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Schröder V, Gherghel D, Apetroaei MR, Gîjiu CL, Isopescu R, Dinculescu D, Apetroaei MM, Enache LE, Mihai CT, Rău I, Vochița G. α-Chitosan and β-Oligochitosan Mixtures-Based Formula for In Vitro Assessment of Melanocyte Cells Response. Int J Mol Sci 2024; 25:6768. [PMID: 38928474 DOI: 10.3390/ijms25126768] [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: 05/16/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Chitosan is a natural polymer with numerous biomedical applications. The cellular activity of chitosan has been studied in various types of cancer, including melanoma, and indicates that these molecules can open new perspectives on antiproliferative action and anticancer therapy. This study analyzes how different chitosan conformations, such as α-chitosan (CH) or β-oligochitosan (CO), with various degrees of deacetylation (DDA) and molar mass (MM), both in different concentrations and in CH-CO mixtures, influence the cellular processes of SK-MEL-28 melanocytes, to estimate the reactivity of these cells to the applied treatments. The in vitro evaluation was carried out, aiming at the cellular metabolism (MTT assay), cellular morphology, and chitinase-like glycoprotein YKL-40 expression. The in vitro effect of the CH-CO mixture application on melanocytes is obvious at low concentrations of α-chitosan/β-oligochitosan (1:2 ratio), with the cell's response supporting the hypothesis that β-oligo-chitosan amplifies the effect. This oligochitosan mixture, favored by the β conformation and its small size, penetrates faster into the cells, being more reactive when interacting with some cellular components. Morphological effects expressed by the loss of cell adhesion and the depletion of YKL-40 synthesis are significant responses of melanocytes. β-oligochitosan (1.5 kDa) induces an extension of cytophysiological effects and limits the cell viability compared to α-chitosan (400-900 kDa). Statistical analysis using multivariate techniques showed differences between the CH samples and CH-CO mixtures.
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Affiliation(s)
- Verginica Schröder
- Departament of Cellular and Molecular Biology, Faculty of Pharmacy, Ovidius University of Constanta, 6 Capt. Aviator Al. Șerbănescu Street, Campus C, 900470 Constanta, Romania
| | - Daniela Gherghel
- Institute of Biological Research Iasi, Branch of NIRDBS-National Institute of Research and Development of Biological Sciences Bucharest, 47 Lascar Catargi, 700107 Iasi, Romania
| | - Manuela Rossemary Apetroaei
- Department of Marine Electric and Electronic Engineering, Faculty of Marine Engineering, Mircea cel Batran Naval Academy, 1 Fulgerului Street, 900218 Constanta, Romania
| | - Cristiana Luminița Gîjiu
- Faculty of Chemical Engineering and Biotechnologies, National University of Science and Technology POLITEHNICA Bucharest, 011061 Bucharest, Romania
| | - Raluca Isopescu
- Faculty of Chemical Engineering and Biotechnologies, National University of Science and Technology POLITEHNICA Bucharest, 011061 Bucharest, Romania
| | - Daniel Dinculescu
- Faculty of Chemical Engineering and Biotechnologies, National University of Science and Technology POLITEHNICA Bucharest, 011061 Bucharest, Romania
| | - Miruna-Maria Apetroaei
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania
| | - Laura Elena Enache
- Faculty of Chemical Engineering and Biotechnologies, National University of Science and Technology POLITEHNICA Bucharest, 011061 Bucharest, Romania
| | | | - Ileana Rău
- Faculty of Chemical Engineering and Biotechnologies, National University of Science and Technology POLITEHNICA Bucharest, 011061 Bucharest, Romania
| | - Gabriela Vochița
- Institute of Biological Research Iasi, Branch of NIRDBS-National Institute of Research and Development of Biological Sciences Bucharest, 47 Lascar Catargi, 700107 Iasi, Romania
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2
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Di Leo L, Pagliuca C, Kishk A, Rizza S, Tsiavou C, Pecorari C, Dahl C, Pacheco MP, Tholstrup R, Brewer JR, Berico P, Hernando E, Cecconi F, Ballotti R, Bertolotto C, Filomeni G, Gjerstorff MF, Sauter T, Lovat P, Guldberg P, De Zio D. AMBRA1 levels predict resistance to MAPK inhibitors in melanoma. Proc Natl Acad Sci U S A 2024; 121:e2400566121. [PMID: 38870061 PMCID: PMC11194594 DOI: 10.1073/pnas.2400566121] [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: 01/16/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024] Open
Abstract
Intrinsic and acquired resistance to mitogen-activated protein kinase inhibitors (MAPKi) in melanoma remains a major therapeutic challenge. Here, we show that the clinical development of resistance to MAPKi is associated with reduced tumor expression of the melanoma suppressor Autophagy and Beclin 1 Regulator 1 (AMBRA1) and that lower expression levels of AMBRA1 predict a poor response to MAPKi treatment. Functional analyses show that loss of AMBRA1 induces phenotype switching and orchestrates an extracellular signal-regulated kinase (ERK)-independent resistance mechanism by activating focal adhesion kinase 1 (FAK1). In both in vitro and in vivo settings, melanomas with low AMBRA1 expression exhibit intrinsic resistance to MAPKi therapy but higher sensitivity to FAK1 inhibition. Finally, we show that the rapid development of resistance in initially MAPKi-sensitive melanomas can be attributed to preexisting subclones characterized by low AMBRA1 expression and that cotreatment with MAPKi and FAK1 inhibitors (FAKi) effectively prevents the development of resistance in these tumors. In summary, our findings underscore the value of AMBRA1 expression for predicting melanoma response to MAPKi and supporting the therapeutic efficacy of FAKi to overcome MAPKi-induced resistance.
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Affiliation(s)
- Luca Di Leo
- Melanoma Research Team, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen2100, Denmark
| | - Chiara Pagliuca
- Melanoma Research Team, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen2100, Denmark
| | - Ali Kishk
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux4365, Luxembourg
| | - Salvatore Rizza
- Redox Biology Group, Danish Cancer Institute, Copenhagen2100, Denmark
| | - Christina Tsiavou
- Melanoma Research Team, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen2100, Denmark
| | - Chiara Pecorari
- Redox Biology Group, Danish Cancer Institute, Copenhagen2100, Denmark
| | - Christina Dahl
- Molecular Diagnostics Group, Danish Cancer Institute, Copenhagen2100, Denmark
| | - Maria Pires Pacheco
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux4365, Luxembourg
| | - Rikke Tholstrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense5230, Denmark
| | - Jonathan Richard Brewer
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense5230, Denmark
| | - Pietro Berico
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
| | - Eva Hernando
- Department of Pathology, New York University Grossman School of Medicine, New York, NY10016
| | - Francesco Cecconi
- Cell Stress and Survival, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen2100, Denmark
- Faculty of Medicine and Surgery, Università Cattolica del “Sacro Cuore”, Fondazione Policlinico Gemelli—Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome00136, Italy
| | - Robert Ballotti
- Université Côte d’Azur, Nice06200, France
- Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020, Centre Méditerranéen de Médecine Moléculaire, Nice06200, France
| | - Corine Bertolotto
- Université Côte d’Azur, Nice06200, France
- Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020, Centre Méditerranéen de Médecine Moléculaire, Nice06200, France
| | - Giuseppe Filomeni
- Redox Biology Group, Danish Cancer Institute, Copenhagen2100, Denmark
| | - Morten Frier Gjerstorff
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense5230, Denmark
- Department of Oncology, Odense University Hospital, Odense5000, Denmark
| | - Thomas Sauter
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux4365, Luxembourg
| | - Penny Lovat
- Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Per Guldberg
- Molecular Diagnostics Group, Danish Cancer Institute, Copenhagen2100, Denmark
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense5230, Denmark
| | - Daniela De Zio
- Melanoma Research Team, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen2100, Denmark
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense5230, Denmark
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3
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El-Hachem N, Leclercq M, Susaeta Ruiz M, Vanleyssem R, Shostak K, Körner PR, Capron C, Martin-Morales L, Roncarati P, Lavergne A, Blomme A, Turchetto S, Goffin E, Thandapani P, Tarassov I, Nguyen L, Pirotte B, Chariot A, Marine JC, Herfs M, Rapino F, Agami R, Close P. Valine aminoacyl-tRNA synthetase promotes therapy resistance in melanoma. Nat Cell Biol 2024:10.1038/s41556-024-01439-2. [PMID: 38849541 DOI: 10.1038/s41556-024-01439-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 05/12/2024] [Indexed: 06/09/2024]
Abstract
Transfer RNA dynamics contribute to cancer development through regulation of codon-specific messenger RNA translation. Specific aminoacyl-tRNA synthetases can either promote or suppress tumourigenesis. Here we show that valine aminoacyl-tRNA synthetase (VARS) is a key player in the codon-biased translation reprogramming induced by resistance to targeted (MAPK) therapy in melanoma. The proteome rewiring in patient-derived MAPK therapy-resistant melanoma is biased towards the usage of valine and coincides with the upregulation of valine cognate tRNAs and of VARS expression and activity. Strikingly, VARS knockdown re-sensitizes MAPK-therapy-resistant patient-derived melanoma in vitro and in vivo. Mechanistically, VARS regulates the messenger RNA translation of valine-enriched transcripts, among which hydroxyacyl-CoA dehydrogenase mRNA encodes for a key enzyme in fatty acid oxidation. Resistant melanoma cultures rely on fatty acid oxidation and hydroxyacyl-CoA dehydrogenase for their survival upon MAPK treatment. Together, our data demonstrate that VARS may represent an attractive therapeutic target for the treatment of therapy-resistant melanoma.
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Affiliation(s)
- Najla El-Hachem
- Laboratory of Cancer Signaling, GIGA Institute, University of Liège, Liège, Belgium
| | - Marine Leclercq
- Laboratory of Cancer Signaling, GIGA Institute, University of Liège, Liège, Belgium
| | - Miguel Susaeta Ruiz
- Laboratory of Cancer Signaling, GIGA Institute, University of Liège, Liège, Belgium
| | - Raphael Vanleyssem
- Laboratory of Cancer Signaling, GIGA Institute, University of Liège, Liège, Belgium
| | - Kateryna Shostak
- Laboratory of Cancer Biology, GIGA Institute, University of Liège, Liège, Belgium
| | - Pierre-René Körner
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Coralie Capron
- Laboratory of Cancer Stemness, GIGA Institute, University of Liège, Liège, Belgium
| | | | - Patrick Roncarati
- Laboratory of Experimental Pathology, GIGA Institute, University of Liège, Liège, Belgium
| | - Arnaud Lavergne
- Bioinformatics platform, GIGA Institute, University of Liège, Liège, Belgium
| | - Arnaud Blomme
- Laboratory of Cancer Signaling, GIGA Institute, University of Liège, Liège, Belgium
| | - Silvia Turchetto
- Laboratory of Molecular Regulation of Neurogenesis, GIGA Institute, University of Liège, Liège, Belgium
| | - Eric Goffin
- Center for Interdisciplinary Research on Medicines-Laboratory of Medicinal Chemistry, University of Liège, Liège, Belgium
| | - Palaniraja Thandapani
- Department of Hematopoietic Biology and Malignancy, MD Anderson Cancer Center, Houston, TX, USA
| | - Ivan Tarassov
- UMR 7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg/CNRS, Strasbourg, France
| | - Laurent Nguyen
- Laboratory of Molecular Regulation of Neurogenesis, GIGA Institute, University of Liège, Liège, Belgium
- WELBIO department, WEL Research Institute, Wavre, Belgium
| | - Bernard Pirotte
- Center for Interdisciplinary Research on Medicines-Laboratory of Medicinal Chemistry, University of Liège, Liège, Belgium
| | - Alain Chariot
- Laboratory of Cancer Biology, GIGA Institute, University of Liège, Liège, Belgium
- WELBIO department, WEL Research Institute, Wavre, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Michael Herfs
- Laboratory of Experimental Pathology, GIGA Institute, University of Liège, Liège, Belgium
| | - Francesca Rapino
- Laboratory of Cancer Stemness, GIGA Institute, University of Liège, Liège, Belgium
- WELBIO department, WEL Research Institute, Wavre, Belgium
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Erasmus MC, Department of Genetics, Rotterdam University, Rotterdam, The Netherlands
| | - Pierre Close
- Laboratory of Cancer Signaling, GIGA Institute, University of Liège, Liège, Belgium.
- WELBIO department, WEL Research Institute, Wavre, Belgium.
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4
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Schmidt M, Avagyan S, Reiche K, Binder H, Loeffler-Wirth H. A Spatial Transcriptomics Browser for Discovering Gene Expression Landscapes across Microscopic Tissue Sections. Curr Issues Mol Biol 2024; 46:4701-4720. [PMID: 38785552 PMCID: PMC11119626 DOI: 10.3390/cimb46050284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
A crucial feature of life is its spatial organization and compartmentalization on the molecular, cellular, and tissue levels. Spatial transcriptomics (ST) technology has opened a new chapter of the sequencing revolution, emerging rapidly with transformative effects across biology. This technique produces extensive and complex sequencing data, raising the need for computational methods for their comprehensive analysis and interpretation. We developed the ST browser web tool for the interactive discovery of ST images, focusing on different functional aspects such as single gene expression, the expression of functional gene sets, as well as the inspection of the spatial patterns of cell-cell interactions. As a unique feature, our tool applies self-organizing map (SOM) machine learning to the ST data. Our SOM data portrayal method generates individual gene expression landscapes for each spot in the ST image, enabling its downstream analysis with high resolution. The performance of the spatial browser is demonstrated by disentangling the intra-tumoral heterogeneity of melanoma and the microarchitecture of the mouse brain. The integration of machine-learning-based SOM portrayal into an interactive ST analysis environment opens novel perspectives for the comprehensive knowledge mining of the organization and interactions of cellular ecosystems.
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Affiliation(s)
- Maria Schmidt
- Interdisciplinary Centre for Bioinformatics (IZBI), Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.S.); (H.B.)
| | - Susanna Avagyan
- Armenian Bioinformatics Institute, 3/6 Nelson Stepanyan Str., Yerevan 0062, Armenia
| | - Kristin Reiche
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstrasse 1, 04103 Leipzig, Germany
- Institute for Clinical Immunology, University Hospital of Leipzig, 04103 Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics (IZBI), Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.S.); (H.B.)
