1
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Waddell A, Grbic N, Leibowitz K, Wyant WA, Choudhury S, Park K, Collard M, Cole PA, Alani RM. p300 KAT Regulates SOX10 Stability and Function in Human Melanoma. CANCER RESEARCH COMMUNICATIONS 2024; 4:1894-1907. [PMID: 38994683 PMCID: PMC11293458 DOI: 10.1158/2767-9764.crc-24-0124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/15/2024] [Accepted: 07/09/2024] [Indexed: 07/13/2024]
Abstract
SOX10 is a lineage-specific transcription factor critical for melanoma tumor growth; on the other hand, SOX10 loss-of-function drives the emergence of therapy-resistant, invasive melanoma phenotypes. A major challenge has been developing therapeutic strategies targeting SOX10's role in melanoma proliferation while preventing a concomitant increase in tumor cell invasion. In this study, we report that the lysine acetyltransferase (KAT) EP300 and SOX10 gene loci on chromosome 22 are frequently co-amplified in melanomas, including UV-associated and acral tumors. We further show that p300 KAT activity mediates SOX10 protein stability and that the p300 inhibitor A-485 downregulates SOX10 protein levels in melanoma cells via proteasome-mediated degradation. Additionally, A-485 potently inhibits proliferation of SOX10+ melanoma cells while decreasing invasion in AXLhigh/MITFlow melanoma cells through downregulation of metastasis-related genes. We conclude that the SOX10/p300 axis is critical to melanoma growth and invasion and that inhibition of p300 KAT activity through A-485 may be a worthwhile therapeutic approach for SOX10-reliant tumors. SIGNIFICANCE The p300 KAT inhibitor A-485 blocks SOX10-dependent proliferation and SOX10-independent invasion in hard-to-treat melanoma cells.
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Affiliation(s)
- Aaron Waddell
- Department of Dermatology, Boston University Aram V. Chobanian and Edward Avedisian School of Medicine, Boston, Massachusetts.
| | - Nicole Grbic
- Department of Dermatology, Boston University Aram V. Chobanian and Edward Avedisian School of Medicine, Boston, Massachusetts.
| | - Kassidy Leibowitz
- Department of Dermatology, Boston University Aram V. Chobanian and Edward Avedisian School of Medicine, Boston, Massachusetts.
| | - William Austin Wyant
- Department of Dermatology, Boston University Aram V. Chobanian and Edward Avedisian School of Medicine, Boston, Massachusetts.
| | - Sabah Choudhury
- Department of Dermatology, Boston University Aram V. Chobanian and Edward Avedisian School of Medicine, Boston, Massachusetts.
| | - Kihyun Park
- Department of Dermatology, Boston University Aram V. Chobanian and Edward Avedisian School of Medicine, Boston, Massachusetts.
| | - Marianne Collard
- Department of Dermatology, Boston University Aram V. Chobanian and Edward Avedisian School of Medicine, Boston, Massachusetts.
| | - Philip A. Cole
- Division of Genetics, Department of Medicine, Harvard Medical School and Brigham and Women’s Hospital, Boston, Massachusetts.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women’s Hospital, Boston, Massachusetts.
| | - Rhoda M. Alani
- Department of Dermatology, Boston University Aram V. Chobanian and Edward Avedisian School of Medicine, Boston, Massachusetts.
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2
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Nocente MC, Mesihovic Karamitsos A, Drouineau E, Soleil M, Albawardi W, Dulary C, Ribierre F, Picaud H, Alibert O, Acker J, Kervella M, Aude JC, Gilbert N, Ochsenbein F, Chantalat S, Gérard M. cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers. Nat Struct Mol Biol 2024:10.1038/s41594-024-01344-0. [PMID: 38956169 DOI: 10.1038/s41594-024-01344-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/03/2024] [Indexed: 07/04/2024]
Abstract
The canonical BRG/BRM-associated factor (cBAF) complex is essential for chromatin opening at enhancers in mammalian cells. However, the nature of the open chromatin remains unclear. Here, we show that, in addition to producing histone-free DNA, cBAF generates stable hemisome-like subnucleosomal particles containing the four core histones associated with 50-80 bp of DNA. Our genome-wide analysis indicates that cBAF makes these particles by targeting and splitting fragile nucleosomes. In mouse embryonic stem cells, these subnucleosomes become an in vivo binding substrate for the master transcription factor OCT4 independently of the presence of OCT4 DNA motifs. At enhancers, the OCT4-subnucleosome interaction increases OCT4 occupancy and amplifies the genomic interval bound by OCT4 by up to one order of magnitude compared to the region occupied on histone-free DNA. We propose that cBAF-dependent subnucleosomes orchestrate a molecular mechanism that projects OCT4 function in chromatin opening beyond its DNA motifs.
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Affiliation(s)
- Marina C Nocente
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Anida Mesihovic Karamitsos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Emilie Drouineau
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Manon Soleil
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Waad Albawardi
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Cécile Dulary
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Florence Ribierre
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Hélène Picaud
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Olivier Alibert
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Joël Acker
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Marie Kervella
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jean-Christophe Aude
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Nick Gilbert
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Françoise Ochsenbein
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sophie Chantalat
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Matthieu Gérard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
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3
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Basurto-Cayuela L, Guerrero-Martínez JA, Gómez-Marín E, Sánchez-Escabias E, Escaño-Maestre M, Ceballos-Chávez M, Reyes JC. SWI/SNF-dependent genes are defined by their chromatin landscape. Cell Rep 2024; 43:113855. [PMID: 38427563 DOI: 10.1016/j.celrep.2024.113855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 11/23/2023] [Accepted: 02/08/2024] [Indexed: 03/03/2024] Open
Abstract
SWI/SNF complexes are evolutionarily conserved, ATP-dependent chromatin remodeling machines. Here, we characterize the features of SWI/SNF-dependent genes using BRM014, an inhibitor of the ATPase activity of the complexes. We find that SWI/SNF activity is required to maintain chromatin accessibility and nucleosome occupancy for most enhancers but not for most promoters. SWI/SNF activity is needed for expression of genes with low to medium levels of expression that have promoters with (1) low chromatin accessibility, (2) low levels of active histone marks, (3) high H3K4me1/H3K4me3 ratio, (4) low nucleosomal phasing, and (5) enrichment in TATA-box motifs. These promoters are mostly occupied by the canonical Brahma-related gene 1/Brahma-associated factor (BAF) complex. These genes are surrounded by SWI/SNF-dependent enhancers and mainly encode signal transduction, developmental, and cell identity genes (with almost no housekeeping genes). Machine-learning models trained with different chromatin characteristics of promoters and their surrounding regulatory regions indicate that the chromatin landscape is a determinant for establishing SWI/SNF dependency.
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Affiliation(s)
- Laura Basurto-Cayuela
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - José A Guerrero-Martínez
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Elena Gómez-Marín
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Elena Sánchez-Escabias
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - María Escaño-Maestre
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - María Ceballos-Chávez
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - José C Reyes
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain.
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4
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Podleśny-Drabiniok A, Novikova G, Liu Y, Dunst J, Temizer R, Giannarelli C, Marro S, Kreslavsky T, Marcora E, Goate AM. BHLHE40/41 regulate microglia and peripheral macrophage responses associated with Alzheimer's disease and other disorders of lipid-rich tissues. Nat Commun 2024; 15:2058. [PMID: 38448474 PMCID: PMC10917780 DOI: 10.1038/s41467-024-46315-7] [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: 02/10/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Genetic and experimental evidence suggests that Alzheimer's disease (AD) risk alleles and genes may influence disease susceptibility by altering the transcriptional and cellular responses of macrophages, including microglia, to damage of lipid-rich tissues like the brain. Recently, sc/nRNA sequencing studies identified similar transcriptional activation states in subpopulations of macrophages in aging and degenerating brains and in other diseased lipid-rich tissues. We collectively refer to these subpopulations of microglia and peripheral macrophages as DLAMs. Using macrophage sc/nRNA-seq data from healthy and diseased human and mouse lipid-rich tissues, we reconstructed gene regulatory networks and identified 11 strong candidate transcriptional regulators of the DLAM response across species. Loss or reduction of two of these transcription factors, BHLHE40/41, in iPSC-derived microglia and human THP-1 macrophages as well as loss of Bhlhe40/41 in mouse microglia, resulted in increased expression of DLAM genes involved in cholesterol clearance and lysosomal processing, increased cholesterol efflux and storage, and increased lysosomal mass and degradative capacity. These findings provide targets for therapeutic modulation of macrophage/microglial function in AD and other disorders affecting lipid-rich tissues.
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Affiliation(s)
- Anna Podleśny-Drabiniok
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gloriia Novikova
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- OMNI Bioinformatics Department, Genentech, Inc., South San Francisco, CA, USA
| | - Yiyuan Liu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Josefine Dunst
- Department of Medicine, Division of Immunology and Allergy, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rose Temizer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chiara Giannarelli
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Samuele Marro
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Taras Kreslavsky
- Department of Medicine, Division of Immunology and Allergy, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Edoardo Marcora
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Alison Mary Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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5
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Berns HM, Watkins-Chow DE, Lu S, Louphrasitthiphol P, Zhang T, Brown KM, Moura-Alves P, Goding CR, Pavan WJ. Single-cell profiling of MC1R-inhibited melanocytes. Pigment Cell Melanoma Res 2024; 37:291-308. [PMID: 37972124 DOI: 10.1111/pcmr.13141] [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: 07/12/2023] [Revised: 09/15/2023] [Accepted: 10/05/2023] [Indexed: 11/19/2023]
Abstract
The human red hair color (RHC) trait is caused by increased pheomelanin (red-yellow) and reduced eumelanin (black-brown) pigment in skin and hair due to diminished melanocortin 1 receptor (MC1R) function. In addition, individuals harboring the RHC trait are predisposed to melanoma development. While MC1R variants have been established as causative of RHC and are a well-defined risk factor for melanoma, it remains unclear mechanistically why decreased MC1R signaling alters pigmentation and increases melanoma susceptibility. Here, we use single-cell RNA sequencing (scRNA-seq) of melanocytes isolated from RHC mouse models to define a MC1R-inhibited Gene Signature (MiGS) comprising a large set of previously unidentified genes which may be implicated in melanogenesis and oncogenic transformation. We show that one of the candidate MiGS genes, TBX3, a well-known anti-senescence transcription factor implicated in melanoma progression, binds both E-box and T-box elements to regulate genes associated with melanogenesis and senescence bypass. Our results provide key insights into further mechanisms by which melanocytes with reduced MC1R signaling may regulate pigmentation and offer new candidates of study toward understanding how individuals with the RHC phenotype are predisposed to melanoma.
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Affiliation(s)
- H Matthew Berns
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sizhu Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Pedro Moura-Alves
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, PT, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, PT, Portugal
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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6
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Waddell A, Grbic N, Leibowitz K, Wyant WA, Choudhury S, Park K, Collard M, Cole PA, Alani RM. p300 KAT regulates SOX10 stability and function in human melanoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.20.581224. [PMID: 38469149 PMCID: PMC10926666 DOI: 10.1101/2024.02.20.581224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
SOX10 is a lineage-specific transcription factor critical for melanoma tumor growth, while SOX10 loss-of-function drives the emergence of therapy-resistant, invasive melanoma phenotypes. A major challenge has been developing therapeutic strategies targeting SOX10's role in melanoma proliferation, while preventing a concomitant increase in tumor cell invasion. Here, we report that the lysine acetyltransferase (KAT) EP300 and SOX10 gene loci on Chromosome 22 are frequently co-amplified in melanomas, including UV-associated and acral tumors. We further show that p300 KAT activity mediates SOX10 protein stability and that the p300 inhibitor, A-485, downregulates SOX10 protein levels in melanoma cells via proteasome-mediated degradation. Additionally, A-485 potently inhibits proliferation of SOX10+ melanoma cells while decreasing invasion in AXLhigh/MITFlow melanoma cells through downregulation of metastasis-related genes. We conclude that the SOX10/p300 axis is critical to melanoma growth and invasion, and that inhibition of p300 KAT activity through A-485 may be a worthwhile therapeutic approach for SOX10-reliant tumors.
