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Zhu Y, Koleilat MKI, Roszik J, Kwong MK, Wang Z, Maru DM, Kopetz S, Kwong LN. A Gold Standard-Derived Modular Barcoding Approach to Cancer Transcriptomics. Cancers (Basel) 2024; 16:1886. [PMID: 38791964 PMCID: PMC11120226 DOI: 10.3390/cancers16101886] [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: 03/01/2024] [Revised: 04/22/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
A challenge with studying cancer transcriptomes is in distilling the wealth of information down into manageable portions of information. In this resource, we develop an approach that creates and assembles cancer type-specific gene expression modules into flexible barcodes, allowing for adaptation to a wide variety of uses. Specifically, we propose that modules derived organically from high-quality gold standards such as The Cancer Genome Atlas (TCGA) can accurately capture and describe functionally related genes that are relevant to specific cancer types. We show that such modules can: (1) uncover novel gene relationships and nominate new functional memberships, (2) improve and speed up analysis of smaller or lower-resolution datasets, (3) re-create and expand known cancer subtyping schemes, (4) act as a "decoder" to bridge seemingly disparate established gene signatures, and (5) efficiently apply single-cell RNA sequencing information to other datasets. Moreover, such modules can be used in conjunction with native spreadsheet program commands to create a powerful and rapid approach to hypothesis generation and testing that is readily accessible to non-bioinformaticians. Finally, we provide tools for users to create and interpret their own modules. Overall, the flexible modular nature of the proposed barcoding provides a user-friendly approach to rapidly decoding transcriptome-wide data for research or, potentially, clinical uses.
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Affiliation(s)
- Yan Zhu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
| | - Mohamad Karim I. Koleilat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Man Kam Kwong
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China;
| | - Zhonglin Wang
- Social Science Research Institute, Duke University, Durham, NC 27708, USA;
| | - Dipen M. Maru
- Department of Anatomical Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Lawrence N. Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.Z.); (M.K.I.K.)
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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2
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Fateeva A, Eddy K, Chen S. Current State of Melanoma Therapy and Next Steps: Battling Therapeutic Resistance. Cancers (Basel) 2024; 16:1571. [PMID: 38672652 PMCID: PMC11049326 DOI: 10.3390/cancers16081571] [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: 03/05/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Melanoma is the most aggressive and deadly form of skin cancer due to its high propensity to metastasize to distant organs. Significant progress has been made in the last few decades in melanoma therapeutics, most notably in targeted therapy and immunotherapy. These approaches have greatly improved treatment response outcomes; however, they remain limited in their abilities to hinder disease progression due, in part, to the onset of acquired resistance. In parallel, intrinsic resistance to therapy remains an issue to be resolved. In this review, we summarize currently available therapeutic options for melanoma treatment and focus on possible mechanisms that drive therapeutic resistance. A better understanding of therapy resistance will provide improved rational strategies to overcome these obstacles.
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Affiliation(s)
- Anna Fateeva
- Susan Lehman Cullman Laboratory for Cancer Research, Rutgers University, Piscataway, NJ 08854, USA; (A.F.); (K.E.)
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, NJ 08854, USA
| | - Kevinn Eddy
- Susan Lehman Cullman Laboratory for Cancer Research, Rutgers University, Piscataway, NJ 08854, USA; (A.F.); (K.E.)
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, NJ 08854, USA
| | - Suzie Chen
- Susan Lehman Cullman Laboratory for Cancer Research, Rutgers University, Piscataway, NJ 08854, USA; (A.F.); (K.E.)
