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Jin J, Wang K, Lu C, Yao C, Xie F. NEDD4L Inhibits the Proliferation and Migration of Keloid Fibroblasts by Regulating YY1 Ubiquitination-Mediated Glycolytic Metabolic Reprogramming. Exp Dermatol 2024; 33:e70008. [PMID: 39494931 DOI: 10.1111/exd.70008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 08/19/2024] [Accepted: 10/13/2024] [Indexed: 11/05/2024]
Abstract
Keloid scarring is a complex fibroproliferative disorder characterised by excessive fibroblast proliferation. Inhibition of cellular glycolysis effectively suppresses the proliferation of keloid fibroblasts (KFs). Neural precursor cell-expressed developmentally downregulated gene 4-like (NEDD4L), a ubiquitin ligase, regulates cell proliferation in different diseases. This study investigated the effects of NEDD4L on glucose metabolism, proliferation and migration in KFs. Primary KFs were isolated from keloid skin tissues obtained from patients with active-stage keloids. Cell transfection was used to upregulate or downregulate NEDD4L and Yin Yang 1 (YY1) in KFs. Protein expression was assessed by immunohistochemistry and western blotting. The viability, proliferative capacity and migration ability of KFs were evaluated using the MTT method and the EdU and wound healing assays, respectively. The regulatory effect of NEDD4L on YY1 ubiquitination was examined by coimmunoprecipitation. The interaction between YY1 and hexokinase 2 (HK2) was confirmed by a dual-luciferase reporter assay. NEDD4L was downregulated, whereas YY1 and HK2 were highly expressed in keloid tissues compared with normal skin. Overexpression of NEDD4L inhibited the proliferation and migration of KFs. NEDD4L promoted YY1 degradation in KFs by inducing its ubiquitination. Upregulation of YY1 induced glucose consumption and lactate production in KFs via the transcriptional regulation of HK2. Increased expression of YY1 reversed the reduced viability, proliferation, and migration of KFs overexpressing NEDD4L. YY1 also reversed the NEDD4L-induced inhibition of glucose consumption and lactate production in KFs. Additionally, an in vivo study confirmed the inhibitory roles of NEDD4L overexpression and YY1 knockdown in keloid formation. NEDD4L suppressed the viability, proliferation and migration of KFs by regulating YY1 ubiquitination-mediated glycolysis through HK2. These findings suggest a novel regulatory axis, NEDD4L/YY1/HK2, that mediates glucose metabolism in keloid formation.
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Affiliation(s)
- Jun Jin
- Department of Plastic Surgery, Henan Provincial People's Hospital (Zhengzhou University People's Hospital), Zhengzhou, China
| | - Kai Wang
- Department of Plastic Surgery, Henan Provincial People's Hospital (Zhengzhou University People's Hospital), Zhengzhou, China
| | - Chenxi Lu
- Department of Plastic Surgery, Henan Provincial People's Hospital (Zhengzhou University People's Hospital), Zhengzhou, China
| | - Chenghao Yao
- Department of Plastic Surgery, Henan Provincial People's Hospital (Zhengzhou University People's Hospital), Zhengzhou, China
| | - Feng Xie
- Department of Plastic Surgery, Henan Provincial People's Hospital (Zhengzhou University People's Hospital), Zhengzhou, China
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2
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Roider E, Lakatos AIT, McConnell AM, Wang P, Mueller A, Kawakami A, Tsoi J, Szabolcs BL, Ascsillán AA, Suita Y, Igras V, Lo JA, Hsiao JJ, Lapides R, Pál DMP, Lengyel AS, Navarini A, Okazaki A, Iliopoulos O, Németh I, Graeber TG, Zon L, Giese RW, Kemeny LV, Fisher DE. MITF regulates IDH1, NNT, and a transcriptional program protecting melanoma from reactive oxygen species. Sci Rep 2024; 14:21527. [PMID: 39277608 PMCID: PMC11401838 DOI: 10.1038/s41598-024-72031-9] [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: 03/26/2024] [Accepted: 09/03/2024] [Indexed: 09/17/2024] Open
Abstract
Microphthalmia-associated transcription factor (MITF) is a master regulator of melanocyte function, development and plays a significant role in melanoma pathogenesis. MITF genomic amplification promotes melanoma development, and it can facilitate resistance to multiple therapies. Here, we show that MITF regulates a global antioxidant program that increases survival of melanoma cell lines by protecting the cells from reactive oxygen species (ROS)-induced damage. In addition, this redox program is correlated with MITF expression in human melanoma cell lines and patient-derived melanoma samples. Using a zebrafish melanoma model, we show that MITF decreases ROS-mediated DNA damage in vivo. Some of the MITF target genes involved, such as IDH1 and NNT, are regulated through direct MITF binding to canonical enhancer box (E-BOX) sequences proximal to their promoters. Utilizing functional experiments, we demonstrate the role of MITF and its target genes in reducing cytosolic and mitochondrial ROS. Collectively, our data identify MITF as a significant driver of the cellular antioxidant state.
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Affiliation(s)
- Elisabeth Roider
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA.
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA.
- Department of Dermatology, University Hospital of Basel, Basel, Switzerland.
| | - Alexandra I T Lakatos
- HCEMM-SU Translational Dermatology Research Group, Semmelweis University, Budapest, Hungary
- Department of Physiology, Semmelweis University, Budapest, Hungary
- Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Alicia M McConnell
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Massachusetts and the Howard Hughes Medical Institute, Boston, USA
| | - Poguang Wang
- Department of Pharmaceutical Sciences, Department of Chemistry and Chemical Biology, and Barnett Institute, Bouve College, Northeastern University, Boston, MA, 02115, USA
| | - Alina Mueller
- Department of Dermatology, University Hospital of Basel, Basel, Switzerland
| | - Akinori Kawakami
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Jennifer Tsoi
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- UCLA Metabolomics Center, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Botond L Szabolcs
- HCEMM-SU Translational Dermatology Research Group, Semmelweis University, Budapest, Hungary
- Department of Physiology, Semmelweis University, Budapest, Hungary
- Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Anna A Ascsillán
- HCEMM-SU Translational Dermatology Research Group, Semmelweis University, Budapest, Hungary
- Department of Physiology, Semmelweis University, Budapest, Hungary
- Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Yusuke Suita
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Vivien Igras
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Jennifer A Lo
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Jennifer J Hsiao
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Rebecca Lapides
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Robert Larner, College of Medicine at the University of Vermont, Burlington, USA
| | - Dorottya M P Pál
- HCEMM-SU Translational Dermatology Research Group, Semmelweis University, Budapest, Hungary
- Department of Physiology, Semmelweis University, Budapest, Hungary
- Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Anna S Lengyel
- HCEMM-SU Translational Dermatology Research Group, Semmelweis University, Budapest, Hungary
- Department of Physiology, Semmelweis University, Budapest, Hungary
- Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Alexander Navarini
- Department of Dermatology, University Hospital of Basel, Basel, Switzerland
| | - Arimichi Okazaki
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA
| | - Othon Iliopoulos
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA
| | - István Németh
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- UCLA Metabolomics Center, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA, USA
| | - Leonard Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Massachusetts and the Howard Hughes Medical Institute, Boston, USA
| | - Roger W Giese
- Department of Pharmaceutical Sciences, Department of Chemistry and Chemical Biology, and Barnett Institute, Bouve College, Northeastern University, Boston, MA, 02115, USA
| | - Lajos V Kemeny
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA.
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA.
- HCEMM-SU Translational Dermatology Research Group, Semmelweis University, Budapest, Hungary.
- Department of Physiology, Semmelweis University, Budapest, Hungary.
- Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, Budapest, Hungary.
| | - David E Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, USA.
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA.
- Lancer Professorship of Dermatology, Harvard Medical School, Boston, USA.
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3
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Khan DA, Adhikary T, Sultana MT, Toukir IA. A comprehensive identification of potential molecular targets and small drugs candidate for melanoma cancer using bioinformatics and network-based screening approach. J Biomol Struct Dyn 2024; 42:7349-7369. [PMID: 37534476 DOI: 10.1080/07391102.2023.2240409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023]
Abstract
Melanoma is the third most common malignant skin tumor and has increased in morbidity and mortality over the previous decade due to its rapid spread into the bloodstream or lymphatic system. This study used integrated bioinformatics and network-based methodologies to reliably identify molecular targets and small molecular medicines that may be more successful for Melanoma diagnosis, prognosis and treatment. The statistical LIMMA approach utilized for bioinformatics analysis in this study found 246 common differentially expressed genes (cDEGs) between case and control samples from two microarray gene-expression datasets (GSE130244 and GSE15605). Protein-protein interaction network study revealed 15 cDEGs (PTK2, STAT1, PNO1, CXCR4, WASL, FN1, RUNX2, SOCS3, ITGA4, GNG2, CDK6, BRAF, AGO2, GTF2H1 and AR) to be critical in the development of melanoma (KGs). According to regulatory network analysis, the most important transcriptional and post-transcriptional regulators of DEGs and hub-DEGs are ten transcription factors and three miRNAs. We discovered the pathogenetic mechanisms of MC by studying DEGs' biological processes, molecular function, cellular components and KEGG pathways. We used molecular docking and dynamics modeling to select the four most expressed genes responsible for melanoma malignancy to identify therapeutic candidates. Then, utilizing the Connectivity Map (CMap) database, we analyzed the top 4-hub-DEGs-guided repurposable drugs. We validated four melanoma cancer drugs (Fisetin, Epicatechin Gallate, 1237586-97-8 and PF 431396) using molecular dynamics simulation with their target proteins. As a result, the results of this study may provide resources to researchers and medical professionals for the wet-lab validation of MC diagnosis, prognosis and treatments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dhrubo Ahmed Khan
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Tonmoy Adhikary
- Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Mst Tania Sultana
- Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Imran Ahamed Toukir
- Department of Chemical Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
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4
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Lu Y, Travnickova J, Badonyi M, Rambow F, Coates A, Khan Z, Marques J, Murphy LC, Garcia-Martinez P, Marais R, Louphrasitthiphol P, Chan AHY, Schofield CJ, von Kriegsheim A, Marsh JA, Pavet V, Sansom OJ, Illingworth RS, Patton EE. ALDH1A3-acetaldehyde metabolism potentiates transcriptional heterogeneity in melanoma. Cell Rep 2024; 43:114406. [PMID: 38963759 PMCID: PMC11290356 DOI: 10.1016/j.celrep.2024.114406] [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: 09/26/2023] [Revised: 05/08/2024] [Accepted: 06/11/2024] [Indexed: 07/06/2024] Open
Abstract
Cancer cellular heterogeneity and therapy resistance arise substantially from metabolic and transcriptional adaptations, but how these are interconnected is poorly understood. Here, we show that, in melanoma, the cancer stem cell marker aldehyde dehydrogenase 1A3 (ALDH1A3) forms an enzymatic partnership with acetyl-coenzyme A (CoA) synthetase 2 (ACSS2) in the nucleus to couple high glucose metabolic flux with acetyl-histone H3 modification of neural crest (NC) lineage and glucose metabolism genes. Importantly, we show that acetaldehyde is a metabolite source for acetyl-histone H3 modification in an ALDH1A3-dependent manner, providing a physiologic function for this highly volatile and toxic metabolite. In a zebrafish melanoma residual disease model, an ALDH1-high subpopulation emerges following BRAF inhibitor treatment, and targeting these with an ALDH1 suicide inhibitor, nifuroxazide, delays or prevents BRAF inhibitor drug-resistant relapse. Our work reveals that the ALDH1A3-ACSS2 couple directly coordinates nuclear acetaldehyde-acetyl-CoA metabolism with specific chromatin-based gene regulation and represents a potential therapeutic vulnerability in melanoma.