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Affiliation(s)
- Aaron Waddell
- Department of Dermatology, Boston University Aram V. Chobanian & Edward Avedisian School of Medicine, 609 Albany Street, Boston, MA, USA 02118
| | - Nicole Grbic
- Department of Dermatology, Boston University Aram V. Chobanian & Edward Avedisian School of Medicine, 609 Albany Street, Boston, MA, USA 02118
| | - Kassidy Leibowitz
- Department of Dermatology, Boston University Aram V. Chobanian & Edward Avedisian School of Medicine, 609 Albany Street, Boston, MA, USA 02118
| | - W. Austin Wyant
- Department of Dermatology, Boston University Aram V. Chobanian & Edward Avedisian School of Medicine, 609 Albany Street, Boston, MA, USA 02118
| | - Sabah Choudhury
- Department of Dermatology, Boston University Aram V. Chobanian & Edward Avedisian School of Medicine, 609 Albany Street, Boston, MA, USA 02118
| | - Kihyun Park
- Department of Dermatology, Boston University Aram V. Chobanian & Edward Avedisian School of Medicine, 609 Albany Street, Boston, MA, USA 02118
| | - Marianne Collard
- Department of Dermatology, Boston University Aram V. Chobanian & Edward Avedisian School of Medicine, 609 Albany Street, Boston, MA, USA 02118
| | - Philip A. Cole
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | - Rhoda M. Alani
- Department of Dermatology, Boston University Aram V. Chobanian & Edward Avedisian School of Medicine, 609 Albany Street, Boston, MA, USA 02118
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7
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Binet R, Lambert JP, Tomkova M, Tischfield S, Baggiolini A, Picaud S, Sarkar S, Louphrasitthiphol P, Dias D, Carreira S, Humphrey TC, Fillipakopoulos P, White R, Goding CR. DNA damage remodels the MITF interactome to increase melanoma genomic instability. Genes Dev 2024; 38:70-94. [PMID: 38316520 PMCID: PMC10903946 DOI: 10.1101/gad.350740.123] [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: 04/21/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024]
Abstract
Since genome instability can drive cancer initiation and progression, cells have evolved highly effective and ubiquitous DNA damage response (DDR) programs. However, some cells (for example, in skin) are normally exposed to high levels of DNA-damaging agents. Whether such high-risk cells possess lineage-specific mechanisms that tailor DNA repair to the tissue remains largely unknown. Using melanoma as a model, we show here that the microphthalmia-associated transcription factor MITF, a lineage addition oncogene that coordinates many aspects of melanocyte and melanoma biology, plays a nontranscriptional role in shaping the DDR. On exposure to DNA-damaging agents, MITF is phosphorylated at S325, and its interactome is dramatically remodeled; most transcription cofactors dissociate, and instead MITF interacts with the MRE11-RAD50-NBS1 (MRN) complex. Consequently, cells with high MITF levels accumulate stalled replication forks and display defects in homologous recombination-mediated repair associated with impaired MRN recruitment to DNA damage. In agreement with this, high MITF levels are associated with increased single-nucleotide and copy number variant burdens in melanoma. Significantly, the SUMOylation-defective MITF-E318K melanoma predisposition mutation recapitulates the effects of DNA-PKcs-phosphorylated MITF. Our data suggest that a nontranscriptional function of a lineage-restricted transcription factor contributes to a tissue-specialized modulation of the DDR that can impact cancer initiation.
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Affiliation(s)
- Romuald Binet
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center, Université Laval, Québec City, Québec G1V 4G2, Canada
- Endocrinology-Nephrology Axis, CHU de Québec-Université Laval Research Center, Québec City, Québec G1V 4G2, Canada
| | - Marketa Tomkova
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, USA
| | - Samuel Tischfield
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Arianna Baggiolini
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Sovan Sarkar
- Cancer Research UK, Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Diogo Dias
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Suzanne Carreira
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
| | - Timothy C Humphrey
- Cancer Research UK, Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Panagis Fillipakopoulos
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Richard White
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom;
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8
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Brahma S, Henikoff S. The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes. Nat Genet 2024; 56:100-111. [PMID: 38049663 PMCID: PMC10786724 DOI: 10.1038/s41588-023-01603-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 10/30/2023] [Indexed: 12/06/2023]
Abstract
Chromatin accessibility is a hallmark of active transcription and entails ATP-dependent nucleosome remodeling, which is carried out by complexes such as Brahma-associated factor (BAF). However, the mechanistic links between transcription, nucleosome remodeling and chromatin accessibility are unclear. Here, we used a chemical-genetic approach coupled with time-resolved chromatin profiling to dissect the interplay between RNA Polymerase II (RNAPII), BAF and DNA-sequence-specific transcription factors in mouse embryonic stem cells. We show that BAF dynamically unwraps and evicts nucleosomes at accessible chromatin regions, while RNAPII promoter-proximal pausing stabilizes BAF chromatin occupancy and enhances ATP-dependent nucleosome eviction by BAF. We find that although RNAPII and BAF dynamically probe both transcriptionally active and Polycomb-repressed genomic regions, pluripotency transcription factor chromatin binding confers locus specificity for productive chromatin remodeling and nucleosome eviction by BAF. Our study suggests a paradigm for how functional synergy between dynamically acting chromatin factors regulates locus-specific nucleosome organization and chromatin accessibility.
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Affiliation(s)
- Sandipan Brahma
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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9
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Berico P, Nogaret M, Cigrang M, Lallement A, Vand-Rajabpour F, Flores-Yanke A, Gambi G, Davidson G, Seno L, Obid J, Vokshi BH, Le Gras S, Mengus G, Ye T, Cordero CF, Dalmasso M, Compe E, Bertolotto C, Hernando E, Davidson I, Coin F. Super-enhancer-driven expression of BAHCC1 promotes melanoma cell proliferation and genome stability. Cell Rep 2023; 42:113363. [PMID: 37924516 DOI: 10.1016/j.celrep.2023.113363] [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: 11/02/2022] [Revised: 07/27/2023] [Accepted: 10/16/2023] [Indexed: 11/06/2023] Open
Abstract
Super-enhancers (SEs) are stretches of enhancers ensuring a high level of expression of key genes associated with cell function. The identification of cancer-specific SE-driven genes is a powerful means for the development of innovative therapeutic strategies. Here, we identify a MITF/SOX10/TFIIH-dependent SE promoting the expression of BAHCC1 in a broad panel of melanoma cells. BAHCC1 is highly expressed in metastatic melanoma and is required for tumor engraftment, growth, and dissemination. Integrative genomics analyses reveal that BAHCC1 is a transcriptional regulator controlling expression of E2F/KLF-dependent cell-cycle and DNA-repair genes. BAHCC1 associates with BRG1-containing remodeling complexes at the promoters of these genes. BAHCC1 silencing leads to decreased cell proliferation and delayed DNA repair. Consequently, BAHCC1 deficiency cooperates with PARP inhibition to induce melanoma cell death. Our study identifies BAHCC1 as an SE-driven gene expressed in melanoma and demonstrates how its inhibition can be exploited as a therapeutic target.
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Affiliation(s)
- Pietro Berico
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France; Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Maguelone Nogaret
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Max Cigrang
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Antonin Lallement
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Fatemeh Vand-Rajabpour
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Amanda Flores-Yanke
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Giovanni Gambi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Leane Seno
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Julian Obid
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Bujamin H Vokshi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Stephanie Le Gras
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Gabrielle Mengus
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Carlos Fernandez Cordero
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Mélanie Dalmasso
- Université Côte d'Azur, Nice, France; INSERM, Biology and Pathologies of Melanocytes, Equipe labellisée "Ligue contre le Cancer 2020" and Equipe labellisée "Fondation ARC 2022", Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Corine Bertolotto
- Université Côte d'Azur, Nice, France; INSERM, Biology and Pathologies of Melanocytes, Equipe labellisée "Ligue contre le Cancer 2020" and Equipe labellisée "Fondation ARC 2022", Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Eva Hernando
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France.
| | - Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labéllisée, "Ligue contre le Cancer 2022", BP 163, 67404 Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France.
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10
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Glasheen MQ, Caksa S, Young AG, Wilski NA, Ott CA, Chervoneva I, Flaherty KT, Herlyn M, Xu X, Aplin AE, Capparelli C. Targeting Upregulated cIAP2 in SOX10-Deficient Drug Tolerant Melanoma. Mol Cancer Ther 2023; 22:1087-1099. [PMID: 37343247 PMCID: PMC10527992 DOI: 10.1158/1535-7163.mct-23-0025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/07/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
Drug tolerance and minimal residual disease (MRD) are likely to prelude acquired resistance to targeted therapy. Mechanisms that allow persister cells to survive in the presence of targeted therapy are being characterized but selective vulnerabilities for these subpopulations remain uncertain. We identified cellular inhibitor of apoptosis protein 2 (cIAP2) as being highly expressed in SOX10-deficient drug tolerant persister (DTP) melanoma cells. Here, we show that cIAP2 is sufficient to induce tolerance to MEK inhibitors, likely by decreasing the levels of cell death. Mechanistically, cIAP2 is upregulated at the transcript level in SOX10-deficient cells and the AP-1 complex protein, JUND, is required for its expression. Using a patient-derived xenograft model, we demonstrate that treatment with the cIAP1/2 inhibitor, birinapant, during the MRD phase delays the onset of resistance to BRAF inhibitor and MEK inhibitor combination therapy. Together, our data suggest that cIAP2 upregulation in SOX10-deficient subpopulations of melanoma cells induces drug tolerance to MAPK targeting agents and provides a rationale to test a novel therapeutical approach to target MRD.
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Affiliation(s)
- McKenna Q Glasheen
- Department of Pharmacology, Physiology and Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Signe Caksa
- Department of Pharmacology, Physiology and Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Amelia G Young
- Department of Pharmacology, Physiology and Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Nicole A Wilski
- Department of Pharmacology, Physiology and Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Connor A Ott
- Department of Pharmacology, Physiology and Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Inna Chervoneva
- Department of Pharmacology, Physiology and Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Keith T Flaherty
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program, Philadelphia, Pennsylvania
- The Wistar Institute, Philadelphia, Pennsylvania
| | - Xiaowei Xu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrew E Aplin
- Department of Pharmacology, Physiology and Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Claudia Capparelli
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
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11
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Song JS, Manjunath M. Predicting the molecular functions of regulatory genetic variants associated with cancer. Oncotarget 2023; 14:775-777. [PMID: 37646780 PMCID: PMC10467629 DOI: 10.18632/oncotarget.28451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Indexed: 09/01/2023] Open
Affiliation(s)
- Jun S. Song
- Correspondence to:Jun S. Song, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA email
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12
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Ovadia S, Cui G, Elkon R, Cohen-Gulkar M, Zuk-Bar N, Tuoc T, Jing N, Ashery-Padan R. SWI/SNF complexes are required for retinal pigmented epithelium differentiation and for the inhibition of cell proliferation and neural differentiation programs. Development 2023; 150:dev201488. [PMID: 37522516 PMCID: PMC10482007 DOI: 10.1242/dev.201488] [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: 11/27/2022] [Accepted: 07/14/2023] [Indexed: 08/01/2023]
Abstract
During embryonic development, tissue-specific transcription factors and chromatin remodelers function together to ensure gradual, coordinated differentiation of multiple lineages. Here, we define this regulatory interplay in the developing retinal pigmented epithelium (RPE), a neuroectodermal lineage essential for the development, function and maintenance of the adjacent retina. We present a high-resolution spatial transcriptomic atlas of the developing mouse RPE and the adjacent ocular mesenchyme obtained by geographical position sequencing (Geo-seq) of a single developmental stage of the eye that encompasses young and more mature ocular progenitors. These transcriptomic data, available online, reveal the key transcription factors and their gene regulatory networks during RPE and ocular mesenchyme differentiation. Moreover, conditional inactivation followed by Geo-seq revealed that this differentiation program is dependent on the activity of SWI/SNF complexes, shown here to control the expression and activity of RPE transcription factors and, at the same time, inhibit neural progenitor and cell proliferation genes. The findings reveal the roles of the SWI/SNF complexes in controlling the intersection between RPE and neural cell fates and the coupling of cell-cycle exit and differentiation.
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Affiliation(s)
- Shai Ovadia
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guizhong Cui
- Guangzhou National Laboratory, Department of Basic Research, Guangzhou 510005, China
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Mazal Cohen-Gulkar
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nitay Zuk-Bar
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tran Tuoc
- Department of Human Genetics, Ruhr University of Bochum, 44791 Bochum, Germany
| | - Naihe Jing
- Guangzhou National Laboratory, Department of Basic Research, Guangzhou 510005, China
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
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13
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Vu HN, Valdimarsson MM, Sigurbjörnsdóttir S, Bergsteinsdóttir K, Debbache J, Bismuth K, Swing DA, Hallsson JH, Larue L, Arnheiter H, Copeland NG, Jenkins NA, Heidarsson PO, Steingrímsson E. Novel mechanisms of MITF regulation and melanoma predisposition identified in a mouse suppressor screen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.551952. [PMID: 37786677 PMCID: PMC10541597 DOI: 10.1101/2023.08.04.551952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
MITF, a basic-Helix-Loop-Helix Zipper (bHLHZip) transcription factor, plays vital roles in melanocyte development and functions as an oncogene. To explore MITF regulation and its role in melanoma, we conducted a genetic screen for suppressors of the Mitf-associated pigmentation phenotype. An intragenic Mitf mutation was identified, leading to termination of MITF at the K316 SUMOylation site and loss of the C-end intrinsically disordered region (IDR). The resulting protein is more nuclear but less stable than wild-type MITF and retains DNA-binding ability. Interestingly, as a dimer, it can translocate wild-type and mutant MITF partners into the nucleus, improving its own stability and ensuring an active nuclear MITF supply. Interactions between K316 SUMOylation and S409 phosphorylation sites across monomers largely explain the observed effects. Notably, the recurrent melanoma-associated E318K mutation in MITF, which affects K316 SUMOylation, also alters protein regulation in concert with S409, unraveling a novel regulatory mechanism with unexpected disease insights.
