1
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Davalos V, Lovell CD, Von Itter R, Dolgalev I, Agrawal P, Baptiste G, Kahler DJ, Sokolova E, Moran S, Piqué L, Vega-Saenz de Miera E, Fontanals-Cirera B, Karz A, Tsirigos A, Yun C, Darvishian F, Etchevers HC, Osman I, Esteller M, Schober M, Hernando E. An epigenetic switch controls an alternative NR2F2 isoform that unleashes a metastatic program in melanoma. Nat Commun 2023; 14:1867. [PMID: 37015919 PMCID: PMC10073109 DOI: 10.1038/s41467-023-36967-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/24/2023] [Indexed: 04/06/2023] Open
Abstract
Metastatic melanoma develops once transformed melanocytic cells begin to de-differentiate into migratory and invasive melanoma cells with neural crest cell (NCC)-like and epithelial-to-mesenchymal transition (EMT)-like features. However, it is still unclear how transformed melanocytes assume a metastatic melanoma cell state. Here, we define DNA methylation changes that accompany metastatic progression in melanoma patients and discover Nuclear Receptor Subfamily 2 Group F, Member 2 - isoform 2 (NR2F2-Iso2) as an epigenetically regulated metastasis driver. NR2F2-Iso2 is transcribed from an alternative transcriptional start site (TSS) and it is truncated at the N-terminal end which encodes the NR2F2 DNA-binding domain. We find that NR2F2-Iso2 expression is turned off by DNA methylation when NCCs differentiate into melanocytes. Conversely, this process is reversed during metastatic melanoma progression, when NR2F2-Iso2 becomes increasingly hypomethylated and re-expressed. Our functional and molecular studies suggest that NR2F2-Iso2 drives metastatic melanoma progression by modulating the activity of full-length NR2F2 (Isoform 1) over EMT- and NCC-associated target genes. Our findings indicate that DNA methylation changes play a crucial role during metastatic melanoma progression, and their control of NR2F2 activity allows transformed melanocytes to acquire NCC-like and EMT-like features. This epigenetically regulated transcriptional plasticity facilitates cell state transitions and metastatic spread.
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Affiliation(s)
- Veronica Davalos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA.
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain.
| | - Claudia D Lovell
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Richard Von Itter
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Igor Dolgalev
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Praveen Agrawal
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine/ Montefiore, Bronx, NY, 10461, USA
| | - Gillian Baptiste
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - David J Kahler
- High Throughput Biology Core, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Elena Sokolova
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Sebastian Moran
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Laia Piqué
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Eleazar Vega-Saenz de Miera
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
- The Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Barbara Fontanals-Cirera
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Alcida Karz
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Chi Yun
- High Throughput Biology Core, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Farbod Darvishian
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | | | - Iman Osman
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
- The Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red, Cancer (CIBERONC), Madrid, Spain
| | - Markus Schober
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA.
- The Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Cell Biology, New York Grossman University School of Medicine, New York, NY, 10016, USA.
| | - Eva Hernando
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA.
