1
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Jackson JT, Nutt SL, McCormack MP. The Haematopoietically-expressed homeobox transcription factor: roles in development, physiology and disease. Front Immunol 2023; 14:1197490. [PMID: 37398663 PMCID: PMC10313424 DOI: 10.3389/fimmu.2023.1197490] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023] Open
Abstract
The Haematopoietically expressed homeobox transcription factor (Hhex) is a transcriptional repressor that is of fundamental importance across species, as evident by its evolutionary conservation spanning fish, amphibians, birds, mice and humans. Indeed, Hhex maintains its vital functions throughout the lifespan of the organism, beginning in the oocyte, through fundamental stages of embryogenesis in the foregut endoderm. The endodermal development driven by Hhex gives rise to endocrine organs such as the pancreas in a process which is likely linked to its role as a risk factor in diabetes and pancreatic disorders. Hhex is also required for the normal development of the bile duct and liver, the latter also importantly being the initial site of haematopoiesis. These haematopoietic origins are governed by Hhex, leading to its crucial later roles in definitive haematopoietic stem cell (HSC) self-renewal, lymphopoiesis and haematological malignancy. Hhex is also necessary for the developing forebrain and thyroid gland, with this reliance on Hhex evident in its role in endocrine disorders later in life including a potential role in Alzheimer's disease. Thus, the roles of Hhex in embryological development throughout evolution appear to be linked to its later roles in a variety of disease processes.
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Affiliation(s)
- Jacob T. Jackson
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Stephen L. Nutt
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Matthew P. McCormack
- The Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
- iCamuno Biotherapeutics, Melbourne, VIC, Australia
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2
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González-Jiménez A, López-Cotarelo P, Agudo-Jiménez T, Martínez-Ginés M, García-Domínguez JM, Urcelay E, Espino-Paisán L. Unraveling the Influence of HHEX Risk Polymorphism rs7923837 on Multiple Sclerosis Pathogenesis. Int J Mol Sci 2022; 23:ijms23147956. [PMID: 35887298 PMCID: PMC9321666 DOI: 10.3390/ijms23147956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 02/04/2023] Open
Abstract
One of the multiple sclerosis (MS) risk polymorphisms, rs7923837, maps near the HHEX (hematopoietically-expressed homeobox) gene. This variant has also been associated with type 2 diabetes susceptibility and with triglyceride levels, suggesting its metabolic involvement. HHEX plays a relevant role as a negative regulator of inflammatory genes in microglia. A reciprocal repression was reported between HHEX and BCL6, another putative risk factor in MS. The present study evidenced statistically significant lower HHEX mRNA levels in lymphocytes of MS patients compared to those of controls, showing a similar trend in MS patients to the already described eQTL effect in blood from healthy individuals. Even though no differences were found in protein expression according to HHEX genotypes, statistically significant divergent subcellular distributions of HHEX appeared in patients and controls. The epistatic interaction detected between BCL6 and HHEX MS-risk variants in healthy individuals was absent in patients, indicative of a perturbed reciprocal regulation in the latter. Lymphocytes from MS carriers of the homozygous mutant genotype exhibited a distinctive, more energetic profile, both in resting and activated conditions, and significantly increased glycolytic rates in resting conditions when compared to controls sharing the HHEX genotype. In contrast, significantly higher mitochondrial mass was evidenced in homozygous mutant controls.
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Affiliation(s)
- Adela González-Jiménez
- Laboratorio de Genética de Enfermedades Complejas, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain; (A.G.-J.); (P.L.-C.); (T.A.-J.); (E.U.)
- Redes de Investigación Cooperativa Orientada a Resultados en Salud (RICORS), 28029 Madrid, Spain
| | - Pilar López-Cotarelo
- Laboratorio de Genética de Enfermedades Complejas, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain; (A.G.-J.); (P.L.-C.); (T.A.-J.); (E.U.)
| | - Teresa Agudo-Jiménez
- Laboratorio de Genética de Enfermedades Complejas, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain; (A.G.-J.); (P.L.-C.); (T.A.-J.); (E.U.)
| | - Marisa Martínez-Ginés
- Servicio de Neurología, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain; (M.M.-G.); (J.M.G.-D.)
| | - Jose Manuel García-Domínguez
- Servicio de Neurología, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain; (M.M.-G.); (J.M.G.-D.)
| | - Elena Urcelay
- Laboratorio de Genética de Enfermedades Complejas, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain; (A.G.-J.); (P.L.-C.); (T.A.-J.); (E.U.)