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Affiliation(s)
- Yuting Lu
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XU, UK; Edinburgh Cancer Research, CRUK Scotland Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Jana Travnickova
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XU, UK; Edinburgh Cancer Research, CRUK Scotland Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Mihaly Badonyi
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Florian Rambow
- Department of Applied Computational Cancer Research, Institute for AI in Medicine (IKIM), University Hospital Essen, 45131 Essen, Germany; University of Duisburg-Essen, 45141 Essen, Germany
| | - Andrea Coates
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XU, UK; Edinburgh Cancer Research, CRUK Scotland Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Zaid Khan
- Edinburgh Cancer Research, CRUK Scotland Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Jair Marques
- Edinburgh Cancer Research, CRUK Scotland Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Laura C Murphy
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Pablo Garcia-Martinez
- Insitute of Genetics and Cancer, The Univeristy of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Richard Marais
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park SK10 4TG, UK; Oncodrug Ltd, Alderley Park, Macclesfield SK10 4TG, UK
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Alex H Y Chan
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 5JJ, UK
| | - Christopher J Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 5JJ, UK
| | - Alex von Kriegsheim
- Edinburgh Cancer Research, CRUK Scotland Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Valeria Pavet
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park SK10 4TG, UK; Cancer Research UK Beatson Institute, CRUK Scotland Centre, Garscube Estate, Switchback Road, Bearsden Glasgow G61 1BD, UK
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, CRUK Scotland Centre, Garscube Estate, Switchback Road, Bearsden Glasgow G61 1BD, UK; School of Cancer Sciences, University of Glasgow, Glasgow G12 0ZD, UK
| | - Robert S Illingworth
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
| | - E Elizabeth Patton
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XU, UK; Edinburgh Cancer Research, CRUK Scotland Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XR, UK.
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5
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Roider E, Lakatos AIT, McConnell AM, Wang P, Mueller A, Kawakami A, Tsoi J, Szabolcs BL, Ascsillán AA, Suita Y, Igras V, Lo JA, Hsiao JJ, Lapides R, Pál DMP, Lengyel AS, Navarini A, Okazaki A, Iliopoulos O, Németh I, Graeber TG, Zon L, Giese RW, Kemeny LV, Fisher DE. MITF regulates IDH1 and NNT and drives a transcriptional program protecting cutaneous melanoma from reactive oxygen species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.564582. [PMID: 38014031 PMCID: PMC10680652 DOI: 10.1101/2023.11.10.564582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Microphthalmia-associated transcription factor (MITF) plays pivotal roles in melanocyte development, function, and melanoma pathogenesis. MITF amplification occurs in melanoma and has been associated with resistance to targeted therapies. Here, we show that MITF regulates a global antioxidant program that increases survival of melanoma cell lines by protecting the cells from reactive oxygen species (ROS)-induced damage. In addition, this redox program is correlated with MITF expression in human melanoma cell lines and patient-derived melanoma samples. Using a zebrafish melanoma model, we show that MITF decreases ROS-mediated DNA damage in vivo . Some of the MITF target genes involved, such as IDH1 and NNT , are regulated through direct MITF binding to canonical enhancer box (E-BOX) sequences proximal to their promoters. Utilizing functional experiments, we demonstrate the role of MITF and its target genes in reducing cytosolic and mitochondrial ROS. Collectively, our data identify MITF as a significant driver of the cellular antioxidant state. One Sentence Summary MITF promote melanoma survival via increasing ROS tolerance.
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Nasrin M, Ahmed O, Han X, Nojebuzzaman M, Abo-Ahmed AI, Yazawa S, Osawa M. Generation of Pmel-dependent conditional and inducible Cre-driver mouse line for melanocytic-targeted gene manipulation. Pigment Cell Melanoma Res 2023; 36:53-70. [PMID: 36318272 DOI: 10.1111/pcmr.13074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/07/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Conditional and inducible gene targeting using Cre/loxP-mediated recombination is a powerful reverse genetics approach used to study spatiotemporal gene functions in specified cell types. To enable temporal gene manipulation in the melanocyte lineage, we established a novel inducible Cre-driver mouse line by targeting an all-in-one tetracycline/doxycycline (Dox)-inducible Cre expression cassette into the Pmel locus (PmelP2A-TetON3G-TRE3G-iCre ), a gene locus preferentially expressed in pigment cells. By crossing these Cre-driver mice with a strong Cre-reporter mouse line, Gt(ROSA)26Sortm9(CAG-tdTomato)Hze , we show the effectiveness of the PmelP2A-TetON3G-TRE3G-iCre mouse line in facilitating Dox-inducible Cre/loxP recombination in a wide variety of pigment cell lineages including hair follicle melanocytes and their stem cells. Furthermore, to demonstrate proof of concept, we ablated Notch signaling postnatally in the PmelP2A-TetON3G-TRE3G-iCre mice. In agreement with the previously reported phenotype, induced ablation of Notch signaling in the melanocyte lineage resulted in premature hair graying, demonstrating the utility of the PmelP2A-TetON3G-TRE3G-iCre allele. Therefore, the PmelP2A-TetON3G-TRE3G-iCre mouse line is suitable for assessing gene functions in melanocytes using an in vivo inducible reverse genetics approach. Furthermore, we unexpectedly identified previously unrecognized PMEL-expressing cells in non-pigmentary organs in the mice, suggesting unanticipated functions of PMEL other than melanosome formation.
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Affiliation(s)
- Morsheda Nasrin
- Department of Regeneration and Applied Biomedical Sciences, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Osama Ahmed
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Benha University, Toukh, Egypt
| | - Xujun Han
- Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Md Nojebuzzaman
- Department of Regeneration and Applied Biomedical Sciences, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Ahmed I Abo-Ahmed
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Benha University, Toukh, Egypt
| | - Shigenobu Yazawa
- Department of Regeneration and Applied Biomedical Sciences, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Masatake Osawa
- Department of Regeneration and Applied Biomedical Sciences, Graduate School of Medicine, Gifu University, Gifu, Japan
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7
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Dreier MR, de la Serna IL. SWI/SNF Chromatin Remodeling Enzymes in Melanoma. EPIGENOMES 2022; 6:epigenomes6010010. [PMID: 35323214 PMCID: PMC8947417 DOI: 10.3390/epigenomes6010010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Melanoma is an aggressive malignancy that arises from the transformation of melanocytes on the skin, mucosal membranes, and uvea of the eye. SWI/SNF chromatin remodeling enzymes are multi-subunit complexes that play important roles in the development of the melanocyte lineage and in the response to ultraviolet radiation, a key environmental risk factor for developing cutaneous melanoma. Exome sequencing has revealed frequent loss of function mutations in genes encoding SWI/SNF subunits in melanoma. However, some SWI/SNF subunits have also been demonstrated to have pro-tumorigenic roles in melanoma and to affect sensitivity to therapeutics. This review summarizes studies that have implicated SWI/SNF components in melanomagenesis and have evaluated how SWI/SNF subunits modulate the response to current therapeutics.
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8
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Chen L, Qiao L, Guo Y, Huang Y, Luo W, Feng Y. Localization and regulatory function of Yin Yang 1 (YY1) in chicken testis. Mol Genet Genomics 2021; 297:113-123. [PMID: 34854981 DOI: 10.1007/s00438-021-01840-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 11/17/2021] [Indexed: 11/25/2022]
Abstract
In mammals, Yin Yang 1 (YY1), a pervasively expressed transcription factor related to many biological processes as an activator or inhibitor of the transcription of various genes, plays a critical role in the development of male gonads and spermatogenesis. Although the role of YY1 on the development of male gonads and spermatogenesis in mammals has been reported, its function on chicken testis are yet to be clarified. In this study, we used immunofluorescence analysis to investigate the location of YY1 in chicken testis. In embryo testis, YY1 was detected in spermatogonia and Sertoli cells, while in adult testis, YY1 was shown to be expressed in spermatogenic cells and Sertoli cells, but not in spermatozoa. Furthermore, we investigated the regulatory functions of YY1 in chicken testicular Sertoli cells by combining overexpression with RNA-sequencing. Overexpression of YY1 in Sertoli cells revealed a total of 2955 differentially expressed genes involved in various biological processes, such as male gonad development and seminiferous tubule development. Overexpression of YY1 also caused significant differences in the expression of the androgen receptor gene and the inhibin βA gene, two major genes involved in the regulation of spermatogonia in Sertoli cells. These observations indicate that YY1 may regulate the development and function of the gonads by affecting the secretion of cytokines and hormones in Sertoli cells to mediate the production and differentiation of spermatogonia.
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Affiliation(s)
- Ligen Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Lingyun Qiao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yan Guo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Ying Huang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Wei Luo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yanping Feng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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9
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Pan G, Diamanti K, Cavalli M, Lara Gutiérrez A, Komorowski J, Wadelius C. Multifaceted regulation of hepatic lipid metabolism by YY1. Life Sci Alliance 2021; 4:4/7/e202000928. [PMID: 34099540 PMCID: PMC8200296 DOI: 10.26508/lsa.202000928] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 12/20/2022] Open
Abstract
This study shows that YY1 regulates hepatic lipid metabolism by directly or indirectly regulating the expression of several key upstream transcription factors and their coactivators. Recent studies suggested that dysregulated YY1 plays a pivotal role in many liver diseases. To obtain a detailed view of genes and pathways regulated by YY1 in the liver, we carried out RNA sequencing in HepG2 cells after YY1 knockdown. A rigid set of 2,081 differentially expressed genes was identified by comparing the YY1-knockdown samples (n = 8) with the control samples (n = 14). YY1 knockdown significantly decreased the expression of several key transcription factors and their coactivators in lipid metabolism. This is illustrated by YY1 regulating PPARA expression through binding to its promoter and enhancer regions. Our study further suggest that down-regulation of the key transcription factors together with YY1 knockdown significantly decreased the cooperation between YY1 and these transcription factors at various regulatory regions, which are important in regulating the expression of genes in hepatic lipid metabolism. This was supported by the finding that the expression of SCD and ELOVL6, encoding key enzymes in lipogenesis, were regulated by the cooperation between YY1 and PPARA/RXRA complex over their promoters.
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Affiliation(s)
- Gang Pan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Klev Diamanti
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Marco Cavalli
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ariadna Lara Gutiérrez
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jan Komorowski
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,Swedish Collegium for Advanced Study, Uppsala, Sweden.,Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.,Washington National Primate Research Center, Seattle, WA, USA
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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10
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Abstract
Accumulating evidence strongly indicates that the presence of cancer stem cells (CSCs) leads to the emergence of worse clinical scenarios, such as chemo- and radiotherapy resistance, metastasis, and cancer recurrence. CSCs are a highly tumorigenic population characterized by self-renewal capacity and differentiation potential. Thus, CSCs establish a hierarchical intratumor organization that enables tumor adaptation to evade the immune response and resist anticancer therapy. YY1 functions as a transcription factor, RNA-binding protein, and 3D chromatin regulator. Thus, YY1 has multiple effects and regulates several molecular processes. Emerging evidence indicates that the development of lethal YY1-mediated cancer phenotypes is associated with the presence of or enrichment in cancer stem-like cells. Therefore, it is necessary to investigate whether and to what extent YY1 regulates the CSC phenotype. Since CSCs mirror the phenotypic behavior of stem cells, we initially describe the roles played by YY1 in embryonic and adult stem cells. Next, we scrutinize evidence supporting the contributions of YY1 in CSCs from a number of various cancer types. Finally, we identify new areas for further investigation into the YY1-CSCs axis, including the participation of YY1 in the CSC niche.