- Armenian Bioinformatics Institute, 3/6 Nelson Stepanyan Str., Yerevan 0062, Armenia
| | - Henry Loeffler-Wirth
- Interdisciplinary Centre for Bioinformatics (IZBI), Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.S.); (H.B.)
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5
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Zhang Y, Wu B, Liu D, Chen Y, Xu Y, Fu L, Lin Z, Wu G, Huang F. Targeting HIF-1α with Specific DNA Yokes for Effective Anticancer Therapy. Adv Healthc Mater 2024:e2401087. [PMID: 38696899 DOI: 10.1002/adhm.202401087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Indexed: 05/04/2024]
Abstract
Hypoxia, a ubiquitous hallmark in cancer, underscores the significance of targeting HIF-1α, the principal transcriptional factor of hypoxic responses, for effective cancer therapy. Herein, DNA yokes, a novel class of DNA nanomaterials harboring specific HIF-1α binding sequences (hypoxia response elements, HREs), are introduced as nanopharmaceuticals for cancer treatment. Comprising a basal tetrahedral DNA nanostructure and four HRE-bearing overhanging chains, DNA yokes exhibit exceptional stability and prolonged intracellular retention. The investigation reveals their capacity to bind HIF-1α, thereby disrupting its interaction with the downstream genomic DNAs and impeding transcriptional activity. Moreover, DNA yokes facilitate HIF-1α degradation via the ubiquitination pathway, thereby sequestering it from downstream targets and ultimately promoting its degradation. In addition, DNA yokes attenuate cancer cell proliferation, migration, and invasion under hypoxic conditions, while also displaying preferential accumulation within tumors, thereby inhibiting tumor growth and metastasis in vivo. This study pioneers a novel approach to cancer therapy through the development of DNA-based drugs characterized by high stability and low toxicity to normal cells, positioning DNA yokes as promising candidates for cancer treatment.
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Affiliation(s)
- Ying Zhang
- Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350005, China
- Central Laboratory, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China
| | - Bing Wu
- Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350005, China
- Central Laboratory, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China
| | - Danqing Liu
- Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350005, China
- Central Laboratory, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China
| | - Yue Chen
- Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350005, China
- Central Laboratory, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China
| | - Yanfang Xu
- Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350005, China
- Central Laboratory, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China
| | - Lengxi Fu
- Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350005, China
- Central Laboratory, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Gui Wu
- Department of Orthopaedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350005, China
- Department of Orthopaedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China
| | - Fei Huang
- Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350005, China
- Central Laboratory, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China
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6
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Durand S, Tang Y, Pommier RM, Benboubker V, Grimont M, Boivin F, Barbollat-Boutrand L, Cumunel E, Dupeuble F, Eberhardt A, Plaschka M, Dalle S, Caramel J. ZEB1 controls a lineage-specific transcriptional program essential for melanoma cell state transitions. Oncogene 2024; 43:1489-1505. [PMID: 38519642 DOI: 10.1038/s41388-024-03010-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/06/2024] [Indexed: 03/25/2024]
Abstract
Cell plasticity sustains intra-tumor heterogeneity and treatment resistance in melanoma. Deciphering the transcriptional mechanisms governing reversible phenotypic transitions between proliferative/differentiated and invasive/stem-like states is required. Expression of the ZEB1 transcription factor is frequently activated in melanoma, where it fosters adaptive resistance to targeted therapies. Here, we performed a genome-wide characterization of ZEB1 transcriptional targets, by combining ChIP-sequencing and RNA-sequencing, upon phenotype switching in melanoma models. We identified and validated ZEB1 binding peaks in the promoter of key lineage-specific genes crucial for melanoma cell identity. Mechanistically, ZEB1 negatively regulates SOX10-MITF dependent proliferative/melanocytic programs and positively regulates AP-1 driven invasive and stem-like programs. Comparative analyses with breast carcinoma cells revealed lineage-specific ZEB1 binding, leading to the design of a more reliable melanoma-specific ZEB1 regulon. We then developed single-cell spatial multiplexed analyses to characterize melanoma cell states intra-tumoral heterogeneity in human melanoma samples. Combined with scRNA-Seq analyses, our findings confirmed increased ZEB1 expression in Neural-Crest-like cells and mesenchymal cells, underscoring its significance in vivo in both populations. Overall, our results define ZEB1 as a major transcriptional regulator of cell states transitions and provide a better understanding of lineage-specific transcriptional programs sustaining intra-tumor heterogeneity in melanoma.
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Affiliation(s)
- Simon Durand
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Yaqi Tang
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Roxane M Pommier
- Fondation Synergie Lyon Cancer, Plateforme de bio-informatique Gilles Thomas, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, INSERM U1052-CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Valentin Benboubker
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Maxime Grimont
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Felix Boivin
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Laetitia Barbollat-Boutrand
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Eric Cumunel
- Fondation Synergie Lyon Cancer, Plateforme de bio-informatique Gilles Thomas, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, INSERM U1052-CNRS UMR5286, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Florian Dupeuble
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Anaïs Eberhardt
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
- Dermatology Unit, Hospices Civils de Lyon, CH Lyon Sud, 165 chemin du Grand Revoyet, 69495, Pierre Bénite, Cedex, France
| | - Maud Plaschka
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
| | - Stéphane Dalle
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France
- Dermatology Unit, Hospices Civils de Lyon, CH Lyon Sud, 165 chemin du Grand Revoyet, 69495, Pierre Bénite, Cedex, France
| | - Julie Caramel
- "Cancer cell Plasticity in Melanoma" lab, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon1, 69008, Lyon, France.
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7
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Carvalho LADC, Noma IHY, Uehara AH, Siena ÁDD, Osaki LH, Mori MP, Pinto NCDS, Freitas VM, Junior WAS, Smalley KSM, Maria-Engler SS. Modeling Melanoma Heterogeneity In Vitro: Redox, Resistance and Pigmentation Profiles. Antioxidants (Basel) 2024; 13:555. [PMID: 38790661 PMCID: PMC11118096 DOI: 10.3390/antiox13050555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/21/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Microenvironment and transcriptional plasticity generate subpopulations within the tumor, and the use of BRAF inhibitors (BRAFis) contributes to the rise and selection of resistant clones. We stochastically isolated subpopulations (C1, C2, and C3) from naïve melanoma and found that the clones demonstrated distinct morphology, phenotypic, and functional profiles: C1 was less proliferative, more migratory and invasive, less sensitive to BRAFis, less dependent on OXPHOS, more sensitive to oxidative stress, and less pigmented; C2 was more proliferative, less migratory and invasive, more sensitive to BRAFis, less sensitive to oxidative stress, and more pigmented; and C3 was less proliferative, more migratory and invasive, less sensitive to BRAFis, more dependent on OXPHOS, more sensitive to oxidative stress, and more pigmented. Hydrogen peroxide plays a central role in oxidative stress and cell signaling, and PRDXs are one of its main consumers. The intrinsically resistant C1 and C3 clones had lower MITF, PGC-1α, and PRDX1 expression, while C1 had higher AXL and decreased pigmentation markers, linking PRDX1 to clonal heterogeneity and resistance. PRDX2 is depleted in acquired BRAFi-resistant cells and acts as a redox sensor. Our results illustrate that decreased pigmentation markers are related to therapy resistance and decreased antioxidant defense.
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Affiliation(s)
- Larissa Anastacio da Costa Carvalho
- Department of Tumor Biology, Moffitt Cancer Center, Tampa, FL 33612, USA; (L.A.d.C.C.); (K.S.M.S.)
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (I.H.Y.N.); (A.H.U.)
| | - Isabella Harumi Yonehara Noma
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (I.H.Y.N.); (A.H.U.)
| | - Adriana Hiromi Uehara
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (I.H.Y.N.); (A.H.U.)
| | - Ádamo Davi Diógenes Siena
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (Á.D.D.S.); (W.A.S.J.)
| | - Luciana Harumi Osaki
- Department of Cell Biology and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (L.H.O.); (V.M.F.)
| | - Mateus Prates Mori
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, SP, Brazil; (M.P.M.); (N.C.d.S.P.)
| | - Nadja Cristhina de Souza Pinto
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, SP, Brazil; (M.P.M.); (N.C.d.S.P.)
| | - Vanessa Morais Freitas
- Department of Cell Biology and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (L.H.O.); (V.M.F.)
| | - Wilson Araújo Silva Junior
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; (Á.D.D.S.); (W.A.S.J.)
| | - Keiran S. M. Smalley
- Department of Tumor Biology, Moffitt Cancer Center, Tampa, FL 33612, USA; (L.A.d.C.C.); (K.S.M.S.)
| | - Silvya Stuchi Maria-Engler
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (I.H.Y.N.); (A.H.U.)
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8
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Hirsch M, Pal S, Mehrabadi FR, Malikic S, Gruen C, Sassano A, Pérez-Guijarro E, Merlino G, Sahinalp C, Molloy EK, Day CP, Przytycka TM. Stochastic modelling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.588869. [PMID: 38712152 PMCID: PMC11071284 DOI: 10.1101/2024.04.17.588869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Cancer progression is an evolutionary process driven by the selection of cells adapted to gain growth advantage. We present the first formal study on the adaptation of gene expression in subclonal evolution. We model evolutionary changes in gene expression as stochastic Ornstein-Uhlenbeck processes, jointly leveraging the evolutionary history of subclones and single-cell expression data. Applying our model to sublines derived from single cells of a mouse melanoma revealed that sublines with distinct phenotypes are underlined by different patterns of gene expression adaptation, indicating non-genetic mechanisms of cancer evolution. Interestingly, sublines previously observed to be resistant to anti-CTLA-4 treatment showed adaptive expression of genes related to invasion and non-canonical Wnt signaling, whereas sublines that responded to treatment showed adaptive expression of genes related to proliferation and canonical Wnt signaling. Our results suggest that clonal phenotypes emerge as the result of specific adaptivity patterns of gene expression.
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Affiliation(s)
- M.G. Hirsch
- National Library of Medicine, NIH, Bethesda, Maryland, USA
- Department of Computer Science, University of Maryland, College Park, Maryland USA
| | - Soumitra Pal
- Neurobiology Neurodegeneration and Repair Lab, National Eye Institute, NIH, Bethesda, Maryland, USA
| | - Farid Rashidi Mehrabadi
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer institute, NIH, Bethesda, Maryland, USA
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Salem Malikic
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer institute, NIH, Bethesda, Maryland, USA
| | - Charli Gruen
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Antonella Sassano
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Eva Pérez-Guijarro
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
- Instituto de Investigaciones Biomédicas Sols-Morreale, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (IIBM, CSIC-UAM), Madrid, Spain
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Cenk Sahinalp
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer institute, NIH, Bethesda, Maryland, USA
| | - Erin K. Molloy
- Department of Computer Science, University of Maryland, College Park, Maryland USA
- University of Maryland Institute for Advanced Computer Studies, College Park, Maryland USA
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
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9
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Lauss M, Phung B, Borch TH, Harbst K, Kaminska K, Ebbesson A, Hedenfalk I, Yuan J, Nielsen K, Ingvar C, Carneiro A, Isaksson K, Pietras K, Svane IM, Donia M, Jönsson G. Molecular patterns of resistance to immune checkpoint blockade in melanoma. Nat Commun 2024; 15:3075. [PMID: 38594286 PMCID: PMC11004175 DOI: 10.1038/s41467-024-47425-y] [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: 07/27/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024] Open
Abstract
Immune checkpoint blockade (ICB) has improved outcome for patients with metastatic melanoma but not all benefit from treatment. Several immune- and tumor intrinsic features are associated with clinical response at baseline. However, we need to further understand the molecular changes occurring during development of ICB resistance. Here, we collect biopsies from a cohort of 44 patients with melanoma after progression on anti-CTLA4 or anti-PD1 monotherapy. Genetic alterations of antigen presentation and interferon gamma signaling pathways are observed in approximately 25% of ICB resistant cases. Anti-CTLA4 resistant lesions have a sustained immune response, including immune-regulatory features, as suggested by multiplex spatial and T cell receptor (TCR) clonality analyses. One anti-PD1 resistant lesion harbors a distinct immune cell niche, however, anti-PD1 resistant tumors are generally immune poor with non-expanded TCR clones. Such immune poor microenvironments are associated with melanoma cells having a de-differentiated phenotype lacking expression of MHC-I molecules. In addition, anti-PD1 resistant tumors have reduced fractions of PD1+ CD8+ T cells as compared to ICB naïve metastases. Collectively, these data show the complexity of ICB resistance and highlight differences between anti-CTLA4 and anti-PD1 resistance that may underlie differential clinical outcomes of therapy sequence and combination.
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Affiliation(s)
- Martin Lauss
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Bengt Phung
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Troels Holz Borch
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Katja Harbst
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Kamila Kaminska
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Anna Ebbesson
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Joan Yuan
- Division of Molecular Hematology, Department of Laboratory Medicine, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Kari Nielsen
- Lund University Cancer Center, LUCC, Lund, Sweden
- Division of Dermatology, Skåne University Hospital and Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Christian Ingvar
- Division of Surgery, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Ana Carneiro
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital Comprehensive Cancer Center, 22185, Lund, Sweden
| | - Karolin Isaksson
- Lund University Cancer Center, LUCC, Lund, Sweden
- Division of Surgery, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Department of Surgery, Kristianstad Hospital, 29133, Kristianstad, Sweden
| | - Kristian Pietras
- Lund University Cancer Center, LUCC, Lund, Sweden
- Division of Translational Cancer Research, Department of Laboratory Medicine, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Inge Marie Svane
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Marco Donia
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Göran Jönsson
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden.
- Lund University Cancer Center, LUCC, Lund, Sweden.
