1
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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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2
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Coutant K, Magne B, Ferland K, Fuentes-Rodriguez A, Chancy O, Mitchell A, Germain L, Landreville S. Melanocytes in regenerative medicine applications and disease modeling. J Transl Med 2024; 22:336. [PMID: 38589876 PMCID: PMC11003097 DOI: 10.1186/s12967-024-05113-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
Melanocytes are dendritic cells localized in skin, eyes, hair follicles, ears, heart and central nervous system. They are characterized by the presence of melanosomes enriched in melanin which are responsible for skin, eye and hair pigmentation. They also have different functions in photoprotection, immunity and sound perception. Melanocyte dysfunction can cause pigmentary disorders, hearing and vision impairments or increased cancer susceptibility. This review focuses on the role of melanocytes in homeostasis and disease, before discussing their potential in regenerative medicine applications, such as for disease modeling, drug testing or therapy development using stem cell technologies, tissue engineering and extracellular vesicles.
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Affiliation(s)
- Kelly Coutant
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada
- Université Laval Cancer Research Center, Quebec City, QC, Canada
| | - Brice Magne
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada
- Department of Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
| | - Karel Ferland
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada
- Department of Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
| | - Aurélie Fuentes-Rodriguez
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada
- Université Laval Cancer Research Center, Quebec City, QC, Canada
| | - Olivier Chancy
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada
- Université Laval Cancer Research Center, Quebec City, QC, Canada
| | - Andrew Mitchell
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada
- Université Laval Cancer Research Center, Quebec City, QC, Canada
| | - Lucie Germain
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada.
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada.
- Department of Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada.
| | - Solange Landreville
- Department of Ophthalmology and Otorhinolaryngology-Cervico-Facial Surgery, Faculty of Medicine, Université Laval, Quebec City, QC, Canada.
- Regenerative Medicine Division, CHU de Québec-Université Laval Research Centre, Quebec City, QC, Canada.
- Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX, Quebec City, QC, Canada.
- Université Laval Cancer Research Center, Quebec City, QC, Canada.
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3
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Ferretti LP, Böhi F, Leslie Pedrioli DM, Cheng PF, Ferrari E, Baumgaertner P, Alvarado-Diaz A, Sella F, Cereghetti A, Turko P, Wright RH, De Bock K, Speiser DE, Ferrari R, Levesque MP, Hottiger MO. Combinatorial Treatment with PARP and MAPK Inhibitors Overcomes Phenotype Switch-Driven Drug Resistance in Advanced Melanoma. Cancer Res 2023; 83:3974-3988. [PMID: 37729428 DOI: 10.1158/0008-5472.can-23-0485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/07/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
Metastatic melanoma is either intrinsically resistant or rapidly acquires resistance to targeted therapy treatments, such as MAPK inhibitors (MAPKi). A leading cause of resistance to targeted therapy is a dynamic transition of melanoma cells from a proliferative to a highly invasive state, a phenomenon called phenotype switching. Mechanisms regulating phenotype switching represent potential targets for improving treatment of patients with melanoma. Using a drug screen targeting chromatin regulators in patient-derived three-dimensional MAPKi-resistant melanoma cell cultures, we discovered that PARP inhibitors (PARPi) restore sensitivity to MAPKis, independent of DNA damage repair pathways. Integrated transcriptomic, proteomic, and epigenomic analyses demonstrated that PARPis induce lysosomal autophagic cell death, accompanied by enhanced mitochondrial lipid metabolism that ultimately increases antigen presentation and sensitivity to T-cell cytotoxicity. Moreover, transcriptomic and epigenetic rearrangements induced by PARP inhibition reversed epithelial-mesenchymal transition-like phenotype switching, which redirected melanoma cells toward a proliferative and MAPKi-sensitive state. The combination of PARP and MAPKis synergistically induced cancer cell death both in vitro and in vivo in patient-derived xenograft models. Therefore, this study provides a scientific rationale for treating patients with melanoma with PARPis in combination with MAPKis to abrogate acquired therapy resistance. SIGNIFICANCE PARP inhibitors can overcome resistance to MAPK inhibitors by activating autophagic cell death and reversing phenotype switching, suggesting that this synergistic combination could help improve the prognosis of patients with melanoma.
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Affiliation(s)
- Lorenza P Ferretti
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Flurina Böhi
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | | | - Phil F Cheng
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Elena Ferrari
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Petra Baumgaertner
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Abdiel Alvarado-Diaz
- Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach, Switzerland
| | - Federica Sella
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Alessandra Cereghetti
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Patrick Turko
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Roni H Wright
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Barcelona
| | - Katrien De Bock
- Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach, Switzerland
| | - Daniel E Speiser
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Roberto Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Mitchell P Levesque
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
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4
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Godoy PM, Oyedeji A, Mudd JL, Morikis VA, Zarov AP, Longmore GD, Fields RC, Kaufman CK. Functional analysis of recurrent CDC20 promoter variants in human melanoma. Commun Biol 2023; 6:1216. [PMID: 38030698 PMCID: PMC10686982 DOI: 10.1038/s42003-023-05526-2] [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: 09/05/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
Small nucleotide variants in non-coding regions of the genome can alter transcriptional regulation, leading to changes in gene expression which can activate oncogenic gene regulatory networks. Melanoma is heavily burdened by non-coding variants, representing over 99% of total genetic variation, including the well-characterized TERT promoter mutation. However, the compendium of regulatory non-coding variants is likely still functionally under-characterized. We developed a pipeline to identify hotspots, i.e. recurrently mutated regions, in melanoma containing putatively functional non-coding somatic variants that are located within predicted melanoma-specific regulatory regions. We identified hundreds of statistically significant hotspots, including the hotspot containing the TERT promoter variants, and focused on a hotspot in the promoter of CDC20. We found that variants in the promoter of CDC20, which putatively disrupt an ETS motif, lead to lower transcriptional activity in reporter assays. Using CRISPR/Cas9, we generated an indel in the CDC20 promoter in human A375 melanoma cell lines and observed decreased expression of CDC20, changes in migration capabilities, increased growth of xenografts, and an altered transcriptional state previously associated with a more proliferative and less migratory state. Overall, our analysis prioritized several recurrent functional non-coding variants that, through downregulation of CDC20, led to perturbation of key melanoma phenotypes.
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Affiliation(s)
- Paula M Godoy
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Abimbola Oyedeji
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
| | - Jacqueline L Mudd
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
| | - Vasilios A Morikis
- Departments of Medicine (Oncology) and Cell Biology and Physiology and the ICCE Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anna P Zarov
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gregory D Longmore
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
- Departments of Medicine (Oncology) and Cell Biology and Physiology and the ICCE Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ryan C Fields
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
| | - Charles K Kaufman
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA.
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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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Skinner OS, Blanco-Fernández J, Goodman RP, Kawakami A, Shen H, Kemény LV, Joesch-Cohen L, Rees MG, Roth JA, Fisher DE, Mootha VK, Jourdain AA. Salvage of ribose from uridine or RNA supports glycolysis in nutrient-limited conditions. Nat Metab 2023; 5:765-776. [PMID: 37198474 PMCID: PMC10229423 DOI: 10.1038/s42255-023-00774-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/03/2023] [Indexed: 05/19/2023]
Abstract
Glucose is vital for life, serving as both a source of energy and carbon building block for growth. When glucose is limiting, alternative nutrients must be harnessed. To identify mechanisms by which cells can tolerate complete loss of glucose, we performed nutrient-sensitized genome-wide genetic screens and a PRISM growth assay across 482 cancer cell lines. We report that catabolism of uridine from the medium enables the growth of cells in the complete absence of glucose. While previous studies have shown that uridine can be salvaged to support pyrimidine synthesis in the setting of mitochondrial oxidative phosphorylation deficiency1, our work demonstrates that the ribose moiety of uridine or RNA can be salvaged to fulfil energy requirements via a pathway based on: (1) the phosphorylytic cleavage of uridine by uridine phosphorylase UPP1/UPP2 into uracil and ribose-1-phosphate (R1P), (2) the conversion of uridine-derived R1P into fructose-6-P and glyceraldehyde-3-P by the non-oxidative branch of the pentose phosphate pathway and (3) their glycolytic utilization to fuel ATP production, biosynthesis and gluconeogenesis. Capacity for glycolysis from uridine-derived ribose appears widespread, and we confirm its activity in cancer lineages, primary macrophages and mice in vivo. An interesting property of this pathway is that R1P enters downstream of the initial, highly regulated steps of glucose transport and upper glycolysis. We anticipate that 'uridine bypass' of upper glycolysis could be important in the context of disease and even exploited for therapeutic purposes.
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Affiliation(s)
- Owen S Skinner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Russell P Goodman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Akinori Kawakami
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Hongying Shen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
- Yale Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Lajos V Kemény
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
- Department of Dermatology, Venereology and Dermatooncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | | | | | | | - David E Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Vamsi K Mootha
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Alexis A Jourdain
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
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7
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Zhao L, Han H, Li Y, Pang Q. Effects of MITF on marker protein expression of multivesicular bodies and miRNA omics of extracellular vesicles of mice melanocyte cell line. Acta Histochem 2023; 125:152011. [PMID: 36736273 DOI: 10.1016/j.acthis.2023.152011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 01/29/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023]
Abstract
Extracellular vesicles (EVs) are heterogeneous membrane-bound complexes of cell-derived and nanosized structures originating from the endosomal system and subsequently released from the plasma membrane. EVs contribute significantly to intercellular communication and are involved in pigmentation processes that rely on tight communication between keratinocytes and melanocytes in the epidermis. Microphthalmia-associated transcription factor (MITF) induces melanogenesis and modulates the expression factors involved in melanosome biogenesis, maturation and dispersal in melanocytes. Here, we evaluated the effects of MITF on the fate of multivesicular bodies and the biogenesis of extracellular vesicles of melanocytes. It was found that MITF increased the expression of subunits of the endosomal sorting complex, required for transport (ESCRT), including VPS37, VPS36B, and tetraspanin CD81, which are key mediators of multivesicular body biogenesis. Over 110 miRNAs, including miR-211-5p, miR-335-5p, let-7g-5p and miR-28a-3p, were differentially expressed in melanocyte-derived EVs after overexpression of MITF in melanocytes. These miRNAs have been reported to be key regulators of plasma protein binding, changes in the cell membrane system and transferase activity. These results suggest that while enhancing melanogenesis, melanocytes may mediate intercellular communication with surrounding cells by serving as EV delivery vehicles.
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Affiliation(s)
- Lijun Zhao
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, Shanxi Province, China; National & Local Joint Engineering Laboratory of Stem Cell and Biotherapy, Henan Hualong Biotechnology Company LTD, Xinxiang 453000, Henan Province, China.
| | - Hongyu Han
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, Shanxi Province, China.
| | - Yang Li
- National & Local Joint Engineering Laboratory of Stem Cell and Biotherapy, Henan Hualong Biotechnology Company LTD, Xinxiang 453000, Henan Province, China.
| | - Quanhai Pang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, Shanxi Province, China.