- Redes de Investigación Cooperativa Orientada a Resultados en Salud (RICORS), 28029 Madrid, Spain
| | - Laura Espino-Paisán
- Laboratorio de Genética de Enfermedades Complejas, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain; (A.G.-J.); (P.L.-C.); (T.A.-J.); (E.U.)
- Redes de Investigación Cooperativa Orientada a Resultados en Salud (RICORS), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-913303389
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3
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Kitchen P, Gaston K, Jayaraman PS. Transcription Factor Chromatin Immunoprecipitation in Endothelial Cells. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2441:257-275. [PMID: 35099743 DOI: 10.1007/978-1-0716-2059-5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interactions between DNA and proteins are crucial for the regulation of gene expression. Chromatin immunoprecipitation (ChIP) is a powerful technique that allows the study of specific protein-DNA interactions in cultured cells and fresh or fixed tissue. Chromatin is isolated and sheared, and antibodies against the protein(s) of interest are used to isolate specific protein-DNA complexes. Subsequent analysis by real-time polymerase chain reaction (qPCR) or next-generation sequencing (NGS) allows identification and quantification of the co-purified DNA fragments, and NGS also gives insight into the genomic binding sites of a protein. Here we describe a cross-linking ChIP (X-ChIP) protocol, based around the example of a myc-tagged Proline-Rich Homeodomain (PRH) protein expressed in human umbilical vein endothelial cells. We also describe how to analyse specific known or suspected binding sites using quantitative PCR as well as how to analyse genome-wide binding from ChIP sequencing data.
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Affiliation(s)
- Philip Kitchen
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Kevin Gaston
- Biodiscovery Institute and Division of Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
| | - Padma-Sheela Jayaraman
- Biodiscovery Institute and Division of Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK.
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4
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Zhang K, Zhao Q, Li Z, Fu F, Zhang H, Fu J, Zheng M, Zhang S. Clinicopathological Significances of Cancer Stem Cell-Associated HHEX Expression in Breast Cancer. Front Cell Dev Biol 2020; 8:605744. [PMID: 33425911 PMCID: PMC7785851 DOI: 10.3389/fcell.2020.605744] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
Aberrant expression of the transcription factor hematopoietic ally expressed homeobox/proline-rich homeodomain (HHEX/PRH) is implicated in numerous cancers. However, the association of HHEX with breast cancer (BC) remains unclear. In this study, HHEX mRNA and protein expression were analyzed using the Oncomine, UALCAN, GEPIA, TCGAportal, and HPA databases. We evaluated the effect of HHEX on clinicopathological parameters using Kaplan–Meier plotter, OncoLnc, TCGAportal, PROGgeneV2, and BC-GenExMiner. Western blotting was performed to compare the level of HHEX in breast samples of Tientsin Albino 2 mice, human breast precancerous lesions, benign breast tumors, and BC. The correlation between HHEX and cancer stem cells was investigated using the GEO (GSE52327 and GSE94865) and GEPIA datasets. Networks between HHEX and survival-related gene marker sets and microRNAs were analyzed using GEPIA, StarBase, and Cytoscape. Results of this study showed that HHEX expression in BC was significantly lower than those in breast precancerous lesions and benign breast tumors at both mRNA and protein levels. BC patients with lower HHEX expression had significantly worse overall survival and disease-free survival. Moreover, HHEX significantly affected the clinicopathology of BC. Specifically, low HHEX expression was correlated with the following groups of patients: age ≤51 years, ER-negative or PR-negative patients, HER-2 positive, triple-negative breast cancer, and basal-like BC. Immunohistochemical analysis of the breast samples showed significant differences of HHEX staining index (P < 0.001) among the three groups. To further investigate the mechanism, we determined the intersection of differentially expressed genes related to BC stem cells and those genes after HHEX expression was altered. This led to the identification of four potentially regulated genes-CXL12, BLNK, PAG1, and LPXN. Using StarBase and km-plotter, the negative regulation of HHEX expression and survival trends, including miR-130b, miR-30e, and miR-301b were joined into miRNA-HHEX-mRNA potential regulatory network. The abilities of proliferation, migration and invasion increased in MDA-MB-231 and BT-549 breast cancer cell lines after HHEX down expression and decreased after HHEX overexpression compared them in the control cells. In conclusion, these data suggest that HHEX expression is downregulated in BC and HHEX may regulate the development of BC through the stem cell-related genes.