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2
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Karz A, Dimitrova M, Kleffman K, Alvarez-Breckenridge C, Atkins MB, Boire A, Bosenberg M, Brastianos P, Cahill DP, Chen Q, Ferguson S, Forsyth P, Glitza Oliva IC, Goldberg SB, Holmen SL, Knisely JPS, Merlino G, Nguyen DX, Pacold ME, Perez-Guijarro E, Smalley KSM, Tawbi HA, Wen PY, Davies MA, Kluger HM, Mehnert JM, Hernando E. Melanoma central nervous system metastases: An update to approaches, challenges, and opportunities. Pigment Cell Melanoma Res 2022; 35:554-572. [PMID: 35912544 PMCID: PMC10171356 DOI: 10.1111/pcmr.13059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/29/2022] [Indexed: 01/27/2023]
Abstract
Brain metastases are the most common brain malignancy. This review discusses the studies presented at the third annual meeting of the Melanoma Research Foundation in the context of other recent reports on the biology and treatment of melanoma brain metastases (MBM). Although symptomatic MBM patients were historically excluded from immunotherapy trials, efforts from clinicians and patient advocates have resulted in more inclusive and even dedicated clinical trials for MBM patients. The results of checkpoint inhibitor trials were discussed in conversation with current standards of care for MBM patients, including steroids, radiotherapy, and targeted therapy. Advances in the basic scientific understanding of MBM, including the role of astrocytes and metabolic adaptations to the brain microenvironment, are exposing new vulnerabilities which could be exploited for therapeutic purposes. Technical advances including single-cell omics and multiplex imaging are expanding our understanding of the MBM ecosystem and its response to therapy. This unprecedented level of spatial and temporal resolution is expected to dramatically advance the field in the coming years and render novel treatment approaches that might improve MBM patient outcomes.
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Affiliation(s)
- Alcida Karz
- Department of Pathology, NYU Grossman School of Medicine, New York, USA.,Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, USA
| | - Maya Dimitrova
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, USA.,Department of Medicine, NYU Grossman School of Medicine, New York, USA
| | - Kevin Kleffman
- Department of Pathology, NYU Grossman School of Medicine, New York, USA.,Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, USA
| | | | - Michael B Atkins
- Georgetown-Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Adrienne Boire
- Human Oncology and Pathogenesis Program, Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Marcus Bosenberg
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research NCI, NIH, USA
| | - Priscilla Brastianos
- MGH Cancer Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Qing Chen
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Sherise Ferguson
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Peter Forsyth
- Department of Neuro-Oncology and Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Isabella C Glitza Oliva
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sarah B Goldberg
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, Connecticut, USA
| | - Sheri L Holmen
- Huntsman Cancer Institute and Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Jonathan P S Knisely
- Meyer Cancer Center and Department of Radiation Oncology, Weill Cornell Medicine, New York, New York, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research NCI, NIH, USA
| | - Don X Nguyen
- Department of Pathology, Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michael E Pacold
- Department of Radiation Oncology, NYU Langone Health and NYU Grossman School of Medicine, New York, New York, USA
| | - Eva Perez-Guijarro
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research NCI, NIH, USA
| | - Keiran S M Smalley
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Hussein A Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, United States, Boston, Massachusetts, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Harriet M Kluger
- Department of Medicine (Medical Oncology), Yale School of Medicine, New Haven, Connecticut, USA
| | - Janice M Mehnert
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, USA.,Department of Medicine, NYU Grossman School of Medicine, New York, USA
| | - Eva Hernando
- Department of Pathology, NYU Grossman School of Medicine, New York, USA.,Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, USA
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3
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Biermann J, Melms JC, Amin AD, Wang Y, Caprio LA, Karz A, Tagore S, Barrera I, Ibarra-Arellano MA, Andreatta M, Fullerton BT, Gretarsson KH, Sahu V, Mangipudy VS, Nguyen TTT, Nair A, Rogava M, Ho P, Koch PD, Banu M, Humala N, Mahajan A, Walsh ZH, Shah SB, Vaccaro DH, Caldwell B, Mu M, Wünnemann F, Chazotte M, Berhe S, Luoma AM, Driver J, Ingham M, Khan SA, Rapisuwon S, Slingluff CL, Eigentler T, Röcken M, Carvajal R, Atkins MB, Davies MA, Agustinus A, Bakhoum SF, Azizi E, Siegelin M, Lu C, Carmona SJ, Hibshoosh H, Ribas A, Canoll P, Bruce JN, Bi WL, Agrawal P, Schapiro D, Hernando E, Macosko EZ, Chen F, Schwartz GK, Izar B. Dissecting the treatment-naive ecosystem of human melanoma brain metastasis. Cell 2022; 185:2591-2608.e30. [PMID: 35803246 PMCID: PMC9677434 DOI: 10.1016/j.cell.2022.06.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/08/2022] [Accepted: 06/06/2022] [Indexed: 10/17/2022]