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11
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Association between brown eye colour in rs12913832:GG individuals and SNPs in TYR, TYRP1, and SLC24A4. PLoS One 2020; 15:e0239131. [PMID: 32915910 PMCID: PMC7485777 DOI: 10.1371/journal.pone.0239131] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/31/2020] [Indexed: 01/04/2023] Open
Abstract
The genotype of a single SNP, rs12913832, is the primary predictor of blue and brown eye colours. The genotypes rs12913832:AA and rs12913832:GA are most often observed in individuals with brown eye colours, whereas rs12913832:GG is most often observed in individuals with blue eye colours. However, approximately 3% of Europeans with the rs12913832:GG genotype have brown eye colours. The purpose of the study presented here was to identify variants that explain brown eye colour formation in individuals with the rs12913832:GG genotype. Genes and regulatory regions surrounding SLC24A4, TYRP1, SLC24A5, IRF4, TYR, and SLC45A2, as well as the upstream region of OCA2 within the HERC2 gene were sequenced in a study comprising 40 individuals with the rs12913832:GG genotype. Of these, 24 individuals were considered to have blue eye colours and 16 individuals were considered to have brown eye colours. We identified 211 variants within the SLC24A4, TYRP1, IRF4, and TYR target regions associated with eye colour. Based on in silico analyses of predicted variant effects we recognized four variants, TYRP1 rs35866166:C, TYRP1 rs62538956:C, SLC24A4 rs1289469:C, and TYR rs1126809:G, to be the most promising candidates for explanation of brown eye colour in individuals with the rs12913832:GG genotype. Of the 16 individuals with brown eye colours, 14 individuals had four alleles, whereas the alleles were rare in the blue eyed individuals. rs35866166, rs62538956, and rs1289469 were for the first time found to be associated with pigmentary traits, whilst rs1126809 was previously found to be associated with pigmentary variation. To improve prediction of eye colours we suggest that future eye colour prediction models should include rs35866166, rs62538956, rs1289469, and rs1126809.
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12
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Kato S, Weng QY, Insco ML, Chen KY, Muralidhar S, Pozniak J, Diaz JMS, Drier Y, Nguyen N, Lo JA, van Rooijen E, Kemeny LV, Zhan Y, Feng Y, Silkworth W, Powell CT, Liau BB, Xiong Y, Jin J, Newton-Bishop J, Zon LI, Bernstein BE, Fisher DE. Gain-of-Function Genetic Alterations of G9a Drive Oncogenesis. Cancer Discov 2020; 10:980-997. [PMID: 32269030 PMCID: PMC7334057 DOI: 10.1158/2159-8290.cd-19-0532] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 02/05/2020] [Accepted: 04/03/2020] [Indexed: 11/16/2022]
Abstract
Epigenetic regulators, when genomically altered, may become driver oncogenes that mediate otherwise unexplained pro-oncogenic changes lacking a clear genetic stimulus, such as activation of the WNT/β-catenin pathway in melanoma. This study identifies previously unrecognized recurrent activating mutations in the G9a histone methyltransferase gene, as well as G9a genomic copy gains in approximately 26% of human melanomas, which collectively drive tumor growth and an immunologically sterile microenvironment beyond melanoma. Furthermore, the WNT pathway is identified as a key tumorigenic target of G9a gain-of-function, via suppression of the WNT antagonist DKK1. Importantly, genetic or pharmacologic suppression of mutated or amplified G9a using multiple in vitro and in vivo models demonstrates that G9a is a druggable target for therapeutic intervention in melanoma and other cancers harboring G9a genomic aberrations. SIGNIFICANCE: Oncogenic G9a abnormalities drive tumorigenesis and the "cold" immune microenvironment by activating WNT signaling through DKK1 repression. These results reveal a key druggable mechanism for tumor development and identify strategies to restore "hot" tumor immune microenvironments.This article is highlighted in the In This Issue feature, p. 890.
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Affiliation(s)
- Shinichiro Kato
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Qing Yu Weng
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Megan L Insco
- Howard Hughes Medical Institute, Chevy Chase, Maryland
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Kevin Y Chen
- Howard Hughes Medical Institute, Chevy Chase, Maryland
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, Massachusetts
| | - Sathya Muralidhar
- Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Joanna Pozniak
- Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Joey Mark S Diaz
- Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Yotam Drier
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nhu Nguyen
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Jennifer A Lo
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Ellen van Rooijen
- Howard Hughes Medical Institute, Chevy Chase, Maryland
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Lajos V Kemeny
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Yao Zhan
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Yang Feng
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Whitney Silkworth
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - C Thomas Powell
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmaceutical Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmaceutical Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Julia Newton-Bishop
- Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Leonard I Zon
- Howard Hughes Medical Institute, Chevy Chase, Maryland
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Bradley E Bernstein
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - David E Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts.
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13
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Choi J, Zhang T, Vu A, Ablain J, Makowski MM, Colli LM, Xu M, Hennessey RC, Yin J, Rothschild H, Gräwe C, Kovacs MA, Funderburk KM, Brossard M, Taylor J, Pasaniuc B, Chari R, Chanock SJ, Hoggart CJ, Demenais F, Barrett JH, Law MH, Iles MM, Yu K, Vermeulen M, Zon LI, Brown KM. Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma. Nat Commun 2020; 11:2718. [PMID: 32483191 PMCID: PMC7264232 DOI: 10.1038/s41467-020-16590-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 05/12/2020] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified ~20 melanoma susceptibility loci, most of which are not functionally characterized. Here we report an approach integrating massively-parallel reporter assays (MPRA) with cell-type-specific epigenome and expression quantitative trait loci (eQTL) to identify susceptibility genes/variants from multiple GWAS loci. From 832 high-LD variants, we identify 39 candidate functional variants from 14 loci displaying allelic transcriptional activity, a subset of which corroborates four colocalizing melanocyte cis-eQTL genes. Among these, we further characterize the locus encompassing the HIV-1 restriction gene, MX2 (Chr21q22.3), and validate a functional intronic variant, rs398206. rs398206 mediates the binding of the transcription factor, YY1, to increase MX2 levels, consistent with the cis-eQTL of MX2 in primary human melanocytes. Melanocyte-specific expression of human MX2 in a zebrafish model demonstrates accelerated melanoma formation in a BRAFV600E background. Our integrative approach streamlines GWAS follow-up studies and highlights a pleiotropic function of MX2 in melanoma susceptibility. There are more than 20 known melanoma susceptibility genes. Here, using a massively parallel reporter assay, the authors identify risk-associated variants that alter gene transcription, and demonstrate that expression of one such gene, MX2, leads to the promotion of melanoma in a zebrafish model.
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Affiliation(s)
- Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Andrew Vu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Julien Ablain
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Matthew M Makowski
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 XZ, Nijmegen, The Netherlands
| | - Leandro M Colli
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Mai Xu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Rebecca C Hennessey
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Jinhu Yin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Harriet Rothschild
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 XZ, Nijmegen, The Netherlands
| | - Michael A Kovacs
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Karen M Funderburk
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Myriam Brossard
- Université de Paris, UMRS-1124, Institut National de la Santé et de la Recherche Médicale (INSERM), F-75006, Paris, France
| | - John Taylor
- Leeds Institute for Data Analytics, School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90024, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Lab for Cancer Research, National Cancer Institute, Frederick, MD, 21701, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Clive J Hoggart
- Department of Medicine, Imperial College London, London, SW7 2BU, UK
| | - Florence Demenais
- Université de Paris, UMRS-1124, Institut National de la Santé et de la Recherche Médicale (INSERM), F-75006, Paris, France
| | - Jennifer H Barrett
- Leeds Institute for Data Analytics, School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Mark M Iles
- Leeds Institute for Data Analytics, School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 XZ, Nijmegen, The Netherlands
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA.
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14
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Varum S, Baggiolini A, Zurkirchen L, Atak ZK, Cantù C, Marzorati E, Bossart R, Wouters J, Häusel J, Tuncer E, Zingg D, Veen D, John N, Balz M, Levesque MP, Basler K, Aerts S, Zamboni N, Dummer R, Sommer L. Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation. Cell Stem Cell 2020; 24:637-653.e9. [PMID: 30951662 DOI: 10.1016/j.stem.2019.03.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/29/2019] [Accepted: 03/11/2019] [Indexed: 01/07/2023]
Abstract
Increasing evidence suggests that cancer cells highjack developmental programs for disease initiation and progression. Melanoma arises from melanocytes that originate during development from neural crest stem cells (NCSCs). Here, we identified the transcription factor Yin Yang 1 (Yy1) as an NCSCs regulator. Conditional deletion of Yy1 in NCSCs resulted in stage-dependent hypoplasia of all major neural crest derivatives due to decreased proliferation and increased cell death. Moreover, conditional ablation of one Yy1 allele in a melanoma mouse model prevented tumorigenesis, indicating a particular susceptibility of melanoma cells to reduced Yy1 levels. Combined RNA sequencing (RNA-seq), chromatin immunoprecipitation (ChIP)-seq, and untargeted metabolomics demonstrated that YY1 governs multiple metabolic pathways and protein synthesis in both NCSCs and melanoma. In addition to directly regulating a metabolic gene set, YY1 can act upstream of MITF/c-MYC as part of a gene regulatory network controlling metabolism. Thus, both NCSC development and melanoma formation depend on an intricate YY1-controlled metabolic program.
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Affiliation(s)
- Sandra Varum
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | | | - Luis Zurkirchen
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Zeynep Kalender Atak
- VIB Center for Brain & Disease Research, Laboratory of Computational Biology, 3000 Leuven, Belgium; Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Claudio Cantù
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Elisa Marzorati
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Raphaël Bossart
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Jasper Wouters
- VIB Center for Brain & Disease Research, Laboratory of Computational Biology, 3000 Leuven, Belgium; Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Jessica Häusel
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Eylül Tuncer
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Daniel Zingg
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Dominiek Veen
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Nessy John
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Marcel Balz
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University of Zurich Hospital, 8091 Zurich, Switzerland
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Laboratory of Computational Biology, 3000 Leuven, Belgium; Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University of Zurich Hospital, 8091 Zurich, Switzerland
| | - Lukas Sommer
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland.