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
- U.S. Department of Veterans Affairs, New Jersey Health Care System, East Orange, NJ 07018, USA
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3
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Liguoro D, Frigerio R, Ortolano A, Sacconi A, Acunzo M, Romano G, Nigita G, Bellei B, Madonna G, Capone M, Ascierto PA, Mancini R, Ciliberto G, Fattore L. The MITF/mir-579-3p regulatory axis dictates BRAF-mutated melanoma cell fate in response to MAPK inhibitors. Cell Death Dis 2024; 15:208. [PMID: 38472212 DOI: 10.1038/s41419-024-06580-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024]
Abstract
Therapy of melanoma has improved dramatically over the last years thanks to the development of targeted therapies (MAPKi) and immunotherapies. However, drug resistance continues to limit the efficacy of these therapies. Our research group has provided robust evidence as to the involvement of a set of microRNAs in the development of resistance to target therapy in BRAF-mutated melanomas. Among them, a pivotal role is played by the oncosuppressor miR-579-3p. Here we show that miR-579-3p and the microphthalmia-associated transcription factor (MITF) influence reciprocally their expression through positive feedback regulatory loops. In particular we show that miR-579-3p is specifically deregulated in BRAF-mutant melanomas and that its expression levels mirror those of MITF. Luciferase and ChIP studies show that MITF is a positive regulator of miR-579-3p, which is located in the intron 11 of the human gene ZFR (Zink-finger recombinase) and is co-transcribed with its host gene. Moreover, miR-579-3p, by targeting BRAF, is able to stabilize MITF protein thus inducing its own transcription. From biological points of view, early exposure to MAPKi or, alternatively miR-579-3p transfection, induce block of proliferation and trigger senescence programs in BRAF-mutant melanoma cells. Finally, the long-term development of resistance to MAPKi is able to select cells characterized by the loss of both miR-579-3p and MITF and the same down-regulation is also present in patients relapsing after treatments. Altogether these findings suggest that miR-579-3p/MITF interplay potentially governs the balance between proliferation, senescence and resistance to therapies in BRAF-mutant melanomas.
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Affiliation(s)
- Domenico Liguoro
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Rachele Frigerio
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, 88100, Catanzaro, Italy
| | - Arianna Ortolano
- Department of Anatomy, Histology, Forensic- Medicine and Orthopedics, Sapienza University of Rome, 00161, Rome, Italy
| | - Andrea Sacconi
- Clinical Trial Center, Biostatistics and Bioinformatics Unit, IRCCS Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Mario Acunzo
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Giulia Romano
- Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Barbara Bellei
- Laboratory of Cutaneous Physiopathology, San Gallicano Dermatological Institute, IRCCS, 00144, Rome, Italy
| | - Gabriele Madonna
- Unit of Melanoma, Cancer Immunotherapy and Development Therapeutics, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, 80131, Naples, Italy
| | - Mariaelena Capone
- Unit of Melanoma, Cancer Immunotherapy and Development Therapeutics, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, 80131, Naples, Italy
| | - Paolo Antonio Ascierto
- Unit of Melanoma, Cancer Immunotherapy and Development Therapeutics, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, 80131, Naples, Italy
| | - Rita Mancini
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, 00161, Rome, Italy
- Faculty of Medicine and Psychology, Department Clinical and Molecular Medicine, Sant'Andrea Hospital-Sapienza University of Rome, 00118, Rome, Italy
| | - Gennaro Ciliberto
- Scientific Directorate, IRCSS Regina Elena National Cancer Institute, 00144, Rome, Italy.