Abstract
Melanoma brain metastasis (MBM) frequently occurs in patients with advanced melanoma; yet, our understanding of the underlying salient biology is rudimentary. Here, we performed single-cell/nucleus RNA-seq in 22 treatment-naive MBMs and 10 extracranial melanoma metastases (ECMs) and matched spatial single-cell transcriptomics and T cell receptor (TCR)-seq. Cancer cells from MBM were more chromosomally unstable, adopted a neuronal-like cell state, and enriched for spatially variably expressed metabolic pathways. Key observations were validated in independent patient cohorts, patient-derived MBM/ECM xenograft models, RNA/ATAC-seq, proteomics, and multiplexed imaging. Integrated spatial analyses revealed distinct geography of putative cancer immune evasion and evidence for more abundant intra-tumoral B to plasma cell differentiation in lymphoid aggregates in MBM. MBM harbored larger fractions of monocyte-derived macrophages and dysfunctional TOX+CD8+ T cells with distinct expression of immune checkpoints. This work provides comprehensive insights into MBM biology and serves as a foundational resource for further discovery and therapeutic exploration.
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Affiliation(s)
- Jana Biermann
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA
| | - Lindsay A Caprio
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alcida Karz
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Somnath Tagore
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Irving Barrera
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Miguel A Ibarra-Arellano
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
| | - Massimo Andreatta
- Department of Oncology UNIL CHUV, Lausanne Branch, Ludwig Institute for Cancer Research Lausanne, CHUV and University of Lausanne, Lausanne, 1066 Épalinges, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Benjamin T Fullerton
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kristjan H Gretarsson
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Varun Sahu
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Vaibhav S Mangipudy
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Trang T T Nguyen
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Ajay Nair
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Patricia Ho
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter D Koch
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Matei Banu
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nelson Humala
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aayushi Mahajan
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zachary H Walsh
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Shivem B Shah
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Daniel H Vaccaro
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Blake Caldwell
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Michael Mu
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Florian Wünnemann
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
| | - Margot Chazotte
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
| | - Simon Berhe
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Adrienne M Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA
| | - Joseph Driver
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Ingham
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shaheer A Khan
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Suthee Rapisuwon
- Division of Hematology/Oncology, Medstar Washington Cancer Institute, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Craig L Slingluff
- Department of Surgery, University of Virginia, Charlottesville, VA, USA
| | - Thomas Eigentler
- Department of Dermatology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Dermatology, Venereology and Allergology, 10117, Berlin, Germany
| | - Martin Röcken
- Department of Dermatology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Richard Carvajal
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michael B Atkins
- Georgetown-Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Albert Agustinus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pharmacology, Weill Cornell Graduate School, New York, NY 10065, USA
| | - Samuel F Bakhoum
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elham Azizi
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA
| | - Markus Siegelin
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Santiago J Carmona
- Department of Oncology UNIL CHUV, Lausanne Branch, Ludwig Institute for Cancer Research Lausanne, CHUV and University of Lausanne, Lausanne, 1066 Épalinges, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Antoni Ribas
- Department of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90024, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Jeffrey N Bruce
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Praveen Agrawal
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Denis Schapiro
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Eva Hernando
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gary K Schwartz
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.