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Affiliation(s)
- Kexin Zhang
- Nankai University School of Medicine, Nankai University, Tianjin, China.,Department of Pathology, Tianjin Union Medical Center, Tianjin, China
| | - Qi Zhao
- Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Zugui Li
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China.,Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Fangmei Fu
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China.,Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hao Zhang
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China.,Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Junjie Fu
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
| | - Minying Zheng
- Nankai University School of Medicine, Nankai University, Tianjin, China.,Department of Pathology, Tianjin Union Medical Center, Tianjin, China
| | - Shiwu Zhang
- Nankai University School of Medicine, Nankai University, Tianjin, China.,Department of Pathology, Tianjin Union Medical Center, Tianjin, China
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5
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Gao C, Huang W, Gao Y, Lo LJ, Luo L, Huang H, Chen J, Peng J. Zebrafish hhex-null mutant develops an intrahepatic intestinal tube due to de-repression of cdx1b and pdx1. J Mol Cell Biol 2020; 11:448-462. [PMID: 30428031 PMCID: PMC6604603 DOI: 10.1093/jmcb/mjy068] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/13/2018] [Indexed: 12/17/2022] Open
Abstract
The hepatopancreatic duct (HPD) system links the liver and pancreas to the intestinal tube and is composed of the extrahepatic biliary duct, gallbladder, and pancreatic duct. Haematopoietically expressed-homeobox (Hhex) protein plays an essential role in the establishment of HPD; however, the molecular mechanism remains elusive. Here, we show that zebrafish hhex-null mutants fail to develop the HPD system characterized by lacking the biliary marker Annexin A4 and the HPD marker sox9b. The hepatobiliary duct part of the mutant HPD system is replaced by an intrahepatic intestinal tube characterized by expressing the intestinal marker fatty acid-binding protein 2a (fabp2a). Cell lineage analysis showed that this intrahepatic intestinal tube is not originated from hepatocytes or cholangiocytes. Further analysis revealed that cdx1b and pdx1 are expressed ectopically in the intrahepatic intestinal tube and knockdown of cdx1b and pdx1 could restore the expression of sox9b in the mutant. Chromatin-immunoprecipitation analysis showed that Hhex binds to the promoters of pdx1 and cdx1b genes to repress their expression. We therefore propose that Hhex, Cdx1b, Pdx1, and Sox9b form a genetic network governing the patterning and morphogenesis of the HPD and digestive tract systems in zebrafish.
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Affiliation(s)
- Ce Gao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, China
| | - Weidong Huang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, China
| | - Yuqi Gao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, China
| | - Li Jan Lo
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, China
| | - Lingfei Luo
- College of Life Sciences, Southwest University, Chongqing, China
| | - Honghui Huang
- College of Life Sciences, Southwest University, Chongqing, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, China
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6
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Kitchen P, Lee KY, Clark D, Lau N, Lertsuwan J, Sawasdichai A, Satayavivad J, Oltean S, Afford S, Gaston K, Jayaraman PS. A Runaway PRH/HHEX-Notch3-Positive Feedback Loop Drives Cholangiocarcinoma and Determines Response to CDK4/6 Inhibition. Cancer Res 2019; 80:757-770. [PMID: 31843982 DOI: 10.1158/0008-5472.can-19-0942] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 10/16/2019] [Accepted: 12/10/2019] [Indexed: 12/21/2022]
Abstract
Aberrant Notch and Wnt signaling are known drivers of cholangiocarcinoma (CCA), but the underlying factors that initiate and maintain these pathways are not known. Here, we show that the proline-rich homeodomain protein/hematopoietically expressed homeobox (PRH/HHEX) transcription factor forms a positive transcriptional feedback loop with Notch3 that is critical in CCA. PRH/HHEX expression is elevated in CCA, and depletion of PRH reduces CCA tumor growth in a xenograft model. Overexpression of PRH in primary human biliary epithelial cells is sufficient to increase cell proliferation and produce an invasive phenotype. Interrogation of the gene networks regulated by PRH and Notch3 reveals that unlike Notch3, PRH directly activates canonical Wnt signaling. These data indicate that hyperactivation of Notch and Wnt signaling is independent of the underlying mutational landscape and has a common origin in dysregulation of PRH. Moreover, they suggest new therapeutic options based on the dependence of specific Wnt, Notch, and CDK4/6 inhibitors on PRH activity. SIGNIFICANCE: The PRH/HHEX transcription factor is an oncogenic driver in cholangiocarcinoma that confers sensitivity to CDK4/6 inhibitors.