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15
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Raja DA, Gotherwal V, Burse SA, Subramaniam YJ, Sultan F, Vats A, Gautam H, Sharma B, Sharma S, Singh A, Sivasubbu S, Gokhale RS, Natarajan VT. pH-controlled histone acetylation amplifies melanocyte differentiation downstream of MITF. EMBO Rep 2020; 21:e48333. [PMID: 31709752 PMCID: PMC6945066 DOI: 10.15252/embr.201948333] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 10/04/2019] [Accepted: 10/15/2019] [Indexed: 12/20/2022] Open
Abstract
Tanning response and melanocyte differentiation are mediated by the central transcription factor MITF. This involves the rapid and selective induction of melanocyte maturation genes, while concomitantly the expression of other effector genes is maintained. In this study, using cell-based and zebrafish model systems, we report on a pH-mediated feed-forward mechanism of epigenetic regulation that enables selective amplification of the melanocyte maturation program. We demonstrate that MITF activation directly elevates the expression of the enzyme carbonic anhydrase 14 (CA14). Nuclear localization of CA14 leads to an increase of the intracellular pH, resulting in the activation of the histone acetyl transferase p300/CBP. In turn, enhanced H3K27 histone acetylation at selected differentiation genes facilitates their amplified expression via MITF. CRISPR-mediated targeted missense mutation of CA14 in zebrafish results in the formation of immature acidic melanocytes with decreased pigmentation, establishing a central role for this mechanism during melanocyte differentiation in vivo. Thus, we describe an epigenetic control system via pH modulation that reinforces cell fate determination by altering chromatin dynamics.
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Affiliation(s)
- Desingu Ayyappa Raja
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
| | - Vishvabandhu Gotherwal
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
| | - Shaunak A Burse
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
| | - Yogaspoorthi J Subramaniam
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
| | - Farina Sultan
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
| | - Archana Vats
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
| | - Hemlata Gautam
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
| | - Babita Sharma
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
| | - Sachin Sharma
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
- Present address:
National Institute of ImmunologyNew DelhiIndia
| | - Archana Singh
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
| | | | - Rajesh S Gokhale
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Present address:
National Institute of ImmunologyNew DelhiIndia
| | - Vivek T Natarajan
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative ResearchTaramani, Chennai
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16
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Liu EM, Martinez-Fundichely A, Diaz BJ, Aronson B, Cuykendall T, MacKay M, Dhingra P, Wong EWP, Chi P, Apostolou E, Sanjana NE, Khurana E. Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes. Cell Syst 2019; 8:446-455.e8. [PMID: 31078526 PMCID: PMC6917527 DOI: 10.1016/j.cels.2019.04.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 11/20/2018] [Accepted: 04/02/2019] [Indexed: 12/15/2022]
Abstract
Recent studies have shown that mutations at non-coding elements, such as promoters and enhancers, can act as cancer drivers. However, an important class of non-coding elements, namely CTCF insulators, has been overlooked in the previous driver analyses. We used insulator annotations from CTCF and cohesin ChIA-PET and analyzed somatic mutations in 1,962 whole genomes from 21 cancer types. Using the heterogeneous patterns of transcription-factor-motif disruption, functional impact, and recurrence of mutations, we developed a computational method that revealed 21 insulators showing signals of positive selection. In particular, mutations in an insulator in multiple cancer types, including 16% of melanoma samples, are associated with TGFB1 up-regulation. Using CRISPR-Cas9, we find that alterations at two of the most frequently mutated regions in this insulator increase cell growth by 40%-50%, supporting the role of this boundary element as a cancer driver. Thus, our study reveals several CTCF insulators as putative cancer drivers.
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Affiliation(s)
- Eric Minwei Liu
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Alexander Martinez-Fundichely
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Bianca Jay Diaz
- New York Genome Center, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10003, USA
| | - Boaz Aronson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Tawny Cuykendall
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Matthew MacKay
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Priyanka Dhingra
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Elissa W P Wong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ping Chi
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Effie Apostolou
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Neville E Sanjana
- New York Genome Center, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10003, USA
| | - Ekta Khurana
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY 10065, USA.
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17
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Lu Z, Hong CC, Kong G, Assumpção ALFV, Ong IM, Bresnick EH, Zhang J, Pan X. Polycomb Group Protein YY1 Is an Essential Regulator of Hematopoietic Stem Cell Quiescence. Cell Rep 2019; 22:1545-1559. [PMID: 29425509 PMCID: PMC6140794 DOI: 10.1016/j.celrep.2018.01.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 10/25/2017] [Accepted: 01/08/2018] [Indexed: 01/04/2023] Open
Abstract
Yin yang 1 (YY1) is a ubiquitous transcription factor and mammalian polycomb group protein (PcG) with important functions to regulate embryonic development, lineage differentiation, and cell proliferation. YY1 mediates stable PcG-dependent transcriptional repression via recruitment of PcG proteins that catalyze histone modifications. Many questions remain unanswered regarding how cell- and tissue-specificity is achieved by PcG proteins. Here, we demonstrate that a conditional knockout of Yy1 in hematopoietic stem cells (HSCs) decreases long-term repopulating activity and ectopic YY1 expression expands HSCs. Although the YY1 PcG domain is required for Igk chain rearrangement in B cells, the YY1 mutant lacking the PcG domain retained the capacity to stimulate HSC self-renewal. YY1 deficiency deregulated the genetic network governing HSC cell proliferation and impaired stem cell factor/c-Kit signaling, disrupting mechanisms conferring HSC quiescence. These results reveal a mechanism for how a ubiquitously expressed transcriptional repressor mediates lineage-specific functions to control adult hematopoiesis. Lu et al. investigate the function of the polycomb group (PcG) protein YY1 in hematopoietic stem cells. Independent of its REPO domain/PcG function, YY1 promotes hematopoietic stem cell selfrenewal and quiescence, suggesting that REPO domain/PcG function is not utilized in all contexts within the hematopoietic hierarchy.
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Affiliation(s)
- Zhanping Lu
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA
| | - Courtney C Hong
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA
| | - Guangyao Kong
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 1111 Highland Ave., Madison, WI 53705, USA; National Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PRC; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA
| | - Anna L F V Assumpção
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA
| | - Irene M Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, 1111 Highland Ave., Madison, WI 53705, USA; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, 1111 Highland Ave., Madison, WI 53705, USA; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA
| | - Jing Zhang
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 1111 Highland Ave., Madison, WI 53705, USA; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA
| | - Xuan Pan
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA; Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53706, USA.
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18
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Adhikari K, Mendoza-Revilla J, Sohail A, Fuentes-Guajardo M, Lampert J, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Acuña-Alonzo V, Jaramillo C, Arias W, Lozano RB, Everardo P, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hunemeier T, Ramallo V, Schuler-Faccini L, Salzano FM, Gonzalez-José R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Tobin DJ, Fumagalli M, Balding D, Ruiz-Linares A. A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia. Nat Commun 2019; 10:358. [PMID: 30664655 PMCID: PMC6341102 DOI: 10.1038/s41467-018-08147-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/20/2018] [Indexed: 12/17/2022] Open
Abstract
We report a genome-wide association scan in >6,000 Latin Americans for pigmentation of skin and eyes. We found eighteen signals of association at twelve genomic regions. These include one novel locus for skin pigmentation (in 10q26) and three novel loci for eye pigmentation (in 1q32, 20q13 and 22q12). We demonstrate the presence of multiple independent signals of association in the 11q14 and 15q13 regions (comprising the GRM5/TYR and HERC2/OCA2 genes, respectively) and several epistatic interactions among independently associated alleles. Strongest association with skin pigmentation at 19p13 was observed for an Y182H missense variant (common only in East Asians and Native Americans) in MFSD12, a gene recently associated with skin pigmentation in Africans. We show that the frequency of the derived allele at Y182H is significantly correlated with lower solar radiation intensity in East Asia and infer that MFSD12 was under selection in East Asians, probably after their split from Europeans. Pigmentation variation in humans is influenced by complex genetic architecture in different populations. Here, the authors perform a genome-wide association analysis involving > 6,000 Latin Americans for pigmentation of skin and eyes, and identify known and novel genetic associations.
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Affiliation(s)
- Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Anood Sohail
- Department of Genetics, Cambridge University, Cambridge, CB2 3EH, UK
| | - Macarena Fuentes-Guajardo
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica, 1000000, Chile
| | - Jodie Lampert
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Juan Camilo Chacón-Duque
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Victor Acuña-Alonzo
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,National Institute of Anthropology and History, Mexico City, 4510, Mexico
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Rodrigo Barquera Lozano
- National Institute of Anthropology and History, Mexico City, 4510, Mexico.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Paola Everardo
- National Institute of Anthropology and History, Mexico City, 4510, Mexico
| | - Jorge Gómez-Valdés
- National Institute of Anthropology and History, Mexico City, 4510, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, 4510, Mexico
| | - Caio C Silva de Cerqueira
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Tábita Hunemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil.,Instituto Patagonico de Ciencias Sociales y Humanas, Centro Nacional Patagonico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Rolando Gonzalez-José
- Instituto Patagonico de Ciencias Sociales y Humanas, Centro Nacional Patagonico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Peru
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapaca, Arica, 1000000, Chile.,Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8320000, Chile
| | - Desmond J Tobin
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, BD7 1DP, West Yorkshire, UK.,The Charles Institute of Dermatology, University College Dublin, Dublin, D4, Ireland
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park campus, Imperial College London, Ascot, SL5 7PY, UK
| | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China. .,Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France.
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19
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Hejna M, Moon WM, Cheng J, Kawakami A, Fisher DE, Song JS. Local genomic features predict the distinct and overlapping binding patterns of the bHLH-Zip family oncoproteins MITF and MYC-MAX. Pigment Cell Melanoma Res 2018; 32:500-509. [PMID: 30548162 DOI: 10.1111/pcmr.12762] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 11/21/2018] [Accepted: 11/29/2018] [Indexed: 12/31/2022]
Abstract
MITF and MYC are well-known oncoproteins and members of the basic helix-loop-helix leucine zipper (bHLH-Zip) family of transcription factors (TFs) recognizing hexamer E-box motifs. MITF and MYC not only share the core binding motif, but are also the two most highly expressed bHLH-Zip transcription factors in melanocytes, raising the possibility that they may compete for the same binding sites in select oncogenic targets. Mechanisms determining the distinct and potentially overlapping binding modes of these critical oncoproteins remain uncharacterized. We introduce computational predictive models using local sequence features, including a boosted convolutional decision tree framework, to distinguish MITF versus MYC-MAX binding sites with up to 80% accuracy genomewide. Select E-box locations that can be bound by both MITF and MYC-MAX form a separate class of MITF binding sites characterized by differential sequence content in the flanking region, diminished interaction with SOX10, higher evolutionary conservation, and less tissue-specific chromatin organization.