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4
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Kleffman K, Levinson G, Rose IV, Blumenberg L, Shadaloey SA, Dhabaria A, Wong E, Galán-Echevarría F, Karz A, Argibay D, Von-Itter R, Floristán A, Baptiste G, Eskow N, Tranos J, Chen J, de Miera ECVS, Call M, Rogers R, Jour G, Wadghiri YZ, Osman I, Li YM, Mathews P, Demattos R, Ueberheide B, Ruggles K, Liddelow SA, Schneider RJ, Hernando E. Abstract LB052: Melanoma-secreted amyloid beta suppresses neuroinflammation and promotes brain metastasis. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-lb052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Brain metastasis is a significant cause of morbidity and mortality in multiple cancer types and represents an unmet clinical need. The mechanisms that mediate metastatic cancer growth in the brain parenchyma are largely unknown. Melanoma, which has the highest rate of brain metastasis among common cancer types, is an ideal model to study how cancer cells adapt to the brain parenchyma. Our unbiased proteomics analysis of melanoma short-term cultures revealed that proteins implicated in neurodegenerative pathologies are differentially expressed in melanoma cells explanted from brain metastases compared to those derived from extracranial metastases. We showed that melanoma cells require amyloid beta (Aβ) for growth and survival in the brain parenchyma. Melanoma-secreted Aβ activates surrounding astrocytes to a prometastatic, anti-inflammatory phenotype and prevents phagocytosis of melanoma by microglia. Finally, we demonstrate that pharmacological inhibition of Aβ decreases brain metastatic burden. Our results reveal a novel mechanistic connection between brain metastasis and Alzheimer’s disease - two previously unrelated pathologies, establish Aβ as a promising therapeutic target for brain metastasis, and demonstrate suppression of neuroinflammation as a critical feature of metastatic adaptation to the brain parenchyma.
Citation Format: Kevin Kleffman, Grace Levinson, Indigo V. Rose, Lili Blumenberg, Sorin A. Shadaloey, Avantika Dhabaria, Eitan Wong, Francisco Galán-Echevarría, Alcida Karz, Diana Argibay, Richard Von-Itter, Alfredo Floristán, Gillian Baptiste, Nicole Eskow, James Tranos, Jenny Chen, Eleazar C. Vega Saenz de Miera, Melissa Call, Robert Rogers, George Jour, Youssef Zaim Wadghiri, Iman Osman, Yue Ming Li, Paul Mathews, Ronald Demattos, Beatrix Ueberheide, Kelly Ruggles, Shane A. Liddelow, Robert J. Schneider, Eva Hernando. Melanoma-secreted amyloid beta suppresses neuroinflammation and promotes brain metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB052.
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Affiliation(s)
| | | | | | | | | | | | - Eitan Wong
- 2Memorial Sloan Kettering Cancer Center, New York, NY
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5
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Shadaloey AAS, Karz A, Moubarak RS, Agrawal P, Levinson G, Kleffman K, Aristizabal O, Osman I, Wadghiri YZ, Hernando E. A Robust Discovery Platform for the Identification of Novel Mediators of Melanoma Metastasis. J Vis Exp 2022. [DOI: 10.3791/63186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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6
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Kleffman K, Levinson G, Rose IVL, Blumenberg LM, Shadaloey SAA, Dhabaria A, Wong E, Galan-Echevarria F, Karz A, Argibay D, Von Itter R, Floristan A, Baptiste G, Eskow NM, Tranos JA, Chen J, Vega Y Saenz de Miera EC, Call M, Rogers R, Jour G, Wadghiri YZ, Osman I, Li YM, Mathews P, DeMattos R, Ueberheide B, Ruggles KV, Liddelow SA, Schneider RJ, Hernando E. Melanoma-secreted Amyloid Beta Suppresses Neuroinflammation and Promotes Brain Metastasis. Cancer Discov 2022; 12:1314-1335. [PMID: 35262173 PMCID: PMC9069488 DOI: 10.1158/2159-8290.cd-21-1006] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/21/2021] [Accepted: 02/18/2022] [Indexed: 11/16/2022]
Abstract
Brain metastasis is a significant cause of morbidity and mortality in multiple cancer types and represents an unmet clinical need. The mechanisms that mediate metastatic cancer growth in the brain parenchyma are largely unknown. Melanoma, which has the highest rate of brain metastasis among common cancer types, is an ideal model to study how cancer cells adapt to the brain parenchyma. Our unbiased proteomics analysis of melanoma short-term cultures revealed that proteins implicated in neurodegenerative pathologies are differentially expressed in melanoma cells explanted from brain metastases compared to those derived from extracranial metastases. We showed that melanoma cells require amyloid beta (AB) for growth and survival in the brain parenchyma. Melanoma-secreted AB activates surrounding astrocytes to a pro-metastatic, anti-inflammatory phenotype and prevents phagocytosis of melanoma by microglia. Finally, we demonstrate that pharmacological inhibition of AB decreases brain metastatic burden.