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8
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Lee HJ, Kim SH, Kim YH, Kim SH, Oh GS, Bae JE, Kim JB, Park NY, Park K, Yeom E, Jeong K, Kim P, Jo DS, Cho DH. Nalfurafine Hydrochloride, a κ-Opioid Receptor Agonist, Induces Melanophagy via PKA Inhibition in B16F1 Cells. Cells 2022; 12:cells12010146. [PMID: 36611940 PMCID: PMC9818167 DOI: 10.3390/cells12010146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/01/2023] Open
Abstract
Selective autophagy controls cellular homeostasis by degrading unnecessary or damaged cellular components. Melanosomes are specialized organelles that regulate the biogenesis, storage, and transport of melanin in melanocytes. However, the mechanisms underlying melanosomal autophagy, known as the melanophagy pathway, are poorly understood. To better understand the mechanism of melanophagy, we screened an endocrine-hormone chemical library and identified nalfurafine hydrochlorides, a κ-opioid receptor agonist, as a potent inducer of melanophagy. Treatment with nalfurafine hydrochloride increased autophagy and reduced melanin content in alpha-melanocyte-stimulating hormone (α-MSH)-treated cells. Furthermore, inhibition of autophagy blocked melanosomal degradation and reversed the nalfurafine hydrochloride-induced decrease in melanin content in α-MSH-treated cells. Consistently, treatment with other κ-opioid receptor agonists, such as MCOPPB or mianserin, inhibited excessive melanin production but induced autophagy in B16F1 cells. Furthermore, nalfurafine hydrochloride inhibited protein kinase A (PKA) activation, which was notably restored by forskolin, a PKA activator. Additionally, forskolin treatment further suppressed melanosomal degradation as well as the anti-pigmentation activity of nalfurafine hydrochloride in α-MSH-treated cells. Collectively, our data suggest that stimulation of κ-opioid receptors induces melanophagy by inhibiting PKA activation in α-MSH-treated B16F1 cells.
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Affiliation(s)
- Ha Jung Lee
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seong Hyun Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yong Hwan Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - So Hyun Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Gyeong Seok Oh
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ji-Eun Bae
- Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Joon Bum Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Na Yeon Park
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyuhee Park
- Bio-center, Gyeonggido Business & Science Accelerator, Gyeonggido, Suwon 16229, Republic of Korea
| | - Eunbyul Yeom
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kwiwan Jeong
- Bio-center, Gyeonggido Business & Science Accelerator, Gyeonggido, Suwon 16229, Republic of Korea
| | - Pansoo Kim
- Bio-center, Gyeonggido Business & Science Accelerator, Gyeonggido, Suwon 16229, Republic of Korea
| | - Doo Sin Jo
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Correspondence: (D.S.J.); (D.-H.C.); Tel.: +82-53-950-5382 (D.S.J. & D.-H.C.)
| | - Dong-Hyung Cho
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
- OGASIS Corp. 260, Changyong-daero, Yongtong-gu, Suwon 08826, Republic of Korea
- Correspondence: (D.S.J.); (D.-H.C.); Tel.: +82-53-950-5382 (D.S.J. & D.-H.C.)
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9
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Xing L, Liu S, Zhang L, Yang H, Sun L. MITF Contributes to the Body Color Differentiation of Sea Cucumbers Apostichopus japonicus through Expression Differences and Regulation of Downstream Genes. BIOLOGY 2022; 12:biology12010001. [PMID: 36671694 PMCID: PMC9854957 DOI: 10.3390/biology12010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Melanin, which is a pigment produced in melanocytes, is an important contributor to sea cucumber body color. MITF is one of the most critical genes in melanocyte development and melanin synthesis pathways. However, how MITF regulates body color and differentiation in sea cucumbers is poorly understood. In this study, we analyzed the expression level and location of MITF in white, purple, and green sea cucumbers and identified the genes regulated by MITF using chromatin immunoprecipitation followed by sequencing. The mRNA and protein expression levels of MITF were all highest in purple morphs and lowest in white morphs. In situ hybridization indicated that MITF mRNA were mainly expressed in the epidermis. We also identified 984, 732, and 1191 peaks of MITF binding in green, purple, and white sea cucumbers, which were associated with 727, 557, and 887 genes, respectively. Our findings suggested that MITF contributed to the body color differentiation of green, purple, and white sea cucumbers through expression differences and regulation of downstream genes. These results provided a basis for future studies to determine the mechanisms underlying body color formation and provided insights into gene regulation in sea cucumbers.
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Affiliation(s)
- Lili Xing
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilin Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430071, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel./Fax: +86-532-8289-8610
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10
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Chauhan JS, Hölzel M, Lambert JP, Buffa FM, Goding CR. The MITF regulatory network in melanoma. Pigment Cell Melanoma Res 2022; 35:517-533. [PMID: 35771179 PMCID: PMC9545041 DOI: 10.1111/pcmr.13053] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/09/2022] [Accepted: 06/28/2022] [Indexed: 12/02/2022]
Abstract
Bidirectional interactions between plastic tumor cells and the microenvironment critically impact tumor evolution and metastatic dissemination by enabling cancer cells to adapt to microenvironmental stresses by switching phenotype. In melanoma, a key determinant of phenotypic identity is the microphthalmia‐associated transcription factor MITF that promotes proliferation, suppresses senescence, and anticorrelates with immune infiltration and therapy resistance. What determines whether MITF can activate or repress genes associated with specific phenotypes, or how signaling regulating MITF might impact immune infiltration is poorly understood. Here, we find that MITF binding to genes associated with high MITF is via classical E/M‐box motifs, but genes downregulated when MITF is high contain FOS/JUN/AP1/ATF3 sites. Significantly, the repertoire of MITF‐interacting factors identified here includes JUN and ATF3 as well as many previously unidentified interactors. As high AP1 activity is a hallmark of MITFLow, invasive, slow‐cycling, therapy resistant cells, the ability of MITF to repress AP1‐regulated genes provides an insight into how MITF establishes and maintains a pro‐proliferative phenotype. Moreover, although β‐catenin has been linked to immune exclusion, many Hallmark β‐catenin signaling genes are associated with immune infiltration. Instead, low MITF together with Notch signaling is linked to immune infiltration in both mouse and human melanoma tumors.
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Affiliation(s)
- Jagat S Chauhan
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Michael Hölzel
- Institute of Experimental Oncology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Quebec, Canada.,Endocrinology - Nephrology Axis, CHU de Québec - Université Laval Research Center, QC, Canada.,CHU de Québec Research Center, CHUL, 2705 Boulevard Laurier, Quebec, Canada
| | - Francesca M Buffa
- Department of Oncology, University of Oxford, Headington, Oxford, UK
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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11
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Colombo S, Petit V, Wagner RY, Champeval D, Yajima I, Gesbert F, Aktary Z, Davidson I, Delmas V, Larue L. Stabilization of β-catenin promotes melanocyte specification at the expense of the Schwann cell lineage. Development 2021; 149:274086. [PMID: 34878101 PMCID: PMC8917410 DOI: 10.1242/dev.194407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/25/2021] [Indexed: 11/20/2022]
Abstract
The canonical Wnt/β-catenin pathway governs a multitude of developmental processes in various cell lineages, including the melanocyte lineage. Indeed, β-catenin regulates transcription of Mitf-M, the master regulator of this lineage. The first wave of melanocytes to colonize the skin is directly derived from neural crest cells, whereas the second wave of melanocytes is derived from Schwann cell precursors (SCPs). We investigated the influence of β-catenin in the development of melanocytes of the first and second waves by generating mice expressing a constitutively active form of β-catenin in cells expressing tyrosinase. Constitutive activation of β-catenin did not affect the development of truncal melanoblasts but led to marked hyperpigmentation of the paws. By activating β-catenin at various stages of development (E8.5-E11.5), we showed that the activation of β-catenin in bipotent SCPs favored melanoblast specification at the expense of Schwann cells in the limbs within a specific temporal window. Furthermore, in vitro hyperactivation of the Wnt/β-catenin pathway, which is required for melanocyte development, induces activation of Mitf-M, in turn repressing FoxD3 expression. In conclusion, β-catenin overexpression promotes SCP cell fate decisions towards the melanocyte lineage. Summary: Activation of β-catenin in bipotent Schwann cell precursors during a specific developmental window induces Mitf and represses FoxD3 to promote melanoblast cell fate at the expense of Schwann cells in limbs.
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Affiliation(s)
- Sophie Colombo
- Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, Orsay, France.,Univ Paris-Sud, Univ Paris-Saclay, CNRS UMR 3347, Orsay, France.,Equipes Labellisées Ligue Contre le Cancer, France
| | - Valérie Petit
- Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, Orsay, France.,Univ Paris-Sud, Univ Paris-Saclay, CNRS UMR 3347, Orsay, France.,Equipes Labellisées Ligue Contre le Cancer, France
| | - Roselyne Y Wagner
- Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, Orsay, France.,Univ Paris-Sud, Univ Paris-Saclay, CNRS UMR 3347, Orsay, France.,Equipes Labellisées Ligue Contre le Cancer, France
| | - Delphine Champeval
- Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, Orsay, France.,Univ Paris-Sud, Univ Paris-Saclay, CNRS UMR 3347, Orsay, France.,Equipes Labellisées Ligue Contre le Cancer, France
| | - Ichiro Yajima
- Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, Orsay, France.,Univ Paris-Sud, Univ Paris-Saclay, CNRS UMR 3347, Orsay, France.,Equipes Labellisées Ligue Contre le Cancer, France
| | - Franck Gesbert
- Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, Orsay, France.,Univ Paris-Sud, Univ Paris-Saclay, CNRS UMR 3347, Orsay, France.,Equipes Labellisées Ligue Contre le Cancer, France
| | - Zackie Aktary
- Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, Orsay, France.,Univ Paris-Sud, Univ Paris-Saclay, CNRS UMR 3347, Orsay, France.,Equipes Labellisées Ligue Contre le Cancer, France
| | - Irwin Davidson
- Equipes Labellisées Ligue Contre le Cancer, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404 Illkirch Cedex. Department of Functional Genomics and Cancer, France
| | - Véronique Delmas
- Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, Orsay, France.,Univ Paris-Sud, Univ Paris-Saclay, CNRS UMR 3347, Orsay, France.,Equipes Labellisées Ligue Contre le Cancer, France
| | - Lionel Larue
- Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, Orsay, France.,Univ Paris-Sud, Univ Paris-Saclay, CNRS UMR 3347, Orsay, France.,Equipes Labellisées Ligue Contre le Cancer, France
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12
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Cho H, Shen Q, Zhang LH, Okumura M, Kawakami A, Ambrose J, Sigoillot F, Miller HR, Gleim S, Cobos-Correa A, Wang Y, Piechon P, Roma G, Eggimann F, Moore C, Aspesi P, Mapa FA, Burks H, Ross NT, Krastel P, Hild M, Maimone TJ, Fisher DE, Nomura DK, Tallarico JA, Canham SM, Jenkins JL, Forrester WC. CYP27A1-dependent anti-melanoma activity of limonoid natural products targets mitochondrial metabolism. Cell Chem Biol 2021; 28:1407-1419.e6. [PMID: 33794192 DOI: 10.1016/j.chembiol.2021.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/24/2021] [Accepted: 03/09/2021] [Indexed: 01/18/2023]
Abstract
Three limonoid natural products with selective anti-proliferative activity against BRAF(V600E) and NRAS(Q61K)-mutation-dependent melanoma cell lines were identified. Differential transcriptome analysis revealed dependency of compound activity on expression of the mitochondrial cytochrome P450 oxidase CYP27A1, a transcriptional target of melanogenesis-associated transcription factor (MITF). We determined that CYP27A1 activity is necessary for the generation of a reactive metabolite that proceeds to inhibit cellular proliferation. A genome-wide small interfering RNA screen in combination with chemical proteomics experiments revealed gene-drug functional epistasis, suggesting that these compounds target mitochondrial biogenesis and inhibit tumor bioenergetics through a covalent mechanism. Our work suggests a strategy for melanoma-specific targeting by exploiting the expression of MITF target gene CYP27A1 and inhibiting mitochondrial oxidative phosphorylation in BRAF mutant melanomas.