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Affiliation(s)
- Miroslav Hejna
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Wooyoung M Moon
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Jeffrey Cheng
- Department of Dermatology, University of California, San Francisco, California
| | - Akinori Kawakami
- Cutaneous Biology Research Center and Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - David E Fisher
- Cutaneous Biology Research Center and Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jun S Song
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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20
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Nordlinger A, Dror S, Elkahloun A, Del Rio J, Stubbs E, Golan T, Malcov H, Pricket TD, Cronin JC, Parikh S, Labes S, Thomas L, Yankovitz G, Tabach Y, Levy C, Samuels Y, Khaled M. Mutated MITF-E87R in Melanoma Enhances Tumor Progression via S100A4. J Invest Dermatol 2018; 138:2216-2223. [DOI: 10.1016/j.jid.2018.03.1524] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 02/13/2018] [Accepted: 03/15/2018] [Indexed: 01/16/2023]
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21
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Priprem A, Lee YC, Limphirat W, Tiyaworanant S, Saodaeng K, Chotitumnavee J, Kowtragoon N. Eucalyptus ash alters secondary protein conformation of human grey hair and facilitates anthocyanin dyeing. PLoS One 2018; 13:e0199696. [PMID: 29965982 PMCID: PMC6028099 DOI: 10.1371/journal.pone.0199696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 06/12/2018] [Indexed: 11/30/2022] Open
Abstract
Wood ashes infused with water have been traditionally used as hair cosmetics, but little or no research has examined the effects of ash on human hair. This study investigated the effect of eucalyptus ash on the structure and morphology of excised human grey hair and its potential use as a pretreatment in natural hair dyeing using anthocyanins extracted from purple cops of Zea mays. Tensile characteristics and surface morphology of ash-pretreated hair was monitored by texture analysis, scanning electron microscopy and atomic force microscopy. The biochemical characteristics of ash-treated hair were analyzed by synchrotron radiation-FTIR and sulfur K-edge X-ray absorption near edge. Dyeing with anthocyanins was analyzed by Lab color scale and adsorption of anthocyanins. Ash-treated hair was elastically and plastically deformed with microscopic alterations to the ridges of the cuticle cells, similar to ammonia-treated hair. The ash extract significantly changed the relative proportion of alpha-helices in the cuticle and cortex layers (p < 0.05), but did not affect the interaction of S-bonds with neighboring atoms (p > 0.05). Ash-treated hair showed significantly enhanced adsorption of anthocyanins (p < 0.05) which changed the color of the grey hair. The alteration of secondary proteins in the cuticle and cortex layers of the grey hair by ash extract pre-treatment, enhanced anthocyanin adsorption. The eucalyptus ash could potentially be useful as a natural hair dyeing pre-treatment.
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Affiliation(s)
- Aroonsri Priprem
- Department of Pharmaceutical Technology, Faculty of Pharmaceutical Science, Khon Kaen University, Muang, Khon Kaen, Thailand
| | - Yao-Chang Lee
- National Synchrotron Radiation Research Center, Hsinchu City, Taiwan, Republic of China
| | - Wanwisa Limphirat
- National Synchrotron Research Institute of Thailand, Muang, Nakornratchasima, Thailand
| | - Suppachai Tiyaworanant
- Department of Pharmacognosy and Toxicology, Faculty of Pharmaceutical Science, Khon Kaen University, Muang, Khon Kaen, Thailand
| | - Kedsarin Saodaeng
- Postgraduate program, Master degree in Pharmaceutical Chemistry and Natural Products, Graduate School, Khon Kaen University, Muang, Khon Kaen, Thailand
| | - Jiranan Chotitumnavee
- Undergraduate program in Doctor of Pharmacy, Faculty of Pharmaceutical Science, Khon Kaen University, Muang, Khon Kaen, Thailand
| | - Nuttanunth Kowtragoon
- Undergraduate program in Doctor of Pharmacy, Faculty of Pharmaceutical Science, Khon Kaen University, Muang, Khon Kaen, Thailand
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22
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Bagati A, Bianchi-Smiraglia A, Moparthy S, Kolesnikova K, Fink EE, Kolesnikova M, Roll MV, Jowdy P, Wolff DW, Polechetti A, Yun DH, Lipchick BC, Paul LM, Wrazen B, Moparthy K, Mudambi S, Morozevich GE, Georgieva SG, Wang J, Shafirstein G, Liu S, Kandel ES, Berman AE, Box NF, Paragh G, Nikiforov MA. FOXQ1 controls the induced differentiation of melanocytic cells. Cell Death Differ 2018; 25:1040-1049. [PMID: 29463842 PMCID: PMC5988681 DOI: 10.1038/s41418-018-0066-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/26/2017] [Accepted: 01/11/2018] [Indexed: 01/08/2023] Open
Abstract
Oncogenic transcription factor FOXQ1 has been implicated in promotion of multiple transformed phenotypes in carcinoma cells. Recently, we have characterized FOXQ1 as a melanoma tumor suppressor that acts via repression of N-cadherin gene, and invasion and metastasis. Here we report that FOXQ1 induces differentiation in normal and transformed melanocytic cells at least partially via direct transcriptional activation of MITF gene, melanocytic lineage-specific regulator of differentiation. Importantly, we demonstrate that pigmentation induced in cultured melanocytic cells and in mice by activation of cAMP/CREB1 pathway depends in large part on FOXQ1. Moreover, our data reveal that FOXQ1 acts as a critical mediator of BRAFV600E-dependent regulation of MITF levels, thus providing a novel link between two major signal transduction pathways controlling MITF and differentiation in melanocytic cells.
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Affiliation(s)
- Archis Bagati
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Smith Building, SM-0728, 450 Brookline Ave, Boston, MA, 02215, USA
| | | | - Sudha Moparthy
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kateryna Kolesnikova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Emily E Fink
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Masha Kolesnikova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Matthew V Roll
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Peter Jowdy
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - David W Wolff
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Anthony Polechetti
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Dong Hyun Yun
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Brittany C Lipchick
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Leslie M Paul
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Brian Wrazen
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kalyana Moparthy
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Shaila Mudambi
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | | | | | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Gal Shafirstein
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Eugene S Kandel
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Albert E Berman
- Orekhovich Institute of Biomedical Chemistry, Moscow, 119121, Russia
| | - Neil F Box
- Department of Dermatology, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA
| | - Gyorgy Paragh
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
- Department of Dermatology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Mikhail A Nikiforov
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA.
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23
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Seberg HE, Van Otterloo E, Cornell RA. Beyond MITF: Multiple transcription factors directly regulate the cellular phenotype in melanocytes and melanoma. Pigment Cell Melanoma Res 2018. [PMID: 28649789 DOI: 10.1111/pcmr.12611] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MITF governs multiple steps in the development of melanocytes, including specification from neural crest, growth, survival, and terminal differentiation. In addition, the level of MITF activity determines the phenotype adopted by melanoma cells, whether invasive, proliferative, or differentiated. However, MITF does not act alone. Here, we review literature on the transcription factors that co-regulate MITF-dependent genes. ChIP-seq studies have indicated that the transcription factors SOX10, YY1, and TFAP2A co-occupy subsets of regulatory elements bound by MITF in melanocytes. Analyses at single loci also support roles for LEF1, RB1, IRF4, and PAX3 acting in combination with MITF, while sequence motif analyses suggest that additional transcription factors colocalize with MITF at many melanocyte-specific regulatory elements. However, the precise biochemical functions of each of these MITF collaborators and their contributions to gene expression remain to be elucidated. Analogous to the transcriptional networks in morphogen-patterned tissues during embryogenesis, we anticipate that the level of MITF activity is controlled not only by the concentration of activated MITF, but also by additional transcription factors that either quantitatively or qualitatively influence the expression of MITF-target genes.
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Affiliation(s)
- Hannah E Seberg
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
| | - Eric Van Otterloo
- SDM-Craniofacial Biology, University of Colorado - Anschutz Medical Campus, Aurora, CO, USA
| | - Robert A Cornell
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA.,Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA, USA
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24
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Ji K, Zhang P, Zhang J, Fan R, Liu Y, Yang S, Hu S, Liu X, Dong C. MicroRNA 143-5p regulates alpaca melanocyte migration, proliferation and melanogenesis. Exp Dermatol 2018; 27:166-171. [PMID: 29230879 DOI: 10.1111/exd.13480] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2017] [Indexed: 01/14/2023]
Abstract
microRNAs (miRNAs) have been shown to be closely involved in the control of melanogenesis and hair colour in mammals. Previous data also indicate that miR-143 regulates cell growth in melanoma. Here, we aimed to investigate the role of miR-143-5p in alpaca melanocytes. We found that miR-143-5p was highly expressed in the cytoplasm of alpaca melanocytes as demonstrated by an in situ hybridization assay. Prediction analysis revealed that miR-143-5p could regulate TGF-β-activated kinase 1 (TAK1) expression, which we confirmed by luciferase reporter assay, indicating that miR-143-5p controls TAK1 expression by directly targeting its 3' untranslated region (UTR). miR-143-5p overexpression decreased TAK1 expression, which led to increased melanocyte migration and proliferation, and downregulation of microphthalmia-associated transcription factor (MITF), which regulates melanin production. These results support a functional role for miR-143-5p in regulating alpaca melanocyte migration, proliferation and melanogenesis through direct targeting of TAK1.
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Affiliation(s)
- Kaiyuan Ji
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Pengqian Zhang
- The Department of Ecology Research, Beijing Milu Ecological Research Center, Beijing, China
| | - Junzhen Zhang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Ruiwen Fan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Yu Liu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Shanshan Yang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Shuaipeng Hu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Xuexian Liu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Changsheng Dong
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, China
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25
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The master role of microphthalmia-associated transcription factor in melanocyte and melanoma biology. J Transl Med 2017; 97:649-656. [PMID: 28263292 DOI: 10.1038/labinvest.2017.9] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/07/2017] [Accepted: 01/10/2017] [Indexed: 12/20/2022] Open
Abstract
Certain transcription factors have vital roles in lineage development, including specification of cell types and control of differentiation. Microphthalmia-associated transcription factor (MITF) is a key transcription factor for melanocyte development and differentiation. MITF regulates expression of numerous pigmentation genes to promote melanocyte differentiation, as well as fundamental genes for maintaining cell homeostasis, including genes encoding proteins involved in apoptosis (eg, BCL2) and the cell cycle (eg, CDK2). Loss-of-function mutations of MITF cause Waardenburg syndrome type IIA, whose phenotypes include depigmentation due to melanocyte loss, whereas amplification or specific mutation of MITF can be an oncogenic event that is seen in a subset of familial or sporadic melanomas. In this article, we review basic features of MITF biological function and highlight key unresolved questions regarding this remarkable transcription factor.
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26
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Laurette P, Koludrovic D, Coassolo S, Davidson I. [Epigenetic regulation of gene expression in malignant melanoma]. Biol Aujourdhui 2017; 210:283-295. [PMID: 28327285 DOI: 10.1051/jbio/2016028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Indexed: 06/06/2023]
Abstract
Malignant melanoma is a highly aggressive cancer with a propensity for early metastasis. Melanocyte transformation results predominantly from oncogenic mutations in BRAF, NRAS or NF1 leading to constitutive activation of the MAP kinase pathway driving cell proliferation and second site mutations such as loss of CDKN1A, or PTEN or activating mutations in the beta-catenin pathway that allow escape from oncogene induced senescence. Nevertheless, irrespective of the nature of the driver mutations, melanoma cell physiology is strongly regulated by transcription factors and epigenetic mechanisms. MITF (Microphthalmia-associated Transcription Factor) and SOX10 are two major transcription factors that regulate both normal melanocyte and melanoma cell physiology. Using a combination of mouse genetics, biochemistry and high throughput genomics we have identified cofactors for MITF and addressed the mechanisms by which MITF, SOX10 and their cofactors regulate gene expression in melanocytes and melanoma.