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10
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Stauffer PE, Brinkley J, Jacobson D, Quaranta V, Tyson DR. Purinergic Ca 2+ signaling as a novel mechanism of drug tolerance in BRAF mutant melanoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.03.565532. [PMID: 37961267 PMCID: PMC10635130 DOI: 10.1101/2023.11.03.565532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Drug tolerance is a major cause of relapse after cancer treatment. In spite of intensive efforts1-9, its molecular basis remains poorly understood, hampering actionable intervention. We report a previously unrecognized signaling mechanism supporting drug tolerance in BRAF-mutant melanoma treated with BRAF inhibitors that could be of general relevance to other cancers. Its key features are cell-intrinsic intracellular Ca2+ signaling initiated by P2X7 receptors (purinergic ligand-gated cation channels), and an enhanced ability for these Ca2+ signals to reactivate ERK1/2 in the drug-tolerant state. Extracellular ATP, virtually ubiquitous in living systems, is the ligand that can initiate Ca2+ spikes via P2X7 channels. ATP is abundant in the tumor microenvironment and is released by dying cells, ironically implicating treatment-initiated cancer cell death as a source of trophic stimuli that leads to ERK reactivation and drug tolerance. Such a mechanism immediately offers an explanation of the inevitable relapse after BRAFi treatment in BRAF-mutant melanoma, and points to actionable strategies to overcome it.
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Affiliation(s)
- Philip E Stauffer
- Department of Pharmacology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, USA
| | - Jordon Brinkley
- Department of Pharmacology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, USA
| | - David Jacobson
- Departments of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, USA
| | - Vito Quaranta
- Department of Pharmacology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, USA
| | - Darren R Tyson
- Department of Pharmacology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, USA
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11
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Hanrahan AJ, Chen Z, Rosen N, Solit DB. BRAF - a tumour-agnostic drug target with lineage-specific dependencies. Nat Rev Clin Oncol 2024; 21:224-247. [PMID: 38278874 DOI: 10.1038/s41571-023-00852-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/28/2024]
Abstract
In June 2022, the FDA granted Accelerated Approval to the BRAF inhibitor dabrafenib in combination with the MEK inhibitor trametinib for the treatment of adult and paediatric patients (≥6 years of age) with unresectable or metastatic BRAFV600E-mutant solid tumours, except for BRAFV600E-mutant colorectal cancers. The histology-agnostic approval of dabrafenib plus trametinib marks the culmination of two decades of research into the landscape of BRAF mutations in human cancers, the biochemical mechanisms underlying BRAF-mediated tumorigenesis, and the clinical development of selective RAF and MEK inhibitors. Although the majority of patients with BRAFV600E-mutant tumours derive clinical benefit from BRAF inhibitor-based combinations, resistance to treatment develops in most. In this Review, we describe the biochemical basis for oncogenic BRAF-induced activation of MAPK signalling and pan-cancer and lineage-specific mechanisms of intrinsic, adaptive and acquired resistance to BRAF inhibitors. We also discuss novel RAF inhibitors and drug combinations designed to delay the emergence of treatment resistance and/or expand the population of patients with BRAF-mutant cancers who benefit from molecularly targeted therapies.
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Affiliation(s)
- Aphrothiti J Hanrahan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ziyu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Physiology, Biophysics & Systems Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Neal Rosen
- Molecular Pharmacology Program, Sloan Kettering Institute for Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, Cornell University, New York, NY, USA.
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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12
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Uddin MH, Zhang D, Muqbil I, El-Rayes BF, Chen H, Philip PA, Azmi AS. Deciphering cellular plasticity in pancreatic cancer for effective treatments. Cancer Metastasis Rev 2024; 43:393-408. [PMID: 38194153 DOI: 10.1007/s10555-023-10164-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/19/2023] [Indexed: 01/10/2024]
Abstract
Cellular plasticity and therapy resistance are critical features of pancreatic cancer, a highly aggressive and fatal disease. The pancreas, a vital organ that produces digestive enzymes and hormones, is often affected by two main types of cancer: the pre-dominant ductal adenocarcinoma and the less common neuroendocrine tumors. These cancers are difficult to treat due to their complex biology characterized by cellular plasticity leading to therapy resistance. Cellular plasticity refers to the capability of cancer cells to change and adapt to different microenvironments within the body which includes acinar-ductal metaplasia, epithelial to mesenchymal/epigenetic/metabolic plasticity, as well as stemness. This plasticity allows heterogeneity of cancer cells, metastasis, and evasion of host's immune system and develops resistance to radiation, chemotherapy, and targeted therapy. To overcome this resistance, extensive research is ongoing exploring the intrinsic and extrinsic factors through cellular reprogramming, chemosensitization, targeting metabolic, key survival pathways, etc. In this review, we discussed the mechanisms of cellular plasticity involving cellular adaptation and tumor microenvironment and provided a comprehensive understanding of its role in therapy resistance and ways to overcome it.
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Affiliation(s)
- Md Hafiz Uddin
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R, HWCRC 740, Detroit, MI, 48201, USA.
| | - Dingqiang Zhang
- Department of Natural Sciences, Lawrence Technological University, 21000 W 10 Mile Rd, Southfield, MI, 48075, USA
| | - Irfana Muqbil
- Department of Natural Sciences, Lawrence Technological University, 21000 W 10 Mile Rd, Southfield, MI, 48075, USA
| | - Bassel F El-Rayes
- Division of Hematology and Oncology, Department of Medicine, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, 35233, USA
| | - Herbert Chen
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Philip A Philip
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R, HWCRC 740, Detroit, MI, 48201, USA
- Henry Ford Health Systems, Detroit, MI, 48202, USA
| | - Asfar S Azmi
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, 4100 John R, HWCRC 740, Detroit, MI, 48201, USA.
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13
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Singvogel K, Schittek B. Dormancy of cutaneous melanoma. Cancer Cell Int 2024; 24:88. [PMID: 38419052 PMCID: PMC10903048 DOI: 10.1186/s12935-024-03278-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
Many cancer-related deaths including melanoma result from metastases that develop months or years after the initial cancer therapy. Even the most effective drugs and immune therapies rarely eradicate all tumor cells. Instead, they strongly reduce cancer burden, permitting dormant cancer cells to persist in niches, where they establish a cellular homeostasis with their host without causing clinical symptoms. Dormant cancers respond poorly to most drugs and therapies since they do not proliferate and hide in niches. It therefore remains a major challenge to develop novel therapies for dormant cancers. In this review we focus on the mechanisms regulating the initiation of cutaneous melanoma dormancy as well as those which are involved in reawakening of dormant cutaneous melanoma cells. In recent years the role of neutrophils and niche components in reawakening of melanoma cells came into focus and indicate possible future therapeutic applications. Sophisticated in vitro and in vivo melanoma dormancy models are needed to make progress in this field and are discussed.
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Affiliation(s)
- Kathrin Singvogel
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Liebermeisterstr. 25, D -72076 , Tübingen, Germany
| | - Birgit Schittek
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Liebermeisterstr. 25, D -72076 , Tübingen, Germany.
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.
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14
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Taglialatela I, Indini A, Santanelli G, Di Liberti G, Di Guardo L, De Braud F, Del Vecchio M. Melanoma and sex hormones: Pathogenesis, progressive disease and response to treatments. TUMORI JOURNAL 2024:3008916241231687. [PMID: 38372040 DOI: 10.1177/03008916241231687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Cutaneous melanoma represents the fifth tumor in terms of incidence in young adults, with a major involvement of males than females. Despite the significant changes in available effective treatments for cutaneous melanoma, there is still a proportion of patients that do not benefit long-term disease control with immune checkpoint inhibitors and/or BRAF/MEK inhibitors, and eventually develop progressive disease. In addition to the emerging biomarkers under investigation to understand resistance to treatments, recent studies resumed the role of sex hormones (estrogens, progesterone and androgens) in melanoma patients. In the last decades, the impact of sex hormones has been considered controversial in melanoma patients, but actual growing preclinical and clinical evidence underline the potential influence on melanoma cells' growth, tumor microenvironment, the immune system and consequently on the course of disease.This review will provide available insights on the role of sex hormones in melanoma pathogenesis, disease progression and response/resistance to systemic treatments. We will also offer an overview on the recent studies on the theme, describing the hormonal contribution to disease response and the interaction with targeted therapies and immune-checkpoint inhibitors in cutaneous melanoma patients, illustrating an insight into future research in this field.
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Affiliation(s)
- Ida Taglialatela
- Melanoma Medical Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Alice Indini
- Melanoma Medical Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Giulia Santanelli
- Melanoma Medical Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Giorgia Di Liberti
- Melanoma Medical Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Lorenza Di Guardo
- Melanoma Medical Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Filippo De Braud
- Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
- Università degli studi di Milano, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Michele Del Vecchio
- Melanoma Medical Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
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15
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Mendelson K, Martin TC, Nguyen CB, Hsu M, Xu J, Lang C, Dummer R, Saenger Y, Messina JL, Sondak VK, Desman G, Hasson D, Bernstein E, Parsons RE, Celebi JT. Differential histone acetylation and super-enhancer regulation underlie melanoma cell dedifferentiation. JCI Insight 2024; 9:e166611. [PMID: 38319712 PMCID: PMC11063936 DOI: 10.1172/jci.insight.166611] [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: 10/31/2022] [Accepted: 02/02/2024] [Indexed: 02/07/2024] Open
Abstract
Dedifferentiation or phenotype switching refers to the transition from a proliferative to an invasive cellular state. We previously identified a 122-gene epigenetic gene signature that classifies primary melanomas as low versus high risk (denoted as Epgn1 or Epgn3). We found that the transcriptomes of the Epgn1 low-risk and Epgn3 high-risk cells are similar to the proliferative and invasive cellular states, respectively. These signatures were further validated in melanoma tumor samples. Examination of the chromatin landscape revealed differential H3K27 acetylation in the Epgn1 low-risk versus Epgn3 high-risk cell lines that corroborated with a differential super-enhancer and enhancer landscape. Melanocytic lineage genes (MITF, its targets and regulators) were associated with super-enhancers in the Epgn1 low-risk state, whereas invasiveness genes were linked with Epgn3 high-risk status. We identified the ITGA3 gene as marked by a super-enhancer element in the Epgn3 invasive cells. Silencing of ITGA3 enhanced invasiveness in both in vitro and in vivo systems, suggesting it as a negative regulator of invasion. In conclusion, we define chromatin landscape changes associated with Epgn1/Epgn3 and phenotype switching during early steps of melanoma progression that regulate transcriptional reprogramming. This super-enhancer and enhancer-driven epigenetic regulatory mechanism resulting in major changes in the transcriptome could be important in future therapeutic targeting efforts.
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Affiliation(s)
- Karen Mendelson
- Department of Dermatology, NYU Grossman School of Medicine, New York, New York, USA
| | - Tiphaine C. Martin
- Department of Oncological Sciences and
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christie B. Nguyen
- Department of Oncological Sciences and
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biological Sciences, Icahn School of Medicine, New York, New York, USA
| | - Min Hsu
- Department of Dermatology, NYU Grossman School of Medicine, New York, New York, USA
| | - Jia Xu
- Department of Oncological Sciences and
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Claudia Lang
- Department of Dermatology, University Hospital of Zurich, Zurich, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University Hospital of Zurich, Zurich, Switzerland
| | - Yvonne Saenger
- Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Jane L. Messina
- Department of Pathology and Cell Biology, USF Morsani College of Medicine, Tampa, Florida, USA
- Moffitt Cancer Center, Tampa, Florida, USA
| | - Vernon K. Sondak
- Department of Pathology and Cell Biology, USF Morsani College of Medicine, Tampa, Florida, USA
- Moffitt Cancer Center, Tampa, Florida, USA
| | - Garrett Desman
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dan Hasson
- Department of Oncological Sciences and
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biological Sciences, Icahn School of Medicine, New York, New York, USA
| | - Emily Bernstein
- Department of Oncological Sciences and
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biological Sciences, Icahn School of Medicine, New York, New York, USA
| | - Ramon E. Parsons
- Department of Oncological Sciences and
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Julide Tok Celebi
- Department of Dermatology, NYU Grossman School of Medicine, New York, New York, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
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16
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Runel G, Lopez-Ramirez N, Barbollat-Boutrand L, Cario M, Durand S, Grimont M, Schartl M, Dalle S, Caramel J, Chlasta J, Masse I. Cancer Cell Biomechanical Properties Accompany Tspan8-Dependent Cutaneous Melanoma Invasion. Cancers (Basel) 2024; 16:694. [PMID: 38398085 PMCID: PMC10887418 DOI: 10.3390/cancers16040694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
The intrinsic biomechanical properties of cancer cells remain poorly understood. To decipher whether cell stiffness modulation could increase melanoma cells' invasive capacity, we performed both in vitro and in vivo experiments exploring cell stiffness by atomic force microscopy (AFM). We correlated stiffness properties with cell morphology adaptation and the molecular mechanisms underlying epithelial-to-mesenchymal (EMT)-like phenotype switching. We found that melanoma cell stiffness reduction was systematically associated with the acquisition of invasive properties in cutaneous melanoma cell lines, human skin reconstructs, and Medaka fish developing spontaneous MAP-kinase-induced melanomas. We observed a systematic correlation of stiffness modulation with cell morphological changes towards mesenchymal characteristic gains. We accordingly found that inducing melanoma EMT switching by overexpressing the ZEB1 transcription factor, a major regulator of melanoma cell plasticity, was sufficient to decrease cell stiffness and transcriptionally induce tetraspanin-8-mediated dermal invasion. Moreover, ZEB1 expression correlated with Tspan8 expression in patient melanoma lesions. Our data suggest that intrinsic cell stiffness could be a highly relevant marker for human cutaneous melanoma development.