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Affiliation(s)
- Hyelim Cho
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Qiong Shen
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Lydia H Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Mikiko Okumura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Akinori Kawakami
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jessi Ambrose
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Frederic Sigoillot
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Howard R Miller
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Scott Gleim
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Amanda Cobos-Correa
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Ying Wang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Philippe Piechon
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Fabian Eggimann
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Charles Moore
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Peter Aspesi
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Felipa A Mapa
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Heather Burks
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Nathan T Ross
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Philipp Krastel
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Marc Hild
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Thomas J Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - David E Fisher
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94720, USA
| | - John A Tallarico
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Stephen M Canham
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Jeremy L Jenkins
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - William C Forrester
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
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13
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Melixetian M, Bossi D, Mihailovich M, Punzi S, Barozzi I, Marocchi F, Cuomo A, Bonaldi T, Testa G, Marine JC, Leucci E, Minucci S, Pelicci PG, Lanfrancone L. Long non-coding RNA TINCR suppresses metastatic melanoma dissemination by preventing ATF4 translation. EMBO Rep 2021; 22:e50852. [PMID: 33586907 PMCID: PMC7926219 DOI: 10.15252/embr.202050852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 12/20/2022] Open
Abstract
Transition from proliferative‐to‐invasive phenotypes promotes metastasis and therapy resistance in melanoma. Reversion of the invasive phenotype, however, is challenged by the poor understanding of mechanisms underlying its maintenance. Here, we report that the lncRNA TINCR is down‐regulated in metastatic melanoma and its silencing increases the expression levels of invasive markers, in vitro migration, in vivo tumor growth, and resistance to BRAF and MEK inhibitors. The critical mediator is ATF4, a central player of the integrated stress response (ISR), which is activated in TINCR‐depleted cells in the absence of starvation and eIF2α phosphorylation. TINCR depletion increases global protein synthesis and induces translational reprogramming, leading to increased translation of mRNAs encoding ATF4 and other ISR proteins. Strikingly, re‐expression of TINCR in metastatic melanoma suppresses the invasive phenotype, reduces numbers of tumor‐initiating cells and metastasis formation, and increases drug sensitivity. Mechanistically, TINCR interacts with mRNAs associated with the invasive phenotype, including ATF4, preventing their binding to ribosomes. Thus, TINCR is a suppressor of the melanoma invasive phenotype, which functions in nutrient‐rich conditions by repressing translation of selected ISR RNAs.
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Affiliation(s)
- Marine Melixetian
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Daniela Bossi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Marija Mihailovich
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Simona Punzi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Federica Marocchi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giuseppe Testa
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Department of Oncology, KULeuven, Leuven, Belgium.,Center for Cancer Biology, VIB, Leuven, Belgium
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, KULeuven, Leuven, Belgium
| | - Saverio Minucci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Biosciences, University of Milan, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Luisa Lanfrancone
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
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14
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Dilshat R, Fock V, Kenny C, Gerritsen I, Lasseur RMJ, Travnickova J, Eichhoff OM, Cerny P, Möller K, Sigurbjörnsdóttir S, Kirty K, Einarsdottir BÓ, Cheng PF, Levesque M, Cornell RA, Patton EE, Larue L, de Tayrac M, Magnúsdóttir E, Ögmundsdóttir MH, Steingrimsson E. MITF reprograms the extracellular matrix and focal adhesion in melanoma. eLife 2021; 10:e63093. [PMID: 33438577 PMCID: PMC7857731 DOI: 10.7554/elife.63093] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/11/2021] [Indexed: 12/20/2022] Open
Abstract
The microphthalmia-associated transcription factor (MITF) is a critical regulator of melanocyte development and differentiation. It also plays an important role in melanoma where it has been described as a molecular rheostat that, depending on activity levels, allows reversible switching between different cellular states. Here, we show that MITF directly represses the expression of genes associated with the extracellular matrix (ECM) and focal adhesion pathways in human melanoma cells as well as of regulators of epithelial-to-mesenchymal transition (EMT) such as CDH2, thus affecting cell morphology and cell-matrix interactions. Importantly, we show that these effects of MITF are reversible, as expected from the rheostat model. The number of focal adhesion points increased upon MITF knockdown, a feature observed in drug-resistant melanomas. Cells lacking MITF are similar to the cells of minimal residual disease observed in both human and zebrafish melanomas. Our results suggest that MITF plays a critical role as a repressor of gene expression and is actively involved in shaping the microenvironment of melanoma cells in a cell-autonomous manner.
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Affiliation(s)
- Ramile Dilshat
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of IcelandReykjavikIceland
| | - Valerie Fock
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of IcelandReykjavikIceland
| | - Colin Kenny
- Department of Anatomy and Cell biology, Carver College of Medicine, University of IowaIowa CityUnited States
| | - Ilse Gerritsen
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of IcelandReykjavikIceland
| | - Romain Maurice Jacques Lasseur
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of IcelandReykjavikIceland
| | - Jana Travnickova
- MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit, University of EdinburghEdinburghUnited Kingdom
| | - Ossia M Eichhoff
- Department of Dermatology, University Hospital ZurichZurichSwitzerland
| | - Philipp Cerny
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of IcelandReykjavikIceland
| | - Katrin Möller
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of IcelandReykjavikIceland
| | - Sara Sigurbjörnsdóttir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of IcelandReykjavikIceland
| | - Kritika Kirty
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of IcelandReykjavikIceland
| | - Berglind Ósk Einarsdottir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of IcelandReykjavikIceland
| | - Phil F Cheng
- Department of Dermatology, University Hospital ZurichZurichSwitzerland
| | - Mitchell Levesque
- Department of Dermatology, University Hospital ZurichZurichSwitzerland
| | - Robert A Cornell
- Department of Anatomy and Cell biology, Carver College of Medicine, University of IowaIowa CityUnited States
| | - E Elizabeth Patton
- MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit, University of EdinburghEdinburghUnited Kingdom
| | - Lionel Larue
- Institut Curie, CNRS UMR3347, INSERM U1021, Centre UniversitaireOrsayFrance
| | - Marie de Tayrac
- Service de Génétique Moléculaire et Génomique, CHURennesFrance
- Univ Rennes1, CNRS, IGDR (Institut de Génétique et Développement de Rennes)RennesFrance
| | - Erna Magnúsdóttir
- Department of Anatomy, BioMedical Center, Faculty of Medicine, University of IcelandReykjavikIceland
| | - Margrét Helga Ögmundsdóttir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of IcelandReykjavikIceland
| | - Eirikur Steingrimsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of IcelandReykjavikIceland
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15
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Ballotti R, Cheli Y, Bertolotto C. The complex relationship between MITF and the immune system: a Melanoma ImmunoTherapy (response) Factor? Mol Cancer 2020; 19:170. [PMID: 33276788 PMCID: PMC7718690 DOI: 10.1186/s12943-020-01290-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/29/2020] [Indexed: 12/18/2022] Open
Abstract
The clinical benefit of immune checkpoint inhibitory therapy (ICT) in advanced melanomas is limited by primary and acquired resistance. The molecular determinants of the resistance have been extensively studied, but these discoveries have not yet been translated into therapeutic benefits. As such, a paradigm shift in melanoma treatment, to surmount the therapeutic impasses linked to the resistance, is an important ongoing challenge.This review outlines the multifaceted interplay between microphthalmia-associated transcription factor (MITF), a major determinant of the biology of melanoma cells, and the immune system. In melanomas, MITF functions downstream oncogenic pathways and microenvironment stimuli that restrain the immune responses. We highlight how MITF, by controlling differentiation and genome integrity, may regulate melanoma-specific antigen expression by interfering with the endolysosomal pathway, KARS1, and antigen processing and presentation. MITF also modulates the expression of coinhibitory receptors, i.e., PD-L1 and HVEM, and the production of an inflammatory secretome, which directly affects the infiltration and/or activation of the immune cells.Furthermore, MITF is also a key determinant of melanoma cell plasticity and tumor heterogeneity, which are undoubtedly one of the major hurdles for an effective immunotherapy. Finally, we briefly discuss the role of MITF in kidney cancer, where it also plays a key role, and in immune cells, establishing MITF as a central mediator in the regulation of immune responses in melanoma and other cancers.We propose that a better understanding of MITF and immune system intersections could help in the tailoring of current ICT in melanomas and pave the way for clinical benefits and long-lasting responses.
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Affiliation(s)
- Robert Ballotti
- Université Côte d'Azur, Nice, France
- Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2019, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Yann Cheli
- Université Côte d'Azur, Nice, France
- Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2019, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Corine Bertolotto
- Université Côte d'Azur, Nice, France.
- Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2019, Centre Méditerranéen de Médecine Moléculaire, Nice, France.
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16
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Hsiao YJ, Chang WH, Chen HY, Hsu YC, Chiu SC, Chiang CC, Chang GC, Chen YJ, Wang CY, Chen YM, Lin CY, Chen YJ, Yang PC, Chen JJW, Yu SL. MITF functions as a tumor suppressor in non-small cell lung cancer beyond the canonically oncogenic role. Aging (Albany NY) 2020; 13:646-674. [PMID: 33293474 PMCID: PMC7835003 DOI: 10.18632/aging.202171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Abstract
Microphthalamia-associated transcription factor (MITF) is a critical mediator in melanocyte differentiation and exerts oncogenic functions in melanoma progression. However, the role of MITF in non-small cell lung cancer (NSCLC) is still unknown. We found that MITF is dominantly expressed in the low-invasive CL1-0 lung adenocarcinoma cells and paired adjacent normal lung tissues. MITF expression is significantly associated with better overall survival and disease-free survival in NSCLC and serves as an independent prognostic marker. Silencing MITF promotes tumor cell migration, invasion and colony formation in lung adenocarcinoma cells. In xenograft mouse model, MITF knockdown enhances metastasis and tumorigenesis, but decreases angiogenesis in the Matrigel plug assay. Whole transcriptome profiling of the landscape of MITF regulation in lung adenocarcinoma indicates that MITF is involved in cell development, cell cycle, inflammation and WNT signaling pathways. Chromatin immunoprecipitation assays revealed that MITF targets the promoters of FZD7, PTGR1 and ANXA1. Moreover, silencing FZD7 reduces the invasiveness that is promoted by silencing MITF. Strikingly, MITF has significantly inverse correlations with the expression of its downstream genes in lung adenocarcinoma. In summary, we demonstrate the suppressive role of MITF in lung cancer progression, which is opposite to the canonical oncogenic function of MITF in melanoma.
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Affiliation(s)
- Yi-Jing Hsiao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Hsin Chang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsuan-Yu Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Yin-Chen Hsu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Su-Chin Chiu
- Inservice Master Program in Life Sciences, College of Life Sciences, National Chung-Hsing University, Taichung, Taiwan
| | - Ching-Cheng Chiang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Gee-Chen Chang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yi-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chia-Yu Wang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yan-Ming Chen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chien-Yu Lin
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Pan-Chyr Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jeremy J W Chen
- Institute of Biomedical Sciences, National Chung-Hsing University, Taichung, Taiwan
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Centers for Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
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17
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Human Endogenous Retrovirus K Rec forms a Regulatory Loop with MITF that Opposes the Progression of Melanoma to an Invasive Stage. Viruses 2020; 12:v12111303. [PMID: 33202765 PMCID: PMC7696977 DOI: 10.3390/v12111303] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/19/2022] Open
Abstract
The HML2 subfamily of HERV-K (henceforth HERV-K) represents the most recently endogenized retrovirus in the human genome. While the products of certain HERV-K genomic copies are expressed in normal tissues, they are upregulated in several pathological conditions, including various tumors. It remains unclear whether HERV-K(HML2)-encoded products overexpressed in cancer contribute to disease progression or are merely by-products of tumorigenesis. Here, we focus on the regulatory activities of the Long Terminal Repeats (LTR5_Hs) of HERV-K and the potential role of the HERV-K-encoded Rec in melanoma. Our regulatory genomics analysis of LTR5_Hs loci indicates that Melanocyte Inducing Transcription Factor (MITF) (also known as binds to a canonical E-box motif (CA(C/T)GTG) within these elements in proliferative type of melanoma, and that depletion of MITF results in reduced HERV-K expression. In turn, experimentally depleting Rec in a proliferative melanoma cell line leads to lower mRNA levels of MITF and its predicted target genes. Furthermore, Rec knockdown leads to an upregulation of epithelial-to-mesenchymal associated genes and an enhanced invasion phenotype of proliferative melanoma cells. Together these results suggest the existence of a regulatory loop between MITF and Rec that may modulate the transition from proliferative to invasive stages of melanoma. Because HERV-K(HML2) elements are restricted to hominoid primates, these findings might explain certain species-specific features of melanoma progression and point to some limitations of animal models in melanoma studies.