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Affiliation(s)
- Philip Kitchen
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Ka Ying Lee
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Danielle Clark
- Department of Biochemistry, Medical School, University of Bristol, Bristol, United Kingdom
| | - Nikki Lau
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jomnarong Lertsuwan
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, Thailand
| | - Anyaporn Sawasdichai
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, Thailand
| | | | - Sebastian Oltean
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, United Kingdom
| | - Simon Afford
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Kevin Gaston
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom.
| | - Padma-Sheela Jayaraman
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom.
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7
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Homeobox protein Hhex negatively regulates Treg cells by inhibiting Foxp3 expression and function. Proc Natl Acad Sci U S A 2019; 116:25790-25799. [PMID: 31792183 DOI: 10.1073/pnas.1907224116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Regulatory T (Treg) cells play an essential role in maintaining immune homeostasis, but the suppressive function of Treg cells can be an obstacle in the treatment of cancer and chronic infectious diseases. Here, we identified the homeobox protein Hhex as a negative regulator of Treg cells. The expression of Hhex was lower in Treg cells than in conventional T (Tconv) cells. Hhex expression was repressed in Treg cells by TGF-β/Smad3 signaling. Retroviral overexpression of Hhex inhibited the differentiation of induced Treg (iTreg) cells and the stability of thymic Treg (tTreg) cells by significantly reducing Foxp3 expression. Moreover, Hhex-overexpressing Treg cells lost their immunosuppressive activity and failed to prevent colitis in a mouse model of inflammatory bowel disease (IBD). Hhex expression was increased; however, Foxp3 expression was decreased in Treg cells in a delayed-type hypersensitivity (DTH) reaction, a type I immune reaction. Hhex directly bound to the promoters of Foxp3 and other Treg signature genes, including Il2ra and Ctla4, and repressed their transactivation. The homeodomain and N-terminal repression domain of Hhex were critical for inhibiting Foxp3 and other Treg signature genes. Thus, Hhex plays an essential role in inhibiting Treg cell differentiation and function via inhibition of Foxp3.
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8
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CK2 abrogates the inhibitory effects of PRH/HHEX on prostate cancer cell migration and invasion and acts through PRH to control cell proliferation. Oncogenesis 2017; 6:e293. [PMID: 28134934 PMCID: PMC5294245 DOI: 10.1038/oncsis.2016.82] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 12/16/2015] [Accepted: 01/26/2016] [Indexed: 01/02/2023] Open
Abstract
PRH/HHEX (proline-rich homeodomain protein/haematopoietically expressed homeobox protein) is a transcription factor that controls cell proliferation, cell differentiation and cell migration. Our previous work has shown that in haematopoietic cells, Protein Kinase CK2-dependent phosphorylation of PRH results in the inhibition of PRH DNA-binding activity, increased cleavage of PRH by the proteasome and the misregulation of PRH target genes. Here we show that PRH and hyper-phosphorylated PRH are present in normal prostate epithelial cells, and that hyper-phosphorylated PRH levels are elevated in benign prostatic hyperplasia, prostatic adenocarcinoma, and prostate cancer cell lines. A reduction in PRH protein levels increases the motility of normal prostate epithelial cells and conversely, PRH over-expression inhibits prostate cancer cell migration and blocks the ability of these cells to invade an extracellular matrix. We show that CK2 over-expression blocks the repression of prostate cancer cell migration and invasion by PRH. In addition, we show that PRH knockdown in normal immortalised prostate cells results in an increase in the population of cells capable of colony formation in Matrigel, as well as increased cell invasion and decreased E-cadherin expression. Inhibition of CK2 reduces PRH phosphorylation and reduces prostate cell proliferation but the effects of CK2 inhibition on cell proliferation are abrogated in PRH knockdown cells. These data suggest that the increased phosphorylation of PRH in prostate cancer cells increases both cell proliferation and tumour cell migration/invasion.