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Affiliation(s)
- Kevin Kleffman
- NYU Langone Medical Center, New York, New York, United States
| | - Grace Levinson
- NYU Langone Medical Center, New York, New York, United States
| | - Indigo V L Rose
- NYU Langone Medical Center, New York, New York, United States
| | | | | | - Avantika Dhabaria
- Proteomics Laboratory, Division of Advanced Research and Technology, NYU Langone Health, New York, New York., New York, NY, United States
| | - Eitan Wong
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | | | - Alcida Karz
- NYU Langone Medical Center, New York, New York, United States
| | - Diana Argibay
- NYU Langone Medical Center, New York, NY, United States
| | | | | | - Gillian Baptiste
- New York University Grossman School of Medicine, New York, NY, United States
| | | | - James A Tranos
- NYU Langone Medical Center, New York, New York, United States
| | - Jenny Chen
- NYU Langone Medical Center, New York, New York, United States
| | | | - Melissa Call
- NYU Langone Medical Center, New York, New York, United States
| | - Robert Rogers
- NYU Langone Medical Center, New York, New York, United States
| | - George Jour
- New York University, New York, New York, United States
| | | | - Iman Osman
- New York University School of Medicine, New York, New York, United States
| | - Yue-Ming Li
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Paul Mathews
- NYU Langone Medical Center, New York, New York, United States
| | - Ronald DeMattos
- Eli Lilly (United States), Indianapolis, Indiana, United States
| | - Beatrix Ueberheide
- Proteomics Laboratory, Division of Advanced Research and Technology, NYU Langone Health, New York, New York., United States
| | - Kelly V Ruggles
- New York University Langone Medical Center, New York, United States
| | | | | | - Eva Hernando
- NYU Langone Medical Center, New York, NY, United States
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7
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Moubarak RS, de Pablos-Aragoneses A, Ortiz-Barahona V, Gong Y, Gowen M, Dolgalev I, Shadaloey SAA, Argibay D, Karz A, Von Itter R, Vega-Sáenz de Miera EC, Sokolova E, Darvishian F, Tsirigos A, Osman I, Hernando E. The histone demethylase PHF8 regulates TGFβ signaling and promotes melanoma metastasis. Sci Adv 2022; 8:eabi7127. [PMID: 35179962 PMCID: PMC8856617 DOI: 10.1126/sciadv.abi7127] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 12/14/2021] [Indexed: 05/17/2023]
Abstract
The contribution of epigenetic dysregulation to metastasis remains understudied. Through a meta-analysis of gene expression datasets followed by a mini-screen, we identified Plant Homeodomain Finger protein 8 (PHF8), a histone demethylase of the Jumonji C protein family, as a previously unidentified prometastatic gene in melanoma. Loss- and gain-of-function approaches demonstrate that PHF8 promotes cell invasion without affecting proliferation in vitro and increases dissemination but not subcutaneous tumor growth in vivo, thus supporting its specific contribution to the acquisition of metastatic potential. PHF8 requires its histone demethylase activity to enhance melanoma cell invasion. Transcriptomic and epigenomic analyses revealed that PHF8 orchestrates a molecular program that directly controls the TGFβ signaling pathway and, as a consequence, melanoma invasion and metastasis. Our findings bring a mechanistic understanding of epigenetic regulation of metastatic fitness in cancer, which may pave the way for improved therapeutic interventions.