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18
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Ballesteros-Álvarez J, Dilshat R, Fock V, Möller K, Karl L, Larue L, Ögmundsdóttir MH, Steingrímsson E. MITF and TFEB cross-regulation in melanoma cells. PLoS One 2020; 15:e0238546. [PMID: 32881934 PMCID: PMC7470386 DOI: 10.1371/journal.pone.0238546] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/18/2020] [Indexed: 01/24/2023] Open
Abstract
The MITF, TFEB, TFE3 and TFEC (MiT-TFE) proteins belong to the basic helix-loop-helix family of leucine zipper transcription factors. MITF is crucial for melanocyte development and differentiation, and has been termed a lineage-specific oncogene in melanoma. The three related proteins MITF, TFEB and TFE3 have been shown to be involved in the biogenesis and function of lysosomes and autophagosomes, regulating cellular clearance pathways. Here we investigated the cross-regulatory relationship of MITF and TFEB in melanoma cells. Like MITF, the TFEB and TFE3 genes are expressed in melanoma cells as well as in melanoma tumors, albeit at lower levels. We show that the MITF and TFEB proteins, but not TFE3, directly affect each other's mRNA and protein expression. In addition, the subcellular localization of MITF and TFEB is subject to regulation by the mTOR signaling pathway, which impacts their cross-regulatory relationship at the transcriptional level. Our work shows that the relationship between MITF and TFEB is multifaceted and that the cross-regulatory interactions of these factors need to be taken into account when considering pathways regulated by these proteins.
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Affiliation(s)
- Josué Ballesteros-Álvarez
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavík, Iceland
| | - Ramile Dilshat
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavík, Iceland
| | - Valerie Fock
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavík, Iceland
| | - Katrín Möller
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavík, Iceland
| | - Ludwig Karl
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavík, Iceland
| | - Lionel Larue
- Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- Univ Paris-Sud, Univ Paris-Saclay, CNRS UMR 3347, Orsay, France
- Equipe Labellisée Ligue Contre le Cancer
| | | | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavík, Iceland
- * E-mail:
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19
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Johansson JA, Marie KL, Lu Y, Brombin A, Santoriello C, Zeng Z, Zich J, Gautier P, von Kriegsheim A, Brunsdon H, Wheeler AP, Dreger M, Houston DR, Dooley CM, Sims AH, Busch-Nentwich EM, Zon LI, Illingworth RS, Patton EE. PRL3-DDX21 Transcriptional Control of Endolysosomal Genes Restricts Melanocyte Stem Cell Differentiation. Dev Cell 2020; 54:317-332.e9. [PMID: 32652076 PMCID: PMC7435699 DOI: 10.1016/j.devcel.2020.06.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/06/2020] [Accepted: 06/09/2020] [Indexed: 01/22/2023]
Abstract
Melanocytes, replenished throughout life by melanocyte stem cells (MSCs), play a critical role in pigmentation and melanoma. Here, we reveal a function for the metastasis-associated phosphatase of regenerating liver 3 (PRL3) in MSC regeneration. We show that PRL3 binds to the RNA helicase DDX21, thereby restricting productive transcription by RNAPII at master transcription factor (MITF)-regulated endolysosomal vesicle genes. In zebrafish, this mechanism controls premature melanoblast expansion and differentiation from MSCs. In melanoma patients, restricted transcription of this endolysosomal vesicle pathway is a hallmark of PRL3-high melanomas. Our work presents the conceptual advance that PRL3-mediated control of transcriptional elongation is a differentiation checkpoint mechanism for activated MSCs and has clinical relevance for the activity of PRL3 in regenerating tissue and cancer.
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Affiliation(s)
- Jeanette A Johansson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Kerrie L Marie
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuting Lu
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Alessandro Brombin
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Cristina Santoriello
- Stem Cell Program and Division of Hematology, Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, USA
| | - Zhiqiang Zeng
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Judith Zich
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Alex von Kriegsheim
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Hannah Brunsdon
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ann P Wheeler
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Marcel Dreger
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Douglas R Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology, Waddington Building, King's Buildings, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Christopher M Dooley
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Max-Planck-Institute for Developmental Biology, Department ECNV, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Andrew H Sims
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Elisabeth M Busch-Nentwich
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology, Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, USA
| | - Robert S Illingworth
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, UK.
| | - E Elizabeth Patton
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.
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20
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Vanni I, Tanda ET, Dalmasso B, Pastorino L, Andreotti V, Bruno W, Boutros A, Spagnolo F, Ghiorzo P. Non-BRAF Mutant Melanoma: Molecular Features and Therapeutical Implications. Front Mol Biosci 2020; 7:172. [PMID: 32850962 PMCID: PMC7396525 DOI: 10.3389/fmolb.2020.00172] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023] Open
Abstract
Melanoma is one of the most aggressive tumors of the skin, and its incidence is growing worldwide. Historically considered a drug resistant disease, since 2011 the therapeutic landscape of melanoma has radically changed. Indeed, the improved knowledge of the immune system and its interactions with the tumor, and the ever more thorough molecular characterization of the disease, has allowed the development of immunotherapy on the one hand, and molecular target therapies on the other. The increased availability of more performing technologies like Next-Generation Sequencing (NGS), and the availability of increasingly large genetic panels, allows the identification of several potential therapeutic targets. In light of this, numerous clinical and preclinical trials are ongoing, to identify new molecular targets. Here, we review the landscape of mutated non-BRAF skin melanoma, in light of recent data deriving from Whole-Exome Sequencing (WES) or Whole-Genome Sequencing (WGS) studies on melanoma cohorts for which information on the mutation rate of each gene was available, for a total of 10 NGS studies and 992 samples, focusing on available, or in experimentation, targeted therapies beyond those targeting mutated BRAF. Namely, we describe 33 established and candidate driver genes altered with frequency greater than 1.5%, and the current status of targeted therapy for each gene. Only 1.1% of the samples showed no coding mutations, whereas 30% showed at least one mutation in the RAS genes (mostly NRAS) and 70% showed mutations outside of the RAS genes, suggesting potential new roads for targeted therapy. Ongoing clinical trials are available for 33.3% of the most frequently altered genes.
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Affiliation(s)
- Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | | | - Bruna Dalmasso
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | - Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | - Virginia Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | - Andrea Boutros
- Medical Oncology, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
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21
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Lavelle TJ, Alver TN, Heintz KM, Wernhoff P, Nygaard V, Nakken S, Øy GF, Bøe SL, Urbanucci A, Hovig E. Dysregulation of MITF Leads to Transformation in MC1R-Defective Melanocytes. Cancers (Basel) 2020; 12:cancers12071719. [PMID: 32605315 PMCID: PMC7408466 DOI: 10.3390/cancers12071719] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/20/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
The MC1R/cAMP/MITF pathway is a key determinant for growth, differentiation, and survival of melanocytes and melanoma. MITF-M is the melanocyte-specific isoform of Microphthalmia-associated Transcription Factor (MITF) in human melanoma. Here we use two melanocyte cell lines to show that forced expression of hemagglutinin (HA) -tagged MITF-M through lentiviral transduction represents an oncogenic insult leading to consistent cell transformation of the immortalized melanocyte cell line Hermes 4C, being a melanocortin-1 receptor (MC1R) compound heterozygote, while not causing transformation of the MC1R wild type cell line Hermes 3C. The transformed HA-tagged MITF-M transduced Hermes 4C cells form colonies in soft agar and tumors in mice. Further, Hermes 4C cells display increased MITF chromatin binding, and transcriptional reprogramming consistent with an invasive melanoma phenotype. Mechanistically, forced expression of MITF-M drives the upregulation of the AXL tyrosine receptor kinase (AXL), with concomitant downregulation of phosphatase and tensin homolog (PTEN), leading to increased activation of the PI3K/AKT pathway. Treatment with AXL inhibitors reduces growth of the transformed cells by reverting AKT activation. In conclusion, we present a model system of melanoma development, driven by MITF-M in the context of MC1R loss of function, and independent of UV exposure. This model provides a basis for further studies of critical changes in the melanocyte transformation process.
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Affiliation(s)
- Timothy J. Lavelle
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; (T.J.L.); (T.N.A.); (K.-M.H.); (P.W.); (V.N.); (S.N.); (G.F.Ø.)
| | - Tine Norman Alver
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; (T.J.L.); (T.N.A.); (K.-M.H.); (P.W.); (V.N.); (S.N.); (G.F.Ø.)
| | - Karen-Marie Heintz
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; (T.J.L.); (T.N.A.); (K.-M.H.); (P.W.); (V.N.); (S.N.); (G.F.Ø.)
| | - Patrik Wernhoff
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; (T.J.L.); (T.N.A.); (K.-M.H.); (P.W.); (V.N.); (S.N.); (G.F.Ø.)
| | - Vegard Nygaard
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; (T.J.L.); (T.N.A.); (K.-M.H.); (P.W.); (V.N.); (S.N.); (G.F.Ø.)
| | - Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; (T.J.L.); (T.N.A.); (K.-M.H.); (P.W.); (V.N.); (S.N.); (G.F.Ø.)
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0424 Oslo, Norway
| | - Geir Frode Øy
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; (T.J.L.); (T.N.A.); (K.-M.H.); (P.W.); (V.N.); (S.N.); (G.F.Ø.)
| | - Sigurd Leinæs Bøe
- Department of Medical Biochemistry, Oslo University Hospital, Radiumhospitalet, 0424 Oslo, Norway;
| | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; (T.J.L.); (T.N.A.); (K.-M.H.); (P.W.); (V.N.); (S.N.); (G.F.Ø.)
- Correspondence: (A.U.); (E.H.)
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; (T.J.L.); (T.N.A.); (K.-M.H.); (P.W.); (V.N.); (S.N.); (G.F.Ø.)
- Department of Informatics, University of Oslo, 0316 Oslo, Norway
- Correspondence: (A.U.); (E.H.)