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Affiliation(s)
- Hong Nhung Vu
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 102 Reykjavík, Iceland
| | - Matti Már Valdimarsson
- Department of Biochemistry, Science Institute, School of Engineering and Natural Sciences, University of Iceland, Sturlugata 7, 102 Reykjavík, Iceland
| | - Sara Sigurbjörnsdóttir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 102 Reykjavík, Iceland
| | - Kristín Bergsteinsdóttir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 102 Reykjavík, Iceland
| | - Julien Debbache
- Mammalian Development Section, NINDS, NIH, Bethesda, MD 20892-3706
| | - Keren Bismuth
- Mammalian Development Section, NINDS, NIH, Bethesda, MD 20892-3706
| | | | - Jón H. Hallsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 102 Reykjavík, Iceland
| | - Lionel Larue
- Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, 91405, Orsay, France
| | - Heinz Arnheiter
- Mammalian Development Section, NINDS, NIH, Bethesda, MD 20892-3706
| | - Neal G. Copeland
- Mouse Cancer Genetics Program, NCI, Frederick, MD 21702-1201
- Current address: Genetics Department, MD Anderson Cancer Center, Houston, TX 77030
| | - Nancy A. Jenkins
- Mouse Cancer Genetics Program, NCI, Frederick, MD 21702-1201
- Current address: Genetics Department, MD Anderson Cancer Center, Houston, TX 77030
| | - Petur O. Heidarsson
- Department of Biochemistry, Science Institute, School of Engineering and Natural Sciences, University of Iceland, Sturlugata 7, 102 Reykjavík, Iceland
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 102 Reykjavík, Iceland
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14
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Vokshi BH, Davidson G, Tawanaie Pour Sedehi N, Helleux A, Rippinger M, Haller AR, Gantzer J, Thouvenin J, Baltzinger P, Bouarich R, Manriquez V, Zaidi S, Rao P, Msaouel P, Su X, Lang H, Tricard T, Lindner V, Surdez D, Kurtz JE, Bourdeaut F, Tannir NM, Davidson I, Malouf GG. SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance. Nat Commun 2023; 14:3034. [PMID: 37236926 DOI: 10.1038/s41467-023-38472-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Renal medullary carcinoma (RMC) is an aggressive tumour driven by bi-allelic loss of SMARCB1 and tightly associated with sickle cell trait. However, the cell-of-origin and oncogenic mechanism remain poorly understood. Using single-cell sequencing of human RMC, we defined transformation of thick ascending limb (TAL) cells into an epithelial-mesenchymal gradient of RMC cells associated with loss of renal epithelial transcription factors TFCP2L1, HOXB9 and MITF and gain of MYC and NFE2L2-associated oncogenic and ferroptosis resistance programs. We describe the molecular basis for this transcriptional switch that is reversed by SMARCB1 re-expression repressing the oncogenic and ferroptosis resistance programs leading to ferroptotic cell death. Ferroptosis resistance links TAL cell survival with the high extracellular medullar iron concentrations associated with sickle cell trait, an environment propitious to the mutagenic events associated with RMC development. This unique environment may explain why RMC is the only SMARCB1-deficient tumour arising from epithelial cells, differentiating RMC from rhabdoid tumours arising from neural crest cells.
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Affiliation(s)
- Bujamin H Vokshi
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Guillaume Davidson
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Nassim Tawanaie Pour Sedehi
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Alexandra Helleux
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Marc Rippinger
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Alexandre R Haller
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Justine Gantzer
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
- Department of Medical Oncology, Institut de Cancérologie Strasbourg Europe, 67200, Strasbourg, France
| | - Jonathan Thouvenin
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
- Department of Medical Oncology, Institut de Cancérologie Strasbourg Europe, 67200, Strasbourg, France
| | - Philippe Baltzinger
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France
| | - Rachida Bouarich
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie Research Centre, 75005, Paris, France
| | - Valeria Manriquez
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie Research Centre, 75005, Paris, France
| | - Sakina Zaidi
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie Research Centre, 75005, Paris, France
| | - Priya Rao
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Pavlos Msaouel
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hervé Lang
- Department of Urology, CHRU Strasbourg, Strasbourg University, 67000, Strasbourg, France
| | - Thibault Tricard
- Department of Urology, CHRU Strasbourg, Strasbourg University, 67000, Strasbourg, France
| | - Véronique Lindner
- Department of Pathology, CHRU Strasbourg, Strasbourg University, 67200, Strasbourg, France
| | - Didier Surdez
- Balgrist University Hospital, University of Zurich, Zurich, Switzerland
- INSERM, U830, Pediatric Translational Research, PSL Research University, SIREDO Oncology Center, Institut Curie, Paris, France
| | - Jean-Emmanuel Kurtz
- Department of Medical Oncology, Institut de Cancérologie Strasbourg Europe, 67200, Strasbourg, France
| | - Franck Bourdeaut
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie Research Centre, 75005, Paris, France
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Irwin Davidson
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France.
- 'Équipe Labellisée' Ligue National contre le Cancer, Paris, France.
| | - Gabriel G Malouf
- Department of Cancer and Functional Genomics, Institute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRA, 67400, Illkirch, France.
- Department of Medical Oncology, Institut de Cancérologie Strasbourg Europe, 67200, Strasbourg, France.
- 'Équipe Labellisée' Ligue National contre le Cancer, Paris, France.
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15
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Binet R, Lambert JP, Tomkova M, Tischfield S, Baggiolini A, Picaud S, Sarkar S, Louphrasitthiphol P, Dias D, Carreira S, Humphrey T, Fillipakopoulos P, White R, Goding CR. DNA damage-induced interaction between a lineage addiction oncogenic transcription factor and the MRN complex shapes a tissue-specific DNA Damage Response and cancer predisposition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537819. [PMID: 37131595 PMCID: PMC10153263 DOI: 10.1101/2023.04.21.537819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Since genome instability can drive cancer initiation and progression, cells have evolved highly effective and ubiquitous DNA Damage Response (DDR) programs. However, some cells, in skin for example, are normally exposed to high levels of DNA damaging agents. Whether such high-risk cells possess lineage-specific mechanisms that tailor DNA repair to the tissue remains largely unknown. Here we show, using melanoma as a model, that the microphthalmia-associated transcription factor MITF, a lineage addition oncogene that coordinates many aspects of melanocyte and melanoma biology, plays a non-transcriptional role in shaping the DDR. On exposure to DNA damaging agents, MITF is phosphorylated by ATM/DNA-PKcs, and unexpectedly its interactome is dramatically remodelled; most transcription (co)factors dissociate, and instead MITF interacts with the MRE11-RAD50-NBS1 (MRN) complex. Consequently, cells with high MITF levels accumulate stalled replication forks, and display defects in homologous recombination-mediated repair associated with impaired MRN recruitment to DNA damage. In agreement, high MITF levels are associated with increased SNV burden in melanoma. Significantly, the SUMOylation-defective MITF-E318K melanoma predisposition mutation recapitulates the effects of ATM/DNA-PKcs-phosphorylated MITF. Our data suggest that a non-transcriptional function of a lineage-restricted transcription factor contributes to a tissue-specialised modulation of the DDR that can impact cancer initiation.
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Affiliation(s)
- Romuald Binet
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center and Big Data Research Center, Université Laval, Quebec, Canada; Endocrinology – Nephrology Axis, CHU de Québec – Université Laval Research Center, Quebec City, QC, Canada, G1V 4G2
| | - Marketa Tomkova
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- Department of Biochemistry and Molecular Medicine, University of California, Davis, USA
| | - Samuel Tischfield
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Arianna Baggiolini
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Sovan Sarkar
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Diogo Dias
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Suzanne Carreira
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Timothy Humphrey
- CRUK MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Panagis Fillipakopoulos
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Richard White
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - 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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16
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Berns HM, Watkins-Chow DE, Lu S, Louphrasitthiphol P, Zhang T, Brown KM, Moura-Alves P, Goding CR, Pavan WJ. Loss of MC1R signaling implicates TBX3 in pheomelanogenesis and melanoma predisposition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.10.532018. [PMID: 37090624 PMCID: PMC10120706 DOI: 10.1101/2023.03.10.532018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The human Red Hair Color (RHC) trait is caused by increased pheomelanin (red-yellow) and reduced eumelanin (black-brown) pigment in skin and hair due to diminished melanocortin 1 receptor (MC1R) function. In addition, individuals harboring the RHC trait are predisposed to melanoma development. While MC1R variants have been established as causative of RHC and are a well-defined risk factor for melanoma, it remains unclear mechanistically why decreased MC1R signaling alters pigmentation and increases melanoma susceptibility. Here, we use single-cell RNA-sequencing (scRNA-seq) of melanocytes isolated from RHC mouse models to reveal a Pheomelanin Gene Signature (PGS) comprising genes implicated in melanogenesis and oncogenic transformation. We show that TBX3, a well-known anti-senescence transcription factor implicated in melanoma progression, is part of the PGS and binds both E-box and T-box elements to regulate genes associated with melanogenesis and senescence bypass. Our results provide key insights into mechanisms by which MC1R signaling regulates pigmentation and how individuals with the RHC phenotype are predisposed to melanoma.
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Affiliation(s)
- H. Matthew Berns
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Dawn E. Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sizhu Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - 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, Tsukuba, Japan
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, 13 USA
| | - Kevin M. Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, 13 USA
| | - Pedro Moura-Alves
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, PT
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, PT
| | - Colin R. Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - William J. Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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17
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Podlesny-Drabiniok A, Novikova G, Liu Y, Dunst J, Temizer R, Giannarelli C, Marro S, Kreslavsky T, Marcora E, Goate AM. BHLHE40/41 regulate macrophage/microglia responses associated with Alzheimer's disease and other disorders of lipid-rich tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528372. [PMID: 36824752 PMCID: PMC9948946 DOI: 10.1101/2023.02.13.528372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Background Genetic and experimental evidence strongly implicates myeloid cells in the etiology of AD and suggests that AD-associated alleles and genes may modulate disease risk by altering the transcriptional and cellular responses of macrophages (like microglia) to damage of lipid-rich tissues (like the brain). Specifically, recent single-cell/nucleus RNA sequencing (sc/nRNA-seq) studies identified a transcriptionally distinct state of subsets of macrophages in aging or degenerating brains (usually referred to as disease-associated microglia or DAM) and in other diseased lipid-rich tissues (e.g., obese adipose tissue, fatty liver, and atherosclerotic plaques). We collectively refer to these subpopulations as lipid-associated macrophages or LAMs. Importantly, this particular activation state is characterized by increased expression of genes involved in the phagocytic clearance of lipid-rich cellular debris (efferocytosis), including several AD risk genes. Methods We used sc/nRNA-seq data from human and mouse microglia from healthy and diseased brains and macrophages from other lipid-rich tissues to reconstruct gene regulatory networks and identify transcriptional regulators whose regulons are enriched for LAM response genes (LAM TFs) across species. We then used gene knock-down/knock-out strategies to validate some of these LAM TFs in human THP-1 macrophages and iPSC-derived microglia in vitro, as well as mouse microglia in vivo. Results We nominate 11 strong candidate LAM TFs shared across human and mouse networks (BHLHE41, HIF1A, ID2, JUNB, MAF, MAFB, MEF2A, MEF2C, NACA, POU2F2 and SPI1). We also demonstrate a strong enrichment of AD risk alleles in the cistrome of BHLHE41 (and its close homolog BHLHE40), thus implicating its regulon in the modulation of disease susceptibility. Loss or reduction of BHLHE40/41 expression in human THP-1 macrophages and iPSC-derived microglia, as well as loss of Bhlhe40/41 in mouse microglia led to increased expression of LAM response genes, specifically those involved in cholesterol clearance and lysosomal processing, with a concomitant increase in cholesterol efflux and storage, as well as lysosomal mass and degradative capacity. Conclusions Taken together, this study nominates transcriptional regulators of the LAM response, experimentally validates BHLHE40/41 in human and mouse macrophages/microglia, and provides novel targets for therapeutic modulation of macrophage/microglia function in AD and other disorders of lipid-rich tissues.
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Affiliation(s)
- Anna Podlesny-Drabiniok
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gloriia Novikova
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
- OMNI Bioinformatics Department and Neuroscience Department, Genentech, Inc., South San Francisco, CA, USA
| | - Yiyuan Liu
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Josefine Dunst
- Department of Medicine, Division of Immunology and Allergy, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rose Temizer
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chiara Giannarelli
- Department of Medicine (C.G.), Cardiology, NYU Grossman School of Medicine
- Department of Pathology (C.G.), Cardiology, NYU Grossman School of Medicine
| | - Samuele Marro
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Taras Kreslavsky
- Department of Medicine, Division of Immunology and Allergy, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Edoardo Marcora
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alison Mary Goate
- Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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18
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Basuroy T, Dreier M, Baum C, Blomquist T, Trumbly R, Filipp FV, de la Serna IL. Epigenetic and pharmacological control of pigmentation via Bromodomain Protein 9 (BRD9). Pigment Cell Melanoma Res 2023; 36:19-32. [PMID: 36112085 PMCID: PMC10091956 DOI: 10.1111/pcmr.13068] [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: 05/25/2022] [Revised: 08/01/2022] [Accepted: 09/14/2022] [Indexed: 12/31/2022]
Abstract
Lineage-specific differentiation programs are activated by epigenetic changes in chromatin structure. Melanin-producing melanocytes maintain a gene expression program ensuring appropriate enzymatic conversion of metabolites into the pigment, melanin, and transfer to surrounding cells. During neuroectodermal development, SMARCA4 (BRG1), the catalytic subunit of SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complexes, is essential for lineage specification. SMARCA4 is also required for development of multipotent neural crest precursors into melanoblasts, which differentiate into pigment-producing melanocytes. In addition to the catalytic domain, SMARCA4 and several SWI/SNF subunits contain bromodomains which are amenable to pharmacological inhibition. We investigated the effects of pharmacological inhibitors of SWI/SNF bromodomains on melanocyte differentiation. Strikingly, treatment of murine melanoblasts and human neonatal epidermal melanocytes with selected bromodomain inhibitors abrogated melanin synthesis and visible pigmentation. Using functional genomics, iBRD9, a small molecule selective for the bromodomain of BRD9 was found to repress pigmentation-specific gene expression. Depletion of BRD9 confirmed a requirement for expression of pigmentation genes in the differentiation program from melanoblasts into pigmented melanocytes and in melanoma cells. Chromatin immunoprecipitation assays showed that iBRD9 disrupts the occupancy of BRD9 and the catalytic subunit SMARCA4 at melanocyte-specific loci. These data indicate that BRD9 promotes melanocyte pigmentation whereas pharmacological inhibition of BRD9 is repressive.