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Affiliation(s)
- Gaël Runel
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
- BioMeca, 60F, Bioserra 2, Av. Rockefeller, 69008 Lyon, France
| | - Noémie Lopez-Ramirez
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Laetitia Barbollat-Boutrand
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Muriel Cario
- National Reference Center for Rare Skin Disease, Department of Dermatology, University Hospital, INSERM 1035, 33000 Bordeaux, France
- AquiDerm, University Bordeaux, 33076 Bordeaux, France
| | - Simon Durand
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Maxime Grimont
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Manfred Schartl
- Developmental Biochemistry, University of Würzburg, 97074 Würzburg, Germany
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX 78666, USA
| | - Stéphane Dalle
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
- Dermatology Department, Hôpital Universitaire Lyon Sud, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
| | - Julie Caramel
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Julien Chlasta
- BioMeca, 60F, Bioserra 2, Av. Rockefeller, 69008 Lyon, France
| | - Ingrid Masse
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
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17
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Kharouf N, Flanagan TW, Alamodi AA, Al Hmada Y, Hassan SY, Shalaby H, Santourlidis S, Hassan SL, Haikel Y, Megahed M, Brodell RT, Hassan M. CD133-Dependent Activation of Phosphoinositide 3-Kinase /AKT/Mammalian Target of Rapamycin Signaling in Melanoma Progression and Drug Resistance. Cells 2024; 13:240. [PMID: 38334632 PMCID: PMC10854812 DOI: 10.3390/cells13030240] [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: 11/29/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024] Open
Abstract
Melanoma frequently harbors genetic alterations in key molecules leading to the aberrant activation of PI3K and its downstream pathways. Although the role of PI3K/AKT/mTOR in melanoma progression and drug resistance is well documented, targeting the PI3K/AKT/mTOR pathway showed less efficiency in clinical trials than might have been expected, since the suppression of the PI3K/mTOR signaling pathway-induced feedback loops is mostly associated with the activation of compensatory pathways such as MAPK/MEK/ERK. Consequently, the development of intrinsic and acquired resistance can occur. As a solid tumor, melanoma is notorious for its heterogeneity. This can be expressed in the form of genetically divergent subpopulations including a small fraction of cancer stem-like cells (CSCs) and non-cancer stem cells (non-CSCs) that make the most of the tumor mass. Like other CSCs, melanoma stem-like cells (MSCs) are characterized by their unique cell surface proteins/stemness markers and aberrant signaling pathways. In addition to its function as a robust marker for stemness properties, CD133 is crucial for the maintenance of stemness properties and drug resistance. Herein, the role of CD133-dependent activation of PI3K/mTOR in the regulation of melanoma progression, drug resistance, and recurrence is reviewed.
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Affiliation(s)
- Naji Kharouf
- Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France; (N.K.); (Y.H.)
- Department of Operative Dentistry and Endodontics, Dental Faculty, University of Strasbourg, 67000 Strasbourg, France
| | - Thomas W. Flanagan
- Department of Pharmacology and Experimental Therapeutics, LSU Health Sciences Center, New Orleans, LA 70112, USA;
| | | | - Youssef Al Hmada
- Department of Pathology, University of Mississippi Medical Center, Jackson, MS 39216, USA; (Y.A.H.); (R.T.B.)
| | - Sofie-Yasmin Hassan
- Department of Pharmacy, Faculty of Science, Heinrich-Heine University Duesseldorf, 40225 Dusseldorf, Germany;
| | - Hosam Shalaby
- Department of Urology, School of Medicine, Tulane University, New Orleans, LA 70112, USA;
| | - Simeon Santourlidis
- Epigenetics Core Laboratory, Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, 40225 Duesseldorf, Germany;
| | - Sarah-Lilly Hassan
- Department of Chemistry, Faculty of Science, Heinrich-Heine University Duesseldorf, 40225 Dusseldorf, Germany;
| | - Youssef Haikel
- Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France; (N.K.); (Y.H.)
- Department of Operative Dentistry and Endodontics, Dental Faculty, University of Strasbourg, 67000 Strasbourg, France
- Pôle de Médecine et Chirurgie Bucco-Dentaire, Hôpital Civil, Hôpitaux Universitaire de Strasbourg, 67000 Strasbourg, France
| | - Mossad Megahed
- Clinic of Dermatology, University Hospital of Aachen, 52074 Aachen, Germany;
| | - Robert T. Brodell
- Department of Pathology, University of Mississippi Medical Center, Jackson, MS 39216, USA; (Y.A.H.); (R.T.B.)
| | - Mohamed Hassan
- Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France; (N.K.); (Y.H.)
- Department of Operative Dentistry and Endodontics, Dental Faculty, University of Strasbourg, 67000 Strasbourg, France
- Research Laboratory of Surgery-Oncology, Department of Surgery, Tulane University School of Medicine, New Orleans, LA 70112, USA
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18
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Al Hmada Y, Brodell RT, Kharouf N, Flanagan TW, Alamodi AA, Hassan SY, Shalaby H, Hassan SL, Haikel Y, Megahed M, Santourlidis S, Hassan M. Mechanisms of Melanoma Progression and Treatment Resistance: Role of Cancer Stem-like Cells. Cancers (Basel) 2024; 16:470. [PMID: 38275910 PMCID: PMC10814963 DOI: 10.3390/cancers16020470] [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: 12/05/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Melanoma is the third most common type of skin cancer, characterized by its heterogeneity and propensity to metastasize to distant organs. Melanoma is a heterogeneous tumor, composed of genetically divergent subpopulations, including a small fraction of melanoma-initiating cancer stem-like cells (CSCs) and many non-cancer stem cells (non-CSCs). CSCs are characterized by their unique surface proteins associated with aberrant signaling pathways with a causal or consequential relationship with tumor progression, drug resistance, and recurrence. Melanomas also harbor significant alterations in functional genes (BRAF, CDKN2A, NRAS, TP53, and NF1). Of these, the most common are the BRAF and NRAS oncogenes, with 50% of melanomas demonstrating the BRAF mutation (BRAFV600E). While the successful targeting of BRAFV600E does improve overall survival, the long-term efficacy of available therapeutic options is limited due to adverse side effects and reduced clinical efficacy. Additionally, drug resistance develops rapidly via mechanisms involving fast feedback re-activation of MAPK signaling pathways. This article updates information relevant to the mechanisms of melanoma progression and resistance and particularly the mechanistic role of CSCs in melanoma progression, drug resistance, and recurrence.
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Affiliation(s)
- Youssef Al Hmada
- Department of Pathology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA; (Y.A.H.); (R.T.B.)
| | - Robert T. Brodell
- Department of Pathology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA; (Y.A.H.); (R.T.B.)
| | - Naji Kharouf
- Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France; (N.K.); (Y.H.)
- Department of Operative Dentistry and Endodontics, Dental Faculty, University of Strasbourg, 67000 Strasbourg, France
| | - Thomas W. Flanagan
- Department of Pharmacology and Experimental Therapeutics, LSU Health Sciences Center, New Orleans, LA 70112, USA;
| | - Abdulhadi A. Alamodi
- College of Health Sciences, Jackson State University, 310 W Woodrow Wilson Ave Ste 300, Jackson, MS 39213, USA;
| | - Sofie-Yasmin Hassan
- Department of Pharmacy, Faculty of Science, Heinrich-Heine University Duesseldorf, 40225 Dusseldorf, Germany;
| | - Hosam Shalaby
- Department of Urology, Tulane University School of Medicine, New Orleans, LA 70112, USA;
| | - Sarah-Lilly Hassan
- Department of Chemistry, Faculty of Science, Heinrich-Heine University Duesseldorf, 40225 Dusseldorf, Germany;
| | - Youssef Haikel
- Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France; (N.K.); (Y.H.)
- Department of Operative Dentistry and Endodontics, Dental Faculty, University of Strasbourg, 67000 Strasbourg, France
- Pôle de Médecine et Chirurgie Bucco-Dentaire, Hôpital Civil, Hôpitaux Universitaire de Strasbourg, 67000 Strasbourg, France
| | - Mosaad Megahed
- Clinic of Dermatology, University Hospital of Aachen, 52074 Aachen, Germany;
| | - Simeon Santourlidis
- Epigenetics Core Laboratory, Medical Faculty, Institute of Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf, 40225 Dusseldorf, Germany;
| | - Mohamed Hassan
- Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 67000 Strasbourg, France; (N.K.); (Y.H.)
- Department of Operative Dentistry and Endodontics, Dental Faculty, University of Strasbourg, 67000 Strasbourg, France
- Research Laboratory of Surgery-Oncology, Department of Surgery, Tulane University School of Medicine, New Orleans, LA 70112, USA
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19
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Zhang X, Pant SM, Ritch CC, Tang HY, Shao H, Dweep H, Gong YY, Brooks R, Brafford P, Wolpaw AJ, Lee Y, Weeraratna A, Sehgal A, Herlyn M, Kossenkov A, Speicher D, Sorger PK, Santagata S, Dang CV. Cell state dependent effects of Bmal1 on melanoma immunity and tumorigenicity. Nat Commun 2024; 15:633. [PMID: 38245503 PMCID: PMC10799901 DOI: 10.1038/s41467-024-44778-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/05/2024] [Indexed: 01/22/2024] Open
Abstract
The circadian clock regulator Bmal1 modulates tumorigenesis, but its reported effects are inconsistent. Here, we show that Bmal1 has a context-dependent role in mouse melanoma tumor growth. Loss of Bmal1 in YUMM2.1 or B16-F10 melanoma cells eliminates clock function and diminishes hypoxic gene expression and tumorigenesis, which could be rescued by ectopic expression of HIF1α in YUMM2.1 cells. By contrast, over-expressed wild-type or a transcriptionally inactive mutant Bmal1 non-canonically sequester myosin heavy chain 9 (Myh9) to increase MRTF-SRF activity and AP-1 transcriptional signature, and shift YUMM2.1 cells from a Sox10high to a Sox9high immune resistant, mesenchymal cell state that is found in human melanomas. Our work describes a link between Bmal1, Myh9, mouse melanoma cell plasticity, and tumor immunity. This connection may underlie cancer therapeutic resistance and underpin the link between the circadian clock, MRTF-SRF and the cytoskeleton.
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Affiliation(s)
- Xue Zhang
- The Wistar Institute, Philadelphia, PA, USA.
- Ludwig Institute for Cancer Research, New York, NY, USA.
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Shishir M Pant
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Cecily C Ritch
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Yao-Yu Gong
- The Wistar Institute, Philadelphia, PA, USA
- Ludwig Institute for Cancer Research, New York, NY, USA
| | - Rebekah Brooks
- The Wistar Institute, Philadelphia, PA, USA
- Ludwig Institute for Cancer Research, New York, NY, USA
| | - Patricia Brafford
- The Wistar Institute, Philadelphia, PA, USA
- Ludwig Institute for Cancer Research, New York, NY, USA
| | - Adam J Wolpaw
- The Wistar Institute, Philadelphia, PA, USA
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yool Lee
- Department of Translational Medicine and Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Ashani Weeraratna
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Amita Sehgal
- Howard Hughes Medical Institute, Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chi V Dang
- The Wistar Institute, Philadelphia, PA, USA.
- Ludwig Institute for Cancer Research, New York, NY, USA.
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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20
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Fontana F, Sommariva M, Anselmi M, Bianchi F, Limonta P, Gagliano N. Differentiation States of Phenotypic Transition of Melanoma Cells Are Revealed by 3D Cell Cultures. Cells 2024; 13:181. [PMID: 38247872 PMCID: PMC10814891 DOI: 10.3390/cells13020181] [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: 11/02/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Melanoma is characterized by high metastatic potential favored by the epithelial-to-mesenchymal transition (EMT), leading melanoma cells to exhibit a spectrum of typical EMT markers. This study aimed to analyze the expression of EMT markers in A375 and BLM melanoma cell lines cultured in 2D monolayers and 3D spheroids using morphological and molecular methods. The expression of EMT markers was strongly affected by 3D arrangement and revealed a hybrid phenotype for the two cell lines. Indeed, although E-cadherin was almost undetectable in both A375 and BLM cells, cortical actin was detected in A375 2D monolayers and 3D spheroids and was strongly expressed in BLM 3D spheroids. The mesenchymal marker N-cadherin was significantly up-regulated in A375 3D spheroids while undetectable in BLM cells, but vimentin was similarly expressed in both cell lines at the gene and protein levels. This pattern suggests that A375 cells exhibit a more undifferentiated/mesenchymal phenotype, while BLM cells have more melanocytic/differentiated characteristics. Accordingly, the Zeb1 and 2, Slug, Snail and Twist gene expression analyses showed that they were differentially expressed in 2D monolayers compared to 3D spheroids, supporting this view. Furthermore, A375 cells are characterized by a greater invasive potential, strongly influenced by 3D arrangement, compared to the BLM cell line, as evaluated by SDS-zymography and TIMPs gene expression analysis. Finally, TGF-β1, a master controller of EMT, and lysyl oxidase (LOX), involved in melanoma progression, were strongly up-regulated by 3D arrangement in the metastatic BLM cells alone, likely playing a role in the metastatic phases of melanoma progression. Overall, these findings suggest that A375 and BLM cells possess a hybrid/intermediate phenotype in relation to the expression of EMT markers. The former is characterized by a more mesenchymal/undifferentiated phenotype, while the latter shows a more melanocytic/differentiated phenotype. Our results contribute to the characterization of the role of EMT in melanoma cells and confirm that a 3D cell culture model could provide deeper insight into our understanding of the biology of melanoma.
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Affiliation(s)
- Fabrizio Fontana
- Department of Pharmacological and Biomolecular Sciences “Rodolfo Paoletti”, Università degli Studi di Milano, 20133 Milan, Italy; (F.F.); (M.A.); (P.L.)
| | - Michele Sommariva
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, 20133 Milan, Italy; (M.S.); (F.B.)
| | - Martina Anselmi
- Department of Pharmacological and Biomolecular Sciences “Rodolfo Paoletti”, Università degli Studi di Milano, 20133 Milan, Italy; (F.F.); (M.A.); (P.L.)
| | - Francesca Bianchi
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, 20133 Milan, Italy; (M.S.); (F.B.)
- U. O. Laboratorio Morfologia Umana Applicata, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Patrizia Limonta
- Department of Pharmacological and Biomolecular Sciences “Rodolfo Paoletti”, Università degli Studi di Milano, 20133 Milan, Italy; (F.F.); (M.A.); (P.L.)
| | - Nicoletta Gagliano
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, 20133 Milan, Italy; (M.S.); (F.B.)