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Parcy F, Vernoux T, Dumas R. A Glimpse beyond Structures in Auxin-Dependent Transcription. TRENDS IN PLANT SCIENCE 2016; 21:574-583. [PMID: 26994657 DOI: 10.1016/j.tplants.2016.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/09/2016] [Accepted: 02/16/2016] [Indexed: 05/28/2023]
Abstract
Auxin response factors (ARFs), transcription factors (TFs), and their Aux/IAA (IAA) repressors are central components of the auxin signalling pathway. They interact as homo- and heteromultimers. The structure of their interacting domains revealed a PB1 fold mediating electrostatic interactions through positive and negative faces. Detailed structural analysis revealed additional hydrophobic and polar determinants and started unveiling an ARF/IAA interaction code. Structural progress also shed new light on the DNA binding mode of ARFs showing how they dimerize to bind repeated DNA elements. Here, we discuss the in vitro and in vivo significance of these structural properties for the ARF family of TFs and identify some critical missing information on how specificity might be achieved in the auxin signalling pathway.
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Affiliation(s)
- François Parcy
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS UMR5168, CEA/DRF/BIG, INRA UMR 1417, Grenoble, France.
| | - Teva Vernoux
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS de Lyon, UCBL, Université de Lyon, 46 Allée d'Italie, F-69342 Lyon, France.
| | - Renaud Dumas
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS UMR5168, CEA/DRF/BIG, INRA UMR 1417, Grenoble, France
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10
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Sayou C, Nanao MH, Jamin M, Posé D, Thévenon E, Grégoire L, Tichtinsky G, Denay G, Ott F, Peirats Llobet M, Schmid M, Dumas R, Parcy F. A SAM oligomerization domain shapes the genomic binding landscape of the LEAFY transcription factor. Nat Commun 2016; 7:11222. [PMID: 27097556 PMCID: PMC4844672 DOI: 10.1038/ncomms11222] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 03/02/2016] [Indexed: 01/10/2023] Open
Abstract
Deciphering the mechanisms directing transcription factors (TFs) to specific genome regions is essential to understand and predict transcriptional regulation. TFs recognize short DNA motifs primarily through their DNA-binding domain. Some TFs also possess an oligomerization domain suspected to potentiate DNA binding but for which the genome-wide influence remains poorly understood. Here we focus on the LEAFY transcription factor, a master regulator of flower development in angiosperms. We have determined the crystal structure of its conserved amino-terminal domain, revealing an unanticipated Sterile Alpha Motif oligomerization domain. We show that this domain is essential to LEAFY floral function. Moreover, combined biochemical and genome-wide assays suggest that oligomerization is required for LEAFY to access regions with low-affinity binding sites or closed chromatin. This finding shows that domains that do not directly contact DNA can nevertheless have a profound impact on the DNA binding landscape of a TF. The LEAFY transcription factor is a master regulator of flower development in plants. Here the authors describe the structure of a LEAFY oligomerization domain and show that mutations that disrupt oligomerization alter its capacity to bind low affinity and poorly accessible target sites.