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22
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Louphrasitthiphol P, Siddaway R, Loffreda A, Pogenberg V, Friedrichsen H, Schepsky A, Zeng Z, Lu M, Strub T, Freter R, Lisle R, Suer E, Thomas B, Schuster-Böckler B, Filippakopoulos P, Middleton M, Lu X, Patton EE, Davidson I, Lambert JP, Wilmanns M, Steingrímsson E, Mazza D, Goding CR. Tuning Transcription Factor Availability through Acetylation-Mediated Genomic Redistribution. Mol Cell 2020; 79:472-487.e10. [PMID: 32531202 PMCID: PMC7427332 DOI: 10.1016/j.molcel.2020.05.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 04/01/2020] [Accepted: 05/19/2020] [Indexed: 11/06/2022]
Abstract
It is widely assumed that decreasing transcription factor DNA-binding affinity reduces transcription initiation by diminishing occupancy of sequence-specific regulatory elements. However, in vivo transcription factors find their binding sites while confronted with a large excess of low-affinity degenerate motifs. Here, using the melanoma lineage survival oncogene MITF as a model, we show that low-affinity binding sites act as a competitive reservoir in vivo from which transcription factors are released by mitogen-activated protein kinase (MAPK)-stimulated acetylation to promote increased occupancy of their regulatory elements. Consequently, a low-DNA-binding-affinity acetylation-mimetic MITF mutation supports melanocyte development and drives tumorigenesis, whereas a high-affinity non-acetylatable mutant does not. The results reveal a paradoxical acetylation-mediated molecular clutch that tunes transcription factor availability via genome-wide redistribution and couples BRAF to tumorigenesis. Our results further suggest that p300/CREB-binding protein-mediated transcription factor acetylation may represent a common mechanism to control transcription factor availability. Reducing transcription factor DNA-binding affinity increases activity in vivo Acetylation is triggered by MAPK signaling Acetylation leads to genome-wide transcription factor redistribution Acetylation of MITF drives tumorigenesis and melanocyte development
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Affiliation(s)
- Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK; Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Robert Siddaway
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Alessia Loffreda
- Experimental Imaging Center, Cancer Imaging Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy; Fondazione CEN, European Center for Nanomedicine, 20133 Milan, Italy
| | - Vivian Pogenberg
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 25a, 22607 Hamburg, Germany & University Hamburg Medical Centre Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Hans Friedrichsen
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Alexander Schepsky
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK; Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Zhiqiang Zeng
- MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit and Edinburgh Cancer Research UK Centre, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Min Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Thomas Strub
- Institut de Génetique et Biologie Moléculaire et Cellulaire (IGBMC), Equipe labéllisée Ligue contre le Cancer, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Rasmus Freter
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Richard Lisle
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Eda Suer
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Benjamin Thomas
- Central Proteomics Facility, Sir William Dunn Pathology School, Oxford University, Oxford OX1 3RE, UK
| | - Benjamin Schuster-Böckler
- Ludwig Institute for Cancer Research, Big Data Institute, University of Oxford, Headington, Oxford OX3 7LF, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Mark Middleton
- Oxford NIHR Biomedical Research Centre, Department of Oncology, Churchill Hospital, Oxford OX3 7LE, UK
| | - Xin Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - E Elizabeth Patton
- MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit and Edinburgh Cancer Research UK Centre, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Irwin Davidson
- Institut de Génetique et Biologie Moléculaire et Cellulaire (IGBMC), Equipe labéllisée Ligue contre le Cancer, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Quebec, QC, Canada; CHU de Québec Research Center, CHUL, 2705 Boulevard Laurier, Quebec G1V 4G2, QC, Canada
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 25a, 22607 Hamburg, Germany & University Hamburg Medical Centre Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Davide Mazza
- Experimental Imaging Center, Cancer Imaging Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy; Fondazione CEN, European Center for Nanomedicine, 20133 Milan, Italy.
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK.
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23
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Fufa TD, Baxter LL, Wedel JC, Gildea DE, Loftus SK, Pavan WJ. MEK inhibition remodels the active chromatin landscape and induces SOX10 genomic recruitment in BRAF(V600E) mutant melanoma cells. Epigenetics Chromatin 2019; 12:50. [PMID: 31399133 PMCID: PMC6688322 DOI: 10.1186/s13072-019-0297-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/28/2019] [Indexed: 01/03/2023] Open
Abstract
Background The MAPK/ERK signaling pathway is an essential regulator of numerous cell processes that are crucial for normal development as well as cancer progression. While much is known regarding MAPK/ERK signal conveyance from the cell membrane to the nucleus, the transcriptional and epigenetic mechanisms that govern gene expression downstream of MAPK signaling are not fully elucidated. Results This study employed an integrated epigenome analysis approach to interrogate the effects of MAPK/ERK pathway inhibition on the global transcriptome, the active chromatin landscape, and protein–DNA interactions in 501mel melanoma cells. Treatment of these cells with the small-molecule MEK inhibitor AZD6244 induces hyperpigmentation, widespread gene expression changes including alteration of genes linked to pigmentation, and extensive epigenomic reprogramming of transcriptionally distinct regulatory regions associated with the active chromatin mark H3K27ac. Regulatory regions with differentially acetylated H3K27ac regions following AZD6244 treatment are enriched in transcription factor binding motifs of ETV/ETS and ATF family members as well as the lineage-determining factors MITF and SOX10. H3K27ac-dense enhancer clusters known as super-enhancers show similar transcription factor motif enrichment, and furthermore, these super-enhancers are associated with genes encoding MITF, SOX10, and ETV/ETS proteins. Along with genome-wide resetting of the active enhancer landscape, MEK inhibition also results in widespread SOX10 recruitment throughout the genome, including increased SOX10 binding density at H3K27ac-marked enhancers. Importantly, these MEK inhibitor-responsive enhancers marked by H3K27ac and occupied by SOX10 are located near melanocyte lineage-specific and pigmentation genes and overlap numerous human SNPs associated with pigmentation and melanoma phenotypes, highlighting the variants located within these regions for prioritization in future studies. Conclusions These results reveal the epigenetic reprogramming underlying the re-activation of melanocyte pigmentation and developmental transcriptional programs in 501mel cells in response to MEK inhibition and suggest extensive involvement of a MEK-SOX10 axis in the regulation of these processes. The dynamic chromatin changes identified here provide a rich genomic resource for further analyses of the molecular mechanisms governing the MAPK pathway in pigmentation- and melanocyte-associated diseases. Electronic supplementary material The online version of this article (10.1186/s13072-019-0297-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Temesgen D Fufa
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Julia C Wedel
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Derek E Gildea
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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24
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Abstract
In this review, Goding and Arnheiter present the current understanding of MITF's role and regulation in development and disease and highlight key areas where our knowledge of MITF regulation and function is limited. All transcription factors are equal, but some are more equal than others. In the 25 yr since the gene encoding the microphthalmia-associated transcription factor (MITF) was first isolated, MITF has emerged as a key coordinator of many aspects of melanocyte and melanoma biology. Like all transcription factors, MITF binds to specific DNA sequences and up-regulates or down-regulates its target genes. What marks MITF as being remarkable among its peers is the sheer range of biological processes that it appears to coordinate. These include cell survival, differentiation, proliferation, invasion, senescence, metabolism, and DNA damage repair. In this article we present our current understanding of MITF's role and regulation in development and disease, as well as those of the MITF-related factors TFEB and TFE3, and highlight key areas where our knowledge of MITF regulation and function is limited.
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Affiliation(s)
- Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Heinz Arnheiter
- National Institute of Neurological Disorders and Stroke, National Institutes of Heath, Bethesda, Maryland 20824, USA
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25
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MITF has a central role in regulating starvation-induced autophagy in melanoma. Sci Rep 2019; 9:1055. [PMID: 30705290 PMCID: PMC6355916 DOI: 10.1038/s41598-018-37522-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/07/2018] [Indexed: 01/27/2023] Open
Abstract
The MITF transcription factor is a master regulator of melanocyte development and a critical factor in melanomagenesis. The related transcription factors TFEB and TFE3 regulate lysosomal activity and autophagy processes known to be important in melanoma. Here we show that MITF binds the CLEAR-box element in the promoters of lysosomal and autophagosomal genes in melanocytes and melanoma cells. The crystal structure of MITF bound to the CLEAR-box reveals how the palindromic nature of this motif induces symmetric MITF homodimer binding. In metastatic melanoma tumors and cell lines, MITF positively correlates with the expression of lysosomal and autophagosomal genes, which, interestingly, are different from the lysosomal and autophagosomal genes correlated with TFEB and TFE3. Depletion of MITF in melanoma cells and melanocytes attenuates the response to starvation-induced autophagy, whereas the overexpression of MITF in melanoma cells increases the number of autophagosomes but is not sufficient to induce autophagic flux. Our results suggest that MITF and the related factors TFEB and TFE3 have separate roles in regulating a starvation-induced autophagy response in melanoma. Understanding the normal and pathophysiological roles of MITF and related transcription factors may provide important clinical insights into melanoma therapy.
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26
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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: 8] [Impact Index Per Article: 1.3] [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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27
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Genome-wide study of hair colour in UK Biobank explains most of the SNP heritability. Nat Commun 2018; 9:5271. [PMID: 30531825 PMCID: PMC6288091 DOI: 10.1038/s41467-018-07691-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 11/14/2018] [Indexed: 01/22/2023] Open
Abstract
Natural hair colour within European populations is a complex genetic trait. Previous work has established that MC1R variants are the principal genetic cause of red hair colour, but with variable penetrance. Here, we have extensively mapped the genes responsible for hair colour in the white, British ancestry, participants in UK Biobank. MC1R only explains 73% of the SNP heritability for red hair in UK Biobank, and in fact most individuals with two MC1R variants have blonde or light brown hair. We identify other genes contributing to red hair, the combined effect of which accounts for ~90% of the SNP heritability. Blonde hair is associated with over 200 genetic variants and we find a continuum from black through dark and light brown to blonde and account for 73% of the SNP heritability of blonde hair. Many of the associated genes are involved in hair growth or texture, emphasising the cellular connections between keratinocytes and melanocytes in the determination of hair colour. Natural hair colour in Europeans is a complex genetic trait. Here, the authors carry out a genome-wide association study using UK BioBank data, suggesting that in combination with pigmentation genes, variants with roles in hair texture and growth can affect hair colouration or our perception of it.
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28
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Malcov-Brog H, Alpert A, Golan T, Parikh S, Nordlinger A, Netti F, Sheinboim D, Dror I, Thomas L, Cosson C, Gonen P, Stanevsky Y, Brenner R, Perluk T, Frand J, Elgavish S, Nevo Y, Rahat D, Tabach Y, Khaled M, Shen-Orr SS, Levy C. UV-Protection Timer Controls Linkage between Stress and Pigmentation Skin Protection Systems. Mol Cell 2018; 72:444-456.e7. [PMID: 30401431 PMCID: PMC6224604 DOI: 10.1016/j.molcel.2018.09.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 08/15/2018] [Accepted: 09/18/2018] [Indexed: 11/25/2022]
Abstract
Skin sun exposure induces two protection programs: stress responses and pigmentation, the former within minutes and the latter only hours afterward. Although serving the same physiological purpose, it is not known whether and how these programs are coordinated. Here, we report that UVB exposure every other day induces significantly more skin pigmentation than the higher frequency of daily exposure, without an associated increase in stress responses. Using mathematical modeling and empirical studies, we show that the melanocyte master regulator, MITF, serves to synchronize stress responses and pigmentation and, furthermore, functions as a UV-protection timer via damped oscillatory dynamics, thereby conferring a trade-off between the two programs. MITF oscillations are controlled by multiple negative regulatory loops, one at the transcriptional level involving HIF1α and another post-transcriptional loop involving microRNA-148a. These findings support trait linkage between the two skin protection programs, which, we speculate, arose during furless skin evolution to minimize skin damage. UV exposure frequency reveals a trade-off between skin protection programs MITF dynamics synchronize skin stress responses and pigmentation MITF serves as a UV-protection timer Two negative regulatory loops involving miR-148a and HIF1α underlie MITF dynamics
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Affiliation(s)
- Hagar Malcov-Brog
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ayelet Alpert
- Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Tamar Golan
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shivang Parikh
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Alice Nordlinger
- INSERM U1186, Gustave Roussy Cancer Center, Université Paris-Saclay, Villejuif 94805, France
| | - Francesca Netti
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Danna Sheinboim
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Iris Dror
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Laetitia Thomas
- INSERM U1186, Gustave Roussy Cancer Center, Université Paris-Saclay, Villejuif 94805, France
| | - Camille Cosson
- INSERM U1186, Gustave Roussy Cancer Center, Université Paris-Saclay, Villejuif 94805, France
| | - Pinchas Gonen
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | | | | | | | - Jacob Frand
- E. Wolfson Medical Center, Holon 58100, Israel
| | - Sharona Elgavish
- Bioinformatics Unit of the I-CORE Computation Center, Hebrew University, Jerusalem 91120, Israel
| | - Yuval Nevo
- Bioinformatics Unit of the I-CORE Computation Center, Hebrew University, Jerusalem 91120, Israel
| | - Dolev Rahat
- Department of Developmental Biology and Cancer Research, Hadassah Medical School, Hebrew University, Jerusalem 91120, Israel
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, Hadassah Medical School, Hebrew University, Jerusalem 91120, Israel
| | - Mehdi Khaled
- INSERM U1186, Gustave Roussy Cancer Center, Université Paris-Saclay, Villejuif 94805, France.