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Affiliation(s)
- Rana S. Moubarak
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, NYU Cancer Institute, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | | | | | - Yixiao Gong
- Applied Bioinformatics Laboratories, NYU School of Medicine, NY 10016, USA
| | - Michael Gowen
- NYU School of Medicine Institute for Computational Medicine, New York, NY 10016, USA
| | - Igor Dolgalev
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
- Applied Bioinformatics Laboratories, NYU School of Medicine, NY 10016, USA
| | - Sorin A. A. Shadaloey
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, NYU Cancer Institute, New York, NY 10016, USA
| | - Diana Argibay
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, NYU Cancer Institute, New York, NY 10016, USA
| | - Alcida Karz
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, NYU Cancer Institute, New York, NY 10016, USA
| | - Richard Von Itter
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, NYU Cancer Institute, New York, NY 10016, USA
| | | | - Elena Sokolova
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, NYU Cancer Institute, New York, NY 10016, USA
| | - Farbod Darvishian
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, NYU Cancer Institute, New York, NY 10016, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
- Applied Bioinformatics Laboratories, NYU School of Medicine, NY 10016, USA
- NYU School of Medicine Institute for Computational Medicine, New York, NY 10016, USA
| | - Iman Osman
- Interdisciplinary Melanoma Cooperative Group, NYU Cancer Institute, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
- Ronald O. Perelman Department of Dermatology, NYU School of Medicine, New York, NY 10016, USA
| | - Eva Hernando
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, NYU Cancer Institute, New York, NY 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
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8
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Ho JSY, Di Tullio F, Schwarz M, Low D, Incarnato D, Gay F, Tabaglio T, Zhang J, Wollmann H, Chen L, An O, Chan THM, Hall Hickman A, Zheng S, Roudko V, Chen S, Karz A, Ahmed M, He HH, Greenbaum BD, Oliviero S, Serresi M, Gargiulo G, Mann KM, Hernando E, Mulholland D, Marazzi I, Wee DKB, Guccione E. HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness. eLife 2021; 10:e59654. [PMID: 34075878 PMCID: PMC8346284 DOI: 10.7554/elife.59654] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 05/30/2021] [Indexed: 12/25/2022] Open
Abstract
High spliceosome activity is a dependency for cancer cells, making them more vulnerable to perturbation of the splicing machinery compared to normal cells. To identify splicing factors important for prostate cancer (PCa) fitness, we performed pooled shRNA screens in vitro and in vivo. Our screens identified heterogeneous nuclear ribonucleoprotein M (HNRNPM) as a regulator of PCa cell growth. RNA- and eCLIP-sequencing identified HNRNPM binding to transcripts of key homeostatic genes. HNRNPM binding to its targets prevents aberrant exon inclusion and backsplicing events. In both linear and circular mis-spliced transcripts, HNRNPM preferentially binds to GU-rich elements in long flanking proximal introns. Mimicry of HNRNPM-dependent linear-splicing events using splice-switching-antisense-oligonucleotides was sufficient to inhibit PCa cell growth. This suggests that PCa dependence on HNRNPM is likely a result of mis-splicing of key homeostatic coding and non-coding genes. Our results have further been confirmed in other solid tumors. Taken together, our data reveal a role for HNRNPM in supporting cancer cell fitness. Inhibition of HNRNPM activity is therefore a potential therapeutic strategy in suppressing growth of PCa and other solid tumors.