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Affiliation(s)
- Tupa Basuroy
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Megan Dreier
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Caitlin Baum
- Department of Pathology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Thomas Blomquist
- Department of Pathology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Robert Trumbly
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA.,Department of Medical Education, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Fabian V Filipp
- Metaflux, Broadway, San Diego, California, USA.,Cancer Systems Biology, Institute for Diabetes and Cancer, Helmholtz Zentrum München, Munich, Germany.,School of Life Sciences Weihenstephan, Technical University München, Freising, Germany
| | - Ivana L de la Serna
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
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19
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Gambi G, Mengus G, Davidson G, Demesmaeker E, Cuomo A, Bonaldi T, Katopodi V, Malouf GG, Leucci E, Davidson I. The LncRNA LENOX Interacts with RAP2C to Regulate Metabolism and Promote Resistance to MAPK Inhibition in Melanoma. Cancer Res 2022; 82:4555-4570. [PMID: 36214632 PMCID: PMC9755964 DOI: 10.1158/0008-5472.can-22-0959] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/27/2022] [Accepted: 09/21/2022] [Indexed: 01/24/2023]
Abstract
Tumor heterogeneity is a key feature of melanomas that hinders development of effective treatments. Aiming to overcome this, we identified LINC00518 (LENOX; lincRNA-enhancer of oxidative phosphorylation) as a melanoma-specific lncRNA expressed in all known melanoma cell states and essential for melanoma survival in vitro and in vivo. Mechanistically, LENOX promoted association of the RAP2C GTPase with mitochondrial fission regulator DRP1, increasing DRP1 S637 phosphorylation, mitochondrial fusion, and oxidative phosphorylation. LENOX expression was upregulated following treatment with MAPK inhibitors, facilitating a metabolic switch from glycolysis to oxidative phosphorylation and conferring resistance to MAPK inhibition. Consequently, combined silencing of LENOX and RAP2C synergized with MAPK inhibitors to eradicate melanoma cells. Melanomas are thus addicted to the lncRNA LENOX, which acts to optimize mitochondrial function during melanoma development and progression. SIGNIFICANCE The lncRNA LENOX is a novel regulator of melanoma metabolism, which can be targeted in conjunction with MAPK inhibitors to eradicate melanoma cells.
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Affiliation(s)
- Giovanni Gambi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Gabrielle Mengus
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | | | - Alessandro Cuomo
- Nuclear Proteomics Institute to Study Gene Expression, Milano, Italy
| | - Tiziana Bonaldi
- Nuclear Proteomics Institute to Study Gene Expression, Milano, Italy
| | - Vicky Katopodi
- Laboratory for RNA Cancer Biology, KU Leuven, Leuven, Belgium
| | - Gabriel G. Malouf
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, KU Leuven, Leuven, Belgium.,Corresponding Authors: Irwin Davidson, Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 Rue Laurent Fries, Illkirch, 67404, France. E-mail: ; and Eleonora Leucci, Laboratory for RNA Cancer Biology, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. E-mail:
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Equipe Labélisée Ligue contre le Cancer.,Corresponding Authors: Irwin Davidson, Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 Rue Laurent Fries, Illkirch, 67404, France. E-mail: ; and Eleonora Leucci, Laboratory for RNA Cancer Biology, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. E-mail:
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20
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Cheng ZJ, Dai GF, Hsu JL, Lin JJ, Wu WT, Su CC, Wu YJ. Antimelanogenesis Effect of Methyl Gallate through the Regulation of PI3K/Akt and MEK/ERK in B16F10 Melanoma Cells. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:5092655. [PMID: 36532851 PMCID: PMC9750762 DOI: 10.1155/2022/5092655] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/08/2022] [Accepted: 11/25/2022] [Indexed: 07/30/2023]
Abstract
Methyl gallate is a polyphenolic compound found in many plants, and its antioxidant, antitumor, antibacterial, and anti-inflammatory effects have been extensively studied. More recently, antidepressant-like effects of methyl gallate have been demonstrated in some studies. In the present study, we examined the effects of methyl gallate on melanogenesis, including the tyrosinase inhibitory effect, the melanin content, and the molecular signaling pathways involved in this inhibition. The results showed that methyl gallate inhibited tyrosinase activity and significantly downregulated the expressions of melanin synthesis-associated proteins, including microphthalmia-associated transcription factor (MITF), tyrosinase, dopachrome tautomerase (Dct), and tyrosinase-related protein-1 (TRP1). In conclusion, our findings indicated that activation of MEK/ERK and PI3K/Akt promoted by methyl gallate caused downregulation of MITF and triggered its downstream signaling pathway, thereby inhibiting the production of melanin. In summary, methyl gallate showed significant inhibitory activity against melanin formation, implying that it may be a potential ingredient for application in skin-whitening cosmetics.
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Affiliation(s)
- Zhi Jiao Cheng
- Department of Beauty Science, Meiho University, Pingtung 91202, Taiwan
| | - Guo Fong Dai
- Yu Jun Biotechnology Co., Ltd., Kaoshiung, Taiwan
| | - Jue Liang Hsu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Center for Austronesian Medicine and Agriculture, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Jen Jie Lin
- Yu Jun Biotechnology Co., Ltd., Kaoshiung, Taiwan
- Department of Food and Nutrition, Meiho University, Pingtung 91202, Taiwan
| | - Wen Tung Wu
- Department of Food and Nutrition, Meiho University, Pingtung 91202, Taiwan
| | - Ching Chyuan Su
- Antai Medical Care Corporation Antai Tian-Sheng Memorial Hospital, Pingtung 928, Taiwan
| | - Yu Jen Wu
- Department of Beauty Science, Meiho University, Pingtung 91202, Taiwan
- Yu Jun Biotechnology Co., Ltd., Kaoshiung, Taiwan
- Department of Food and Nutrition, Meiho University, Pingtung 91202, Taiwan
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21
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Mo Y, Duan S, Zhang X, Hua X, Zhou H, Wei HJ, Watanabe J, McQuillan N, Su Z, Gu W, Wu CC, Vakoc CR, Hashizume R, Chang K, Zhang Z. Epigenome Programming by H3.3K27M Mutation Creates a Dependence of Pediatric Glioma on SMARCA4. Cancer Discov 2022; 12:2906-2929. [PMID: 36305747 PMCID: PMC9722525 DOI: 10.1158/2159-8290.cd-21-1492] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 07/20/2022] [Accepted: 09/02/2022] [Indexed: 01/12/2023]
Abstract
Patients with diffuse midline gliomas that are H3K27 altered (DMG) display a dismal prognosis. However, the molecular mechanisms underlying DMG tumorigenesis remain poorly defined. Here we show that SMARCA4, the catalytic subunit of the mammalian SWI/SNF chromatin remodeling complex, is essential for the proliferation, migration, and invasion of DMG cells and tumor growth in patient-derived DMG xenograft models. SMARCA4 colocalizes with SOX10 at gene regulatory elements to control the expression of genes involved in cell growth and the extracellular matrix (ECM). Moreover, SMARCA4 chromatin binding is reduced upon depletion of SOX10 or H3.3K27M, a mutation occurring in about 60% DMG tumors. Furthermore, the SMARCA4 occupancy at enhancers marked by both SOX10 and H3K27 acetylation is reduced the most upon depleting the H3.3K27M mutation. Taken together, our results support a model in which epigenome reprogramming by H3.3K27M creates a dependence on SMARCA4-mediated chromatin remodeling to drive gene expression and the pathogenesis of H3.3K27M DMG. SIGNIFICANCE DMG is a deadly pediatric glioma currently without effective treatments. We discovered that the chromatin remodeler SMARCA4 is essential for the proliferation of DMG with H3K27M mutation in vitro and in vivo, identifying a potentially novel therapeutic approach to this disease. See related commentary by Beytagh and Weiss, p. 2730. See related article by Panditharatna et al., p. 2880. This article is highlighted in the In This Issue feature, p. 2711.
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Affiliation(s)
- Yan Mo
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Shoufu Duan
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Xu Zhang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Hui Zhou
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Hong-Jian Wei
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jun Watanabe
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nicholas McQuillan
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zhenyi Su
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wei Gu
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Cheng-Chia Wu
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Rintaro Hashizume
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
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22
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Fang X, Rao K, Wei Z, Cheng J. SOX10
modulated
SMARCA4
dysregulation alleviates
DNA
replication stress in cutaneous melanoma. J Cell Mol Med 2022; 26:5846-5857. [DOI: 10.1111/jcmm.17607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/21/2022] [Accepted: 10/15/2022] [Indexed: 12/05/2022] Open
Affiliation(s)
- Xiangjian Fang
- Department of Burns and Plastic Surgery Fujian Medical University Affiliated First Quanzhou Hospital Quanzhou Fujian Province China
| | - Keqiang Rao
- School of Medicine Shanghai Jiao Tong University Shanghai China
| | - Zhiyi Wei
- Department of Burns and Plastic Surgery Fujian Medical University Affiliated First Quanzhou Hospital Quanzhou Fujian Province China
| | - Juntao Cheng
- Department of Burns and Plastic Surgery Fujian Medical University Affiliated First Quanzhou Hospital Quanzhou Fujian Province China
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23
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Rubanov A, Berico P, Hernando E. Epigenetic Mechanisms Underlying Melanoma Resistance to Immune and Targeted Therapies. Cancers (Basel) 2022; 14:cancers14235858. [PMID: 36497341 PMCID: PMC9738385 DOI: 10.3390/cancers14235858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
Abstract
Melanoma is an aggressive skin cancer reliant on early detection for high likelihood of successful treatment. Solar UV exposure transforms melanocytes into highly mutated tumor cells that metastasize to the liver, lungs, and brain. Even upon resection of the primary tumor, almost thirty percent of patients succumb to melanoma within twenty years. Identification of key melanoma genetic drivers led to the development of pharmacological BRAFV600E and MEK inhibitors, significantly improving metastatic patient outcomes over traditional cytotoxic chemotherapy or pioneering IFN-α and IL-2 immune therapies. Checkpoint blockade inhibitors releasing the immunosuppressive effects of CTLA-4 or PD-1 proved to be even more effective and are the standard first-line treatment. Despite these major improvements, durable responses to immunotherapy and targeted therapy have been hindered by intrinsic or acquired resistance. In addition to gained or selected genetic alterations, cellular plasticity conferred by epigenetic reprogramming is emerging as a driver of therapy resistance. Epigenetic regulation of chromatin accessibility drives gene expression and establishes distinct transcriptional cell states. Here we review how aberrant chromatin, transcriptional, and epigenetic regulation contribute to therapy resistance and discuss how targeting these programs sensitizes melanoma cells to immune and targeted therapies.
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Affiliation(s)
- Andrey Rubanov
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Pietro Berico
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Eva Hernando
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
- Correspondence:
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24
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Slade L, Biswas D, Kienesberger PC, Pulinilkunnil T. Loss of transcription factor EB dysregulates the G1/S transition and DNA replication in mammary epithelial cells. J Biol Chem 2022; 298:102692. [PMID: 36372230 PMCID: PMC9764199 DOI: 10.1016/j.jbc.2022.102692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022] Open
Abstract
Triple-negative breast cancer (TNBC) poses significant challenges for treatment given the lack of targeted therapies and increased probability of relapse. It is pertinent to identify vulnerabilities in TNBC and develop newer treatments. Our prior research demonstrated that transcription factor EB (TFEB) is necessary for TNBC survival by regulating DNA repair, apoptosis signaling, and the cell cycle. However, specific mechanisms by which TFEB targets DNA repair and cell cycle pathways are unclear, and whether these effects dictate TNBC survival is yet to be determined. Here, we show that TFEB knockdown decreased the expression of genes and proteins involved in DNA replication and cell cycle progression in MDA-MB-231 TNBC cells. DNA replication was decreased in cells lacking TFEB, as measured by EdU incorporation. TFEB silencing in MDA-MB-231 and noncancerous MCF10A cells impaired progression through the S-phase following G1/S synchronization; however, this proliferation defect could not be rescued by co-knockdown of suppressor RB1. Instead, TFEB knockdown reduced origin licensing in G1 and early S-phase MDA-MB-231 cells. TFEB silencing was associated with replication stress in MCF10A but not in TNBC cells. Lastly, we identified that TFEB knockdown renders TNBC cells more sensitive to inhibitors of Aurora Kinase A, a protein facilitating mitosis. Thus, inhibition of TFEB impairs cell cycle progress by decreasing origin licensing, leading to delayed entry into the S-phase, while rendering TNBC cells sensitive to Aurora kinase A inhibitors and decreasing cell viability. In contrast, TFEB silencing in noncancerous cells is associated with replication stress and leads to G1/S arrest.