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21
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Xiao H, Shiu J, Chen CF, Wu J, Zhou P, Telang SS, Ruiz-Vega R, Nie Q, Lander AD, Ganesan AK. Uncovering Minimal Pathways in Melanoma Initiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.08.570336. [PMID: 38106189 PMCID: PMC10723457 DOI: 10.1101/2023.12.08.570336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Cutaneous melanomas are clinically and histologically heterogeneous. Most display activating mutations in Braf or Nras and complete loss of function of one or more tumor suppressor genes. Mouse models that replicate such mutations produce fast-growing, pigmented tumors. However, mice that combine Braf activation with only heterozygous loss of Pten also produce tumors and, as we show here, in an Albino background this occurs even with Braf activation alone. Such tumors arise rarely, grow slowly, and express low levels of pigmentation genes. The timing of their appearance was consistent with a single step stochastic event, but no evidence could be found that it required de novo mutation, suggesting instead the involvement of an epigenetic transition. Single-cell transcriptomic analysis revealed such tumors to be heterogeneous, including a minor cell type we term LNM ( L ow-pigment, N eural- and extracellular M atrix-signature) that displays gene expression resembling "neural crest"-like cell subsets detected in the fast-growing tumors of more heavily-mutated mice, as well as in human biopsy and xenograft samples. We provide evidence that LNM cells pre-exist in normal skin, are expanded by Braf activation, can transition into malignant cells, and persist with malignant cells through multiple rounds of transplantation. We discuss the possibility that LNM cells not only serve as a pre-malignant state in the production of some melanomas, but also as an important intermediate in the development of drug resistance.
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22
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Balderson B, Fane M, Harvey TJ, Piper M, Smith A, Bodén M. Systematic analysis of the transcriptional landscape of melanoma reveals drug-target expression plasticity. Brief Funct Genomics 2024:elad055. [PMID: 38183207 DOI: 10.1093/bfgp/elad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 10/25/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024] Open
Abstract
Metastatic melanoma originates from melanocytes of the skin. Melanoma metastasis results in poor treatment prognosis for patients and is associated with epigenetic and transcriptional changes that reflect the developmental program of melanocyte differentiation from neural crest stem cells. Several studies have explored melanoma transcriptional heterogeneity using microarray, bulk and single-cell RNA-sequencing technologies to derive data-driven models of the transcriptional-state change which occurs during melanoma progression. No study has systematically examined how different models of melanoma progression derived from different data types, technologies and biological conditions compare. Here, we perform a cross-sectional study to identify averaging effects of bulk-based studies that mask and distort apparent melanoma transcriptional heterogeneity; we describe new transcriptionally distinct melanoma cell states, identify differential co-expression of genes between studies and examine the effects of predicted drug susceptibilities of different cell states between studies. Importantly, we observe considerable variability in drug-target gene expression between studies, indicating potential transcriptional plasticity of melanoma to down-regulate these drug targets and thereby circumvent treatment. Overall, observed differences in gene co-expression and predicted drug susceptibility between studies suggest bulk-based transcriptional measurements do not reliably gauge heterogeneity and that melanoma transcriptional plasticity is greater than described when studies are considered in isolation.
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Affiliation(s)
- Brad Balderson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Mitchell Fane
- Fox Chase Cancer Centre, Philadelphia, 19019 Pennsylvania, United States of America
| | - Tracey J Harvey
- School of Biomedical Sciences, University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Michael Piper
- School of Biomedical Sciences, University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Aaron Smith
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, 4072 Queensland, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072 Queensland, Australia
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23
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Pozniak J, Pedri D, Landeloos E, Van Herck Y, Antoranz A, Vanwynsberghe L, Nowosad A, Roda N, Makhzami S, Bervoets G, Maciel LF, Pulido-Vicuña CA, Pollaris L, Seurinck R, Zhao F, Flem-Karlsen K, Damsky W, Chen L, Karagianni D, Cinque S, Kint S, Vandereyken K, Rombaut B, Voet T, Vernaillen F, Annaert W, Lambrechts D, Boecxstaens V, Saeys Y, van den Oord J, Bosisio F, Karras P, Shain AH, Bosenberg M, Leucci E, Paschen A, Rambow F, Bechter O, Marine JC. A TCF4-dependent gene regulatory network confers resistance to immunotherapy in melanoma. Cell 2024; 187:166-183.e25. [PMID: 38181739 DOI: 10.1016/j.cell.2023.11.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 08/23/2023] [Accepted: 11/29/2023] [Indexed: 01/07/2024]
Abstract
To better understand intrinsic resistance to immune checkpoint blockade (ICB), we established a comprehensive view of the cellular architecture of the treatment-naive melanoma ecosystem and studied its evolution under ICB. Using single-cell, spatial multi-omics, we showed that the tumor microenvironment promotes the emergence of a complex melanoma transcriptomic landscape. Melanoma cells harboring a mesenchymal-like (MES) state, a population known to confer resistance to targeted therapy, were significantly enriched in early on-treatment biopsies from non-responders to ICB. TCF4 serves as the hub of this landscape by being a master regulator of the MES signature and a suppressor of the melanocytic and antigen presentation transcriptional programs. Targeting TCF4 genetically or pharmacologically, using a bromodomain inhibitor, increased immunogenicity and sensitivity of MES cells to ICB and targeted therapy. We thereby uncovered a TCF4-dependent regulatory network that orchestrates multiple transcriptional programs and contributes to resistance to both targeted therapy and ICB in melanoma.
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Affiliation(s)
- Joanna Pozniak
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium.
| | - Dennis Pedri
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium; Laboratory for Membrane Trafficking, Center for Brain and Disease Research, VIB, Leuven, Belgium
| | - Ewout Landeloos
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium; Department of General Medical Oncology, UZ Leuven, Leuven, Belgium
| | | | - Asier Antoranz
- Laboratory of Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven and UZ Leuven, Leuven, Belgium
| | - Lukas Vanwynsberghe
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Ada Nowosad
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Niccolò Roda
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Samira Makhzami
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Greet Bervoets
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Lucas Ferreira Maciel
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Carlos Ariel Pulido-Vicuña
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Lotte Pollaris
- Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Ruth Seurinck
- Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Fang Zhao
- Laboratory of Molecular Tumor Immunology, Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany
| | - Karine Flem-Karlsen
- Department of Dermatology, Yale University, 15 York Street, New Haven, CT 05610, USA
| | - William Damsky
- Departments of Dermatology and Pathology, Yale University, 15 York Street, New Haven, CT 05610, USA
| | - Limin Chen
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Despoina Karagianni
- Immune Regulation and Tumor Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, London WC1E 6DD, UK
| | - Sonia Cinque
- Laboratory for RNA Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sam Kint
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | - Katy Vandereyken
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | - Benjamin Rombaut
- Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | | | - Wim Annaert
- Laboratory for Membrane Trafficking, Center for Brain and Disease Research, VIB, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB, Leuven, Belgium; Center for Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Yvan Saeys
- Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Joost van den Oord
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, UZ Leuven, Leuven, Belgium
| | - Francesca Bosisio
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, UZ Leuven, Leuven, Belgium
| | - Panagiotis Karras
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - A Hunter Shain
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Marcus Bosenberg
- Departments of Dermatology, Pathology and Immunobiology, Yale University, New Haven, CT 05610, USA
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Annette Paschen
- Laboratory of Molecular Tumor Immunology, Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany
| | - Florian Rambow
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium; Department of Applied Computational Cancer Research, Institute for AI in Medicine (IKIM), University Hospital Essen, Essen, Germany; University Duisburg-Essen, Essen, Germany.
| | - Oliver Bechter
- Department of General Medical Oncology, UZ Leuven, Leuven, Belgium.
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium.
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24
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Taskaeva YS, Shatruk AY, Lomakin AI, Bgatova NP, Fursov SA. Assessment of Autophagy in Tumor Cells of Human Skin Melanoma of Different Stages. Bull Exp Biol Med 2024; 176:376-381. [PMID: 38340197 DOI: 10.1007/s10517-024-06027-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Indexed: 02/12/2024]
Abstract
High levels of autophagy can increase the viability of tumor cells as well as their resistance to chemotherapy. Evaluation of the dynamics of autophagy processes at different stages of carcinogenesis can extend our understanding of melanoma pathogenesis to develop new therapeutic approaches. We performed a comparative study of tumor cell autophagy in stages II and III human skin melanoma. Tumor cells were characterized by high content of structures associated with autophagy (autophagosomes and autolysosomes). In stage III melanoma characterized by the presence of regional metastases in the lymph nodes, tumor cells showed higher expression of the autophagy marker protein LC3beta in comparison with stage II melanoma cells, which can indicate the involvement of autophagy processes in tumor progression and the formation of metastases in the lymph nodes.
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Affiliation(s)
- Yu S Taskaeva
- Research Institute of Clinical and Experimental Lymphology - Branch of Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia.
| | - A Yu Shatruk
- Research Institute of Clinical and Experimental Lymphology - Branch of Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A I Lomakin
- Novosibirsk Regional Clinical Oncology Dispensary, Novosibirsk, Russia
| | - N P Bgatova
- Research Institute of Clinical and Experimental Lymphology - Branch of Federal Research Center Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - S A Fursov
- Novosibirsk Regional Clinical Oncology Dispensary, Novosibirsk, Russia
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25
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Santasusagna S, Zhu S, Jawalagatti V, Carceles-Cordon M, Ertel A, Garcia-Longarte S, Song WM, Fujiwara N, Li P, Mendizabal I, Petrylak DP, Kelly WK, Reddy EP, Wang L, Schiewer MJ, Lujambio A, Karnes J, Knudsen KE, Cordon-Cardo C, Dong H, Huang H, Carracedo A, Hoshida Y, Rodriguez-Bravo V, Domingo-Domenech J. Master Transcription Factor Reprogramming Unleashes Selective Translation Promoting Castration Resistance and Immune Evasion in Lethal Prostate Cancer. Cancer Discov 2023; 13:2584-2609. [PMID: 37676710 PMCID: PMC10714140 DOI: 10.1158/2159-8290.cd-23-0306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/28/2023] [Accepted: 09/05/2023] [Indexed: 09/08/2023]
Abstract
Signaling rewiring allows tumors to survive therapy. Here we show that the decrease of the master regulator microphthalmia transcription factor (MITF) in lethal prostate cancer unleashes eukaryotic initiation factor 3B (eIF3B)-dependent translation reprogramming of key mRNAs conferring resistance to androgen deprivation therapy (ADT) and promoting immune evasion. Mechanistically, MITF represses through direct promoter binding eIF3B, which in turn regulates the translation of specific mRNAs. Genome-wide eIF3B enhanced cross-linking immunoprecipitation sequencing (eCLIP-seq) showed specialized binding to a UC-rich motif present in subsets of 5' untranslated regions. Indeed, translation of the androgen receptor and major histocompatibility complex I (MHC-I) through this motif is sensitive to eIF3B amount. Notably, pharmacologic targeting of eIF3B-dependent translation in preclinical models sensitizes prostate cancer to ADT and anti-PD-1 therapy. These findings uncover a hidden connection between transcriptional and translational rewiring promoting therapy-refractory lethal prostate cancer and provide a druggable mechanism that may transcend into effective combined therapeutic strategies. SIGNIFICANCE Our study shows that specialized eIF3B-dependent translation of specific mRNAs released upon downregulation of the master transcription factor MITF confers castration resistance and immune evasion in lethal prostate cancer. Pharmacologic targeting of this mechanism delays castration resistance and increases immune-checkpoint efficacy. This article is featured in Selected Articles from This Issue, p. 2489.
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Affiliation(s)
- Sandra Santasusagna
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Shijia Zhu
- Department of Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Vijayakumar Jawalagatti
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | | | - Adam Ertel
- Department of Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Saioa Garcia-Longarte
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Won-Min Song
- Department of Genetics and Genome Sciences, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Naoto Fujiwara
- Department of Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Peiyao Li
- Department of Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Isabel Mendizabal
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Daniel P. Petrylak
- Department of Oncology, Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - William Kevin Kelly
- Department of Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - E. Premkumar Reddy
- Department of Oncological Sciences, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Liguo Wang
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Matthew J. Schiewer
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Amaia Lujambio
- Department of Oncological Sciences, Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jeffrey Karnes
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Karen E. Knudsen
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Carlos Cordon-Cardo
- Department of Pathology. Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Haidong Dong
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Immunology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Haojie Huang
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Arkaitz Carracedo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Traslational prostate cancer Research Lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
- CIBERONC, Madrid, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Yujin Hoshida
- Department of Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Veronica Rodriguez-Bravo
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
| | - Josep Domingo-Domenech
- Department of Urology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
- Department of Biochemistry and Molecular Biology, Mayo Comprehensive Cancer Center, Rochester, Minnesota
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Chen L, Fang C, Yuan X, Liu M, Wu P, Zhong L, Chen Z. Has-miR-300-GADD45B promotes melanoma growth via cell cycle. Aging (Albany NY) 2023; 15:13920-13943. [PMID: 38070141 PMCID: PMC10756120 DOI: 10.18632/aging.205276] [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: 06/15/2023] [Accepted: 10/16/2023] [Indexed: 12/21/2023]
Abstract
Response to oncogenic factors like UV, GADD45 family in skin participates in scavenging ROS, DNA repair and cell cycle control. Because of this, the previous study of the chronic UVB injury model has found that hsa-miR-300 can conduct intercellular transport by exosomes and target regulation of GADD45B. Whether the hsa-miR-300-GADD45B still regulates tumor development by cell cycle pathway is unclear. Through transcriptomic analysis of primary (n=39) and metastatic (n=102) melanoma, it was confirmed that in metastatic samples, some of the 97 down-regulated genes participate in maintaining skin homeostasis while 42 up-regulated genes were enriched in cancer-related functions. Furthermore, CDKN1A, CDKN2A, CXCR4 and RAD51 in the melanoma pathway, were also differentially expressed between normal skin and melanoma. CDKN1A and CDKN2A were also found to be involved in TP53-dependent cell cycle regulation. In conclusion, it was speculated that CDKN1A, CDKN2A, TP53, GADD45B and hsa-miR-300 may have regulatory relationships. It was demonstrated that there is a bidirectional regulation between hsa-miR-300 and TP53. In addition, miR-300 can regulate CDKN1A by GADD45B/TP53 and promote melanoma growth by accelerating the cell cycle transition from G1/S to G2 phase.