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Kim JS, Chae JH, Cheon YP, Kim CG. Reciprocal localization of transcription factors YY1 and CP2c in spermatogonial stem cells and their putative roles during spermatogenesis. Acta Histochem 2016; 118:685-692. [PMID: 27612612 DOI: 10.1016/j.acthis.2016.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 08/24/2016] [Accepted: 08/24/2016] [Indexed: 01/12/2023]
Abstract
Maintaining stemness and permitting differentiation mediated by combinations of transcription factors (TFs) are key aspects of mammalian spermatogenesis. It has been established that yin yang 1 (YY1), a target factor of mammalian polycomb repressive complex 2 (PRC2) and a regulator of stemness, is involved in the stable maintenance of prophase stage spermatocytes. Recently, we have demonstrated that the TF CP2c partners with YY1 in some cells to antagonistically regulate the other protein's function. To date, the functional roles of YY1 and CP2c in spermatogonial stem cells and their derived germ cells remain unclear. Here, we investigated the expression of YY1 and CP2c in mouse gonocytes and germ cells using tissue immunohistochemical and immunofluorescence analyses. At E14.5, both YY1 and CP2c were stained in gonocytes and Sertoli cells in testicular cords, showing different proportion and density of immunoreactivity. However, in adult testes, YY1 was localized in the nuclei of spermatogonial stem cells and spermatocytes, but not in spermatozoa. It was also detected in spermatogonia and spermatids in a stage-specific manner during spermatogenic cycle. CP2c could be detected mostly in the cytoplasm of spermatocytes but not at all in spermatogonial stem cells, indicating mutually exclusive expression of CP2c and YY1. Interestingly, however, CP2c was stained in the cytoplasm and nucleus of spermatogonia at elongation and release stages, and co-localized with YY1 in the nucleus at grouping, maturation, and releasing stages. Neither YY1 nor CP2c was expressed in spermatozoa. Our data indicate that YY1 strongly localizes in the spermatogonial stem cells and co-localizes heterogeneously with CP2c to permit spermatogenesis, and also suggest that YY1 is essential for stemness of spermatogonial stem cells (SCs) whereas CP2c is critical for the commitment of spermatogonia and during the progression of spermatogonia to spermatids. This evaluation expands our understanding of the molecular mechanism of spermatogonia formation as well as spermatogenesis in general.
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Affiliation(s)
- Ji Sook Kim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Ji Hyung Chae
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Yong-Pil Cheon
- Division of Developmental Biology and Physiology, Department of Biology, Institute for Basic Sciences, Sungshin University, Seoul 02844, Republic of Korea.
| | - Chul Geun Kim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea.
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Elias KM, Emori MM, Westerling T, Long H, Budina-Kolomets A, Li F, MacDuffie E, Davis MR, Holman A, Lawney B, Freedman ML, Quackenbush J, Brown M, Drapkin R. Epigenetic remodeling regulates transcriptional changes between ovarian cancer and benign precursors. JCI Insight 2016; 1. [PMID: 27617304 DOI: 10.1172/jci.insight.87988] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Regulation of lineage-restricted transcription factors has been shown to influence malignant transformation in several types of cancer. Whether similar mechanisms are involved in ovarian cancer pathogenesis is unknown. PAX8 is a nuclear transcription factor that controls the embryologic development of the Müllerian system, including the fallopian tubes. Recent studies have shown that fallopian tube secretory epithelial cells (FTSECs) give rise to the most common form of ovarian cancer, high-grade serous ovarian carcinomas (HGSOCs). We designed the present study in order to understand whether changes in gene expression between FTSECs and HGSOCs relate to alterations in PAX8 binding to chromatin. Using whole transcriptome shotgun sequencing (RNA-Seq) after PAX8 knockdown and ChIP-Seq, we show that FTSECs and HGSOCs are distinguished by marked reprogramming of the PAX8 cistrome. Genes that are significantly altered between FTSECs and HGSOCs are enriched near PAX8 binding sites. These sites are also near TEAD binding sites, and these transcriptional changes may be related to PAX8 interactions with the TEAD/YAP1 signaling pathway. These data suggest that transcriptional changes after transformation in ovarian cancer are closely related to epigenetic remodeling in lineage-specific transcription factors.
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Affiliation(s)
- Kevin M Elias
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA.; Harvard Medical School, Boston, Massachusetts, USA
| | - Megan M Emori
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.; Graduate School of Arts and Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Thomas Westerling
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Anna Budina-Kolomets
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Fugen Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Emily MacDuffie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Michelle R Davis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA.; Harvard Medical School, Boston, Massachusetts, USA
| | - Alexander Holman
- Computational Biology and Functional Genomics Laboratory, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Brian Lawney
- Computational Biology and Functional Genomics Laboratory, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.; Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - John Quackenbush
- Computational Biology and Functional Genomics Laboratory, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ronny Drapkin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.; Harvard Medical School, Boston, Massachusetts, USA.; Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Jiang S, Yu X, Dong C. MiR-137 affects melanin synthesis in mouse melanocyte by repressing the expression of c-Kit and Tyrp2 in SCF/c-Kit signaling pathway. Biosci Biotechnol Biochem 2016; 80:2115-2121. [PMID: 27323927 DOI: 10.1080/09168451.2016.1200455] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Previously, we created miR-137 overexpressing transgenic mice that produced lighten color phenotypes including gray mice phenotype. However, the miR-137 functional role in coat color regulation is still not well understood. In this study, the quantity of melanin granule and the relative expression of TYRP2 in gray miR-137 overexpression transgenic mouse skin were significantly lower than that in C57BL/6J black mouse skin. The mRNA and protein expression level of c-Kit and c-Kit downstream gene Tyrp2 in miR-137 expression plasmid-transfected melanocytes were significantly down-regulated comparing with that of the control melanocytes. In melanocytes, miR-137 overexpression could decrease the enhanced expression of c-Kit and Tyrp2 and the increased melanin production caused by UV treatment. The target relationship of miR-137 and c-Kit was identified by luciferase assay. The results suggest that miR-137 could inhibit melanogenesis in mouse skin melanocytes by repressing the expression of c-Kit and Tyrp2 in SCF/c-Kit signaling pathway.
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Affiliation(s)
- Shan Jiang
- a College of Animal Science and Veterinary Medicine , Shanxi Agricultural University , Taigu , China
| | - Xiuju Yu
- a College of Animal Science and Veterinary Medicine , Shanxi Agricultural University , Taigu , China
| | - Changsheng Dong
- a College of Animal Science and Veterinary Medicine , Shanxi Agricultural University , Taigu , China
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Tayarani-Najaran Z, Akaberi M, Vatani M, Emami SA. Evaluation of antioxidant and anti-melanogenic activities of different extracts from aerial parts of Nepeta binaludensis Jamzad in murine melanoma B16F10 cells. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2016; 19:662-9. [PMID: 27482348 PMCID: PMC4951606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVES Nepeta binaludensis Jamzad (Lamiaceae) has been used in folk medicine of Iran to cure various diseases. The plant is an endemic species to the country that has recently been identified in Razavi Khorasan province. To evaluate the antioxidant and anti-melanogenesis of N. binaludensis, in this study the inhibitory activity of different extracts of N. binaludensis in murine melanoma B16F10 cells is investigated. MATERIALS AND METHODS The effects of petroleum ether, dichloromethane, ethyl acetate, and methanol extracts isolated from the plant on melanogenesis in B16 melanoma cells were investigated. To assess the inhibitory effects of this plant on melanogenesis, various assays were used including cytotoxicity, inhibition of mushroom tyrosinase and cellular tyrosinase, determination of melanin content, the effect of extracts on reactive oxygen species and western blot analysis of proteins involved in melanogenesis process. RESULTS The content of melanin and the activity of tyrosinase were significantly reduced with different extracts of N. binaludensis in cells. Reactive oxygen species was also significantly decreased following the treatment of cell with the mentioned extracts, while a resazurin assay showed no cytotoxicity. Furthermore, we have found that the plant decreased the amount of tyrosinase and microphthalmia-associated transcription factor proteins, which verify the role of suppression of microphthalmia-associated transcription factor protein in melanogenesis inhibition. CONCLUSION Taken together the data indicate that N. binaludensis has inhibitory activity on melanin synthesis with no cytotoxic effects in B16 melanoma cells. Therefore, it merits future investigations to apply as whitening agent in hyperpigmentation.
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Affiliation(s)
- Zahra Tayarani-Najaran
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran,Corresponding author: Zahra Tayarani-Najaran Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran. Tel: +98-51-38823255;
| | - Maryam Akaberi
- Department of Pharmacognosy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohsen Vatani
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Ahmad Emami
- Department of Pharmacognosy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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Shiu WL, Huang KR, Hung JC, Wu JL, Hong JR. Knockdown of zebrafish YY1a can downregulate the phosphatidylserine (PS) receptor expression, leading to induce the abnormal brain and heart development. J Biomed Sci 2016; 23:31. [PMID: 26924789 PMCID: PMC4770675 DOI: 10.1186/s12929-016-0248-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 02/16/2016] [Indexed: 01/08/2023] Open
Abstract
Background Yin Yang 1 (YY1) is a ubiquitously expressed GLI-Kruppel zinc finger-containing transcriptional regulator. YY1 plays a fundamental role in normal biologic processes such as embryogenesis, differentiation, and cellular proliferation. YY1 effects on the genes involved in these processes are mediated via initiation, activation, or repression of transcription depending upon the context in which it binds. The role of the multifunctional transcription factor Yin Yang 1 (YY1) in tissue development is poorly understood. In the present, we investigated YY1a role in developing zebrafish on PSR-mediated apoptotic cell engulfment during organic morphogenesis. Results YY1a is first expressed 0.5 h post-fertilization (hpf), in the whole embryo 12 hpf, and in brain, eyes, and heart 72 hpf by in situ hybridization assay. The nucleotide sequence of zebrafish YY1a transcription factor (clone zfYY1a; HQ 166834) was found to be similar to that of zebrafish YY1a (99 % sequence identity; NM 212617). With the loss-of-function assay, YY1a knockdown by a morpholino oligonucleotide led to downregulation of the phosphatidylserine engulfing receptor zfPSR during embryonic segmentation and to the accumulation of a large number of dead apoptotic cells throughout the entire early embryo, especially in the posterior area. Up to 24 hpf, these cells interfered with embryonic cell migration and cell-cell interactions that normally occur in the brain, heart, eye, and notochord. Finally, with gain-of-function assay, defective morphants could be rescued by injecting both YY1a mRNA and PSR mRNA and trigger resumption of normal development. Conclusions Taken together, our results suggest that YY1a regulates PS receptor expression that linked to function of PSR-phagocyte mediated apoptotic cell engulfment during development, especially the development of organs such as the brain and heart. YY1a/PSR-mediated engulfing system may involve in diseases.
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Affiliation(s)
- Wei-Lun Shiu
- Laboratory of Molecular Virology and Biotechnology, Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Kuan-Rong Huang
- Laboratory of Molecular Virology and Biotechnology, Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Jo-Chi Hung
- Laboratory of Molecular Virology and Biotechnology, Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan, ROC
| | - Jen-Leih Wu
- Laboratory of Marine Molecular Biology and Biotechnology, Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, ROC
| | - Jiann-Ruey Hong
- Laboratory of Molecular Virology and Biotechnology, Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan, ROC.