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25
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Nyberg WA, Velasquez‐Pulgarin DA, He T, Sjöstrand M, Pellé L, Covacu R, Espinosa A. The bromodomain protein TRIM28 controls the balance between growth and invasiveness in melanoma. EMBO Rep 2022; 24:e54944. [PMID: 36341538 PMCID: PMC9827549 DOI: 10.15252/embr.202254944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
Melanoma tumors are highly metastatic partly due to the ability of melanoma cells to transition between invasive and proliferative states. However, the mechanisms underlying this plasticity are still not fully understood. To identify new epigenetic regulators of melanoma plasticity, we combined data mining, tumor models, proximity proteomics, and CUT&RUN sequencing. We focus on the druggable family of bromodomain epigenetic readers and identify TRIM28 as a new regulator of melanoma plasticity. We find that TRIM28 promotes the expression of pro-invasive genes and that TRIM28 controls the balance between invasiveness and growth of melanoma cells. We demonstrate that TRIM28 acts via the transcription factor JUNB that directly regulates the expression of pro-invasive and pro-growth genes. Mechanistically, TRIM28 controls the expression of JUNB by negatively regulating its transcriptional elongation by RNA polymerase II. In conclusion, our results demonstrate that a TRIM28-JUNB axis controls the balance between invasiveness and growth in melanoma tumors and suggest that the bromodomain protein TRIM28 could be targeted to reduce tumor spread.
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Affiliation(s)
- William A Nyberg
- Department of Medicine, Center for Molecular Medicine, Karolinska InstitutetKarolinska University HospitalStockholmSweden,Present address:
Department of MedicineUniversity of California San FranciscoSan FranciscoCAUSA
| | - Diego A Velasquez‐Pulgarin
- Department of Medicine, Center for Molecular Medicine, Karolinska InstitutetKarolinska University HospitalStockholmSweden,Department of Biomedical EngineeringUniversity of MemphisMemphisTNUSA
| | - Tianlin He
- Department of Medicine, Center for Molecular Medicine, Karolinska InstitutetKarolinska University HospitalStockholmSweden
| | - Maria Sjöstrand
- Department of Medicine, Center for Molecular Medicine, Karolinska InstitutetKarolinska University HospitalStockholmSweden,Present address:
Department of Medicine, Center for Cell EngineeringMemorial Sloan‐Kettering Cancer CenterNew YorkNYUSA
| | - Lucia Pellé
- Department of Medicine, Center for Molecular Medicine, Karolinska InstitutetKarolinska University HospitalStockholmSweden
| | - Ruxandra Covacu
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska InstitutetKarolinska University HospitalStockholmSweden
| | - Alexander Espinosa
- Department of Medicine, Center for Molecular Medicine, Karolinska InstitutetKarolinska University HospitalStockholmSweden
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26
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Yan X, Cheng Y, Zhang X, Hu Y, Huang H, Ren J, Wen B, Yang Y, Xiao K, Hu W, Wang W. NICD3 regulates the expression of MUC5AC and MUC2 by recruiting SMARCA4 and is involved in the differentiation of mucinous colorectal adenocarcinoma. Mol Oncol 2022; 16:3509-3532. [PMID: 35900231 PMCID: PMC9533685 DOI: 10.1002/1878-0261.13296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/08/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022] Open
Abstract
Adenocarcinoma is the most prevalent histological subtype of colorectal cancer (CRC), with mucinous colorectal adenocarcinoma (MCA) being a unique form. Although the mucinous subtype is known to elicit a worse response to chemotherapy and immunotherapy than the nonmucinous subtype, its pathogenesis remains poorly understood. Neurogenic locus notch homolog protein 3 (NOTCH3), a member of the NOTCH subfamilies, is highly expressed in CRC. In the past three decades, many studies have been performed evaluating the biological role of NOTCH3 in CRC. However, the precise activities of NOTCH3 in MCA, as well as the mechanisms involved in its transcriptional control, are yet to be elucidated. Our finding showed that the critical transcriptional regulatory factor transcription activator BRG1 (SMARCA4) directly binds to the intracellular domain of NOTCH3 to control transcriptional regulation. Moreover, RNA‐sequencing results indicated a common targeting effect on the transcriptional activity of mucin‐5AC (MUC5AC) and mucin‐2 (MUC2) in CRC cells by NOTCH3 and SMARCA4. Furthermore, NOTCH3 was found to control the expressions of MUC5AC and MUC2 in a SMARCA4‐dependent manner. MUC5AC and MUC2, which encode two secreted mucins, are located on chromosome 11p15.5, and are linked to the development of MCA. This finding suggests that the interaction between NOTCH3 and SMARCA4 may be involved in MCA differentiation by jointly targeting MUC5AC and MUC2. Patients with MCA are often treated in accordance with CRC guidelines. Determining the relationship between NOTCH3 and SMARCA4 by demonstrating their interactions in the pathophysiology of MCA could provide novel therapeutic targets and help identify potential prognostic markers for MCA.
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Affiliation(s)
- Xiaodong Yan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.,Department of Gastrointestinal Surgery, Changzhi People's Hospital, The Affiliated Hospital of Shanxi Medical University, Changzhi, Shanxi Province, 046000, China
| | - Yuan Cheng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Xia Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Yi Hu
- Fuxing Hospital, Capital Medical University, Beijing, 100038, China
| | - Haixia Huang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Jie Ren
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Boye Wen
- School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Yuhui Yang
- School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Keyuan Xiao
- Central laboratory, Changzhi People's Hospital, The Affiliated Hospital of Shanxi Medical University, Changzhi, Shanxi Province, 046000, China
| | - Wenqing Hu
- Department of Gastrointestinal Surgery, Changzhi People's Hospital, The Affiliated Hospital of Shanxi Medical University, Changzhi, Shanxi Province, 046000, China
| | - Wei Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.,Beijing Lab for Cardiovascular Precision Medicine, Capital Medical University, Beijing, 100069, China
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27
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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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28
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Beon J, Han S, Yang H, Park SE, Hyun K, Lee SY, Rhee HW, Seo JK, Kim J, Kim S, Lee D. Inositol polyphosphate multikinase physically binds to the SWI/SNF complex and modulates BRG1 occupancy in mouse embryonic stem cells. eLife 2022; 11:73523. [PMID: 35551737 PMCID: PMC9098221 DOI: 10.7554/elife.73523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Inositol polyphosphate multikinase (IPMK), a key enzyme in inositol polyphosphate (IP) metabolism, is a pleiotropic signaling factor involved in major biological events, including transcriptional control. In the yeast, IPMK and its IP products promote the activity of the chromatin remodeling complex SWI/SNF, which plays a critical role in gene expression by regulating chromatin accessibility. However, the direct link between IPMK and chromatin remodelers remains unclear, raising the question of how IPMK contributes to transcriptional regulation in mammals. By employing unbiased screening approaches and in vivo/in vitro immunoprecipitation, here we demonstrate that mammalian IPMK physically interacts with the SWI/SNF complex by directly binding to SMARCB1, BRG1, and SMARCC1. Furthermore, we identified the specific domains required for IPMK-SMARCB1 binding. Notably, using CUT&RUN and ATAC-seq assays, we discovered that IPMK co-localizes with BRG1 and regulates BRG1 localization as well as BRG1-mediated chromatin accessibility in a genome-wide manner in mouse embryonic stem cells. Together, these findings show that IPMK regulates the promoter targeting of the SWI/SNF complex, thereby contributing to SWI/SNF-meditated chromatin accessibility, transcription, and differentiation in mouse embryonic stem cells.
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Affiliation(s)
- Jiyoon Beon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sungwook Han
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Hyeokjun Yang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Seung Eun Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Kwangbeom Hyun
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Song-Yi Lee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jeong Kon Seo
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Seyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,KAIST Stem Cell Center, KAIST, Daejeon, Republic of Korea.,KAIST Institute for the BioCentury, KAIST, Daejeon, Republic of Korea
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
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29
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Kenny C, Dilshat R, Seberg HE, Van Otterloo E, Bonde G, Helverson A, Franke CM, Steingrímsson E, Cornell RA. TFAP2 paralogs facilitate chromatin access for MITF at pigmentation and cell proliferation genes. PLoS Genet 2022; 18:e1010207. [PMID: 35580127 PMCID: PMC9159589 DOI: 10.1371/journal.pgen.1010207] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/01/2022] [Accepted: 04/19/2022] [Indexed: 12/13/2022] Open
Abstract
In developing melanocytes and in melanoma cells, multiple paralogs of the Activating-enhancer-binding Protein 2 family of transcription factors (TFAP2) contribute to expression of genes encoding pigmentation regulators, but their interaction with Microphthalmia transcription factor (MITF), a master regulator of these cells, is unclear. Supporting the model that TFAP2 facilitates MITF's ability to activate expression of pigmentation genes, single-cell seq analysis of zebrafish embryos revealed that pigmentation genes are only expressed in the subset of mitfa-expressing cells that also express tfap2 paralogs. To test this model in SK-MEL-28 melanoma cells we deleted the two TFAP2 paralogs with highest expression, TFAP2A and TFAP2C, creating TFAP2 knockout (TFAP2-KO) cells. We then assessed gene expression, chromatin accessibility, binding of TFAP2A and of MITF, and the chromatin marks H3K27Ac and H3K27Me3 which are characteristic of active enhancers and silenced chromatin, respectively. Integrated analyses of these datasets indicate TFAP2 paralogs directly activate enhancers near genes enriched for roles in pigmentation and proliferation, and directly repress enhancers near genes enriched for roles in cell adhesion. Consistently, compared to WT cells, TFAP2-KO cells proliferate less and adhere to one another more. TFAP2 paralogs and MITF co-operatively activate a subset of enhancers, with the former necessary for MITF binding and chromatin accessibility. By contrast, TFAP2 paralogs and MITF do not appear to co-operatively inhibit enhancers. These studies reveal a mechanism by which TFAP2 profoundly influences the set of genes activated by MITF, and thereby the phenotype of pigment cells and melanoma cells.
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Affiliation(s)
- Colin Kenny
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Ramile Dilshat
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Hannah E. Seberg
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Eric Van Otterloo
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Gregory Bonde
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Annika Helverson
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Christopher M. Franke
- Department of Surgery, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Robert A. Cornell
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
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30
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Möller E, Praz V, Rajendran S, Dong R, Cauderay A, Xing YH, Lee L, Fusco C, Broye LC, Cironi L, Iyer S, Rengarajan S, Awad ME, Naigles B, Letovanec I, Ormas N, Finzi G, La Rosa S, Sessa F, Chebib I, Petur Nielsen G, Digklia A, Spentzos D, Cote GM, Choy E, Aryee M, Stamenkovic I, Boulay G, Rivera MN, Riggi N. EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in Clear Cell Sarcoma. Nat Commun 2022; 13:2267. [PMID: 35477713 PMCID: PMC9046276 DOI: 10.1038/s41467-022-29910-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 04/07/2022] [Indexed: 11/26/2022] Open
Abstract
Oncogenic fusion proteins generated by chromosomal translocations play major roles in cancer. Among them, fusions between EWSR1 and transcription factors generate oncogenes with powerful chromatin regulatory activities, capable of establishing complex gene expression programs in permissive precursor cells. Here we define the epigenetic and 3D connectivity landscape of Clear Cell Sarcoma, an aggressive cancer driven by the EWSR1-ATF1 fusion gene. We find that EWSR1-ATF1 displays a distinct DNA binding pattern that requires the EWSR1 domain and promotes ATF1 retargeting to new distal sites, leading to chromatin activation and the establishment of a 3D network that controls oncogenic and differentiation signatures observed in primary CCS tumors. Conversely, EWSR1-ATF1 depletion results in a marked reconfiguration of 3D connectivity, including the emergence of regulatory circuits that promote neural crest-related developmental programs. Taken together, our study elucidates the epigenetic mechanisms utilized by EWSR1-ATF1 to establish regulatory networks in CCS, and points to precursor cells in the neural crest lineage as candidate cells of origin for these tumors. The relationship between cellular histogenesis and molecular phenotypes for the EWSR1- ATF1 fusion in clear cell sarcoma (CCS) requires further characterization. Here, the authors investigate the EWSR1-ATF1 gene regulation networks in CCS cell lines, primary tumors, and mesenchymal stem cells.