| | - Luigi Fattore
- SAFU Laboratory, Department of Research, Advanced Diagnostics and Technological Innovation, Translational Research Area, IRCCS Regina Elena National Cancer Institute, 00144, Rome, Italy
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4
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Muraro E, Montico B, Lum B, Colizzi F, Giurato G, Salvati A, Guerrieri R, Rizzo A, Comaro E, Canzonieri V, Anichini A, Del Vecchio M, Mortarini R, Milione M, Weisz A, Pizzichetta MA, Simpson F, Dolcetti R, Fratta E, Sigalotti L. Antibody dependent cellular cytotoxicity-inducing anti-EGFR antibodies as effective therapeutic option for cutaneous melanoma resistant to BRAF inhibitors. Front Immunol 2024; 15:1336566. [PMID: 38510242 PMCID: PMC10950948 DOI: 10.3389/fimmu.2024.1336566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction About 50% of cutaneous melanoma (CM) patients present activating BRAF mutations that can be effectively targeted by BRAF inhibitors (BRAFi). However, 20% of CM patients exhibit intrinsic drug resistance to BRAFi, while most of the others develop adaptive resistance over time. The mechanisms involved in BRAFi resistance are disparate and globally seem to rewire the cellular signaling profile by up-regulating different receptor tyrosine kinases (RTKs), such as the epidermal growth factor receptor (EGFR). RTKs inhibitors have not clearly demonstrated anti-tumor activity in BRAFi resistant models. To overcome this issue, we wondered whether the shared up-regulated RTK phenotype associated with BRAFi resistance could be exploited by using immune weapons as the antibody-dependent cell cytotoxicity (ADCC)-mediated effect of anti-RTKs antibodies, and kill tumor cells independently from the mechanistic roots. Methods and results By using an in vitro model of BRAFi resistance, we detected increased membrane expression of EGFR, both at mRNA and protein level in 4 out of 9 BRAFi-resistant (VR) CM cultures as compared to their parental sensitive cells. Increased EGFR phosphorylation and AKT activation were observed in the VR CM cultures. EGFR signaling appeared dispensable for maintaining resistance, since small molecule-, antibody- and CRISPR-targeting of EGFR did not restore sensitivity of VR cells to BRAFi. Importantly, immune-targeting of EGFR by the anti-EGFR antibody cetuximab efficiently and specifically killed EGFR-expressing VR CM cells, both in vitro and in humanized mouse models in vivo, triggering ADCC by healthy donors' and patients' peripheral blood cells. Conclusion Our data demonstrate the efficacy of immune targeting of RTKs expressed by CM relapsing on BRAFi, providing the proof-of-concept supporting the assessment of anti-RTK antibodies in combination therapies in this setting. This strategy might be expected to concomitantly trigger the crosstalk of adaptive immune response leading to a complementing T cell immune rejection of tumors.
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Affiliation(s)
- Elena Muraro
- Immunopathology and Cancer Biomarkers, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Barbara Montico
- Immunopathology and Cancer Biomarkers, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Benedict Lum
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Francesca Colizzi
- Immunopathology and Cancer Biomarkers, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
- Genome Research Center for Health - CRGS, Baronissi, Italy
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
- Genome Research Center for Health - CRGS, Baronissi, Italy
- Molecular Pathology and Medical Genomics Program, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' University of Salerno and Rete Oncologica Campana, Salerno, Italy
| | - Roberto Guerrieri
- Immunopathology and Cancer Biomarkers, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Aurora Rizzo
- Immunopathology and Cancer Biomarkers, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Elisa Comaro
- Immunopathology and Cancer Biomarkers, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Vincenzo Canzonieri
- Division of Pathology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Andrea Anichini
- Human Tumors Immunobiology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Michele Del Vecchio
- Melanoma Unit, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Roberta Mortarini
- Human Tumors Immunobiology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Massimo Milione
- Pathology Unit 1, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, Italy
- Genome Research Center for Health - CRGS, Baronissi, Italy
- Molecular Pathology and Medical Genomics Program, AOU 'S. Giovanni di Dio e Ruggi d'Aragona' University of Salerno and Rete Oncologica Campana, Salerno, Italy
| | - Maria Antonietta Pizzichetta
- Division of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
- Department of Dermatology, University of Trieste, Trieste, Italy
| | - Fiona Simpson
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Riccardo Dolcetti
- Translational and Clinical Immunotherapy, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Elisabetta Fratta
- Immunopathology and Cancer Biomarkers, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Luca Sigalotti
- Oncogenetics and Functional Oncogenomics Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
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5