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Affiliation(s)
- Camille Sayou
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS UMR5168, CEA/DRF/BIG, INRA UMR 1417, 17, avenue des Martyrs, 38054 Grenoble, France
| | - Max H Nanao
- European Molecular Biology Laboratory, 71, avenue des Martyrs, 38042 Grenoble, France
| | - Marc Jamin
- Institut de Biologie Structurale CEA/DRF, CNRS, Université Grenoble Alpes, 71, avenue des Martyrs, 38044 Grenoble, France
| | - David Posé
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.,Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - Emmanuel Thévenon
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS UMR5168, CEA/DRF/BIG, INRA UMR 1417, 17, avenue des Martyrs, 38054 Grenoble, France
| | - Laura Grégoire
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS UMR5168, CEA/DRF/BIG, INRA UMR 1417, 17, avenue des Martyrs, 38054 Grenoble, France
| | - Gabrielle Tichtinsky
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS UMR5168, CEA/DRF/BIG, INRA UMR 1417, 17, avenue des Martyrs, 38054 Grenoble, France
| | - Grégoire Denay
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS UMR5168, CEA/DRF/BIG, INRA UMR 1417, 17, avenue des Martyrs, 38054 Grenoble, France
| | - Felix Ott
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Marta Peirats Llobet
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS UMR5168, CEA/DRF/BIG, INRA UMR 1417, 17, avenue des Martyrs, 38054 Grenoble, France
| | - Markus Schmid
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.,Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Renaud Dumas
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS UMR5168, CEA/DRF/BIG, INRA UMR 1417, 17, avenue des Martyrs, 38054 Grenoble, France
| | - François Parcy
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS UMR5168, CEA/DRF/BIG, INRA UMR 1417, 17, avenue des Martyrs, 38054 Grenoble, France.,Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada V5Z 4H4
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11
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Gaston K, Tsitsilianos MA, Wadey K, Jayaraman PS. Misregulation of the proline rich homeodomain (PRH/HHEX) protein in cancer cells and its consequences for tumour growth and invasion. Cell Biosci 2016; 6:12. [PMID: 26877867 PMCID: PMC4752775 DOI: 10.1186/s13578-016-0077-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/01/2016] [Indexed: 02/07/2023] Open
Abstract
The proline rich homeodomain protein (PRH), also known as haematopoietically expressed homeobox (HHEX), is an essential transcription factor in embryonic development and in the adult. The PRH protein forms oligomeric complexes that bind to tandemly repeated PRH recognition sequences within or at a distance from PRH-target genes and recruit a variety of PRH-interacting proteins. PRH can also bind to other transcription factors and co-regulate specific target genes either directly through DNA binding, or indirectly through effects on the activity of its partner proteins. In addition, like some other homeodomain proteins, PRH can regulate the translation of specific mRNAs. Altered PRH expression and altered PRH intracellular localisation, are associated with breast cancer, liver cancer and thyroid cancer and some subtypes of leukaemia. This is consistent with the involvement of multiple PRH-interacting proteins, including the oncoprotein c-Myc, translation initiation factor 4E (eIF4E), and the promyelocytic leukaemia protein (PML), in the control of cell proliferation and cell survival. Similarly, multiple PRH target genes, including the genes encoding vascular endothelial growth factor (VEGF), VEGF receptors, Endoglin, and Goosecoid, are known to be important in the control of cell proliferation and cell survival and/or the regulation of cell migration and invasion. In this review, we summarise the evidence that implicates PRH in tumourigenesis and we review the data that suggests PRH levels could be useful in cancer prognosis and in the choice of treatment options.
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Affiliation(s)
- Kevin Gaston
- School of Biochemistry, University Walk, University of Bristol, Bristol, BS8 1TD UK
| | | | - Kerry Wadey
- School of Biochemistry, University Walk, University of Bristol, Bristol, BS8 1TD UK
| | - Padma-Sheela Jayaraman
- Division of Immunity and Infection, School of Medicine, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
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Hhex Is Necessary for the Hepatic Differentiation of Mouse ES Cells and Acts via Vegf Signaling. PLoS One 2016; 11:e0146806. [PMID: 26784346 PMCID: PMC4718667 DOI: 10.1371/journal.pone.0146806] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 12/22/2015] [Indexed: 01/07/2023] Open
Abstract
Elucidating the molecular mechanisms involved in the differentiation of stem cells to hepatic cells is critical for both understanding normal developmental processes as well as for optimizing the generation of functional hepatic cells for therapy. We performed in vitro differentiation of mouse embryonic stem cells (mESCs) with a null mutation in the homeobox gene Hhex and show that Hhex-/- mESCs fail to differentiate from definitive endoderm (Sox17+/Foxa2+) to hepatic endoderm (Alb+/Dlk+). In addition, hepatic culture elicited a >7-fold increase in Vegfa mRNA expression in Hhex-/- cells compared to Hhex+/+ cells. Furthermore, we identified VEGFR2+/ALB+/CD34- in early Hhex+/+ hepatic cultures. These cells were absent in Hhex-/- cultures. Finally, through manipulation of Hhex and Vegfa expression, gain and loss of expression experiments revealed that Hhex shares an inverse relationship with the activity of the Vegf signaling pathway in supporting hepatic differentiation. In summary, our results suggest that Hhex represses Vegf signaling during hepatic differentiation of mouse ESCs allowing for cell-type autonomous regulation of Vegfr2 activity independent of endothelial cells.