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Affiliation(s)
- Emely Möller
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Viviane Praz
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sanalkumar Rajendran
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Rui Dong
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Alexandra Cauderay
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.,Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Yu-Hang Xing
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Lukuo Lee
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Carlo Fusco
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Liliane C Broye
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Luisa Cironi
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sowmya Iyer
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Shruthi Rengarajan
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Mary E Awad
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Beverly Naigles
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Igor Letovanec
- Department of Histopathology, Central Institute, Valais Hospital, Sion, Switzerland.,Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Nicola Ormas
- Department of Pathology, ASST Sette Laghi, Varese, Italy
| | - Giovanna Finzi
- Department of Pathology, ASST Sette Laghi, Varese, Italy
| | - Stefano La Rosa
- Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.,Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Fausto Sessa
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Ivan Chebib
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - G Petur Nielsen
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Antonia Digklia
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dimitrios Spentzos
- Department of Orthopaedic Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Gregory M Cote
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Edwin Choy
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Martin Aryee
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA.,Broad Institute, Cambridge, MA, USA
| | - Ivan Stamenkovic
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gaylor Boulay
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA
| | - Miguel N Rivera
- Department of Pathology and Cancer Center, Massachusetts General Hospital, Charlestown, MA, USA.,Broad Institute, Cambridge, MA, USA
| | - Nicolò Riggi
- Experimental Pathology Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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31
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Understanding Molecular Mechanisms of Phenotype Switching and Crosstalk with TME to Reveal New Vulnerabilities of Melanoma. Cells 2022; 11:cells11071157. [PMID: 35406721 PMCID: PMC8997563 DOI: 10.3390/cells11071157] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 12/15/2022] Open
Abstract
Melanoma cells are notorious for their high plasticity and ability to switch back and forth between various melanoma cell states, enabling the adaptation to sub-optimal conditions and therapeutics. This phenotypic plasticity, which has gained more attention in cancer research, is proposed as a new paradigm for melanoma progression. In this review, we provide a detailed and deep comprehensive recapitulation of the complex spectrum of phenotype switching in melanoma, the key regulator factors, the various and new melanoma states, and corresponding signatures. We also present an extensive description of the role of epigenetic modifications (chromatin remodeling, methylation, and activities of long non-coding RNAs/miRNAs) and metabolic rewiring in the dynamic switch. Furthermore, we elucidate the main role of the crosstalk between the tumor microenvironment (TME) and oxidative stress in the regulation of the phenotype switching. Finally, we discuss in detail several rational therapeutic approaches, such as exploiting phenotype-specific and metabolic vulnerabilities and targeting components and signals of the TME, to improve the response of melanoma patients to treatments.
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32
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Dreier MR, de la Serna IL. SWI/SNF Chromatin Remodeling Enzymes in Melanoma. EPIGENOMES 2022; 6:epigenomes6010010. [PMID: 35323214 PMCID: PMC8947417 DOI: 10.3390/epigenomes6010010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Melanoma is an aggressive malignancy that arises from the transformation of melanocytes on the skin, mucosal membranes, and uvea of the eye. SWI/SNF chromatin remodeling enzymes are multi-subunit complexes that play important roles in the development of the melanocyte lineage and in the response to ultraviolet radiation, a key environmental risk factor for developing cutaneous melanoma. Exome sequencing has revealed frequent loss of function mutations in genes encoding SWI/SNF subunits in melanoma. However, some SWI/SNF subunits have also been demonstrated to have pro-tumorigenic roles in melanoma and to affect sensitivity to therapeutics. This review summarizes studies that have implicated SWI/SNF components in melanomagenesis and have evaluated how SWI/SNF subunits modulate the response to current therapeutics.
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33
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MITF activity is regulated by a direct interaction with RAF proteins in melanoma cells. Commun Biol 2022; 5:101. [PMID: 35091687 PMCID: PMC8799692 DOI: 10.1038/s42003-022-03049-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 01/12/2022] [Indexed: 12/14/2022] Open
Abstract
The MITF transcription factor and the RAS/RAF/MEK/ERK pathway are two interconnected main players in melanoma. Understanding how MITF activity is regulated represents a key question since its dynamic modulation is involved in the phenotypic plasticity of melanoma cells and their resistance to therapy. By investigating the role of ARAF in NRAS-driven mouse melanoma through mass spectrometry experiments followed by a functional siRNA-based screen, we unexpectedly identified MITF as a direct ARAF partner. Interestingly, this interaction is conserved among the RAF protein kinase family since BRAF/MITF and CRAF/MITF complexes were also observed in the cytosol of NRAS-mutated mouse melanoma cells. The interaction occurs through the kinase domain of RAF proteins. Importantly, endogenous BRAF/MITF complexes were also detected in BRAF-mutated human melanoma cells. RAF/MITF complexes modulate MITF nuclear localization by inducing an accumulation of MITF in the cytoplasm, thus negatively controlling its transcriptional activity. Taken together, our study highlights a new level of regulation between two major mediators of melanoma progression, MITF and the MAPK/ERK pathway, which appears more complex than previously anticipated. The MITF transcription factor directly binds to the kinase domain of RAF kinases, including ARAF, BRAF and CRAF in melanoma cells. RAF/MITF complex promotes cytoplasmic accumulation of MITF and thus negatively regulates its transcriptional activity.
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34
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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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35
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Mauduit D, Taskiran II, Minnoye L, de Waegeneer M, Christiaens V, Hulselmans G, Demeulemeester J, Wouters J, Aerts S. Analysis of long and short enhancers in melanoma cell states. eLife 2021; 10:e71735. [PMID: 34874265 PMCID: PMC8691835 DOI: 10.7554/elife.71735] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 12/06/2021] [Indexed: 12/14/2022] Open
Abstract
Understanding how enhancers drive cell-type specificity and efficiently identifying them is essential for the development of innovative therapeutic strategies. In melanoma, the melanocytic (MEL) and the mesenchymal-like (MES) states present themselves with different responses to therapy, making the identification of specific enhancers highly relevant. Using massively parallel reporter assays (MPRAs) in a panel of patient-derived melanoma lines (MM lines), we set to identify and decipher melanoma enhancers by first focusing on regions with state-specific H3K27 acetylation close to differentially expressed genes. An in-depth evaluation of those regions was then pursued by investigating the activity of overlapping ATAC-seq peaks along with a full tiling of the acetylated regions with 190 bp sequences. Activity was observed in more than 60% of the selected regions, and we were able to precisely locate the active enhancers within ATAC-seq peaks. Comparison of sequence content with activity, using the deep learning model DeepMEL2, revealed that AP-1 alone is responsible for the MES enhancer activity. In contrast, SOX10 and MITF both influence MEL enhancer function with SOX10 being required to achieve high levels of activity. Overall, our MPRAs shed light on the relationship between long and short sequences in terms of their sequence content, enhancer activity, and specificity across melanoma cell states.
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Affiliation(s)
- David Mauduit
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
| | - Ibrahim Ihsan Taskiran
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
| | - Liesbeth Minnoye
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
| | - Maxime de Waegeneer
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
| | - Valerie Christiaens
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
| | - Gert Hulselmans
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
| | - Jonas Demeulemeester
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
- Cancer Genomics Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Jasper Wouters
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
| | - Stein Aerts
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
- KU Leuven, Department of Human Genetics KU LeuvenLeuvenBelgium
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36
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Berico P, Cigrang M, Davidson G, Braun C, Sandoz J, Legras S, Vokshi BH, Slovic N, Peyresaubes F, Gene Robles CM, Egly JM, Compe E, Davidson I, Coin F. CDK7 and MITF repress a transcription program involved in survival and drug tolerance in melanoma. EMBO Rep 2021; 22:e51683. [PMID: 34296805 DOI: 10.15252/embr.202051683] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 11/09/2022] Open
Abstract
Melanoma cell phenotype switching between differentiated melanocytic and undifferentiated mesenchymal-like states drives metastasis and drug resistance. CDK7 is the serine/threonine kinase of the basal transcription factor TFIIH. We show that dedifferentiation of melanocytic-type melanoma cells into mesenchymal-like cells and acquisition of tolerance to targeted therapies is achieved through chronic inhibition of CDK7. In addition to emergence of a mesenchymal-type signature, we identify a GATA6-dependent gene expression program comprising genes such as AMIGO2 or ABCG2 involved in melanoma survival or targeted drug tolerance, respectively. Mechanistically, we show that CDK7 drives expression of the melanocyte lineage transcription factor MITF that in turn binds to an intronic region of GATA6 to repress its expression in melanocytic-type cells. We show that GATA6 expression is activated in MITF-low melanoma cells of patient-derived xenografts. Taken together, our data show how the poorly characterized repressive function of MITF in melanoma participates in a molecular cascade regulating activation of a transcriptional program involved in survival and drug resistance in melanoma.
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Affiliation(s)
- Pietro Berico
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Max Cigrang
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Cathy Braun
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Jeremy Sandoz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Stephanie Legras
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bujamin Hektor Vokshi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Nevena Slovic
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - François Peyresaubes
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Carlos Mario Gene Robles
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Frederic Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
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37
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Sheinboim D, Parikh S, Parikh R, Menuchin A, Shapira G, Kapitansky O, Elkoshi N, Ruppo S, Shaham L, Golan T, Elgavish S, Nevo Y, Bell RE, Malcov H, Shomron N, Taub JW, Izraeli S, Levy C. Slow transcription of the 99a/let-7c/125b-2 cluster results in differential miRNA expression and promotes melanoma phenotypic plasticity. J Invest Dermatol 2021; 141:2944-2956.e6. [PMID: 34186058 DOI: 10.1016/j.jid.2021.03.036] [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: 11/09/2020] [Revised: 03/21/2021] [Accepted: 03/31/2021] [Indexed: 10/21/2022]
Abstract
Almost half of human miRNAs are encoded in clusters. Although transcribed as a single unit, the levels of individual mature miRNAs often differ. The mechanisms underlying differential biogenesis of clustered miRNAs and the resulting physiological implications are mostly unknown. Here, we report that the melanoma master transcription regulator MITF regulates the differential expression of the 99a/let-7c/125b-2 cluster by altering the distribution of RNA polymerase II (Pol-II) along the cluster. We discovered that MITF interacts with TRIM28, a known inhibitor of Pol-II transcription elongation, at the let-7c region resulting in Pol-II pausing and causing its elevated expression, whereas low levels of Pol-II occupation over miR-99a and miR-125b-2 regions decreases their biogenesis. Furthermore, we showed that this differential expression affects the phenotypic state of melanoma cells. RNA-seq analysis of proliferative melanoma cells that express miR-99a and miR-125b mimics revealed a transcriptomic shift toward an invasive phenotype. Conversely, expression of a let-7c mimic in invasive melanoma cells induced a shift to a more proliferative state. We confirmed direct target genes of these miRNAs: FGFR3, BAP1, Bcl2, TGFBR1, and CDKN1A. Our study demonstrates a MITF-governed biogenesis mechanism that results in differential expression of clustered 99a/let-7c/125b-2 miRNAs that control melanoma progression.
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Affiliation(s)
- Danna Sheinboim
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shivang Parikh
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Roma Parikh
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Amitai Menuchin
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Guy Shapira
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Oxana Kapitansky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nadav Elkoshi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shmuel Ruppo
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem and Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Lital Shaham
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Division of Pediatric Hematology-Oncology Department, Schneider Children's Medical Center, Petah Tikva 49202, Israel
| | - Tamar Golan
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sharona Elgavish
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem and Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Yuval Nevo
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem and Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Rachel E Bell
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hagar Malcov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Edmond J. Safra Center of Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jeffrey W Taub
- Wayne State University School of Medicine, Detroit, MI 48201, USA; Division of Pediatric Hematology and Oncology, Children's Hospital of Michigan, Detroit, MI 48201, USA
| | - Shai Izraeli
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem and Hadassah Medical Center, Jerusalem 9112102, Israel
| | - Carmit Levy
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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38
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Hamm M, Sohier P, Petit V, Raymond JH, Delmas V, Le Coz M, Gesbert F, Kenny C, Aktary Z, Pouteaux M, Rambow F, Sarasin A, Charoenchon N, Bellacosa A, Sanchez-Del-Campo L, Mosteo L, Lauss M, Meijer D, Steingrimsson E, Jönsson GB, Cornell RA, Davidson I, Goding CR, Larue L. BRN2 is a non-canonical melanoma tumor-suppressor. Nat Commun 2021; 12:3707. [PMID: 34140478 PMCID: PMC8211827 DOI: 10.1038/s41467-021-23973-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 05/27/2021] [Indexed: 12/13/2022] Open
Abstract
While the major drivers of melanoma initiation, including activation of NRAS/BRAF and loss of PTEN or CDKN2A, have been identified, the role of key transcription factors that impose altered transcriptional states in response to deregulated signaling is not well understood. The POU domain transcription factor BRN2 is a key regulator of melanoma invasion, yet its role in melanoma initiation remains unknown. Here, in a BrafV600E PtenF/+ context, we show that BRN2 haplo-insufficiency promotes melanoma initiation and metastasis. However, metastatic colonization is less efficient in the absence of Brn2. Mechanistically, BRN2 directly induces PTEN expression and in consequence represses PI3K signaling. Moreover, MITF, a BRN2 target, represses PTEN transcription. Collectively, our results suggest that on a PTEN heterozygous background somatic deletion of one BRN2 allele and temporal regulation of the other allele elicits melanoma initiation and progression.