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Affiliation(s)
- Long Chen
- Department of Burn Plastic and Cosmetology, Affiliated Fuling Hospital, Chongqing University, Chongqing 408099, China
- College of Bioengineering, Chongqing University, Chongqing 400000, China
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu 610500, Sichuan, China
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu 610500, Sichuan, China
| | - Chenglong Fang
- Department of Rehabilitation, LinYi People’s Hospital, Linyi 276000, Shandong, China
| | - Xiaoxue Yuan
- College of Bioengineering, Chongqing University, Chongqing 400000, China
| | - Mengqi Liu
- College of Bioengineering, Chongqing University, Chongqing 400000, China
| | - Ping Wu
- Department of Burn Plastic and Cosmetology, Affiliated Fuling Hospital, Chongqing University, Chongqing 408099, China
| | - Li Zhong
- College of Bioengineering, Chongqing University, Chongqing 400000, China
| | - Zhiyong Chen
- Department of Burn Plastic and Cosmetology, Affiliated Fuling Hospital, Chongqing University, Chongqing 408099, China
- College of Bioengineering, Chongqing University, Chongqing 400000, China
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27
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Manicardi V, Gugnoni M, Sauta E, Donati B, Vitale E, Torricelli F, Manzotti G, Piana S, Longo C, Ghini F, Ciarrocchi A. Ex vivo mapping of enhancer networks that define the transcriptional program driving melanoma metastasis. Mol Oncol 2023; 17:2728-2742. [PMID: 37408506 DOI: 10.1002/1878-0261.13485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/20/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023] Open
Abstract
Mortality from vmelanoma is associated with metastatic disease, but the mechanisms leading to spreading of the cancer cells remain obscure. Spatial profiling revealed that melanoma is characterized by a high degree of heterogeneity, which is established by the ability of melanoma cells to switch between different phenotypical stages. This plasticity, likely a heritage from embryonic pathways, accounts for a relevant part of the metastatic potential of these lesions, and requires the rapid and efficient reorganization of the transcriptional landscape of melanoma cells. A large part of the non-coding genome cooperates to control gene expression, specifically through the activity of enhancers (ENHs). In this study, we aimed to identify ex vivo the network of active ENHs and to outline their cooperative interactions in supporting transcriptional adaptation during melanoma metastatic progression. We conducted a genome-wide analysis to map active ENHs distribution in a retrospective cohort of 39 melanoma patients, comparing the profiles obtained in primary (N = 19) and metastatic (N = 20) melanoma lesions. Unsupervised clustering showed that the profile for acetylated histone H3 at lysine 27 (H3K27ac) efficiently segregates lesions into three different clusters corresponding to progressive stages of the disease. We reconstructed the map of super-ENHs (SEs) and cooperative ENHs that associate with metastatic progression in melanoma, which showed that cooperation among regulatory elements is a mandatory requirement for transcriptional plasticity. We also showed that these elements carry out specialized and non-redundant functions, and indicated the existence of a hierarchical organization, with SEs on top as masterminds of the entire transcriptional program and classical ENHs as executors. By providing an innovative vision of how the chromatin landscape of melanoma works during metastatic spreading, our data also point out the need to integrate functional profiling in the analysis of cancer lesions to increase definition and improve interpretation of tumor heterogeneity.
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Affiliation(s)
- Veronica Manicardi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Italy
| | - Mila Gugnoni
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | | | - Benedetta Donati
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Emanuele Vitale
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Gloria Manzotti
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | | | - Caterina Longo
- Skin Cancer Unit, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Francesco Ghini
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
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28
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Dos Santos AF, Fazeli G, Xavier da Silva TN, Friedmann Angeli JP. Ferroptosis: mechanisms and implications for cancer development and therapy response. Trends Cell Biol 2023; 33:1062-1076. [PMID: 37230924 DOI: 10.1016/j.tcb.2023.04.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023]
Abstract
As cancer cells develop resistance to apoptosis, non-apoptotic cell death modalities, such as ferroptosis, have emerged as promising strategies to combat therapy-resistant cancers. Cells that develop resistance to conventional therapies or metastatic cancer cells have been shown to have increased sensitivity to ferroptosis. Therefore, targeting the regulatory elements of ferroptosis in cancer could offer novel therapeutic opportunities. In this review, we first provide an overview of the known ferroptosis regulatory networks and discuss recent findings on how they contribute to cancer plasticity. We then expand into the critical role of selenium metabolism in regulating ferroptosis. Finally, we highlight specific cases where induction of ferroptosis could be used to sensitize cancer cells to this form of cell death.
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Affiliation(s)
- Ancély Ferreira Dos Santos
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Chair of Translational Cell Biology, University of Würzburg, Würzburg, Germany
| | - Gholamreza Fazeli
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Chair of Translational Cell Biology, University of Würzburg, Würzburg, Germany
| | - Thamara Nishida Xavier da Silva
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Chair of Translational Cell Biology, University of Würzburg, Würzburg, Germany
| | - José Pedro Friedmann Angeli
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Chair of Translational Cell Biology, University of Würzburg, Würzburg, Germany.
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29
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Ferretti LP, Böhi F, Leslie Pedrioli DM, Cheng PF, Ferrari E, Baumgaertner P, Alvarado-Diaz A, Sella F, Cereghetti A, Turko P, Wright RH, De Bock K, Speiser DE, Ferrari R, Levesque MP, Hottiger MO. Combinatorial Treatment with PARP and MAPK Inhibitors Overcomes Phenotype Switch-Driven Drug Resistance in Advanced Melanoma. Cancer Res 2023; 83:3974-3988. [PMID: 37729428 DOI: 10.1158/0008-5472.can-23-0485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/07/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023]
Abstract
Metastatic melanoma is either intrinsically resistant or rapidly acquires resistance to targeted therapy treatments, such as MAPK inhibitors (MAPKi). A leading cause of resistance to targeted therapy is a dynamic transition of melanoma cells from a proliferative to a highly invasive state, a phenomenon called phenotype switching. Mechanisms regulating phenotype switching represent potential targets for improving treatment of patients with melanoma. Using a drug screen targeting chromatin regulators in patient-derived three-dimensional MAPKi-resistant melanoma cell cultures, we discovered that PARP inhibitors (PARPi) restore sensitivity to MAPKis, independent of DNA damage repair pathways. Integrated transcriptomic, proteomic, and epigenomic analyses demonstrated that PARPis induce lysosomal autophagic cell death, accompanied by enhanced mitochondrial lipid metabolism that ultimately increases antigen presentation and sensitivity to T-cell cytotoxicity. Moreover, transcriptomic and epigenetic rearrangements induced by PARP inhibition reversed epithelial-mesenchymal transition-like phenotype switching, which redirected melanoma cells toward a proliferative and MAPKi-sensitive state. The combination of PARP and MAPKis synergistically induced cancer cell death both in vitro and in vivo in patient-derived xenograft models. Therefore, this study provides a scientific rationale for treating patients with melanoma with PARPis in combination with MAPKis to abrogate acquired therapy resistance. SIGNIFICANCE PARP inhibitors can overcome resistance to MAPK inhibitors by activating autophagic cell death and reversing phenotype switching, suggesting that this synergistic combination could help improve the prognosis of patients with melanoma.
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Affiliation(s)
- Lorenza P Ferretti
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Flurina Böhi
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | | | - Phil F Cheng
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Elena Ferrari
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Petra Baumgaertner
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Abdiel Alvarado-Diaz
- Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach, Switzerland
| | - Federica Sella
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Alessandra Cereghetti
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Patrick Turko
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Roni H Wright
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Barcelona
| | - Katrien De Bock
- Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach, Switzerland
| | - Daniel E Speiser
- Department of Oncology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Roberto Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Mitchell P Levesque
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
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30
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Godoy PM, Oyedeji A, Mudd JL, Morikis VA, Zarov AP, Longmore GD, Fields RC, Kaufman CK. Functional analysis of recurrent CDC20 promoter variants in human melanoma. Commun Biol 2023; 6:1216. [PMID: 38030698 PMCID: PMC10686982 DOI: 10.1038/s42003-023-05526-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
Small nucleotide variants in non-coding regions of the genome can alter transcriptional regulation, leading to changes in gene expression which can activate oncogenic gene regulatory networks. Melanoma is heavily burdened by non-coding variants, representing over 99% of total genetic variation, including the well-characterized TERT promoter mutation. However, the compendium of regulatory non-coding variants is likely still functionally under-characterized. We developed a pipeline to identify hotspots, i.e. recurrently mutated regions, in melanoma containing putatively functional non-coding somatic variants that are located within predicted melanoma-specific regulatory regions. We identified hundreds of statistically significant hotspots, including the hotspot containing the TERT promoter variants, and focused on a hotspot in the promoter of CDC20. We found that variants in the promoter of CDC20, which putatively disrupt an ETS motif, lead to lower transcriptional activity in reporter assays. Using CRISPR/Cas9, we generated an indel in the CDC20 promoter in human A375 melanoma cell lines and observed decreased expression of CDC20, changes in migration capabilities, increased growth of xenografts, and an altered transcriptional state previously associated with a more proliferative and less migratory state. Overall, our analysis prioritized several recurrent functional non-coding variants that, through downregulation of CDC20, led to perturbation of key melanoma phenotypes.
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Affiliation(s)
- Paula M Godoy
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Abimbola Oyedeji
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
| | - Jacqueline L Mudd
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
| | - Vasilios A Morikis
- Departments of Medicine (Oncology) and Cell Biology and Physiology and the ICCE Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anna P Zarov
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gregory D Longmore
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
- Departments of Medicine (Oncology) and Cell Biology and Physiology and the ICCE Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ryan C Fields
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
| | - Charles K Kaufman
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA.
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31
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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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Khorsandi K, Esfahani H, Ghamsari SK, Lakhshehei P. Targeting ferroptosis in melanoma: cancer therapeutics. Cell Commun Signal 2023; 21:337. [PMID: 37996827 PMCID: PMC10666330 DOI: 10.1186/s12964-023-01296-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/25/2023] [Indexed: 11/25/2023] Open
Abstract
Melanoma is an aggressive kind of skin cancer; its rate has risen rapidly over the past few decades. Melanoma reports for only about 1% of skin cancers but leads to a high majority of skin cancer deaths. Thus, new useful therapeutic approaches are currently required, to state effective treatments to consistently enhance the overall survival rate of melanoma patients. Ferroptosis is a recently identified cell death process, which is different from autophagy, apoptosis, necrosis, and pyroptosis in terms of biochemistry, genetics, and morphology which plays an important role in cancer treatment. Ferroptosis happens mostly by accumulating iron and lipid peroxides in the cell. Recently, studies have revealed that ferroptosis has a key role in the tumor's progression. Especially, inducing ferroptosis in cells can inhibit the tumor cells' growth, leading to back warding tumorigenesis. Here, we outline the ferroptosis characteristics from its basic role in melanoma cancer and mention its possible applications in melanoma cancer treatment. Video Abstract.
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Affiliation(s)
- Khatereh Khorsandi
- Department of Photodynamics, Medical Laser Research Center, Yara Institute, ACECR, Tehran, Iran.
| | - HomaSadat Esfahani
- Department of Photodynamics, Medical Laser Research Center, Yara Institute, ACECR, Tehran, Iran
| | | | - Parisa Lakhshehei
- Department of Biochemistry, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
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33
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Ozen M, Lopez CF. Data-driven structural analysis of small cell lung cancer transcription factor network suggests potential subtype regulators and transition pathways. NPJ Syst Biol Appl 2023; 9:55. [PMID: 37907529 PMCID: PMC10618210 DOI: 10.1038/s41540-023-00316-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/12/2023] [Indexed: 11/02/2023] Open
Abstract
Small cell lung cancer (SCLC) is an aggressive disease and challenging to treat due to its mixture of transcriptional subtypes and subtype transitions. Transcription factor (TF) networks have been the focus of studies to identify SCLC subtype regulators via systems approaches. Yet, their structures, which can provide clues on subtype drivers and transitions, are barely investigated. Here, we analyze the structure of an SCLC TF network by using graph theory concepts and identify its structurally important components responsible for complex signal processing, called hubs. We show that the hubs of the network are regulators of different SCLC subtypes by analyzing first the unbiased network structure and then integrating RNA-seq data as weights assigned to each interaction. Data-driven analysis emphasizes MYC as a hub, consistent with recent reports. Furthermore, we hypothesize that the pathways connecting functionally distinct hubs may control subtype transitions and test this hypothesis via network simulations on a candidate pathway and observe subtype transition. Overall, structural analyses of complex networks can identify their functionally important components and pathways driving the network dynamics. Such analyses can be an initial step for generating hypotheses and can guide the discovery of target pathways whose perturbation may change the network dynamics phenotypically.
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Affiliation(s)
- Mustafa Ozen
- Dept. of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Multiscale Modeling Group, SI3, Altos Labs, Redwood City, CA, USA
| | - Carlos F Lopez
- Dept. of Biochemistry, Vanderbilt University, Nashville, TN, USA.
- Multiscale Modeling Group, SI3, Altos Labs, Redwood City, CA, USA.
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34
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Sun L, Kang X, Ju H, Wang C, Yang G, Wang R, Sun S. A human mucosal melanoma organoid platform for modeling tumor heterogeneity and exploring immunotherapy combination options. SCIENCE ADVANCES 2023; 9:eadg6686. [PMID: 37889972 PMCID: PMC10610903 DOI: 10.1126/sciadv.adg6686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023]
Abstract
Mucosal melanoma (MM), an aggressive rare subtype of melanoma, is distinct from cutaneous melanoma and has poor prognoses. We addressed the lack of cell models for MM by establishing 30 organoids of human oral MM (OMM), which retained major histopathological and functional features of parental tumors. Organoid groups derived from chronologically or intratumorally distinct lesions within the same individual displayed heterogeneous genetics, expression profiles, and drug responses, indicating rapid tumor evolution and poor clinical response. Furthermore, transcriptome analysis revealed receptor tyrosine kinases (RTKs) signaling, particularly NGFR, a nerve growth factor receptor, was significantly up-regulated in OMMs and organoids from patients resistant to anti-programmed cell death protein 1 (anti-PD-1) therapy. Combining anti-PD-1 with anlotinib (a phase 2 multitarget RTK inhibitor for OMM) or NGFR knockdown enhanced the effective activity of immune cells in organoid-immune cell coculture systems. Together, our study suggested that OMM organoids serve as faithful models for exploring tumor evolution and immunotherapy combination strategies.