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Affiliation(s)
- Jessica SY Ho
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Department of Microbiology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Federico Di Tullio
- Center for Therapeutics Discovery, department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Oncological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Megan Schwarz
- Center for Therapeutics Discovery, department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Oncological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Diana Low
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Danny Incarnato
- IIGM (Italian Institute for Genomic Medicine)TorinoItaly
- Dipartimento di Scienze della Vita e Biologia dei Sistemi Università di TorinoTorinoItaly
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of GroningenGroningenNetherlands
| | - Florence Gay
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Tommaso Tabaglio
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - JingXian Zhang
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Heike Wollmann
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of SingaporeSingaporeSingapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of SingaporeSingaporeSingapore
| | - Tim Hon Man Chan
- Cancer Science Institute of Singapore, National University of SingaporeSingaporeSingapore
| | - Alexander Hall Hickman
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Simin Zheng
- Department of Microbiology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- NTU Institute of Structural Biology, Nanyang Technological UniversitySingaporeSingapore
| | - Vladimir Roudko
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Oncological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Sujun Chen
- Department of Medical Biophysics, University of TorontoTorontoCanada
- Princess Margaret Cancer Center, University Health NetworkTorontoCanada
- Ontario Institute for Cancer ResearchTorontoCanada
| | - Alcida Karz
- Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical CenterNew YorkUnited States
- Department of Pathology, New York University Langone Medical CenterNew YorkUnited States
| | - Musaddeque Ahmed
- Princess Margaret Cancer Center, University Health NetworkTorontoCanada
| | - Housheng Hansen He
- Department of Medical Biophysics, University of TorontoTorontoCanada
- Princess Margaret Cancer Center, University Health NetworkTorontoCanada
| | - Benjamin D Greenbaum
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Oncological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Pathology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Salvatore Oliviero
- IIGM (Italian Institute for Genomic Medicine)TorinoItaly
- Dipartimento di Scienze della Vita e Biologia dei Sistemi Università di TorinoTorinoItaly
| | - Michela Serresi
- Max Delbruck Center for Molecular MedicineBerlin-BuchGermany
| | | | - Karen M Mann
- Department of Molecular Oncology, Moffitt Cancer CenterTampaUnited States
| | - Eva Hernando
- Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical CenterNew YorkUnited States
- Department of Pathology, New York University Langone Medical CenterNew YorkUnited States
| | - David Mulholland
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Oncological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Dave Keng Boon Wee
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Center for Therapeutics Discovery, department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Oncological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
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9
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Hanniford D, Ulloa-Morales A, Sánchez-Sendra B, Karz A, Moubarak R, Tabaglio T, Berzoti-Coelho MG, Davalos V, Wu P, Vasudevaraja V, Kloetgen A, Lilja K, Imig J, Monteagudo C, Guccione E, Tsirigos A, Osman I, Aifantis I, Hernando E. Abstract PR04: Epigenetic silencing of CDR1as drives IGF2BP3-mediated melanoma invasion and metastasis. Cancer Res 2020. [DOI: 10.1158/1538-7445.mel2019-pr04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Metastasis is the primary cause of death of cancer patients. Dissecting mechanisms governing metastatic spread may uncover new biology and/or yield promising therapeutic insights. Here we investigated the role of circular RNAs (circRNAs), a class of noncoding RNAs lacking characterized functions, in metastasis, using melanoma as a model aggressive tumor. We analyzed RNA-seq of melanocytes and melanoma short-term cultures to characterize the landscape of circRNA in melanocytic cells. We observed silencing of Cerebellar Degeneration Related 1 (CDR1as), a neuronal-enriched circRNA and known regulator of the microRNA miR-7, in melanoma cell lines and short-term cultures compared to cultured melanocytes, and progressive loss from primary to metastatic disease in melanoma patient samples. Moreover, low CDR1as expression in primary tumors associates with poor prognostic histopathologic indicators and patient outcomes. We find that CDR1as loss results from H3K27me3-mediated silencing of its originating lincRNA LINC00632. We observed abundant H3K27me3, the repressive chromatin mark deposited by the PRC2 complex, in regulatory regions of LINC00632 in cell lines lacking CDR1as expression, and pharmacologic inhibition of EZH2 restored expression of both transcripts. Phenotypically, CDR1as depletion in vitro and in vivo enhances melanoma invasion and metastasis, with limited effect on cell proliferation or tumor growth. Surprisingly, we did not observe miR-7 regulation to be a catalyst of the proinvasive effects of CDR1as depletion in our models. Instead, we identified IGF2BP3 as a novel interactor of CDR1as and critical mediator downstream of CDR1as silencing. Finally, we find that CDR1as abundance associates with previously defined cellular states that engender distinct therapeutic responses to MAPK and GPX4 inhibitors. Collectively, our study reveals CDR1as silencing as a hallmark of melanoma progression; documents novel functional, prognostic and predictive roles for CDR1as; and exposes circRNAs as key players in metastasis.