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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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6
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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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7
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Han S, Zhang M, Qu X, Wu Z, Huang Z, Hu Y, Li Y, Cui L, Si L, Liu J, Shao Y. SOX10 deficiency-mediated LAMB3 upregulation determines the invasiveness of MAPKi-resistant melanoma. Oncogene 2024; 43:434-446. [PMID: 38102338 DOI: 10.1038/s41388-023-02917-x] [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: 03/06/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]
Abstract
Melanoma that develops adaptive resistance to MAPK inhibitors (MAPKi) through transcriptional reprograming-mediated phenotype switching is associated with enhanced metastatic potential, yet the underlying mechanism of this improved invasiveness has not been fully elucidated. In this study, we show that MAPKi-resistant melanoma cells are more motile and invasive than the parental cells. We further show that LAMB3, a β subunit of the extracellular matrix protein laminin-332 is upregulated in MAPKi-resistant melanoma cells and that the LAMB3-Integrin α3/α6 signaling mediates the motile and invasive phenotype of resistant cells. In addition, we demonstrate that SOX10 deficiency in MAPKi-resistant melanoma cells drives LAMB3 upregulation through TGF-β signaling. Transcriptome profiling and functional studies further reveal a FAK/MMPs axis mediates the pro-invasiveness effect of LAMB3. Using a mouse lung metastasis model, we demonstrate LAMB3 depletion inhibits the metastatic potential of MAPKi-resistant cells in vivo. In summary, this study identifies a SOX10low/TGF-β/LAMB3/FAK/MMPs signaling pathway that determines the migration and invasion properties of MAPKi-resistant melanoma cells and provide rationales for co-targeting LAMB3 to curb the metastasis of melanoma cells in targeted therapy.
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Affiliation(s)
- Shujun Han
- Frontier Institute of Science and Technology, and Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Mo Zhang
- Frontier Institute of Science and Technology, and Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xiaoyan Qu
- Frontier Institute of Science and Technology, and Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Zihao Wu
- Frontier Institute of Science and Technology, and Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Zongguan Huang
- Frontier Institute of Science and Technology, and Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yiming Hu
- Department of Dermatology, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Ying Li
- Department of Dermatology, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Lanlan Cui
- Department of Dermatology, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Lu Si
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Melanoma and Sarcoma, Peking University Cancer Hospital and Research Institute, Beijing, 100142, China
| | - Jiankang Liu
- Frontier Institute of Science and Technology, and Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China.
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266071, China.
| | - Yongping Shao
- Frontier Institute of Science and Technology, and Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China.
- Department of Dermatology, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, 710049, China.
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8
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Chocarro-Calvo A, Jociles-Ortega M, García-Martinez JM, Louphrasitthiphol P, Garcia YV, Ramírez-Sánchez A, Chauhan J, Fiuza MC, Duran M, García-Jiménez C, Goding CR. Phenotype-specific melanoma uptake of fatty acid from human adipocytes activates AXL and CAV1-dependent β-catenin nuclear accumulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.21.576568. [PMID: 38328032 PMCID: PMC10849526 DOI: 10.1101/2024.01.21.576568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Phenotypic diversity of cancer cells within tumors generated through bi-directional interactions with the tumor microenvironment has emerged as a major driver of disease progression and therapy resistance. Nutrient availability plays a critical role in determining phenotype, but whether specific nutrients elicit different responses on distinct phenotypes is poorly understood. Here we show, using melanoma as a model, that only MITF Low undifferentiated cells, but not MITF High cells, are competent to drive lipolysis in human adipocytes. In contrast to MITF High melanomas, adipocyte-derived free fatty acids are taken up by undifferentiated MITF Low cells via a fatty acid transporter (FATP)-independent mechanism. Importantly, oleic acid (OA), a monounsaturated long chain fatty acid abundant in adipose tissue and lymph, reprograms MITF Low undifferentiated melanoma cells to a highly invasive state by ligand-independent activation of AXL, a receptor tyrosine kinase associated with therapy resistance in a wide range of cancers. AXL activation by OA then drives SRC-dependent formation and nuclear translocation of a β-catenin-CAV1 complex. The results highlight how a specific nutritional input drives phenotype-specific activation of a pro-metastasis program with implications for FATP-targeted therapies.