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Affiliation(s)
- Lulu Sun
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
- Shanghai Research Institute of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai 200011, China
| | - Xindan Kang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
- Shanghai Research Institute of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai 200011, China
| | - Houyu Ju
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
- Shanghai Research Institute of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai 200011, China
| | - Chong Wang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
- Shanghai Research Institute of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai 200011, China
| | - Guizhu Yang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
- Shanghai Research Institute of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai 200011, China
| | - Rui Wang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
- Shanghai Research Institute of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai 200011, China
| | - Shuyang Sun
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
- Shanghai Research Institute of Stomatology, Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai 200011, China
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35
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Chen S, Zhou Z, Li Y, Du Y, Chen G. Application of single-cell sequencing to the research of tumor microenvironment. Front Immunol 2023; 14:1285540. [PMID: 37965341 PMCID: PMC10641410 DOI: 10.3389/fimmu.2023.1285540] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
Single-cell sequencing is a technique for detecting and analyzing genomes, transcriptomes, and epigenomes at the single-cell level, which can detect cellular heterogeneity lost in conventional sequencing hybrid samples, and it has revolutionized our understanding of the genetic heterogeneity and complexity of tumor progression. Moreover, the tumor microenvironment (TME) plays a crucial role in the formation, development and response to treatment of tumors. The application of single-cell sequencing has ushered in a new age for the TME analysis, revealing not only the blueprint of the pan-cancer immune microenvironment, but also the heterogeneity and differentiation routes of immune cells, as well as predicting tumor prognosis. Thus, the combination of single-cell sequencing and the TME analysis provides a unique opportunity to unravel the molecular mechanisms underlying tumor development and progression. In this review, we summarize the recent advances in single-cell sequencing and the TME analysis, highlighting their potential applications in cancer research and clinical translation.
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Affiliation(s)
| | | | | | | | - Guoan Chen
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China
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36
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Sahoo S, Ramu S, Nair MG, Pillai M, San Juan BP, Milioli HZ, Mandal S, Naidu CM, Mavatkar AD, Subramaniam H, Neogi AG, Chaffer CL, Prabhu JS, Somarelli JA, Jolly MK. Multi-modal transcriptomic analysis unravels enrichment of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.30.558960. [PMID: 37873432 PMCID: PMC10592858 DOI: 10.1101/2023.09.30.558960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Intra-tumoral phenotypic heterogeneity promotes tumor relapse and therapeutic resistance and remains an unsolved clinical challenge. It manifests along multiple phenotypic axes and decoding the interconnections among these different axes is crucial to understand its molecular origins and to develop novel therapeutic strategies to control it. Here, we use multi-modal transcriptomic data analysis - bulk, single-cell and spatial transcriptomics - from breast cancer cell lines and primary tumor samples, to identify associations between epithelial-mesenchymal transition (EMT) and luminal-basal plasticity - two key processes that enable heterogeneity. We show that luminal breast cancer strongly associates with an epithelial cell state, but basal breast cancer is associated with hybrid epithelial/mesenchymal phenotype(s) and higher phenotypic heterogeneity. These patterns were inherent in methylation profiles, suggesting an epigenetic crosstalk between EMT and lineage plasticity in breast cancer. Mathematical modelling of core underlying gene regulatory networks representative of the crosstalk between the luminal-basal and epithelial-mesenchymal axes recapitulate and thus elucidate mechanistic underpinnings of the observed associations from transcriptomic data. Our systems-based approach integrating multi-modal data analysis with mechanism-based modeling offers a predictive framework to characterize intra-tumor heterogeneity and to identify possible interventions to restrict it.
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Affiliation(s)
- Sarthak Sahoo
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Soundharya Ramu
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Madhumathy G Nair
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | - Maalavika Pillai
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
- Current affiliation: Feinberg School of Medicine, Northwestern University, Chicago, 60611, USA
| | - Beatriz P San Juan
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | | | - Susmita Mandal
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Chandrakala M Naidu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | - Apoorva D Mavatkar
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | - Harini Subramaniam
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Arpita G Neogi
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Christine L Chaffer
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- University of New South Wales, UNSW Medicine, UNSW Sydney, NSW, 2052, Australia
| | - Jyothi S Prabhu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | | | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
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37
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Shinzawa K, Matsumoto S, Sada R, Harada A, Saitoh K, Kato K, Ikeda S, Hirayama A, Yokoi K, Tanemura A, Nimura K, Ikawa M, Soga T, Kikuchi A. GREB1 isoform 4 is specifically transcribed by MITF and required for melanoma proliferation. Oncogene 2023; 42:3142-3156. [PMID: 37658191 PMCID: PMC10575781 DOI: 10.1038/s41388-023-02803-6] [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: 02/15/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
Growth regulation by estrogen in breast cancer 1 (GREB1) is involved in hormone-dependent and -independent tumor development (e.g., hepatoblastoma). In this study, we found that a GREB1 splicing variant, isoform 4 (Is4), which encodes C-terminal half of full-length GREB1, is specifically expressed via microphthalmia-associated transcription factor (MITF) in melanocytic melanoma, and that two MITF-binding E-box CANNTG motifs at the 5'-upstream region of GREB1 exon 19 are necessary for GREB1 Is4 transcription. MITF and GREB1 Is4 were strongly co-expressed in approximately 20% of the melanoma specimens evaluated (17/89 cases) and their expression was associated with tumor thickness. GREB1 Is4 silencing reduced melanoma cell proliferation in association with altered expression of cell proliferation-related genes in vitro. In addition, GREB1 Is4 targeting by antisense oligonucleotide (ASO) decreased melanoma xenograft tumor formation and GREB1 Is4 expression in a BRAFV600E; PTENflox melanoma mouse model promoted melanoma formation, demonstrating the crucial role of GREB1 Is4 for melanoma proliferation in vivo. GREB1 Is4 bound to CAD, the rate-limiting enzyme of pyrimidine metabolism, and metabolic flux analysis revealed that GREBI Is4 is necessary for pyrimidine synthesis. These results suggest that MITF-dependent GREB1 Is4 expression leads to melanoma proliferation and GREB1 Is4 represents a new molecular target in melanoma.
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Affiliation(s)
- Koei Shinzawa
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
| | - Shinji Matsumoto
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
| | - Ryota Sada
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
| | - Akikazu Harada
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
| | - Kaori Saitoh
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Keiko Kato
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Kazunori Yokoi
- Department of Dermatology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Atsushi Tanemura
- Department of Dermatology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Keisuke Nimura
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Gunma University Initiative for Advanced Research, Gunma University, Maebashi, Gunma, Japan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Akira Kikuchi
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan.
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38
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Hartman ML, Koziej P, Kluszczyńska K, Czyz M. Pro-Apoptotic Activity of MCL-1 Inhibitor in Trametinib-Resistant Melanoma Cells Depends on Their Phenotypes and Is Modulated by Reversible Alterations Induced by Trametinib Withdrawal. Cancers (Basel) 2023; 15:4799. [PMID: 37835493 PMCID: PMC10571954 DOI: 10.3390/cancers15194799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Although BRAFV600/MEK inhibitors improved the treatment of melanoma patients, resistance is acquired almost inevitably. METHODS Trametinib withdrawal/rechallenge and MCL-1 inhibition in trametinib-resistance models displaying distinct p-ERK1/2 levels were investigated. RESULTS Trametinib withdrawal/rechallenge caused reversible changes in ERK1/2 activity impacting the balance between pro-survival and pro-apoptotic proteins. Reversible alterations were found in MCL-1 levels and MCL-1 inhibitors, BIM and NOXA. Taking advantage of melanoma cell dependency on MCL-1 for survival, we used S63845. While it was designed to inhibit MCL-1 activity, we showed that it also significantly reduced NOXA levels. S63845-induced apoptosis was detected as the enhancement of Annexin V-positivity, caspase-3/7 activation and histone H2AX phosphorylation. Percentages of Annexin V-positive cells were increased most efficiently in trametinib-resistant melanoma cells displaying the p-ERK1/2low/MCL-1low/BIMhigh/NOXAlow phenotype with EC50 values at concentrations as low as 0.1 μM. Higher ERK1/2 activity associated with increased MCL-1 level and reduced BIM level limited pro-apoptotic activity of S63845 further influenced by a NOXA level. CONCLUSIONS Our study supports the notion that the efficiency of an agent designed to target a single protein can largely depend on the phenotype of cancer cells. Thus, it is important to define appropriate phenotype determinants to stratify the patients for the novel therapy.
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Affiliation(s)
| | | | | | - Małgorzata Czyz
- Department of Molecular Biology of Cancer, Medical University of Lodz, 92-215 Lodz, Poland; (M.L.H.); (P.K.); (K.K.)
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Louphrasitthiphol P, Loffreda A, Pogenberg V, Picaud S, Schepsky A, Friedrichsen H, Zeng Z, Lashgari A, Thomas B, Patton EE, Wilmanns M, Filippakopoulos P, Lambert JP, Steingrímsson E, Mazza D, Goding CR. Acetylation reprograms MITF target selectivity and residence time. Nat Commun 2023; 14:6051. [PMID: 37770430 PMCID: PMC10539308 DOI: 10.1038/s41467-023-41793-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 09/08/2023] [Indexed: 09/30/2023] Open
Abstract
The ability of transcription factors to discriminate between different classes of binding sites associated with specific biological functions underpins effective gene regulation in development and homeostasis. How this is achieved is poorly understood. The microphthalmia-associated transcription factor MITF is a lineage-survival oncogene that plays a crucial role in melanocyte development and melanoma. MITF suppresses invasion, reprograms metabolism and promotes both proliferation and differentiation. How MITF distinguishes between differentiation and proliferation-associated targets is unknown. Here we show that compared to many transcription factors MITF exhibits a very long residence time which is reduced by p300/CBP-mediated MITF acetylation at K206. While K206 acetylation also decreases genome-wide MITF DNA-binding affinity, it preferentially directs DNA binding away from differentiation-associated CATGTG motifs toward CACGTG elements. The results reveal an acetylation-mediated switch that suppresses differentiation and provides a mechanistic explanation of why a human K206Q MITF mutation is associated with Waardenburg syndrome.
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Affiliation(s)
- Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Alessia Loffreda
- Experimental Imaging Center, Ospedale San Raffaele, Milano, Italy
| | - Vivian Pogenberg
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
- Institute of Biochemistry and Signal Transduction, University Hamburg Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
| | - Alexander Schepsky
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Hans Friedrichsen
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
| | - Zhiqiang Zeng
- MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Edinburgh Cancer Research Centre, Edinburgh, UK
| | - Anahita Lashgari
- Department of Molecular Medicine and Cancer Research Center, Université Laval, Quebec, Canada; Endocrinology - Nephrology Axis, CHU de Québec - Université Laval Research Center, Quebec City, QC, Canada
| | - Benjamin Thomas
- Central Proteomics Facility, Sir William Dunn Pathology School, University of Oxford, Oxford, UK
| | - E Elizabeth Patton
- MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Edinburgh Cancer Research Centre, Edinburgh, UK
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
- University Hamburg Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Center, Université Laval, Quebec, Canada; Endocrinology - Nephrology Axis, CHU de Québec - Université Laval Research Center, Quebec City, QC, Canada
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Davide Mazza
- Experimental Imaging Center, Ospedale San Raffaele, Milano, Italy
- Università Vita-Salulte San Raffaele, Milano, Italy
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, UK.
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40
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Kuras M. Exploring the Complex and Multifaceted Interplay between Melanoma Cells and the Tumor Microenvironment. Int J Mol Sci 2023; 24:14403. [PMID: 37762707 PMCID: PMC10531837 DOI: 10.3390/ijms241814403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
Malignant melanoma is a very aggressive skin cancer, characterized by a heterogeneous nature and high metastatic potential. The incidence of melanoma is continuously increasing worldwide, and it is one of the most common cancers in young adults. In the past twenty years, our understanding of melanoma biology has increased profoundly, and disease management for patients with disseminated disease has improved due to the emergence of immunotherapy and targeted therapy. However, a significant fraction of patients relapse or do not respond adequately to treatment. This can partly be explained by the complex signaling between the tumor and its microenvironment, giving rise to melanoma phenotypes with different patterns of disease progression. This review focuses on the key aspects and complex relationship between pathogenesis, genetic abnormalities, tumor microenvironment, cellular plasticity, and metabolic reprogramming in melanoma. By acquiring a deeper understanding of the multifaceted features of melanomagenesis, we can reach a point of more individualized and patient-centered disease management and reduced costs of ineffective treatments.
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Affiliation(s)
- Magdalena Kuras
- Department of Biomedical Engineering, Lund University, 221 00 Lund, Sweden;
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden
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41
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Giraulo C, Turiello R, Orlando L, Leonardelli S, Landsberg J, Belvedere R, Rolshoven G, Müller CE, Hölzel M, Morello S. The CD73 is induced by TGF-β1 triggered by nutrient deprivation and highly expressed in dedifferentiated human melanoma. Biomed Pharmacother 2023; 165:115225. [PMID: 37517292 DOI: 10.1016/j.biopha.2023.115225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/18/2023] [Accepted: 07/23/2023] [Indexed: 08/01/2023] Open
Abstract
CD73 is the key enzyme in the generation of extracellular adenosine, a mediator involved in tumor progression, tumor immune escape and resistance to anti-cancer therapeutics. Microenvironmental conditions influence the expression of CD73 in tumor cells. However how CD73 expression and activity is regulated in a stress condition of lower nutrient availability are largely unknown. Our results indicate that serum starvation leads to a marked up-regulation of CD73 expression on A375 melanoma cells in a time-dependent manner. The cell-surface expression of CD73 is associated with an increased release of TGF-β1 by starved cells. Blockade of TGF-β1 receptors or TGFβ/SMAD3 signaling pathway significantly reduce the expression of CD73 induced by starvation. Treatment of cells with rTGF-β1 up-regulates the expression of CD73 in a concentration-dependent manner, confirming the role of this pathway in regulating CD73 in melanoma A375 cells. The increased expression of CD73 is associated with enhanced AMPase activity, which is selectively reduced by inhibitors of CD73 activity, APCP and PSB-12489. Pharmacological blockade of CD73 significantly inhibits invasion of melanoma cells in a transwell system. Furthermore, using multiplex immunofluorescence imaging we found that, within human melanoma metastases, tumor cells at the dedifferentiated stage show the highest CD73 protein expression. In summary, our data provide new insights into the mechanism regulating the expression/activity of CD73 in melanoma cells in a condition of lower availability of nutrients, which is a common feature of the tumor microenvironment. Within human metastatic melanoma tissues elevated protein expression of CD73 is associated with an invasive-like phenotype.