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Affiliation(s)
- Michael Hamm
- Institut Curie, Université PSL, CNRS UMR3347, Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- Université Paris-Saclay, CNRS UMR3347, Inserm U1021, Signalisation radiobiologie et cancer, Orsay, France
- Equipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Pierre Sohier
- Institut Curie, Université PSL, CNRS UMR3347, Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- Université Paris-Saclay, CNRS UMR3347, Inserm U1021, Signalisation radiobiologie et cancer, Orsay, France
- Equipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Valérie Petit
- Institut Curie, Université PSL, CNRS UMR3347, Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- Université Paris-Saclay, CNRS UMR3347, Inserm U1021, Signalisation radiobiologie et cancer, Orsay, France
- Equipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Jérémy H Raymond
- Institut Curie, Université PSL, CNRS UMR3347, Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- Université Paris-Saclay, CNRS UMR3347, Inserm U1021, Signalisation radiobiologie et cancer, Orsay, France
- Equipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Véronique Delmas
- Institut Curie, Université PSL, CNRS UMR3347, Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- Université Paris-Saclay, CNRS UMR3347, Inserm U1021, Signalisation radiobiologie et cancer, Orsay, France
- Equipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Madeleine Le Coz
- Institut Curie, Université PSL, CNRS UMR3347, Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- Université Paris-Saclay, CNRS UMR3347, Inserm U1021, Signalisation radiobiologie et cancer, Orsay, France
- Equipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Franck Gesbert
- Institut Curie, Université PSL, CNRS UMR3347, Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- Université Paris-Saclay, CNRS UMR3347, Inserm U1021, Signalisation radiobiologie et cancer, Orsay, France
- Equipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Colin Kenny
- Department of Anatomy and Cell biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Zackie Aktary
- Institut Curie, Université PSL, CNRS UMR3347, Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- Université Paris-Saclay, CNRS UMR3347, Inserm U1021, Signalisation radiobiologie et cancer, Orsay, France
- Equipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Marie Pouteaux
- Institut Curie, Université PSL, CNRS UMR3347, Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- Université Paris-Saclay, CNRS UMR3347, Inserm U1021, Signalisation radiobiologie et cancer, Orsay, France
- Equipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Florian Rambow
- Institut Curie, Université PSL, CNRS UMR3347, Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- Université Paris-Saclay, CNRS UMR3347, Inserm U1021, Signalisation radiobiologie et cancer, Orsay, France
- Equipes Labellisées Ligue Contre le Cancer, Paris, France
| | - Alain Sarasin
- Laboratory of Genetic Instability and Oncogenesis, UMR8200 CNRS, Gustave Roussy, Université Paris-Sud, Villejuif, France
| | - Nisamanee Charoenchon
- Institut Curie, Université PSL, CNRS UMR3347, Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France
- Université Paris-Saclay, CNRS UMR3347, Inserm U1021, Signalisation radiobiologie et cancer, Orsay, France
- Equipes Labellisées Ligue Contre le Cancer, Paris, France
- Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Alfonso Bellacosa
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Luis Sanchez-Del-Campo
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
| | - Laura Mosteo
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
| | - Martin Lauss
- Department of Oncology, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Dies Meijer
- Centre of Neuroregeneration, University of Edinburgh, Edinburgh, UK
| | - Eirikur Steingrimsson
- Department of Biochemistry and Molecular Biology, and Department of Anatomy, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Göran B Jönsson
- Department of Oncology, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Robert A Cornell
- Department of Anatomy and Cell biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Irwin Davidson
- Department of Anatomy and Cell biology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UNISTRA, 1 Rue Laurent Fries, 67404, Illkirch, Cedex, France
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK.
| | - Lionel Larue
- Institut Curie, Université PSL, CNRS UMR3347, Inserm U1021, Normal and Pathological Development of Melanocytes, Orsay, France.
- Université Paris-Saclay, CNRS UMR3347, Inserm U1021, Signalisation radiobiologie et cancer, Orsay, France.
- Equipes Labellisées Ligue Contre le Cancer, Paris, France.
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39
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Dilshat R, Vu HN, Steingrímsson E. Epigenetic regulation during melanocyte development and homeostasis. Exp Dermatol 2021; 30:1033-1050. [PMID: 34003523 DOI: 10.1111/exd.14391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/09/2021] [Accepted: 05/09/2021] [Indexed: 12/26/2022]
Abstract
Melanocytes originate in the neural crest as precursor cells which then migrate and proliferate to reach their destination where they differentiate into pigment-producing cells. Melanocytes not only determine the colour of hair, skin and eyes but also protect against the harmful effects of UV irradiation. The establishment of the melanocyte lineage is regulated by a defined set of transcription factors and signalling pathways that direct the specific gene expression programmes underpinning melanoblast specification, survival, migration, proliferation and differentiation. In addition, epigenetic modifiers and replacement histones play key roles in regulating gene expression and its timing during the different steps of this process. Here, we discuss the evidence for the role of epigenetic regulators in melanocyte development and function and how they interact with transcription factors and signalling pathways to establish and maintain this important cell lineage.
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Affiliation(s)
- Ramile Dilshat
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
| | - Hong Nhung Vu
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
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40
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Zhang J, Mou Y, Gong H, Chen H, Xiao H. Microphthalmia-Associated Transcription Factor in Senescence and Age-Related Diseases. Gerontology 2021; 67:708-717. [PMID: 33940580 DOI: 10.1159/000515525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/27/2021] [Indexed: 02/05/2023] Open
Abstract
Although microphthalmia-associated transcription factor (MITF) has been known for decades as a key regulator for melanocytic differentiation, recent studies expanded its other roles in multiple biological processes. Among these newfound roles, the relationship between MITF and aging is attractive; however, the underlying mechanism remains elusive. Here, we review the documented cues that highlight the implication of MITF in the aging process and particularly discuss the possible mechanisms underlying the participation of MITF in cellular senescence. First, it summarizes the association of MITF with melanocytic senescence, including the roles of MITF in cell cycle regulation, DNA damage repair, oxidative stress response, and the generation of senescence-associated secretory phenotype. Then, it collects the information involving MITF-related senescent changes in nonmelanocytes, such as retinal pigment epithelium cells, osteoclasts, and cardiomyocytes. This review may deepen the understanding of MITF function and be helpful to develop new strategies for improving geriatric health.
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Affiliation(s)
- Jian Zhang
- Lab for Aging Research, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Yi Mou
- Geroscience and Chronic Disease Department, The 8th Municipal Hospital for the People, Chengdu, China
| | - Hui Gong
- Lab for Aging Research, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Honghan Chen
- Lab for Aging Research, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Hengyi Xiao
- Lab for Aging Research, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
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41
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Sánchez-Del-Campo L, Martí-Díaz R, Montenegro MF, González-Guerrero R, Hernández-Caselles T, Martínez-Barba E, Piñero-Madrona A, Cabezas-Herrera J, Goding CR, Rodríguez-López JN. MITF induces escape from innate immunity in melanoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:117. [PMID: 33789714 PMCID: PMC8015040 DOI: 10.1186/s13046-021-01916-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/16/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND The application of immune-based therapies has revolutionized cancer treatment. Yet how the immune system responds to phenotypically heterogeneous populations within tumors is poorly understood. In melanoma, one of the major determinants of phenotypic identity is the lineage survival oncogene MITF that integrates diverse microenvironmental cues to coordinate melanoma survival, senescence bypass, differentiation, proliferation, invasion, metabolism and DNA damage repair. Whether MITF also controls the immune response is unknown. METHODS By using several mouse melanoma models, we examine the potential role of MITF to modulate the anti-melanoma immune response. ChIP-seq data analysis, ChIP-qPCR, CRISPR-Cas9 genome editing, and luciferase reporter assays were utilized to identify ADAM10 as a direct MITF target gene. Western blotting, confocal microscopy, flow cytometry, and natural killer (NK) cytotoxicity assays were used to determine the underlying mechanisms by which MITF-driven phenotypic plasticity modulates melanoma NK cell-mediated killing. RESULTS Here we show that MITF regulates expression of ADAM10, a key sheddase that cleaves the MICA/B family of ligands for NK cells. By controlling melanoma recognition by NK-cells MITF thereby controls the melanoma response to the innate immune system. Consequently, while melanoma MITFLow cells can be effectively suppressed by NK-mediated killing, MITF-expressing cells escape NK cell surveillance. CONCLUSION Our results reveal how modulation of MITF activity can impact the anti-melanoma immune response with implications for the application of anti-melanoma immunotherapies.
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Affiliation(s)
- Luis Sánchez-Del-Campo
- Department of Biochemistry and Molecular Biology A, School of Biology, IMIB-University of Murcia, 30100, Murcia, Spain.
| | - Román Martí-Díaz
- Department of Biochemistry and Molecular Biology A, School of Biology, IMIB-University of Murcia, 30100, Murcia, Spain
| | - María F Montenegro
- Department of Biochemistry and Molecular Biology A, School of Biology, IMIB-University of Murcia, 30100, Murcia, Spain
| | - Rebeca González-Guerrero
- Department of Biochemistry and Molecular Biology A, School of Biology, IMIB-University of Murcia, 30100, Murcia, Spain
| | - Trinidad Hernández-Caselles
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Medicine, IMIB-University of Murcia, Murcia, Spain
| | | | | | - Juan Cabezas-Herrera
- Translational Cancer Research Group, University Hospital Virgen de la Arrixaca, IMIB, Murcia, Spain
| | - Colin R Goding
- ResearchNuffield Department of Clinical Medicine, Ludwig Institute for Cancer, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - José Neptuno Rodríguez-López
- Department of Biochemistry and Molecular Biology A, School of Biology, IMIB-University of Murcia, 30100, Murcia, Spain.
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42
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Lee JE, Kim MY. Cancer epigenetics: Past, present and future. Semin Cancer Biol 2021; 83:4-14. [PMID: 33798724 DOI: 10.1016/j.semcancer.2021.03.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 12/14/2022]
Abstract
Cancer was thought to be caused solely by genetic mutations in oncogenes and tumor suppressor genes. In the last 35 years, however, epigenetic changes have been increasingly recognized as another primary driver of carcinogenesis and cancer progression. Epigenetic deregulation in cancer often includes mutations and/or aberrant expression of chromatin-modifying enzymes, their associated proteins, and even non-coding RNAs, which can alter chromatin structure and dynamics. This leads to changes in gene expression that ultimately contribute to the emergence and evolution of cancer cells. Studies of the deregulation of chromatin modifiers in cancer cells have reshaped the way we approach cancer and guided the development of novel anticancer therapeutics that target epigenetic factors. There remain, however, a number of unanswered questions in this field that are the focus of present research. Areas of particular interest include the actions of emerging classes of epigenetic regulators of carcinogenesis and the tumor microenvironment, as well as epigenetic tumor heterogeneity. In this review, we discuss past findings on epigenetic mechanisms of cancer, current trends in the field of cancer epigenetics, and the directions of future research that may lead to the identification of new prognostic markers for cancer and the development of more effective anticancer therapeutics.
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Affiliation(s)
- Jae Eun Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Mi-Young Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea; KAIST Institute for the BioCentury, Cancer Metastasis Control Center, Daejeon, Republic of Korea.
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43
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Coassolo S, Davidson G, Negroni L, Gambi G, Daujat S, Romier C, Davidson I. Citrullination of pyruvate kinase M2 by PADI1 and PADI3 regulates glycolysis and cancer cell proliferation. Nat Commun 2021; 12:1718. [PMID: 33741961 PMCID: PMC7979715 DOI: 10.1038/s41467-021-21960-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/23/2021] [Indexed: 12/11/2022] Open
Abstract
Chromodomain helicase DNA binding protein 4 (CHD4) is an ATPase subunit of the Nucleosome Remodelling and Deacetylation (NuRD) complex that regulates gene expression. CHD4 is essential for growth of multiple patient derived melanoma xenografts and for breast cancer. Here we show that CHD4 regulates expression of PADI1 (Protein Arginine Deiminase 1) and PADI3 in multiple cancer cell types modulating citrullination of arginine residues of the allosterically-regulated glycolytic enzyme pyruvate kinase M2 (PKM2). Citrullination of PKM2 R106 reprogrammes cross-talk between PKM2 ligands lowering its sensitivity to the inhibitors Tryptophan, Alanine and Phenylalanine and promoting activation by Serine. Citrullination thus bypasses normal physiological regulation by low Serine levels to promote excessive glycolysis and reduced cell proliferation. We further show that PADI1 and PADI3 expression is up-regulated by hypoxia where PKM2 citrullination contributes to increased glycolysis. We provide insight as to how conversion of arginines to citrulline impacts key interactions within PKM2 that act in concert to reprogramme its activity as an additional mechanism regulating this important enzyme.
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Affiliation(s)
- Sébastien Coassolo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélise Ligue Contre le Cancer, Illkirch, France
- Centre National de la Recherche Scientifique, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
- Université de Strasbourg, Strasbourg, France
- Discovery Oncology, Genentech, South San Francisco, CA, USA
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélise Ligue Contre le Cancer, Illkirch, France
- Centre National de la Recherche Scientifique, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
- Université de Strasbourg, Strasbourg, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélise Ligue Contre le Cancer, Illkirch, France
- Centre National de la Recherche Scientifique, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
- Université de Strasbourg, Strasbourg, France
| | - Giovanni Gambi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélise Ligue Contre le Cancer, Illkirch, France
- Centre National de la Recherche Scientifique, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
- Université de Strasbourg, Strasbourg, France
| | - Sylvain Daujat
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélise Ligue Contre le Cancer, Illkirch, France
- Centre National de la Recherche Scientifique, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
- Université de Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brandt, Illkirch, France
| | - Christophe Romier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélise Ligue Contre le Cancer, Illkirch, France
- Centre National de la Recherche Scientifique, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
- Université de Strasbourg, Strasbourg, France
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélise Ligue Contre le Cancer, Illkirch, France.
- Centre National de la Recherche Scientifique, Paris, France.
- Institut National de la Santé et de la Recherche Médicale, Paris, France.
- Université de Strasbourg, Strasbourg, France.