This abstract is also being presented as Poster A29.
Citation Format: Douglas Hanniford, Alejandro Ulloa-Morales, Beatriz Sánchez-Sendra, Alcida Karz, Rana Moubarak, Tommaso Tabaglio, Maria Gabriela Berzoti-Coelho, Veronica Davalos, Pamela Wu, Varshini Vasudevaraja, Andreas Kloetgen, Karin Lilja, Jochen Imig, Carlos Monteagudo, Ernesto Guccione, Aristotelis Tsirigos, Iman Osman, Iannis Aifantis, Eva Hernando. Epigenetic silencing of CDR1as drives IGF2BP3-mediated melanoma invasion and metastasis [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr PR04.
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10
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Hanniford D, Ulloa-Morales A, Karz A, Berzoti-Coelho MG, Moubarak RS, Sánchez-Sendra B, Kloetgen A, Davalos V, Imig J, Wu P, Vasudevaraja V, Argibay D, Lilja K, Tabaglio T, Monteagudo C, Guccione E, Tsirigos A, Osman I, Aifantis I, Hernando E. Epigenetic Silencing of CDR1as Drives IGF2BP3-Mediated Melanoma Invasion and Metastasis. Cancer Cell 2020; 37:55-70.e15. [PMID: 31935372 PMCID: PMC7184928 DOI: 10.1016/j.ccell.2019.12.007] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 08/17/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022]
Abstract
Metastasis is the primary cause of death of cancer patients. Dissecting mechanisms governing metastatic spread may uncover important tumor biology and/or yield promising therapeutic insights. Here, we investigated the role of circular RNAs (circRNA) in metastasis, using melanoma as a model aggressive tumor. We identified silencing of cerebellar degeneration-related 1 antisense (CDR1as), a regulator of miR-7, as a hallmark of melanoma progression. CDR1as depletion results from epigenetic silencing of LINC00632, its originating long non-coding RNA (lncRNA) and promotes invasion in vitro and metastasis in vivo through a miR-7-independent, IGF2BP3-mediated mechanism. Moreover, CDR1as levels reflect cellular states associated with distinct therapeutic responses. Our study reveals functional, prognostic, and predictive roles for CDR1as and expose circRNAs as key players in metastasis.
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Affiliation(s)
- Douglas Hanniford
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA.
| | - Alejandro Ulloa-Morales
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Alcida Karz
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Maria Gabriela Berzoti-Coelho
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Department of Clinical Analysis, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Rana S Moubarak
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | | | - Andreas Kloetgen
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Jochen Imig
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Pamela Wu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA
| | - Varshini Vasudevaraja
- Applied Bioinformatics Laboratories, New York University Langone Medical Center, New York, NY, USA
| | - Diana Argibay
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Karin Lilja
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA
| | - Tommaso Tabaglio
- Institute of Molecular and Cell Biology, A(∗)STAR, Singapore, Singapore
| | | | - Ernesto Guccione
- Institute of Molecular and Cell Biology, A(∗)STAR, Singapore, Singapore; Department of Oncological Sciences, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Applied Bioinformatics Laboratories, New York University Langone Medical Center, New York, NY, USA
| | - Iman Osman
- Departments of Urology and Medicine, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Iannis Aifantis
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA
| | - Eva Hernando
- Department of Pathology, New York University Langone Medical Center, New York, NY, USA; Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY, USA.
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