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9
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Lee M, Morris LGT. Genetic alterations in thyroid cancer mediating both resistance to BRAF inhibition and anaplastic transformation. Oncotarget 2024; 15:36-48. [PMID: 38275291 PMCID: PMC10812235 DOI: 10.18632/oncotarget.28544] [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: 10/31/2023] [Accepted: 12/08/2023] [Indexed: 01/27/2024] Open
Abstract
A subset of thyroid cancers present at advanced stage or with dedifferentiated histology and have limited response to standard therapy. Tumors harboring the BRAF V600E mutation may be treated with BRAF inhibitors; however, tumor response is often short lived due to multiple compensatory resistance mechanisms. One mode of resistance is the transition to an alternative cell state, which on rare occasions can correspond to tumor dedifferentiation. DNA sequencing and RNA expression profiling show that thyroid tumors that dedifferentiate after BRAF inhibition are enriched in known genetic alterations that mediate resistance to BRAF blockade, and may also drive tumor dedifferentiation, including mutations in the PI3K/AKT/MTOR (PIK3CA, MTOR), MAP/ERK (MET, NF2, NRAS, RASA1), SWI/SNF chromatin remodeling complex (ARID2, PBRM1), and JAK/STAT pathways (JAK1). Given these findings, recent investigations have evaluated the efficacy of dual-target therapies; however, continued lack of long-term tumor control illustrates the complex and multifactorial nature of these compensatory mechanisms. Transition to an immune-suppressed state is another correlate of BRAF inhibitor resistance and tumor dedifferentiation, suggesting a possible role for concurrent targeted therapy with immunotherapy. Investigations into combined targeted and immunotherapy are ongoing, but early results with checkpoint inhibitors, viral therapies, and CAR T-cells suggest enhanced anti-tumor immune activity with these combinations.
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Affiliation(s)
- Mark Lee
- Department of Otolaryngology-Head and Neck Surgery, New York Presbyterian Hospital, New York, NY 10032, USA
| | - Luc GT Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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10
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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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11
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Gupta PK, Orlovskiy S, Arias-Mendoza F, Nelson DS, Osborne A, Pickup S, Glickson JD, Nath K. Metabolic Imaging Biomarkers of Response to Signaling Inhibition Therapy in Melanoma. Cancers (Basel) 2024; 16:365. [PMID: 38254853 PMCID: PMC10814512 DOI: 10.3390/cancers16020365] [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: 12/14/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Dabrafenib therapy for metastatic melanoma focuses on blocking growth-promoting signals produced by a hyperactive BRAF protein. We report the metabolic differences of four human melanoma cell lines with diverse responses to dabrafenib therapy (30 mg/kg; oral): WM3918 < WM9838BR < WM983B < DB-1. Our goal was to determine if metabolic changes produced by the altered signaling pathway due to BRAF mutations differ in the melanoma models and whether these differences correlate with response to treatment. We assessed metabolic changes in isolated cells using high-resolution proton magnetic resonance spectroscopy (1H MRS) and supplementary biochemical assays. We also noninvasively studied mouse xenografts using proton and phosphorus (1H/31P) MRS. We found consistent changes in lactate and alanine, either in isolated cells or mouse xenografts, correlating with their relative dabrafenib responsiveness. In xenografts, we also observed that a more significant response to dabrafenib correlated with higher bioenergetics (i.e., increased βNTP/Pi). Notably, our noninvasive assessment of the metabolic status of the human melanoma xenografts by 1H/31P MRS demonstrated early metabolite changes preceding therapy response (i.e., tumor shrinkage). Therefore, this noninvasive methodology could be translated to assess in vivo predictive metabolic biomarkers of response in melanoma patients under dabrafenib and probably other signaling inhibition therapies.
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Affiliation(s)
- Pradeep Kumar Gupta
- Molecular Imaging Laboratory, Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; (P.K.G.); (S.O.); (F.A.-M.); (D.S.N.); (A.O.); (S.P.); (J.D.G.)
| | - Stepan Orlovskiy
- Molecular Imaging Laboratory, Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; (P.K.G.); (S.O.); (F.A.-M.); (D.S.N.); (A.O.); (S.P.); (J.D.G.)
| | - Fernando Arias-Mendoza
- Molecular Imaging Laboratory, Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; (P.K.G.); (S.O.); (F.A.-M.); (D.S.N.); (A.O.); (S.P.); (J.D.G.)