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Kershaw RM, Siddiqui YH, Roberts D, Jayaraman PS, Gaston K. PRH/HHex inhibits the migration of breast and prostate epithelial cells through direct transcriptional regulation of Endoglin. Oncogene 2013; 33:5592-600. [PMID: 24240683 DOI: 10.1038/onc.2013.496] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 09/19/2013] [Accepted: 10/11/2013] [Indexed: 12/16/2022]
Abstract
PRH/HHex (proline-rich homeodomain protein) is a transcription factor that controls cell proliferation and cell differentiation in a variety of tissues. Aberrant subcellular localisation of PRH is associated with breast cancer and thyroid cancer. Further, in blast crisis chronic myeloid leukaemia, and a subset of acute myeloid leukaemias, PRH is aberrantly localised and its activity is downregulated. Here we show that PRH is involved in the regulation of cell migration and cancer cell invasion. We show for the first time that PRH is expressed in prostate cells and that a decrease in PRH protein levels increases the migration of normal prostate epithelial cells. We show that a decrease in PRH protein levels also increases the migration of normal breast epithelial cells. Conversely, PRH overexpression inhibits cell migration and cell invasion by PC3 and DU145 prostate cancer cells and MDA-MB-231 breast cancer cells. Previous work has shown that the transforming growth factor-β co-receptor Endoglin inhibits the migration of prostate and breast cancer cells. Here we show that PRH can bind to the Endoglin promoter in immortalised prostate and breast cells. PRH overexpression in these cells results in increased Endoglin protein expression, whereas PRH knockdown results in decreased Endoglin protein expression. Moreover, we demonstrate that Endoglin overexpression abrogates the increased migration shown by PRH knockdown cells. Our data suggest that PRH controls the migration of multiple epithelial cell lineages in part at least through the direct transcriptional regulation of Endoglin. We discuss these results in terms of the functions of PRH in normal cells and the mislocalisation of PRH seen in multiple cancer cell types.
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Affiliation(s)
- R M Kershaw
- Division of Immunity and Infection, School of Medicine, University of Birmingham, Edgbaston, Birmingham, UK
| | - Y H Siddiqui
- School of Biochemistry, University Walk, University of Bristol, Bristol, UK
| | - D Roberts
- Division of Immunity and Infection, School of Medicine, University of Birmingham, Edgbaston, Birmingham, UK
| | - P-S Jayaraman
- Division of Immunity and Infection, School of Medicine, University of Birmingham, Edgbaston, Birmingham, UK
| | - K Gaston
- School of Biochemistry, University Walk, University of Bristol, Bristol, UK
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Noy P, Sawasdichai A, Jayaraman PS, Gaston K. Protein kinase CK2 inactivates PRH/Hhex using multiple mechanisms to de-repress VEGF-signalling genes and promote cell survival. Nucleic Acids Res 2012; 40:9008-20. [PMID: 22844093 PMCID: PMC3467080 DOI: 10.1093/nar/gks687] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein kinase CK2 promotes cell survival and the activity of this kinase is elevated in several cancers including chronic myeloid leukaemia. We have shown previously that phosphorylation of the Proline-Rich Homeodomain protein (PRH/Hhex) by CK2 inhibits the DNA-binding activity of this transcription factor. Furthermore, PRH represses the transcription of multiple genes encoding components of the VEGF-signalling pathway and thereby influences cell survival. Here we show that the inhibitory effects of PRH on cell proliferation are abrogated by CK2 and that CK2 inhibits the binding of PRH at the Vegfr-1 promoter. Phosphorylation of PRH by CK2 also decreases the nuclear association of PRH and induces its cleavage by the proteasome. Moreover, cleavage of phosphorylated PRH produces a stable truncated cleavage product which we have termed PRHΔC (HhexΔC). PRHΔC acts as a transdominant negative regulator of full-length PRH by sequestering TLE proteins that function as PRH co-repressors. We show that this novel regulatory mechanism results in the alleviation of PRH-mediated repression of Vegfr-1. We suggest that the re-establishment of PRH function through inhibition of CK2 could be of value in treatment of myeloid leukaemias, as well as other tumour types in which PRH is inactivated by phosphorylation.