| | - Shai S Shen-Orr
- Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 3200003, Israel.
| | - Carmit Levy
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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29
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Central role of autophagic UVRAG in melanogenesis and the suntan response. Proc Natl Acad Sci U S A 2018; 115:E7728-E7737. [PMID: 30061422 DOI: 10.1073/pnas.1803303115] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
UV-induced cell pigmentation represents an important mechanism against skin cancers. Sun-exposed skin secretes α-MSH, which induces the lineage-specific transcriptional factor MITF and activates melanogenesis in melanocytes. Here, we show that the autophagic tumor suppressor UVRAG plays an integral role in melanogenesis by interaction with the biogenesis of lysosome-related organelles complex 1 (BLOC-1). This interaction is required for BLOC-1 stability and for BLOC-1-mediated cargo sorting and delivery to melanosomes. Absence of UVRAG dispersed BLOC-1 distribution and activity, resulting in impaired melanogenesis in vitro and defective melanocyte development in zebrafish in vivo. Furthermore, our results establish UVRAG as an important effector for melanocytes' response to α-MSH signaling as a direct target of MITF and reveal the molecular basis underlying the association between oncogenic BRAF and compromised UV protection in melanoma.
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30
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Rodrigues P, Patel SA, Harewood L, Olan I, Vojtasova E, Syafruddin SE, Zaini MN, Richardson EK, Burge J, Warren AY, Stewart GD, Saeb-Parsy K, Samarajiwa SA, Vanharanta S. NF-κB-Dependent Lymphoid Enhancer Co-option Promotes Renal Carcinoma Metastasis. Cancer Discov 2018; 8:850-865. [PMID: 29875134 PMCID: PMC6031301 DOI: 10.1158/2159-8290.cd-17-1211] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 03/26/2018] [Accepted: 05/01/2018] [Indexed: 01/10/2023]
Abstract
Metastases, the spread of cancer cells to distant organs, cause the majority of cancer-related deaths. Few metastasis-specific driver mutations have been identified, suggesting aberrant gene regulation as a source of metastatic traits. However, how metastatic gene expression programs arise is poorly understood. Here, using human-derived metastasis models of renal cancer, we identify transcriptional enhancers that promote metastatic carcinoma progression. Specific enhancers and enhancer clusters are activated in metastatic cancer cell populations, and the associated gene expression patterns are predictive of poor patient outcome in clinical samples. We find that the renal cancer metastasis-associated enhancer complement consists of multiple coactivated tissue-specific enhancer modules. Specifically, we identify and functionally characterize a coregulatory enhancer cluster, activated by the renal cancer driver HIF2A and an NF-κB-driven lymphoid element, as a mediator of metastasis in vivo We conclude that oncogenic pathways can acquire metastatic phenotypes through cross-lineage co-option of physiologic epigenetic enhancer states.Significance: Renal cancer is associated with significant mortality due to metastasis. We show that in metastatic renal cancer, functionally important metastasis genes are activated via co-option of gene regulatory enhancer modules from distant developmental lineages, thus providing clues to the origins of metastatic cancer. Cancer Discov; 8(7); 850-65. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 781.
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Affiliation(s)
- Paulo Rodrigues
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Saroor A Patel
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Louise Harewood
- Cancer Research UK/Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Ioana Olan
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Erika Vojtasova
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Saiful E Syafruddin
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Jalan Yaa'cob Latiff, Bandar Tun Razak, Kuala Lumpur, Malaysia
| | - M Nazhif Zaini
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Emma K Richardson
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Johanna Burge
- Academic Urology Group, Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Grant D Stewart
- Academic Urology Group, Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Shamith A Samarajiwa
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Sakari Vanharanta
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom.
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31
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A direct link between MITF, innate immunity, and hair graying. PLoS Biol 2018; 16:e2003648. [PMID: 29723194 PMCID: PMC5933715 DOI: 10.1371/journal.pbio.2003648] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 03/30/2018] [Indexed: 12/03/2022] Open
Abstract
Melanocyte stem cells (McSCs) and mouse models of hair graying serve as useful systems to uncover mechanisms involved in stem cell self-renewal and the maintenance of regenerating tissues. Interested in assessing genetic variants that influence McSC maintenance, we found previously that heterozygosity for the melanogenesis associated transcription factor, Mitf, exacerbates McSC differentiation and hair graying in mice that are predisposed for this phenotype. Based on transcriptome and molecular analyses of Mitfmi-vga9/+ mice, we report a novel role for MITF in the regulation of systemic innate immune gene expression. We also demonstrate that the viral mimic poly(I:C) is sufficient to expose genetic susceptibility to hair graying. These observations point to a critical suppressor of innate immunity, the consequences of innate immune dysregulation on pigmentation, both of which may have implications in the autoimmune, depigmenting disease, vitiligo. Hair pigmentation over the course of a lifetime depends on melanocyte stem cells that reside in the hair follicle. As old hairs fall out and new hairs grow in, melanocyte stem cells serve as a reservoir for the melanocytes that produce the pigment that gives hair its visible color. The loss of these stem cells leads to the growth of nonpigmented, or gray, hairs. Evaluating mouse models of hair graying can reveal key aspects of melanocyte stem cell biology. Using this approach, we discovered a novel role for the melanogenesis associated transcription factor, MITF, in repressing the expression of innate immune genes within cells of the melanocyte lineage. The importance of this repression is revealed in animals that have a predisposition for hair graying. In these animals, artificial elevation of the innate immune response, either through a genetic mechanism or via exposure to viral mimic, results in significant melanocyte and melanocyte stem cell loss and leads to the production of an increased number of gray hairs. These observations highlight the negative effects of innate immune activation on melanocyte and melanocyte stem cell physiology and suggest a connection between viral infection and hair graying.
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32
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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: 11.5] [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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33
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Noncanonical hedgehog pathway activation through SRF-MKL1 promotes drug resistance in basal cell carcinomas. Nat Med 2018; 24:271-281. [PMID: 29400712 PMCID: PMC5839965 DOI: 10.1038/nm.4476] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 12/19/2017] [Indexed: 12/13/2022]
Abstract
Hedgehog pathway-dependent cancers can escape smoothened (SMO) inhibition
through canonical pathway mutations, however, 50% of resistant BCCs lack
additional variants in hedgehog genes. Here we use multi-dimensional genomics in
human and mouse resistant BCCs to identify a non-canonical hedgehog activation
pathway driven by the transcription factor, serum response factor (SRF). Active
SRF along with its co-activator megakaryoblastic leukemia 1 (MKL1) form a novel
protein complex and share chromosomal occupancy with the hedgehog transcription
factor GLI1, causing amplification of GLI1 transcriptional activity. We show
cytoskeletal activation by Rho and the formin family member Diaphanous (mDia)
are required for SRF/MKL-driven GLI1 activation and tumor cell viability.
Remarkably, we use nuclear MKL1 staining in mouse and human patient tumors to
define drug responsiveness to MKL inhibitors highlighting the therapeutic
potential of targeting this pathway. Thus, our studies illuminate for the first
time cytoskeletal-driven transcription as a personalized therapeutic target to
combat drug resistant malignancies.
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Cohen-Solal KA, Kaufman HL, Lasfar A. Transcription factors as critical players in melanoma invasiveness, drug resistance, and opportunities for therapeutic drug development. Pigment Cell Melanoma Res 2017; 31:241-252. [DOI: 10.1111/pcmr.12666] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 10/19/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Karine A. Cohen-Solal
- Rutgers Cancer Institute of New Jersey; New Brunswick NJ USA
- Section of Surgical Oncology Research; Department of Surgery; Rutgers Robert Wood Johnson Medical School; Rutgers, The State University of New Jersey; New Brunswick NJ USA
| | - Howard L. Kaufman
- Department of Surgery; Rutgers University; New Brunswick NJ USA
- Department of Medicine; Rutgers University; New Brunswick NJ USA
| | - Ahmed Lasfar
- Rutgers Cancer Institute of New Jersey; New Brunswick NJ USA
- Department of Pharmacology and Toxicology; Ernest Mario School of Pharmacy; Rutgers, The State University of New Jersey; Piscataway NJ USA
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Long Noncoding RNA MEG3 Is an Epigenetic Determinant of Oncogenic Signaling in Functional Pancreatic Neuroendocrine Tumor Cells. Mol Cell Biol 2017; 37:MCB.00278-17. [PMID: 28847847 DOI: 10.1128/mcb.00278-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/22/2017] [Indexed: 12/26/2022] Open
Abstract
The long noncoding RNA (lncRNA) MEG3 is significantly downregulated in pancreatic neuroendocrine tumors (PNETs). MEG3 loss corresponds with aberrant upregulation of the oncogenic hepatocyte growth factor (HGF) receptor c-MET in PNETs. Meg3 overexpression in a mouse insulin-secreting PNET cell line, MIN6, downregulates c-Met expression. However, the molecular mechanism by which MEG3 regulates c-MET is not known. Using chromatin isolation by RNA purification and sequencing (ChIRP-Seq), we identified Meg3 binding to unique genomic regions in and around the c-Met gene. In the absence of Meg3, these c-Met regions displayed distinctive enhancer-signature histone modifications. Furthermore, Meg3 relied on functional enhancer of zeste homolog 2 (EZH2), a component of polycomb repressive complex 2 (PRC2), to inhibit c-Met expression. Another mechanism of lncRNA-mediated regulation of gene expression utilized triplex-forming GA-GT rich sequences. Transfection of such motifs from Meg3 RNA, termed triplex-forming oligonucleotides (TFOs), in MIN6 cells suppressed c-Met expression and enhanced cell proliferation, perhaps by modulating other targets. This study comprehensively establishes epigenetic mechanisms underlying Meg3 control of c-Met and the oncogenic consequences of Meg3 loss or c-Met gain. These findings have clinical relevance for targeting c-MET in PNETs. There is also the potential for pancreatic islet β-cell expansion through c-MET regulation to ameliorate β-cell loss in diabetes.
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OCT4 impedes cell fate redirection by the melanocyte lineage master regulator MITF in mouse ESCs. Nat Commun 2017; 8:1022. [PMID: 29044103 PMCID: PMC5647326 DOI: 10.1038/s41467-017-01122-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 08/19/2017] [Indexed: 11/09/2022] Open
Abstract
Ectopic expression of lineage master regulators induces transdifferentiation. Whether cell fate transitions can be induced during various developmental stages has not been systemically examined. Here we discover that amongst different developmental stages, mouse embryonic stem cells (mESCs) are resistant to cell fate conversion induced by the melanocyte lineage master regulator MITF. By generating a transgenic system we exhibit that in mESCs, the pluripotency master regulator Oct4, counteracts pro-differentiation induced by Mitf by physical interference with MITF transcriptional activity. We further demonstrate that mESCs must be released from Oct4-maintained pluripotency prior to ectopically induced differentiation. Moreover, Oct4 induction in various differentiated cells represses their lineage identity in vivo. Alongside, chromatin architecture combined with ChIP-seq analysis suggest that Oct4 competes with various lineage master regulators for binding promoters and enhancers. Our analysis reveals pluripotency and transdifferentiation regulatory principles and could open new opportunities in the field of regenerative medicine.