- Advanced Imaging Research, Inc., Cleveland, OH 44114, USA
| | - David S. Nelson
- Molecular Imaging Laboratory, Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; (P.K.G.); (S.O.); (F.A.-M.); (D.S.N.); (A.O.); (S.P.); (J.D.G.)
| | - Aria Osborne
- Molecular Imaging Laboratory, Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; (P.K.G.); (S.O.); (F.A.-M.); (D.S.N.); (A.O.); (S.P.); (J.D.G.)
| | - Stephen Pickup
- Molecular Imaging Laboratory, Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; (P.K.G.); (S.O.); (F.A.-M.); (D.S.N.); (A.O.); (S.P.); (J.D.G.)
| | - Jerry D. Glickson
- Molecular Imaging Laboratory, Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; (P.K.G.); (S.O.); (F.A.-M.); (D.S.N.); (A.O.); (S.P.); (J.D.G.)
| | - Kavindra Nath
- Molecular Imaging Laboratory, Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; (P.K.G.); (S.O.); (F.A.-M.); (D.S.N.); (A.O.); (S.P.); (J.D.G.)
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12
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Murali VS, Rajendran D, Isogai T, DeBerardinis RJ, Danuser G. RhoA activation promotes glucose uptake to elevate proliferation in MAPK inhibitor resistant melanoma cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574940. [PMID: 38260449 PMCID: PMC10802590 DOI: 10.1101/2024.01.09.574940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cutaneous melanomas harboring a B-RafV600E mutation are treated with immune check point inhibitors or kinase inhibitor combination therapies relying on MAPK inhibitors (MAPKi) Dabrafenib and Trametinib (Curti and Faries, 2021). However, cells become resistant to treatments over the timespan of a few months. Resistance to MAPKi has been associated with adoption of an aggressive amoeboid phenotype characterized by elevated RhoA signaling, enhanced contractility and thick cortical filamentous actin (F-actin) structures (Kim et al., 2016; Misek et al., 2020). Targeting active RhoA through Rho-kinase (ROCK) inhibitors, either alone or in combination with immunotherapies, reverts MAPKi-resistance (Misek et al., 2020; Orgaz et al., 2020). Yet, the mechanisms for this behavior remain largely unknown. Given our recent findings of cytoskeleton's role in cancer cell proliferation (Mohan et al., 2019), survival (Weems et al., 2023), and metabolism (Park et al., 2020), we explored possibilities by which RhoA-driven changes in cytoskeleton structure may confer resistance. We confirmed elevated activation of RhoA in a panel of MAPKi-resistant melanoma cell lines, leading to a marked increase in the presence of contractile F-actin bundles. Moreover, these cells had increased glucose uptake and glycolysis, a phenotype disrupted by pharmacological perturbation of ROCK. However, glycolysis was unaffected by disruption of F-actin bundles, indicating that glycolytic stimulation in MAPKi-resistant melanoma is independent of F-actin organization. Instead, our findings highlight a mechanism in which elevated RhoA signaling activates ROCK, leading to the activation of insulin receptor substrate 1 (IRS1) and P85 of the PI3K pathway, which promotes cell surface expression of GLUT1 and elevated glucose uptake. Application of ROCK inhibitor GSK269962A results in reduced glucose uptake and glycolysis, thus impeding cell proliferation. Our study adds a mechanism to the proposed use of ROCK inhibitors for long-term treatments on MAPKi-resistant melanomas.