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32
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Liu F, Visser M, Duffy DL, Hysi PG, Jacobs LC, Lao O, Zhong K, Walsh S, Chaitanya L, Wollstein A, Zhu G, Montgomery GW, Henders AK, Mangino M, Glass D, Bataille V, Sturm RA, Rivadeneira F, Hofman A, van IJcken WFJ, Uitterlinden AG, Palstra RJTS, Spector TD, Martin NG, Nijsten TEC, Kayser M. Genetics of skin color variation in Europeans: genome-wide association studies with functional follow-up. Hum Genet 2015; 134:823-35. [PMID: 25963972 PMCID: PMC4495261 DOI: 10.1007/s00439-015-1559-0] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/20/2015] [Indexed: 02/05/2023]
Abstract
In the International Visible Trait Genetics (VisiGen) Consortium, we investigated the genetics of human skin color by combining a series of genome-wide association studies (GWAS) in a total of 17,262 Europeans with functional follow-up of discovered loci. Our GWAS provide the first genome-wide significant evidence for chromosome 20q11.22 harboring the ASIP gene being explicitly associated with skin color in Europeans. In addition, genomic loci at 5p13.2 (SLC45A2), 6p25.3 (IRF4), 15q13.1 (HERC2/OCA2), and 16q24.3 (MC1R) were confirmed to be involved in skin coloration in Europeans. In follow-up gene expression and regulation studies of 22 genes in 20q11.22, we highlighted two novel genes EIF2S2 and GSS, serving as competing functional candidates in this region and providing future research lines. A genetically inferred skin color score obtained from the 9 top-associated SNPs from 9 genes in 940 worldwide samples (HGDP-CEPH) showed a clear gradual pattern in Western Eurasians similar to the distribution of physical skin color, suggesting the used 9 SNPs as suitable markers for DNA prediction of skin color in Europeans and neighboring populations, relevant in future forensic and anthropological investigations.
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Affiliation(s)
- Fan Liu
- />Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mijke Visser
- />Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - David L. Duffy
- />Queensland Institute of Medical Research, Brisbane, Australia
| | - Pirro G. Hysi
- />Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Leonie C. Jacobs
- />Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Oscar Lao
- />Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
- />CNAG-Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Kaiyin Zhong
- />Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Susan Walsh
- />Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
- />Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202 USA
| | - Lakshmi Chaitanya
- />Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Andreas Wollstein
- />Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
- />Section of Evolutionary Biology, Department of Biology II, University of Munich LMU, Planegg-Martinsried, Germany
| | - Gu Zhu
- />Queensland Institute of Medical Research, Brisbane, Australia
| | | | | | - Massimo Mangino
- />Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Daniel Glass
- />Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Veronique Bataille
- />Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Richard A. Sturm
- />Dermatology Research Centre, The University of Queensland, School of Medicine, Translational Research Institute, Brisbane, Queensland Australia
| | - Fernando Rivadeneira
- />Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
- />Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Albert Hofman
- />Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wilfred F. J. van IJcken
- />Centre for Biomics, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - André G. Uitterlinden
- />Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
- />Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Robert-Jan T. S. Palstra
- />Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
- />Department of Biochemistry, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Timothy D. Spector
- />Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | | | - Tamar E. C. Nijsten
- />Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Manfred Kayser
- />Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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Laurette P, Strub T, Koludrovic D, Keime C, Le Gras S, Seberg H, Van Otterloo E, Imrichova H, Siddaway R, Aerts S, Cornell RA, Mengus G, Davidson I. Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells. eLife 2015; 4. [PMID: 25803486 PMCID: PMC4407272 DOI: 10.7554/elife.06857] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 03/24/2015] [Indexed: 12/17/2022] Open
Abstract
Microphthalmia-associated transcription factor (MITF) is the master regulator of the melanocyte lineage. To understand how MITF regulates transcription, we used tandem affinity purification and mass spectrometry to define a comprehensive MITF interactome identifying novel cofactors involved in transcription, DNA replication and repair, and chromatin organisation. We show that MITF interacts with a PBAF chromatin remodelling complex comprising BRG1 and CHD7. BRG1 is essential for melanoma cell proliferation in vitro and for normal melanocyte development in vivo. MITF and SOX10 actively recruit BRG1 to a set of MITF-associated regulatory elements (MAREs) at active enhancers. Combinations of MITF, SOX10, TFAP2A, and YY1 bind between two BRG1-occupied nucleosomes thus defining both a signature of transcription factors essential for the melanocyte lineage and a specific chromatin organisation of the regulatory elements they occupy. BRG1 also regulates the dynamics of MITF genomic occupancy. MITF-BRG1 interplay thus plays an essential role in transcription regulation in melanoma.
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Affiliation(s)
- Patrick Laurette
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Thomas Strub
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Dana Koludrovic
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Céline Keime
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Stéphanie Le Gras
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Hannah Seberg
- University of Iowa College of Medicine, Iowa City, United States
| | | | - Hana Imrichova
- Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, Leuven, Belgium
| | - Robert Siddaway
- Arthur and Sonia Labatt Brain Tumor Research Centre, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, Canada
| | - Stein Aerts
- Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, Leuven, Belgium
| | - Robert A Cornell
- University of Iowa College of Medicine, Iowa City, United States
| | - Gabrielle Mengus
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
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Visser M, Palstra RJ, Kayser M. Allele-specific transcriptional regulation of IRF4 in melanocytes is mediated by chromatin looping of the intronic rs12203592 enhancer to the IRF4 promoter. Hum Mol Genet 2015; 24:2649-61. [PMID: 25631878 DOI: 10.1093/hmg/ddv029] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/24/2015] [Indexed: 01/07/2023] Open
Abstract
The majority of significant single-nucleotide polymorphisms (SNPs) identified with genome-wide association studies are located in non-coding regions of the genome; it is therefore possible that they are involved in transcriptional regulation of a nearby gene rather than affecting an encoded protein's function. Previously, it was demonstrated that the SNP rs12203592, located in intron 4 of the IRF4 gene, is strongly associated with human skin pigmentation and modulates an enhancer element that controls expression of IRF4. In our study, we investigated the allele-specific effect of rs12203592 on IRF4 expression in epidermal skin samples and in melanocytic cells from donors of different skin color. We focused on the characteristics and activity of the enhancer, and on long-range chromatin interactions in melanocytic cells homozygous and heterozygous for rs12203592. We found that, irrespective of the trans-activating environment, IRF4 transcription is strongly correlated with the allelic status of rs12203592, the activity of the rs12203592 enhancer and that the chromatin features depend on the rs12203592 genotype. Furthermore, we demonstrate that the rs12203592 enhancer physically interacts with the IRF4 promoter through an allele-dependent chromatin loop, and suggest that subsequent allele-specific activation of IRF4 transcription is stabilized by another allele-specific loop from the rs12203592 enhancer to an additional regulatory element in IRF4. We conclude that the non-coding SNP rs12203592 is located in a regulatory region and affects a wide range of enhancer characteristics, resulting into modulation of the enhancer's activity, its interaction with the IRF4 promoter and subsequent allele-specific transcription of IRF4. Our findings provide another example of a non-coding SNP affecting skin color by modulating enhancer-mediated transcriptional regulation.
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Affiliation(s)
- Mijke Visser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Robert-Jan Palstra
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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Capowski EE, Simonett JM, Clark EM, Wright LS, Howden SE, Wallace KA, Petelinsek AM, Pinilla I, Phillips MJ, Meyer JS, Schneider BL, Thomson JA, Gamm DM. Loss of MITF expression during human embryonic stem cell differentiation disrupts retinal pigment epithelium development and optic vesicle cell proliferation. Hum Mol Genet 2014; 23:6332-44. [PMID: 25008112 DOI: 10.1093/hmg/ddu351] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Microphthalmia-associated transcription factor (MITF) is a master regulator of pigmented cell survival and differentiation with direct transcriptional links to cell cycle, apoptosis and pigmentation. In mouse, Mitf is expressed early and uniformly in optic vesicle (OV) cells as they evaginate from the developing neural tube, and null Mitf mutations result in microphthalmia and pigmentation defects. However, homozygous mutations in MITF have not been identified in humans; therefore, little is known about its role in human retinogenesis. We used a human embryonic stem cell (hESC) model that recapitulates numerous aspects of retinal development, including OV specification and formation of retinal pigment epithelium (RPE) and neural retina progenitor cells (NRPCs), to investigate the earliest roles of MITF. During hESC differentiation toward a retinal lineage, a subset of MITF isoforms was expressed in a sequence and tissue distribution similar to that observed in mice. In addition, we found that promoters for the MITF-A, -D and -H isoforms were directly targeted by Visual Systems Homeobox 2 (VSX2), a transcription factor involved in patterning the OV toward a NRPC fate. We then manipulated MITF RNA and protein levels at early developmental stages and observed decreased expression of eye field transcription factors, reduced early OV cell proliferation and disrupted RPE maturation. This work provides a foundation for investigating MITF and other highly complex, multi-purposed transcription factors in a dynamic human developmental model system.
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Affiliation(s)
| | | | | | | | - Sara E Howden
- Morgridge Institute for Research, Madison, WI 53715, USA
| | | | | | - Isabel Pinilla
- Department of Ophthalmology, University Hospital Lozano Blesa, Zaragoza 50009, Spain, Aragon Institute of Health Sciences, Zaragoza 50009, Spain
| | | | - Jason S Meyer
- Department of Biology, Indiana University-Purdue University, Indianapolis, IN 46202, USA
| | - Bernard L Schneider
- Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53715, USA, Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53715, USA and Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - David M Gamm
- Waisman Center, McPherson Eye Research Institute and Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI 53705, USA,
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Visser M, Palstra RJ, Kayser M. Human skin color is influenced by an intergenic DNA polymorphism regulating transcription of the nearby BNC2 pigmentation gene. Hum Mol Genet 2014; 23:5750-62. [PMID: 24916375 DOI: 10.1093/hmg/ddu289] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) found to be statistically significant when associated with human diseases, and other phenotypes are most often located in non-coding regions of the genome. One example is rs10765819 located in the first intron of the BNC2 gene previously associated with (saturation of) human skin color. Here, we demonstrate that a nearby intergenic SNP (rs12350739) in high linkage disequilibrium with rs10756819 is likely the causal DNA variant for the observed BNC2 skin color association. The highly conserved region surrounding rs12350739 functions as an enhancer element regulating BNC2 transcription in human melanocytes, while the activity of this enhancer element depends on the allelic status of rs12350739. When the rs12350739-AA allele is present, the chromatin at the region surrounding rs12350739 is inaccessible and the enhancer element is only slightly active, resulting in low expression of BNC2, corresponding with light skin pigmentation. When the rs12350739-GG allele is present however, the chromatin at the region surrounding rs12350739 is more accessible and the enhancer is active, resulting in a higher expression of BNC2, corresponding with dark skin pigmentation. Overall, we demonstrate the identification of the functional DNA variant that explains the BNC2 skin color association signal, providing another important step towards further understanding human pigmentation genetics beyond statistical association. We thus deliver a clear example of how an intergenic non-coding DNA variant modulates the regulatory potential of the enhancer element it is located within, which in turn results in allele-dependent differential gene expression affecting variation in common human traits.