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Affiliation(s)
- Caterina Giraulo
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy
| | - Roberta Turiello
- Institute of Experimental Oncology, University Hospital Bonn (UKB), University of Bonn, Bonn, Germany
| | - Lavinia Orlando
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Fisciano, Italy
| | - Sonia Leonardelli
- Institute of Experimental Oncology, University Hospital Bonn (UKB), University of Bonn, Bonn, Germany
| | - Jennifer Landsberg
- Laboratory of Experimental Dermatology, Department of Dermatology and Allergy, University of Bonn, Bonn, Germany
| | | | - Georg Rolshoven
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Michael Hölzel
- Institute of Experimental Oncology, University Hospital Bonn (UKB), University of Bonn, Bonn, Germany
| | - Silvana Morello
- Department of Pharmacy, University of Salerno, Fisciano, SA, Italy.
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42
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Castellani G, Buccarelli M, Arasi MB, Rossi S, Pisanu ME, Bellenghi M, Lintas C, Tabolacci C. BRAF Mutations in Melanoma: Biological Aspects, Therapeutic Implications, and Circulating Biomarkers. Cancers (Basel) 2023; 15:4026. [PMID: 37627054 PMCID: PMC10452867 DOI: 10.3390/cancers15164026] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Melanoma is an aggressive form of skin cancer resulting from the malignant transformation of melanocytes. Recent therapeutic approaches, including targeted therapy and immunotherapy, have improved the prognosis and outcome of melanoma patients. BRAF is one of the most frequently mutated oncogenes recognised in melanoma. The most frequent oncogenic BRAF mutations consist of a single point mutation at codon 600 (mostly V600E) that leads to constitutive activation of the BRAF/MEK/ERK (MAPK) signalling pathway. Therefore, mutated BRAF has become a useful target for molecular therapy and the use of BRAF kinase inhibitors has shown promising results. However, several resistance mechanisms invariably develop leading to therapeutic failure. The aim of this manuscript is to review the role of BRAF mutational status in the pathogenesis of melanoma and its impact on differentiation and inflammation. Moreover, this review focuses on the mechanisms responsible for resistance to targeted therapies in BRAF-mutated melanoma and provides an overview of circulating biomarkers including circulating tumour cells, circulating tumour DNA, and non-coding RNAs.
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Affiliation(s)
- Giorgia Castellani
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.C.); (M.B.); (M.B.A.); (S.R.)
| | - Mariachiara Buccarelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.C.); (M.B.); (M.B.A.); (S.R.)
| | - Maria Beatrice Arasi
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.C.); (M.B.); (M.B.A.); (S.R.)
| | - Stefania Rossi
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.C.); (M.B.); (M.B.A.); (S.R.)
| | - Maria Elena Pisanu
- High Resolution NMR Unit, Core Facilities, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Maria Bellenghi
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Carla Lintas
- Research Unit of Medical Genetics, Department of Medicine, Università Campus Bio-Medico di Roma, 00128 Rome, Italy;
- Operative Research Unit of Medical Genetics, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy
| | - Claudio Tabolacci
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.C.); (M.B.); (M.B.A.); (S.R.)
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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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44
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Ning W, Wu T, Wu C, Wang S, Tao Z, Wang G, Zhao X, Diao K, Wang J, Chen J, Chen F, Liu XS. Accurate prediction of pan-cancer types using machine learning with minimal number of DNA methylation sites. J Mol Cell Biol 2023; 15:mjad023. [PMID: 37037781 PMCID: PMC10635511 DOI: 10.1093/jmcb/mjad023] [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: 08/13/2022] [Revised: 02/08/2023] [Accepted: 04/07/2023] [Indexed: 04/12/2023] Open
Abstract
DNA methylation analysis has been applied to determine the primary site of cancer; however, robust and accurate prediction of cancer types with a minimum number of sites is still a significant scientific challenge. To build an accurate and robust cancer type prediction tool with a minimum number of DNA methylation sites, we internally benchmarked different DNA methylation site selection and ranking procedures, as well as different classification models. We used The Cancer Genome Atlas dataset (26 cancer types with 8296 samples) to train and test models and used an independent dataset (17 cancer types with 2738 samples) for model validation. A deep neural network model using a combined feature selection procedure (named MethyDeep) can predict 26 cancer types using 30 methylation sites with superior performance compared with the known methods for both primary and metastatic cancers in independent validation datasets. In conclusion, MethyDeep is an accurate and robust cancer type predictor with the minimum number of DNA methylation sites; it could help the cost-effective clarification of cancer of unknown primary patients and the liquid biopsy-based early screening of cancers.
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Affiliation(s)
- Wei Ning
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Chenxu Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Shixiang Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Ziyu Tao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Guangshuai Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Xiangyu Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Kaixuan Diao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Jinyu Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Jing Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Fuxiang Chen
- Department of Clinical Immunology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Xue-Song Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
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45
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Liang J, Yu D, Luo C, Bennett C, Jedrychowski M, Gygi SP, Widlund HR, Puigserver P. Epigenetic suppression of PGC1α (PPARGC1A) causes collateral sensitivity to HMGCR-inhibitors within BRAF-treatment resistant melanomas. Nat Commun 2023; 14:3251. [PMID: 37277330 PMCID: PMC10241879 DOI: 10.1038/s41467-023-38968-7] [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: 04/09/2022] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
While targeted treatment against BRAF(V600E) improve survival for melanoma patients, many will see their cancer recur. Here we provide data indicating that epigenetic suppression of PGC1α defines an aggressive subset of chronic BRAF-inhibitor treated melanomas. A metabolism-centered pharmacological screen further identifies statins (HMGCR inhibitors) as a collateral vulnerability within PGC1α-suppressed BRAF-inhibitor resistant melanomas. Lower PGC1α levels mechanistically causes reduced RAB6B and RAB27A expression, whereby their combined re-expression reverses statin vulnerability. BRAF-inhibitor resistant cells with reduced PGC1α have increased integrin-FAK signaling and improved extracellular matrix detached survival cues that helps explain their increased metastatic ability. Statin treatment blocks cell growth by lowering RAB6B and RAB27A prenylation that reduces their membrane association and affects integrin localization and downstream signaling required for growth. These results suggest that chronic adaptation to BRAF-targeted treatments drive novel collateral metabolic vulnerabilities, and that HMGCR inhibitors may offer a strategy to treat melanomas recurring with suppressed PGC1α expression.
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Affiliation(s)
- Jiaxin Liang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Deyang Yu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Chi Luo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Parthenon Therapeutics, Boston, MA, 02135, USA
| | - Christopher Bennett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Atavistik Bio, Cambridge, MA, 02139, USA
| | - Mark Jedrychowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steve P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Hans R Widlund
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Pere Puigserver
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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46
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Lumaquin-Yin D, Montal E, Johns E, Baggiolini A, Huang TH, Ma Y, LaPlante C, Suresh S, Studer L, White RM. Lipid droplets are a metabolic vulnerability in melanoma. Nat Commun 2023; 14:3192. [PMID: 37268606 PMCID: PMC10238408 DOI: 10.1038/s41467-023-38831-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/17/2023] [Indexed: 06/04/2023] Open
Abstract
Melanoma exhibits numerous transcriptional cell states including neural crest-like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here, we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets, the specialized organelle responsible for lipid storage. Single-cell RNA-sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake, an increased number of lipid droplets, and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients, these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle.
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Affiliation(s)
- Dianne Lumaquin-Yin
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, NY, 10065, USA
| | - Emily Montal
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Eleanor Johns
- Department of Cancer Biology and Genetics, 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
| | - Ting-Hsiang Huang
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yilun Ma
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, NY, 10065, USA
| | - Charlotte LaPlante
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, NY, 10065, USA
| | - Shruthy Suresh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Lorenz Studer
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Richard M White
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- University of Oxford, Ludwig Cancer Research, Nuffield Department of Medicine, Oxford, UK.
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47
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Biddle A. In vitro cancer models as an approach to identify targetable developmental phenotypes in cancer stem cells. IN VITRO MODELS 2023; 2:83-88. [PMID: 37808201 PMCID: PMC10550853 DOI: 10.1007/s44164-023-00051-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 10/10/2023]
Abstract
Cancer therapeutics are often highly toxic to the patient, and they often elicit rapid resistance in the tumour. Recent advances have suggested a potential new way in which we may improve on this, through two important concepts: (1) that multitudinous pathway alterations converge on a limited number of cancer cellular phenotypes, and (2) that these cancer cellular phenotypes depend on reactivation of developmental processes that are only minimally active in adult tissues. This provides a rationale for pursuing an approach of 'drugging the phenotype' focussed on targeting reactivated cellular processes from embryonic development. In this concepts paper, we cover these recent developments and their implications for the development of new cancer therapeutics that can avoid patient toxicity and acquired resistance. We then propose that in vitro tumour and developmental models can provide an experimental approach to identify and target the specific developmental processes at play, with a focus on the reactivation of developmental processes in the cancer stem cells that drive tumour progression and spread. Ultimately, the aim is to identify cellular processes that are specific to developmental phenotypes, are reactivated in cancer stem cells, and are essential to tumour progression. Therapeutically targeting these cellular processes could represent a new approach of 'drugging the phenotype' that treats the tumour whilst avoiding patient toxicity or the acquisition of therapeutic resistance.
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Affiliation(s)
- Adrian Biddle
- Blizard Institute, Queen Mary University of London, London, UK
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Neuendorf HM, Simmons JL, Boyle GM. Therapeutic targeting of anoikis resistance in cutaneous melanoma metastasis. Front Cell Dev Biol 2023; 11:1183328. [PMID: 37181747 PMCID: PMC10169659 DOI: 10.3389/fcell.2023.1183328] [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: 03/10/2023] [Accepted: 04/14/2023] [Indexed: 05/16/2023] Open
Abstract
The acquisition of resistance to anoikis, the cell death induced by loss of adhesion to the extracellular matrix, is an absolute requirement for the survival of disseminating and circulating tumour cells (CTCs), and for the seeding of metastatic lesions. In melanoma, a range of intracellular signalling cascades have been identified as potential drivers of anoikis resistance, however a full understanding of the process is yet to be attained. Mechanisms of anoikis resistance pose an attractive target for the therapeutic treatment of disseminating and circulating melanoma cells. This review explores the range of small molecule, peptide and antibody inhibitors targeting molecules involved in anoikis resistance in melanoma, and may be repurposed to prevent metastatic melanoma prior to its initiation, potentially improving the prognosis for patients.
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Affiliation(s)
- Hannah M. Neuendorf
- Cancer Drug Mechanisms Group, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jacinta L. Simmons
- Cancer Drug Mechanisms Group, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Glen M. Boyle
- Cancer Drug Mechanisms Group, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
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Howell R, Davies J, Clarke MA, Appios A, Mesquita I, Jayal Y, Ringham-Terry B, Boned Del Rio I, Fisher J, Bennett CL. Localized immune surveillance of primary melanoma in the skin deciphered through executable modeling. SCIENCE ADVANCES 2023; 9:eadd1992. [PMID: 37043573 PMCID: PMC10096595 DOI: 10.1126/sciadv.add1992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
While skin is a site of active immune surveillance, primary melanomas often escape detection. Here, we have developed an in silico model to determine the local cross-talk between melanomas and Langerhans cells (LCs), the primary antigen-presenting cells at the site of melanoma development. The model predicts that melanomas fail to activate LC migration to lymph nodes until tumors reach a critical size, which is determined by a positive TNF-α feedback loop within melanomas, in line with our observations of murine tumors. In silico drug screening, supported by subsequent experimental testing, shows that treatment of primary tumors with MAPK pathway inhibitors may further prevent LC migration. In addition, our in silico model predicts treatment combinations that bypass LC dysfunction. In conclusion, our combined approach of in silico and in vivo studies suggests a molecular mechanism that explains how early melanomas develop under the radar of immune surveillance by LC.
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Affiliation(s)
| | | | - Matthew A. Clarke
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Anna Appios
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Inês Mesquita
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Yashoda Jayal
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Ben Ringham-Terry
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Isabel Boned Del Rio
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
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Ozen M, Lopez CF. Data-driven structural analysis of Small Cell Lung Cancer transcription factor network suggests potential subtype regulators and transition pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.01.535226. [PMID: 37066351 PMCID: PMC10104011 DOI: 10.1101/2023.04.01.535226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Small Cell Lung Cancer (SCLC) is an aggressive disease and challenging to treat due to its mixture of transcriptional subtypes and subtype transitions. Transcription factor (TF) networks have been the focus of studies to identify SCLC subtype regulators via systems approaches. Yet, their structures, which can provide clues on subtype drivers and transitions, are barely investigated. Here, we analyze the structure of an SCLC TF network by using graph theory concepts and identify its structurally important components responsible for complex signal processing, called hubs. We show that the hubs of the network are regulators of different SCLC subtypes by analyzing first the unbiased network structure and then integrating RNA-seq data as weights assigned to each interaction. Data-driven analysis emphasizes MYC as a hub, consistent with recent reports. Furthermore, we hypothesize that the pathways connecting functionally distinct hubs may control subtype transitions and test this hypothesis via network simulations on a candidate pathway and observe subtype transition. Overall, structural analyses of complex networks can identify their functionally important components and pathways driving the network dynamics. Such analyses can be an initial step for generating hypotheses and can guide the discovery of target pathways whose perturbation may change the network dynamics phenotypically.
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Affiliation(s)
- Mustafa Ozen
- Dept. of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA
- Currently at: Computational Innovation Hub, Multiscale Modeling Group, Altos Labs, Redwood City, CA 94065, USA
| | - Carlos F. Lopez
- Dept. of Biochemistry, Vanderbilt University, Nashville, TN 37212, USA
- Currently at: Computational Innovation Hub, Multiscale Modeling Group, Altos Labs, Redwood City, CA 94065, USA
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