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Affiliation(s)
- Peter Noy
- Division of Immunity and Infection, School of Medicine, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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The proline rich homeodomain protein PRH/Hhex forms stable oligomers that are highly resistant to denaturation. PLoS One 2012; 7:e35984. [PMID: 22540015 PMCID: PMC3335068 DOI: 10.1371/journal.pone.0035984] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 03/29/2012] [Indexed: 11/19/2022] Open
Abstract
Background Many transcription factors control gene expression by binding to specific DNA sequences at or near the genes that they regulate. However, some transcription factors play more global roles in the control of gene expression by altering the architecture of sections of chromatin or even the whole genome. The ability to form oligomeric protein assemblies allows many of these proteins to manipulate extensive segments of DNA or chromatin via the formation of structures such as DNA loops or protein-DNA fibres. Principal Findings Here we show that the proline rich homeodomain protein PRH/Hhex forms predominantly octameric and/or hexadecameric species in solution as well as larger assemblies. We show that these assemblies are highly stable resisting denaturation by temperature and chemical denaturants. Conclusion These data indicate that PRH is functionally and structurally related to the Lrp/AsnC family of proteins, a group of proteins that are known to act globally to control gene expression in bacteria and archaea.
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Soufi A, Sawasdichai A, Shukla A, Noy P, Dafforn T, Smith C, Jayaraman PS, Gaston K. DNA compaction by the higher-order assembly of PRH/Hex homeodomain protein oligomers. Nucleic Acids Res 2010; 38:7513-25. [PMID: 20675722 PMCID: PMC2995075 DOI: 10.1093/nar/gkq659] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Protein self-organization is essential for the establishment and maintenance of nuclear architecture and for the regulation of gene expression. We have shown previously that the Proline-Rich Homeodomain protein (PRH/Hex) self-assembles to form oligomeric complexes that bind to arrays of PRH binding sites with high affinity and specificity. We have also shown that many PRH target genes contain suitably spaced arrays of PRH sites that allow this protein to bind and regulate transcription. Here, we use analytical ultracentrifugation and electron microscopy to further characterize PRH oligomers. We use the same techniques to show that PRH oligomers bound to long DNA fragments self-associate to form highly ordered assemblies. Electron microscopy and linear dichroism reveal that PRH oligomers can form protein-DNA fibres and that PRH is able to compact DNA in the absence of other proteins. Finally, we show that DNA compaction is not sufficient for the repression of PRH target genes in cells. We conclude that DNA compaction is a consequence of the binding of large PRH oligomers to arrays of binding sites and that PRH is functionally and structurally related to the Lrp/AsnC family of proteins from bacteria and archaea, a group of proteins formerly thought to be without eukaryotic equivalents.
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Affiliation(s)
- Abdenour Soufi
- Institute for Biomedical Research, Birmingham University Medical School, Edgbaston, Birmingham B15 2TT, UK
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PRH/Hhex controls cell survival through coordinate transcriptional regulation of vascular endothelial growth factor signaling. Mol Cell Biol 2010; 30:2120-34. [PMID: 20176809 DOI: 10.1128/mcb.01511-09] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The proline-rich homeodomain protein (PRH) plays multiple roles in the control of gene expression during embryonic development and in the adult. Vascular endothelial growth factor (VEGF) is a mitogen that stimulates cell proliferation and survival via cell surface receptors including VEGFR-1 and VEGFR-2. VEGF signaling is of critical importance in angiogenesis and hematopoiesis and is elevated in many tumors. Here we show that PRH binds directly to the promoter regions of the Vegf, Vegfr-1, and Vegfr-2 genes and that in each case PRH represses transcription. We demonstrate that overexpression or knockdown of PRH directly impinges on the survival of both leukemic and tumor cells and that the modulation of VEGF and VEGF receptor signaling by PRH mediates these effects. Our findings demonstrate that PRH is a key regulator of the VEGF signaling pathway and describe a mechanism whereby PRH plays an important role in tumorigenesis and leukemogenesis.
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