USA
| | - Mari E Swift
- Department of Pathology, Box 357470, University of Washington, Seattle, WA, USA
| | - Mary L Disis
- Division of Oncology, Box 358050, University of Washington, Seattle, WA, USA
| | - Karen Swisshelm
- Department of Pathology, Box 357470, University of Washington, Seattle, WA, USA
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17
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Segara D, Biankin AV, Kench JG, Langusch CC, Dawson AC, Skalicky DA, Gotley DC, Coleman MJ, Sutherland RL, Henshall SM. Expression of HOXB2, a retinoic acid signaling target in pancreatic cancer and pancreatic intraepithelial neoplasia. Clin Cancer Res 2005; 11:3587-96. [PMID: 15867264 DOI: 10.1158/1078-0432.ccr-04-1813] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PURPOSE Despite significant progress in understanding the molecular pathology of pancreatic cancer and its precursor lesion: pancreatic intraepithelial neoplasia (PanIN), there remain no molecules with proven clinical utility as prognostic or therapeutic markers. Here, we used oligonucleotide microarrays to interrogate mRNA expression of pancreatic cancer tissue and normal pancreas to identify novel molecular pathways dysregulated in the development and progression of pancreatic cancer. EXPERIMENTAL DESIGN RNA was hybridized to Affymetrix Genechip HG-U133 oligonucleotide microarrays. A relational database integrating data from publicly available resources was created to identify candidate genes potentially relevant to pancreatic cancer. The protein expression of one candidate, homeobox B2 (HOXB2), in PanIN and pancreatic cancer was assessed using immunohistochemistry. RESULTS We identified aberrant expression of several components of the retinoic acid (RA) signaling pathway (RARalpha, MUC4, Id-1, MMP9, uPAR, HB-EGF, HOXB6, and HOXB2), many of which are known to be aberrantly expressed in pancreatic cancer and PanIN. HOXB2, a downstream target of RA, was up-regulated 6.7-fold in pancreatic cancer compared with normal pancreas. Immunohistochemistry revealed ectopic expression of HOXB2 in 15% of early PanIN lesions and 48 of 128 (38%) pancreatic cancer specimens. Expression of HOXB2 was associated with nonresectable tumors and was an independent predictor of poor survival in resected tumors. CONCLUSIONS We identified aberrant expression of RA signaling components in pancreatic cancer, including HOXB2, which was expressed in a proportion of PanIN lesions. Ectopic expression of HOXB2 was associated with a poor prognosis for all patients with pancreatic cancer and was an independent predictor of survival in patients who underwent resection.
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Affiliation(s)
- Davendra Segara
- Cancer Research Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
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18
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Dobbs-McAuliffe B, Zhao Q, Linney E. Feedback mechanisms regulate retinoic acid production and degradation in the zebrafish embryo. Mech Dev 2004; 121:339-50. [PMID: 15110044 DOI: 10.1016/j.mod.2004.02.008] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2003] [Revised: 02/23/2004] [Accepted: 02/28/2004] [Indexed: 11/18/2022]
Abstract
Retinoic acid (RA) signaling in vertebrate embryos occurs in a distinct physical and temporal pattern. Regulating this spatial distribution is crucial to the development of the embryo, as RA in excess or in inappropriate tissues is teratogenic. In order to understand how RA availability is determined in zebrafish we have investigated the expression of cyp26a1, an enzyme that inactivates RA, and its relationship to raldh2, one of the enzymes that produce RA from retinal. cyp26a1 expression follows three phases: in presumptive anterior neurectoderm and in a circumblastoporal ring during gastrulation, in the tailbud throughout somitogenesis, and in multiple specific tissue types beginning at mid-somitogenesis and continuing through 48 h postfertilization (hpf). This expression was either adjacent or opposite to those tissues expressing raldh2. We then investigated how RA production might regulate these relationships. Endogenous RA produced by raldhs did not play a role in setting cyp26a1 expression in most tissues. However, exogenous RA regulates expression of both enzymes. cyp26a1 is up regulated in the embryo in a time, concentration, and tissue-dependent manner. Conversely, raldh2 expression is reduced with RA treatment. Tests of the raldh2 promoter in cell transfections proved that RA directly represses its activity. These data demonstrate that the feedback mechanisms regulating production and degradation of RA must be considered in any experiments altering levels of RA in the developing vertebrate embryo.
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Affiliation(s)
- Betsy Dobbs-McAuliffe
- Department of Cell Biology, Duke University Medical Center, Box 3020, Durham, NC 27710, USA
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