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Angus SP, Zawistowski JS, Johnson GL. Epigenetic Mechanisms Regulating Adaptive Responses to Targeted Kinase Inhibitors in Cancer. Annu Rev Pharmacol Toxicol 2017; 58:209-229. [PMID: 28934561 DOI: 10.1146/annurev-pharmtox-010617-052954] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although targeted inhibition of oncogenic kinase drivers has achieved remarkable patient responses in many cancers, the development of resistance has remained a significant challenge. Numerous mechanisms have been identified, including the acquisition of gatekeeper mutations, activating pathway mutations, and copy number loss or gain of the driver or alternate nodes. These changes have prompted the development of kinase inhibitors with increased selectivity, use of second-line therapeutics to overcome primary resistance, and combination treatment to forestall resistance. In addition to genomic resistance mechanisms, adaptive transcriptional and signaling responses seen in tumors are gaining appreciation as alterations that lead to a phenotypic state change-often observed as an epithelial-to-mesenchymal shift or reversion to a cancer stem cell-like phenotype underpinned by remodeling of the epigenetic landscape. This epigenomic modulation driving cell state change is multifaceted and includes modulation of repressive and activating histone modifications, DNA methylation, enhancer remodeling, and noncoding RNA species. Consequently, the combination of kinase inhibitors with drugs targeting components of the transcriptional machinery and histone-modifying enzymes has shown promise in preclinical and clinical studies. Here, we review mechanisms of resistance to kinase inhibition in cancer, with special emphasis on the rewired kinome and transcriptional signaling networks and the potential vulnerabilities that may be exploited to overcome these adaptive signaling changes.
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Affiliation(s)
- Steven P Angus
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA; , ,
| | - Jon S Zawistowski
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA; , ,
| | - Gary L Johnson
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA; , ,
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Kim KH, Lee TR, Cho EG. SH3BP4, a novel pigmentation gene, is inversely regulated by miR-125b and MITF. Exp Mol Med 2017; 49:e367. [PMID: 28819321 PMCID: PMC5579509 DOI: 10.1038/emm.2017.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 02/28/2017] [Accepted: 03/05/2017] [Indexed: 12/30/2022] Open
Abstract
Our previous work has identified miR-125b as a negative regulator of melanogenesis. However, the specific melanogenesis-related genes targeted by this miRNA had not been identified. In this study, we established a screening strategy involving three consecutive analytical approaches—analysis of target genes of miR-125b, expression correlation analysis between each target gene and representative pigmentary genes, and functional analysis of candidate genes related to melanogenesis—to discover melanogenesis-related genes targeted by miR-125b. Through these analyses, we identified SRC homology 3 domain-binding protein 4 (SH3BP4) as a novel pigmentation gene. In addition, by combining bioinformatics analysis and experimental validation, we demonstrated that SH3BP4 is a direct target of miR-125b. Finally, we found that SH3BP4 is transcriptionally regulated by microphthalmia-associated transcription factor as its direct target. These findings provide important insights into the roles of miRNAs and their targets in melanogenesis.
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Affiliation(s)
- Kyu-Han Kim
- Basic Research &Innovation Division, R&D Unit, AmorePacific Corporation, Gyeonggi-do, Korea
| | - Tae Ryong Lee
- Basic Research &Innovation Division, R&D Unit, AmorePacific Corporation, Gyeonggi-do, Korea
| | - Eun-Gyung Cho
- Basic Research &Innovation Division, R&D Unit, AmorePacific Corporation, Gyeonggi-do, Korea
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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: 181] [Impact Index Per Article: 25.9] [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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Seberg HE, Van Otterloo E, Loftus SK, Liu H, Bonde G, Sompallae R, Gildea DE, Santana JF, Manak JR, Pavan WJ, Williams T, Cornell RA. TFAP2 paralogs regulate melanocyte differentiation in parallel with MITF. PLoS Genet 2017; 13:e1006636. [PMID: 28249010 PMCID: PMC5352137 DOI: 10.1371/journal.pgen.1006636] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 03/15/2017] [Accepted: 02/14/2017] [Indexed: 12/20/2022] Open
Abstract
Mutations in the gene encoding transcription factor TFAP2A result in pigmentation anomalies in model organisms and premature hair graying in humans. However, the pleiotropic functions of TFAP2A and its redundantly-acting paralogs have made the precise contribution of TFAP2-type activity to melanocyte differentiation unclear. Defining this contribution may help to explain why TFAP2A expression is reduced in advanced-stage melanoma compared to benign nevi. To identify genes with TFAP2A-dependent expression in melanocytes, we profile zebrafish tissue and mouse melanocytes deficient in Tfap2a, and find that expression of a small subset of genes underlying pigmentation phenotypes is TFAP2A-dependent, including Dct, Mc1r, Mlph, and Pmel. We then conduct TFAP2A ChIP-seq in mouse and human melanocytes and find that a much larger subset of pigmentation genes is associated with active regulatory elements bound by TFAP2A. These elements are also frequently bound by MITF, which is considered the "master regulator" of melanocyte development. For example, the promoter of TRPM1 is bound by both TFAP2A and MITF, and we show that the activity of a minimal TRPM1 promoter is lost upon deletion of the TFAP2A binding sites. However, the expression of Trpm1 is not TFAP2A-dependent, implying that additional TFAP2 paralogs function redundantly to drive melanocyte differentiation, which is consistent with previous results from zebrafish. Paralogs Tfap2a and Tfap2b are both expressed in mouse melanocytes, and we show that mouse embryos with Wnt1-Cre-mediated deletion of Tfap2a and Tfap2b in the neural crest almost completely lack melanocytes but retain neural crest-derived sensory ganglia. These results suggest that TFAP2 paralogs, like MITF, are also necessary for induction of the melanocyte lineage. Finally, we observe a genetic interaction between tfap2a and mitfa in zebrafish, but find that artificially elevating expression of tfap2a does not increase levels of melanin in mitfa hypomorphic or loss-of-function mutants. Collectively, these results show that TFAP2 paralogs, operating alongside lineage-specific transcription factors such as MITF, directly regulate effectors of terminal differentiation in melanocytes. In addition, they suggest that TFAP2A activity, like MITF activity, has the potential to modulate the phenotype of melanoma cells.
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MESH Headings
- Animals
- Base Sequence
- Binding Sites/genetics
- Cell Differentiation/genetics
- Cell Line
- Cell Line, Tumor
- Cells, Cultured
- Embryo, Mammalian/embryology
- Embryo, Mammalian/metabolism
- Embryo, Nonmammalian/embryology
- Embryo, Nonmammalian/metabolism
- Gene Expression Profiling/methods
- Gene Expression Regulation, Developmental
- Humans
- Melanocytes/metabolism
- Mice, Knockout
- Microphthalmia-Associated Transcription Factor/genetics
- Microphthalmia-Associated Transcription Factor/metabolism
- Microscopy, Confocal
- Mutation
- Pigmentation/genetics
- RNA Interference
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Nucleic Acid
- Transcription Factor AP-2/genetics
- Transcription Factor AP-2/metabolism
- Zebrafish
- Zebrafish Proteins/genetics
- Zebrafish Proteins/metabolism
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Affiliation(s)
- Hannah E. Seberg
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
| | - Eric Van Otterloo
- SDM-Craniofacial Biology, University of Colorado – Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Stacie K. Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Huan Liu
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Greg Bonde
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Ramakrishna Sompallae
- Bioinformatics Division, Iowa Institute of Human Genetics, University of Iowa, Iowa City, Iowa, United States of America
| | - Derek E. Gildea
- Bioinformatics and Scientific Programming Core, Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Juan F. Santana
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - J. Robert Manak
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - William J. Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Trevor Williams
- SDM-Craniofacial Biology, University of Colorado – Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Robert A. Cornell
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, United States of America
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41
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Zawistowski JS, Bevill SM, Goulet DR, Stuhlmiller TJ, Beltran AS, Olivares-Quintero JF, Singh D, Sciaky N, Parker JS, Rashid NU, Chen X, Duncan JS, Whittle MC, Angus SP, Velarde SH, Golitz BT, He X, Santos C, Darr DB, Gallagher K, Graves LM, Perou CM, Carey LA, Earp HS, Johnson GL. Enhancer Remodeling during Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacologic Targeting of the P-TEFb Complex. Cancer Discov 2017; 7:302-321. [PMID: 28108460 DOI: 10.1158/2159-8290.cd-16-0653] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 11/16/2022]
Abstract
Targeting the dysregulated BRAF-MEK-ERK pathway in cancer has increasingly emerged in clinical trial design. Despite clinical responses in specific cancers using inhibitors targeting BRAF and MEK, resistance develops often involving nongenomic adaptive bypass mechanisms. Inhibition of MEK1/2 by trametinib in patients with triple-negative breast cancer (TNBC) induced dramatic transcriptional responses, including upregulation of receptor tyrosine kinases (RTK) comparing tumor samples before and after one week of treatment. In preclinical models, MEK inhibition induced genome-wide enhancer formation involving the seeding of BRD4, MED1, H3K27 acetylation, and p300 that drives transcriptional adaptation. Inhibition of the P-TEFb-associated proteins BRD4 and CBP/p300 arrested enhancer seeding and RTK upregulation. BRD4 bromodomain inhibitors overcame trametinib resistance, producing sustained growth inhibition in cells, xenografts, and syngeneic mouse TNBC models. Pharmacologic targeting of P-TEFb members in conjunction with MEK inhibition by trametinib is an effective strategy to durably inhibit epigenomic remodeling required for adaptive resistance.Significance: Widespread transcriptional adaptation to pharmacologic MEK inhibition was observed in TNBC patient tumors. In preclinical models, MEK inhibition induces dramatic genome-wide modulation of chromatin, in the form of de novo enhancer formation and enhancer remodeling. Pharmacologic targeting of P-TEFb complex members at enhancers is an effective strategy to durably inhibit such adaptation. Cancer Discov; 7(3); 302-21. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 235.
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Affiliation(s)
- Jon S Zawistowski
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Samantha M Bevill
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Daniel R Goulet
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Timothy J Stuhlmiller
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Adriana S Beltran
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Jose F Olivares-Quintero
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Darshan Singh
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Noah Sciaky
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Joel S Parker
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Naim U Rashid
- Department of Biostatistics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Xin Chen
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - James S Duncan
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Martin C Whittle
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Steven P Angus
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Sara Hanna Velarde
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Brian T Golitz
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Xiaping He
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Charlene Santos
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - David B Darr
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Kristalyn Gallagher
- Department of Surgery, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Lee M Graves
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Charles M Perou
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Lisa A Carey
- Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - H Shelton Earp
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina.,Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Gary L Johnson
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina.
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Abstract
Enhancer elements function as the logic gates of the genetic regulatory circuitry. One of their most important functions is the integration of extracellular signals with intracellular cell fate information to generate cell type-specific transcriptional responses. Mutations occurring in cancer often misregulate enhancers that normally control the signal-dependent expression of growth-related genes. This misregulation can result from trans-acting mechanisms, such as activation of the transcription factors or epigenetic regulators that control enhancer activity, or can be caused in cis by direct mutations that alter the activity of the enhancer or its target gene specificity. These processes can generate tumour type-specific super-enhancers and establish a 'locked' gene regulatory state that drives the uncontrolled proliferation of cancer cells. Here, we review the role of enhancers in cancer, and their potential as therapeutic targets.