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44
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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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45
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FBXO32 links ubiquitination to epigenetic reprograming of melanoma cells. Cell Death Differ 2021; 28:1837-1848. [PMID: 33462405 PMCID: PMC8184796 DOI: 10.1038/s41418-020-00710-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 12/15/2022] Open
Abstract
Ubiquitination by serving as a major degradation signal of proteins, but also by controlling protein functioning and localization, plays critical roles in most key cellular processes. Here, we show that MITF, the master transcription factor in melanocytes, controls ubiquitination in melanoma cells. We identified FBXO32, a component of the SCF E3 ligase complex as a new MITF target gene. FBXO32 favors melanoma cell migration, proliferation, and tumor development in vivo. Transcriptomic analysis shows that FBXO32 knockdown induces a global change in melanoma gene expression profile. These include the inhibition of CDK6 in agreement with an inhibition of cell proliferation and invasion upon FBXO32 silencing. Furthermore, proteomic analysis identifies SMARC4, a component of the chromatin remodeling complexes BAF/PBAF, as a FBXO32 partner. FBXO32 and SMARCA4 co-localize at loci regulated by FBXO32, such as CDK6 suggesting that FBXO32 controls transcription through the regulation of chromatin remodeling complex activity. FBXO32 and SMARCA4 are the components of a molecular cascade, linking MITF to epigenetics, in melanoma cells.
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46
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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: 42] [Impact Index Per Article: 14.0] [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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47
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Cheli Y, Tulic MK, El Hachem N, Nottet N, Jacquel A, Gesson M, Strub T, Bille K, Picard-Gauci A, Montaudié H, Beranger GE, Passeron T, Close P, Bertolotto C, Ballotti R. ITGBL1 is a new immunomodulator that favors development of melanoma tumors by inhibiting natural killer cells cytotoxicity. Mol Cancer 2021; 20:12. [PMID: 33413419 PMCID: PMC7789764 DOI: 10.1186/s12943-020-01306-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/29/2020] [Indexed: 02/08/2023] Open
Abstract
Resistances to immunotherapies remains a major hurdle towards a cure for melanoma in numerous patients. An increase in the mesenchymal phenotype and a loss of differentiation have been clearly associated with resistance to targeted therapies. Similar phenotypes have been more recently also linked to resistance to immune checkpoint therapies. We demonstrated here that the loss of MIcrophthalmia associated Transcription Factor (MITF), a pivotal player in melanocyte differentiation, favors the escape of melanoma cells from the immune system. We identified Integrin beta-like protein 1 (ITGBL1), a secreted protein, upregulated in anti-PD1 resistant patients and in MITFlow melanoma cells, as the key immunomodulator. ITGBL1 inhibited immune cell cytotoxicity against melanoma cells by inhibiting NK cells cytotoxicity and counteracting beneficial effects of anti-PD1 treatment, both in vitro and in vivo. Mechanistically, MITF inhibited RUNX2, an activator of ITGBL1 transcription. Interestingly, VitaminD3, an inhibitor of RUNX2, improved melanoma cells to death by immune cells. In conclusion, our data suggest that inhibition of ITGBL1 might improve melanoma response to immunotherapies.
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Affiliation(s)
- Yann Cheli
- Université Nice Côte d'Azur, INSERM U1065, Team1 Biology and pathologies of melanocytes. Equipe labellisée ARC 2019, 06000, Nice, France.
| | - Meri K Tulic
- Université Nice Côte d'Azur, INSERM, U1065, Team12 Study of the melanocytic differentiation applied to vitiligo and melanoma, 06000, Nice, France
| | - Najla El Hachem
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium
| | - Nicolas Nottet
- Université Nice Côte d'Azur, INSERM U1065, Team1 Biology and pathologies of melanocytes. Equipe labellisée ARC 2019, 06000, Nice, France
| | - Arnaud Jacquel
- Université Nice Côte d'Azur, INSERM, U1065, Team2 Cell death, differentiation and cancer, 06000, Nice, France
| | - Maeva Gesson
- Université Nice Côte d'Azur, INSERM, U1065, Imaging platform, 06000, Nice, France
| | - Thomas Strub
- Université Nice Côte d'Azur, INSERM U1065, Team1 Biology and pathologies of melanocytes. Equipe labellisée ARC 2019, 06000, Nice, France
| | - Karine Bille
- Université Nice Côte d'Azur, INSERM U1065, Team1 Biology and pathologies of melanocytes. Equipe labellisée ARC 2019, 06000, Nice, France
| | | | | | - Guillaume E Beranger
- Université Nice Côte d'Azur, INSERM U1065, Team1 Biology and pathologies of melanocytes. Equipe labellisée ARC 2019, 06000, Nice, France
- Université Nice Côte d'Azur, INSERM, U1065, Team12 Study of the melanocytic differentiation applied to vitiligo and melanoma, 06000, Nice, France
| | - Thierry Passeron
- Université Nice Côte d'Azur, INSERM, U1065, Team12 Study of the melanocytic differentiation applied to vitiligo and melanoma, 06000, Nice, France
- CHU NICE, Département de Dermatologie, 06000, Nice, France
| | - Pierre Close
- Laboratory of Cancer Signaling, University of Liège, Liège, Belgium
| | - Corine Bertolotto
- Université Nice Côte d'Azur, INSERM U1065, Team1 Biology and pathologies of melanocytes. Equipe labellisée ARC 2019, 06000, Nice, France
| | - Robert Ballotti
- Université Nice Côte d'Azur, INSERM U1065, Team1 Biology and pathologies of melanocytes. Equipe labellisée ARC 2019, 06000, Nice, France
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48
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Wu Y, Fletcher M, Gu Z, Wang Q, Costa B, Bertoni A, Man KH, Schlotter M, Felsberg J, Mangei J, Barbus M, Gaupel AC, Wang W, Weiss T, Eils R, Weller M, Liu H, Reifenberger G, Korshunov A, Angel P, Lichter P, Herrmann C, Radlwimmer B. Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype. Nat Commun 2020; 11:6434. [PMID: 33339831 PMCID: PMC7749178 DOI: 10.1038/s41467-020-20225-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 11/19/2020] [Indexed: 02/08/2023] Open
Abstract
Glioblastoma frequently exhibits therapy-associated subtype transitions to mesenchymal phenotypes with adverse prognosis. Here, we perform multi-omic profiling of 60 glioblastoma primary tumours and use orthogonal analysis of chromatin and RNA-derived gene regulatory networks to identify 38 subtype master regulators, whose cell population-specific activities we further map in published single-cell RNA sequencing data. These analyses identify the oligodendrocyte precursor marker and chromatin modifier SOX10 as a master regulator in RTK I-subtype tumours. In vitro functional studies demonstrate that SOX10 loss causes a subtype switch analogous to the proneural-mesenchymal transition observed in patients at the transcriptomic, epigenetic and phenotypic levels. SOX10 repression in an in vivo syngeneic graft glioblastoma mouse model results in increased tumour invasion, immune cell infiltration and significantly reduced survival, reminiscent of progressive human glioblastoma. These results identify SOX10 as a bona fide master regulator of the RTK I subtype, with both tumour cell-intrinsic and microenvironmental effects.
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Affiliation(s)
- Yonghe Wu
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Michael Fletcher
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Zuguang Gu
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Qi Wang
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Barbara Costa
- Division of Signal Transduction and Growth Control, DKFZ/ZMBH Alliance, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Anna Bertoni
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ka-Hou Man
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Magdalena Schlotter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Jörg Felsberg
- Medical Faculty, Institute of Neuropathology, Heinrich Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner site Essen/Düsseldorf, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Jasmin Mangei
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Martje Barbus
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ann-Christin Gaupel
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Wei Wang
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Tobias Weiss
- Department of Neurology and Brain Tumor Center, University Hospital Zurich, Frauenklinikstrasse 26, CH-8091, Zurich, Switzerland
| | - Roland Eils
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Michael Weller
- Department of Neurology and Brain Tumor Center, University Hospital Zurich, Frauenklinikstrasse 26, CH-8091, Zurich, Switzerland
| | - Haikun Liu
- Division of Molecular Neurogenetics, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Guido Reifenberger
- Medical Faculty, Institute of Neuropathology, Heinrich Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner site Essen/Düsseldorf, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, University of Heidelberg, Im Neuenheimer Feld 220, 69120, Heidelberg, Germany
- Clinical Cooperation Unit, Neuropathology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 220-221, 69120, Heidelberg, Germany
| | - Peter Angel
- Division of Signal Transduction and Growth Control, DKFZ/ZMBH Alliance, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), Partner site Essen/Düsseldorf, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Carl Herrmann
- Health Data Science Unit, Medical Faculty Heidelberg, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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49
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Yu L, Peng F, Dong X, Chen Y, Sun D, Jiang S, Deng C. Sex-Determining Region Y Chromosome-Related High-Mobility-Group Box 10 in Cancer: A Potential Therapeutic Target. Front Cell Dev Biol 2020; 8:564740. [PMID: 33344444 PMCID: PMC7744619 DOI: 10.3389/fcell.2020.564740] [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: 05/22/2020] [Accepted: 11/17/2020] [Indexed: 01/20/2023] Open
Abstract
Sex-determining region Y-related high mobility group-box 10 (SOX10), a member of the SOX family, has recently been highlighted as an essential transcriptional factor involved in developmental biology. Recently, the functionality of SOX 10 has been increasingly revealed by researchers worldwide. It has been reported that SOX10 significantly regulates the proliferation, migration, and apoptosis of tumors and is closely associated with the progression of cancer. In this review, we first introduce the basic background of the SOX family and SOX10 and then discuss the pathophysiological roles of SOX10 in cancer. Besides, we enumerate the application of SOX10 in the pathological diagnosis and therapeutic potential of cancer. Eventually, we summarize the potential directions and perspectives of SOX10 in neoplastic theranostics. The information compiled herein may assist in additional studies and increase the potential of SOX10 as a therapeutic target for cancer.
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Affiliation(s)
- Liming Yu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang, China
| | - Fan Peng
- Department of Cardiology, Xijing Hopspital, The Airforce Military Medical University, Xi'an, China
| | - Xue Dong
- Outpatient Department of Liaoning Military Region, General Hospital of Northern Theater Command, Shenyang, China
| | - Ying Chen
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Dongdong Sun
- Department of Cardiology, Xijing Hopspital, The Airforce Military Medical University, Xi'an, China
| | - Shuai Jiang
- Department of Cardiology, Xijing Hopspital, The Airforce Military Medical University, Xi'an, China
| | - Chao Deng
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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50
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Minnoye L, Taskiran II, Mauduit D, Fazio M, Van Aerschot L, Hulselmans G, Christiaens V, Makhzami S, Seltenhammer M, Karras P, Primot A, Cadieu E, van Rooijen E, Marine JC, Egidy G, Ghanem GE, Zon L, Wouters J, Aerts S. Cross-species analysis of enhancer logic using deep learning. Genome Res 2020; 30:1815-1834. [PMID: 32732264 PMCID: PMC7706731 DOI: 10.1101/gr.260844.120] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/15/2020] [Indexed: 12/23/2022]
Abstract
Deciphering the genomic regulatory code of enhancers is a key challenge in biology because this code underlies cellular identity. A better understanding of how enhancers work will improve the interpretation of noncoding genome variation and empower the generation of cell type-specific drivers for gene therapy. Here, we explore the combination of deep learning and cross-species chromatin accessibility profiling to build explainable enhancer models. We apply this strategy to decipher the enhancer code in melanoma, a relevant case study owing to the presence of distinct melanoma cell states. We trained and validated a deep learning model, called DeepMEL, using chromatin accessibility data of 26 melanoma samples across six different species. We show the accuracy of DeepMEL predictions on the CAGI5 challenge, where it significantly outperforms existing models on the melanoma enhancer of IRF4 Next, we exploit DeepMEL to analyze enhancer architectures and identify accurate transcription factor binding sites for the core regulatory complexes in the two different melanoma states, with distinct roles for each transcription factor, in terms of nucleosome displacement or enhancer activation. Finally, DeepMEL identifies orthologous enhancers across distantly related species, where sequence alignment fails, and the model highlights specific nucleotide substitutions that underlie enhancer turnover. DeepMEL can be used from the Kipoi database to predict and optimize candidate enhancers and to prioritize enhancer mutations. In addition, our computational strategy can be applied to other cancer or normal cell types.
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Affiliation(s)
- Liesbeth Minnoye
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - David Mauduit
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Maurizio Fazio
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Linde Van Aerschot
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
- Laboratory for Disease Mechanisms in Cancer, KU Leuven, 3000 Leuven, Belgium
| | - Gert Hulselmans
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Valerie Christiaens
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Samira Makhzami
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Monika Seltenhammer
- Center for Forensic Medicine, Medical University of Vienna, 1090 Vienna, Austria
- Division of Livestock Sciences (NUWI) - BOKU University of Natural Resources and Life Sciences, 1180 Vienna, Austria
| | - Panagiotis Karras
- VIB-KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium
- KU Leuven, Department of Oncology KU Leuven, 3000 Leuven, Belgium
| | - Aline Primot
- CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, Faculty of Medicine, 35000 Rennes, France
| | - Edouard Cadieu
- CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, Faculty of Medicine, 35000 Rennes, France
| | - Ellen van Rooijen
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Jean-Christophe Marine
- VIB-KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium
- KU Leuven, Department of Oncology KU Leuven, 3000 Leuven, Belgium
| | - Giorgia Egidy
- Université Paris-Saclay, INRA, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Ghanem-Elias Ghanem
- Institut Jules Bordet, Université Libre de Bruxelles, 1000 Brussels, Belgium
| | - Leonard Zon
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Jasper Wouters
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Stein Aerts
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
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