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Affiliation(s)
- Mijke Visser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Robert-Jan Palstra
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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Bérubé-Simard FA, Prudhomme C, Jeannotte L. YY1 acts as a transcriptional activator of Hoxa5 gene expression in mouse organogenesis. PLoS One 2014; 9:e93989. [PMID: 24705708 PMCID: PMC3976385 DOI: 10.1371/journal.pone.0093989] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/11/2014] [Indexed: 12/15/2022] Open
Abstract
The Hox gene family encodes homeodomain-containing transcriptional regulators that confer positional information to axial and paraxial tissues in the developing embryo. The dynamic Hox gene expression pattern requires mechanisms that differentially control Hox transcription in a precise spatio-temporal fashion. This implies an integrated regulation of neighbouring Hox genes achieved through the sharing and the selective use of defined enhancer sequences. The Hoxa5 gene plays a crucial role in lung and gut organogenesis. To position Hoxa5 in the regulatory hierarchy that drives organ morphogenesis, we searched for cis-acting regulatory sequences and associated trans-acting factors required for Hoxa5 expression in the developing lung and gut. Using mouse transgenesis, we identified two DNA regions included in a 1.5-kb XbaI-XbaI fragment located in the Hoxa4-Hoxa5 intergenic domain and known to control Hoxa4 organ expression. The multifunctional YY1 transcription factor binds the two regulatory sequences in vitro and in vivo. Moreover, the mesenchymal deletion of the Yy1 gene function in mice results in a Hoxa5-like lung phenotype with decreased Hoxa5 and Hoxa4 gene expression. Thus, YY1 acts as a positive regulator of Hoxa5 expression in the developing lung and gut. Our data also support a role for YY1 in the coordinated expression of Hox genes for correct organogenesis.
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Affiliation(s)
- Félix-Antoine Bérubé-Simard
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, Canada
- Centre de recherche sur le cancer de l′Université Laval, Québec, Canada
- Centre de recherche du Centre Hospitalier Universitaire de Québec, L'Hôtel-Dieu de Québec, Québec, Canada
| | - Christelle Prudhomme
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, Canada
- Centre de recherche sur le cancer de l′Université Laval, Québec, Canada
- Centre de recherche du Centre Hospitalier Universitaire de Québec, L'Hôtel-Dieu de Québec, Québec, Canada
| | - Lucie Jeannotte
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, Canada
- Centre de recherche sur le cancer de l′Université Laval, Québec, Canada
- Centre de recherche du Centre Hospitalier Universitaire de Québec, L'Hôtel-Dieu de Québec, Québec, Canada
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UV signaling pathways within the skin. J Invest Dermatol 2014; 134:2080-2085. [PMID: 24759085 PMCID: PMC4102648 DOI: 10.1038/jid.2014.161] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/25/2014] [Accepted: 03/12/2014] [Indexed: 11/08/2022]
Abstract
The effects of UVR on the skin include tanning, carcinogenesis, immunomodulation, and synthesis of vitamin D, among others. Melanocortin 1 receptor polymorphisms correlate with skin pigmentation, UV sensitivity, and skin cancer risk. This article reviews pathways through which UVR induces cutaneous stress and the pigmentation response. Modulators of the UV tanning pathway include sunscreen agents, MC1R activators, adenylate cyclase activators, phosphodiesterase 4D3 inhibitors, T oligos, and MITF regulators such as histone deacetylase (HDAC)-inhibitors. UVR, as one of the most ubiquitous carcinogens, represents both a challenge and enormous opportunity in skin cancer prevention.
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Wei S, Zhang L, Zhou X, Du M, Jiang Z, Hausman GJ, Bergen WG, Zan L, Dodson MV. Emerging roles of zinc finger proteins in regulating adipogenesis. Cell Mol Life Sci 2013; 70:4569-84. [PMID: 23760207 PMCID: PMC4100687 DOI: 10.1007/s00018-013-1395-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 05/22/2013] [Accepted: 05/29/2013] [Indexed: 11/30/2022]
Abstract
Proteins containing the zinc finger domain(s) are named zinc finger proteins (ZFPs), one of the largest classes of transcription factors in eukaryotic genomes. A large number of ZFPs have been studied and many of them were found to be involved in regulating normal growth and development of cells and tissues through diverse signal transduction pathways. Recent studies revealed that a small but increasing number of ZFPs could function as key transcriptional regulators involved in adipogenesis. Due to the prevalence of obesity and metabolic disorders, the investigation of molecular regulatory mechanisms of adipocyte development must be more completely understood in order to develop novel and long-term impact strategies for ameliorating obesity. In this review, we discuss recent work that has documented that ZFPs are important functional contributors to the regulation of adipogenesis. Taken together, these data lead to the conclusion that ZFPs may become promising targets to combat human obesity.
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Affiliation(s)
- Shengjuan Wei
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
- Department of Animal Sciences, Washington State University, Pullman, WA 99164 USA
| | - Lifan Zhang
- Department of Animal Sciences, Washington State University, Pullman, WA 99164 USA
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Xiang Zhou
- Department of Animal Sciences, Washington State University, Pullman, WA 99164 USA
| | - Min Du
- Department of Animal Sciences, Washington State University, Pullman, WA 99164 USA
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA 99164 USA
| | - Gary J. Hausman
- Animal Science Department, University of Georgia, Athens, GA 30602-2771 USA
| | - Werner G. Bergen
- Program in Cellular and Molecular Biosciences, Department of Animal Sciences, Auburn University, Auburn, AL 36849 USA
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 Shaanxi People’s Republic of China
| | - Michael V. Dodson
- Department of Animal Sciences, Washington State University, Pullman, WA 99164 USA
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Abstract
Current models of melanoma propose that transition from the proliferative to the invasive stages of tumor development involves a dynamic and reversible switch in cell phenotype. The almost mutually exclusive proliferative and invasive phenotypes are defined by distinct gene expression signatures, which are themselves controlled by the level of functional MITF protein present in the cell. Recently, new signaling pathways and transcription factors that regulate MITF expression have been defined, and high throughput genomics have identified novel MITF target genes. MITF acts both as a transcription activator to promote expression of genes involved in cell cycle, but also as a transcriptional repressor of genes involved in invasion. A novel human germline mutation in MITF has been identified that blocks its sumoylation, thereby altering its transcriptional properties and conferring an increased risk of melanoma. These new studies depict an ever more complex function for MITF in melanoma.
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Affiliation(s)
- Dana Koludrovic
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UDS, 1 Rue Laurent Fries, 67404 Illkirch Cédex, France
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Haq R, Shoag J, Andreu-Perez P, Yokoyama S, Edelman H, Rowe GC, Frederick DT, Hurley AD, Nellore A, Kung AL, Wargo JA, Song JS, Fisher DE, Arany Z, Widlund HR. Oncogenic BRAF regulates oxidative metabolism via PGC1α and MITF. Cancer Cell 2013; 23:302-15. [PMID: 23477830 PMCID: PMC3635826 DOI: 10.1016/j.ccr.2013.02.003] [Citation(s) in RCA: 671] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 11/27/2012] [Accepted: 02/05/2013] [Indexed: 02/08/2023]
Abstract
Activating mutations in BRAF are the most common genetic alterations in melanoma. Inhibition of BRAF by small molecules leads to cell-cycle arrest and apoptosis. We show here that BRAF inhibition also induces an oxidative phosphorylation gene program, mitochondrial biogenesis, and the increased expression of the mitochondrial master regulator, PGC1α. We further show that a target of BRAF, the melanocyte lineage factor MITF, directly regulates the expression of PGC1α. Melanomas with activation of the BRAF/MAPK pathway have suppressed levels of MITF and PGC1α and decreased oxidative metabolism. Conversely, treatment of BRAF-mutated melanomas with BRAF inhibitors renders them addicted to oxidative phosphorylation. Our data thus identify an adaptive metabolic program that limits the efficacy of BRAF inhibitors.
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Affiliation(s)
- Rizwan Haq
- Massachusetts General Hospital Cancer Center, 55 Fruit Street, Boston, MA 02114
- Department of Dermatology and Cutaneous Biology Research Center, 55 Fruit Street, Boston, MA 02114
| | - Jonathan Shoag
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA 02116
| | - Pedro Andreu-Perez
- Department of Dermatology and Cutaneous Biology Research Center, 55 Fruit Street, Boston, MA 02114
| | - Satoru Yokoyama
- Department of Dermatology and Cutaneous Biology Research Center, 55 Fruit Street, Boston, MA 02114
- Division of Pathogenic Biochemistry, Institute of Natural Medicine, University of Toyama, 2630 Sugitani Toyama 930-0194, Japan
| | - Hannah Edelman
- Department of Dermatology and Cutaneous Biology Research Center, 55 Fruit Street, Boston, MA 02114
| | - Glenn C. Rowe
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA 02116
| | - Dennie T. Frederick
- Department of Surgery, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114
| | - Aeron D. Hurley
- Department of Dermatology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Abhinav Nellore
- Institute for Human Genetics and Department of Epidemiology and Biostatistics, University of California, San Francisco
| | - Andrew L. Kung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032
| | - Jennifer A. Wargo
- Department of Surgery, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114
| | - Jun S. Song
- Institute for Human Genetics and Department of Epidemiology and Biostatistics, University of California, San Francisco
| | - David E. Fisher
- Massachusetts General Hospital Cancer Center, 55 Fruit Street, Boston, MA 02114
- Department of Dermatology and Cutaneous Biology Research Center, 55 Fruit Street, Boston, MA 02114
- corresponding authors who contributed equally to this work. Correspondence: Hans Widlund, ; Zolt Arany, ; or David E. Fisher,
| | - Zolt Arany
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Boston, MA 02116
- corresponding authors who contributed equally to this work. Correspondence: Hans Widlund, ; Zolt Arany, ; or David E. Fisher,
| | - Hans R. Widlund
- Department of Dermatology, Brigham and Women’s Hospital, Boston, MA 02115
- corresponding authors who contributed equally to this work. Correspondence: Hans Widlund, ; Zolt Arany, ; or David E. Fisher,
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Guo AM, Sun K, Su X, Wang H, Sun H. YY1TargetDB: an integral information resource for Yin Yang 1 target loci. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat007. [PMID: 23411719 PMCID: PMC3572531 DOI: 10.1093/database/bat007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Yin Yang 1 (YY1), a ubiquitously expressed transcription factor, plays a critical role in regulating cell development, differentiation, cellular proliferation and tumorigenesis. Previous studies identified many YY1-regulated target genes in both human and mouse. Emerging global mapping by Chromatin ImmnoPrecipitation (ChIP)-based high-throughput experiments indicate that YY1 binds to a vast number of loci genome-wide. However, the information is widely scattered in many disparate poorly cross-indexed literatures; a large portion was only published recently by the ENCODE consortium with limited annotation. A centralized database, which annotates and organizes YY1-binding loci and target motifs in a systematic way with easy access, will be valuable resources for the research community. We therefore implemented a web-based YY1 Target loci Database (YY1TargetDB). This database contains YY1-binding loci (binding peaks) from ChIP-seq and ChIP-on-chip experiments, computationally predicated YY1 and cofactor motifs within each locus. It also collects the experimentally verified YY1-binding motifs from individual researchers. The current version of YY1TargetDB contains 92 314 binding loci identified by ChIP-based experiments; 157 200 YY1-binding motifs in which 42 are experimentally verified and 157 158 are computationally predicted; and 130 759 binding motifs for 47 cofactors. Database URL:http://www.myogenesisdb.org/YY1TargetDB
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Affiliation(s)
- Andy M Guo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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