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Affiliation(s)
- Inderpreet Sur
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, and Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Jussi Taipale
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, and Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm SE-171 77, Sweden
- Genome-Scale Biology Program, University of Helsinki, Biomedicum, PO Box 63, Helsinki 00014, Finland
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44
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Tak YG, Farnham PJ. Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome. Epigenetics Chromatin 2015; 8:57. [PMID: 26719772 PMCID: PMC4696349 DOI: 10.1186/s13072-015-0050-4] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/09/2015] [Indexed: 12/13/2022] Open
Abstract
Considerable progress towards an understanding of complex diseases has been made in recent years due to the development of high-throughput genotyping technologies. Using microarrays that contain millions of single-nucleotide polymorphisms (SNPs), Genome Wide Association Studies (GWASs) have identified SNPs that are associated with many complex diseases or traits. For example, as of February 2015, 2111 association studies have identified 15,396 SNPs for various diseases and traits, with the number of identified SNP-disease/trait associations increasing rapidly in recent years. However, it has been difficult for researchers to understand disease risk from GWAS results. This is because most GWAS-identified SNPs are located in non-coding regions of the genome. It is important to consider that the GWAS-identified SNPs serve only as representatives for all SNPs in the same haplotype block, and it is equally likely that other SNPs in high linkage disequilibrium (LD) with the array-identified SNPs are causal for the disease. Because it was hoped that disease-associated coding variants would be identified if the true casual SNPs were known, investigators have expanded their analyses using LD calculation and fine-mapping. However, such analyses also identified risk-associated SNPs located in non-coding regions. Thus, the GWAS field has been left with the conundrum as to how a single-nucleotide change in a non-coding region could confer increased risk for a specific disease. One possible answer to this puzzle is that the variant SNPs cause changes in gene expression levels rather than causing changes in protein function. This review provides a description of (1) advances in genomic and epigenomic approaches that incorporate functional annotation of regulatory elements to prioritize the disease risk-associated SNPs that are located in non-coding regions of the genome for follow-up studies, (2) various computational tools that aid in identifying gene expression changes caused by the non-coding disease-associated SNPs, and (3) experimental approaches to identify target genes of, and study the biological phenotypes conferred by, non-coding disease-associated SNPs.
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Affiliation(s)
- Yu Gyoung Tak
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
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Grimmer MR, Farnham PJ. Can genome engineering be used to target cancer-associated enhancers? Epigenomics 2015; 6:493-501. [PMID: 25431942 DOI: 10.2217/epi.14.30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Transcriptional misregulation is involved in the development of many diseases, especially neoplastic transformation. Distal regulatory elements, such as enhancers, play a major role in specifying cell-specific transcription patterns in both normal and diseased tissues, suggesting that enhancers may be prime targets for therapeutic intervention. By focusing on modulating gene regulation mediated by cell type-specific enhancers, there is hope that normal epigenetic patterning in an affected tissue could be restored with fewer side effects than observed with treatments employing relatively nonspecific inhibitors such as epigenetic drugs. New methods employing genomic nucleases and site-specific epigenetic regulators targeted to specific genomic regions, using either artificial DNA-binding proteins or RNA-DNA interactions, may allow precise genome engineering at enhancers. However, this field is still in its infancy and further refinements that increase specificity and efficiency are clearly required.
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Affiliation(s)
- Matthew R Grimmer
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9601, USA
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Zhang T, Zhou Q, Ogmundsdottir MH, Möller K, Siddaway R, Larue L, Hsing M, Kong SW, Goding CR, Palsson A, Steingrimsson E, Pignoni F. Mitf is a master regulator of the v-ATPase, forming a control module for cellular homeostasis with v-ATPase and TORC1. J Cell Sci 2015; 128:2938-50. [PMID: 26092939 DOI: 10.1242/jcs.173807] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 06/12/2015] [Indexed: 01/29/2023] Open
Abstract
The v-ATPase is a fundamental eukaryotic enzyme that is central to cellular homeostasis. Although its impact on key metabolic regulators such as TORC1 is well documented, our knowledge of mechanisms that regulate v-ATPase activity is limited. Here, we report that the Drosophila transcription factor Mitf is a master regulator of this holoenzyme. Mitf directly controls transcription of all 15 v-ATPase components through M-box cis-sites and this coordinated regulation affects holoenzyme activity in vivo. In addition, through the v-ATPase, Mitf promotes the activity of TORC1, which in turn negatively regulates Mitf. We provide evidence that Mitf, v-ATPase and TORC1 form a negative regulatory loop that maintains each of these important metabolic regulators in relative balance. Interestingly, direct regulation of v-ATPase genes by human MITF also occurs in cells of the melanocytic lineage, showing mechanistic conservation in the regulation of the v-ATPase by MITF family proteins in fly and mammals. Collectively, this evidence points to an ancient module comprising Mitf, v-ATPase and TORC1 that serves as a dynamic modulator of metabolism for cellular homeostasis.
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Affiliation(s)
- Tianyi Zhang
- Department of Ophthalmology, Center for Vision Research and SUNY Eye Institute, Upstate Medical University, Syracuse, 13210 NY, USA
| | - Qingxiang Zhou
- Department of Ophthalmology, Center for Vision Research and SUNY Eye Institute, Upstate Medical University, Syracuse, 13210 NY, USA
| | - Margret Helga Ogmundsdottir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
| | - Katrin Möller
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
| | - Robert Siddaway
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, OX3 7DQ Oxford, UK
| | - Lionel Larue
- Institut Curie, INSERM U1021, CNRS UMR3347, Normal and Pathological Development of Melanocytes, 91405 Orsay, France
| | - Michael Hsing
- Informatics Program, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Sek Won Kong
- Informatics Program, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Colin Ronald Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, OX3 7DQ Oxford, UK
| | - Arnar Palsson
- Life and Environmental Sciences, School of Engineering and Natural Sciences, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
| | - Eirikur Steingrimsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
| | - Francesca Pignoni
- Department of Ophthalmology, Center for Vision Research and SUNY Eye Institute, Upstate Medical University, Syracuse, 13210 NY, USA Departments of Neuroscience and Physiology, Biochemistry and Molecular Biology, Upstate Medical University, Syracuse, 13210 NY, USA
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Lopez-Pajares V, Qu K, Zhang J, Webster DE, Barajas BC, Siprashvili Z, Zarnegar BJ, Boxer LD, Rios EJ, Tao S, Kretz M, Khavari PA. A LncRNA-MAF:MAFB transcription factor network regulates epidermal differentiation. Dev Cell 2015; 32:693-706. [PMID: 25805135 DOI: 10.1016/j.devcel.2015.01.028] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 12/11/2014] [Accepted: 01/21/2015] [Indexed: 02/02/2023]
Abstract
Progenitor differentiation requires remodeling of genomic expression; however, in many tissues, such as epidermis, the spectrum of remodeled genes and the transcription factors (TFs) that control them are not fully defined. We performed kinetic transcriptome analysis during regeneration of differentiated epidermis and identified gene sets enriched in progenitors (594 genes), in early (159 genes), and in late differentiation (387 genes). Module mapping of 1,046 TFs identified MAF and MAFB as necessary and sufficient for progenitor differentiation. MAF:MAFB regulated 393 genes altered in this setting. Integrative analysis identified ANCR and TINCR lncRNAs as essential upstream MAF:MAFB regulators. ChIP-seq analysis demonstrated MAF:MAFB binding to known epidermal differentiation TF genes whose expression they controlled, including GRHL3, ZNF750, KLF4, and PRDM1. Each of these TFs rescued expression of specific MAF:MAFB target gene subsets in the setting of MAF:MAFB loss, indicating they act downstream of MAF:MAFB. A lncRNA-TF network is thus essential for epidermal differentiation.
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Affiliation(s)
| | - Kun Qu
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Jiajing Zhang
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Dan E Webster
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Brook C Barajas
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Zurab Siprashvili
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Brian J Zarnegar
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Lisa D Boxer
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Eon J Rios
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Shiying Tao
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Markus Kretz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA 94304, USA.
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Della Corte CM, Fasano M, Papaccio F, Ciardiello F, Morgillo F. Role of HGF-MET Signaling in Primary and Acquired Resistance to Targeted Therapies in Cancer. Biomedicines 2014; 2:345-358. [PMID: 28548075 PMCID: PMC5344276 DOI: 10.3390/biomedicines2040345] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/11/2014] [Accepted: 11/17/2014] [Indexed: 02/07/2023] Open
Abstract
The Hepatocyte growth factor (HGF)-mesenchymal-epithelial transition (MET) pathway is deregulated in several cancers and is associated with aggressive phenotype and worse prognosis. MET, a tyrosine kinase receptor activated by HGF, plays a physiological role in embryogenesis, promoting cell growth, survival and motility. HGF-MET aberrant activation in tumorigenesis acts through various mechanisms: paracrine/autocrine HGF production, MET overexpression, MET germ-line and sporadic mutations and cross-talk with other growth factor receptors. In addition, MET activation could represent a mechanism of escape from other targeted therapies, through receptor amplification or over-stimulation by the ligand, as demonstrated in non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) models with acquired resistance to epidermal growth factor receptor (EGFR) inhibitors and also in models of melanoma resistant to the BRAF inhibitor vemurafenib. As a consequence, a lot of molecules targeting MET signaling are under clinical investigation as single agent or in combination with other targeted drugs. Patient selection, based on MET expression on tumor samples (eventually, by re-biopsy of new metastatic sites), and pharmacokinetic/pharmacodynamic markers are needed. Authors review the latest data on the role of MET and the molecular mechanism underlying primary or acquired resistance to biological agents, focusing on NSCLC, CRC and melanoma.
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Affiliation(s)
- Carminia Maria Della Corte
- Medical Oncology, Department of Experimental and Internal Medicine "F. Magrassi e A. Lanzara", Second University of Naples, Napoli 80131, Italy.
| | - Morena Fasano
- Medical Oncology, Department of Experimental and Internal Medicine "F. Magrassi e A. Lanzara", Second University of Naples, Napoli 80131, Italy.
| | - Federica Papaccio
- Medical Oncology, Department of Experimental and Internal Medicine "F. Magrassi e A. Lanzara", Second University of Naples, Napoli 80131, Italy.
| | - Fortunato Ciardiello
- Medical Oncology, Department of Experimental and Internal Medicine "F. Magrassi e A. Lanzara", Second University of Naples, Napoli 80131, Italy.
| | - Floriana Morgillo
- Medical Oncology, Department of Experimental and Internal Medicine "F. Magrassi e A. Lanzara", Second University of Naples, Napoli 80131, Italy.
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Zheng GXY, Do BT, Webster DE, Khavari PA, Chang HY. Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs. Nat Struct Mol Biol 2014; 21:585-90. [PMID: 24929436 PMCID: PMC5509563 DOI: 10.1038/nsmb.2842] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/20/2014] [Indexed: 12/19/2022]
Abstract
Long noncoding RNAs (lncRNAs) are important regulators of cell fate, yet little is known about mechanisms controlling lncRNA expression. Here we show that transcription is quantitatively different for lncRNAs and mRNAs--as revealed by deficiency of Dicer (Dcr), a key RNase that generates microRNAs (miRNAs). Dcr loss in mouse embryonic stem cells led unexpectedly to decreased levels of hundreds of lncRNAs. The canonical Dgcr8-Dcr-miRNA pathway is required for robust lncRNA transcriptional initiation and elongation. Computational and genetic epistasis analyses demonstrated that Dcr activation of the oncogenic transcription factor cMyc is partly responsible for lncRNA expression. A quantitative metric of mRNA-lncRNA decoupling revealed that Dcr and cMyc differentially regulate lncRNAs versus mRNAs in diverse cell types and in vivo. Thus, numerous lncRNAs may be modulated as a class in development and disease, notably where Dcr and cMyc act.
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Affiliation(s)
- Grace X Y Zheng
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Brian T Do
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Dan E Webster
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Howard Y Chang
- 1] Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA. [2] Howard Hughes Medical Institute, Stanford, California, USA
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