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Affiliation(s)
- Vasanth Siruvallur Murali
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Divya Rajendran
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tadamoto Isogai
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ralph J. DeBerardinis
- Children’s Research Institute and Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX, USA
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13
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Wei Q, Li P, Yang T, Zhu J, Sun L, Zhang Z, Wang L, Tian X, Chen J, Hu C, Xue J, Ma L, Shimura T, Fang J, Ying J, Guo P, Cheng X. The promise and challenges of combination therapies with antibody-drug conjugates in solid tumors. J Hematol Oncol 2024; 17:1. [PMID: 38178200 PMCID: PMC10768262 DOI: 10.1186/s13045-023-01509-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/06/2023] [Indexed: 01/06/2024] Open
Abstract
Antibody-drug conjugates (ADCs) represent an important class of cancer therapies that have revolutionized the treatment paradigm of solid tumors. To date, many ongoing studies of ADC combinations with a variety of anticancer drugs, encompassing chemotherapy, molecularly targeted agents, and immunotherapy, are being rigorously conducted in both preclinical studies and clinical trial settings. Nevertheless, combination therapy does not always guarantee a synergistic or additive effect and may entail overlapping toxicity risks. Therefore, understanding the current status and underlying mechanisms of ADC combination therapy is urgently required. This comprehensive review analyzes existing evidence concerning the additive or synergistic effect of ADCs with other classes of oncology medicines. Here, we discuss the biological mechanisms of different ADC combination therapy strategies, provide prominent examples, and assess their benefits and challenges. Finally, we discuss future opportunities for ADC combination therapy in clinical practice.
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Affiliation(s)
- Qing Wei
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, China
| | - Peijing Li
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Key Laboratory of Head and Neck Cancer Translational Research of Zhejiang Province, Hangzhou, China
| | - Teng Yang
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Jiayu Zhu
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Lu Sun
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- Department of Gynecologic Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Ziwen Zhang
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
| | - Lu Wang
- Department of Radiation Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Xuefei Tian
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
- College of Molecular Medicine, Hangzhou Institute for Advanced Study (HIAS), University of Chinese Academy of Sciences, Hangzhou, China
| | - Jiahui Chen
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, China
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou, China
| | - Can Hu
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, China
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou, China
| | - Junli Xue
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Letao Ma
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Takaya Shimura
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Jianmin Fang
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Jieer Ying
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China.
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China.
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, China.
| | - Peng Guo
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China.
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, China.
| | - Xiangdong Cheng
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China.
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, China.
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou, China.
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14
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Maltas J, Killarney ST, Singleton KR, Strobl MAR, Washart R, Wood KC, Wood KB. Drug dependence in cancer is exploitable by optimally constructed treatment holidays. Nat Ecol Evol 2024; 8:147-162. [PMID: 38012363 PMCID: PMC10918730 DOI: 10.1038/s41559-023-02255-x] [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: 07/06/2022] [Accepted: 10/19/2023] [Indexed: 11/29/2023]
Abstract
Cancers with acquired resistance to targeted therapy can become simultaneously dependent on the presence of the targeted therapy drug for survival, suggesting that intermittent therapy may slow resistance. However, relatively little is known about which tumours are likely to become dependent and how to schedule intermittent therapy optimally. Here we characterized drug dependence across a panel of over 75 MAPK-inhibitor-resistant BRAFV600E mutant melanoma models at the population and single-clone levels. Melanocytic differentiated models exhibited a much greater tendency to give rise to drug-dependent progeny than their dedifferentiated counterparts. Mechanistically, acquired loss of microphthalmia-associated transcription factor in differentiated melanoma models drives ERK-JunB-p21 signalling to enforce drug dependence. We identified the optimal scheduling of 'drug holidays' using simple mathematical models that we validated across short and long timescales. Without detailed knowledge of tumour characteristics, we found that a simple adaptive therapy protocol can produce near-optimal outcomes using only measurements of total population size. Finally, a spatial agent-based model showed that optimal schedules derived from exponentially growing cells in culture remain nearly optimal in the context of tumour cell turnover and limited environmental carrying capacity. These findings may guide the implementation of improved evolution-inspired treatment strategies for drug-dependent cancers.
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Affiliation(s)
- Jeff Maltas
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Shane T Killarney
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | | | - Maximilian A R Strobl
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Rachel Washart
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
| | - Kevin B Wood
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
- Department of Physics, University of Michigan, Ann Arbor, MI, USA.
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15
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Bahar ME, Kim HJ, Kim DR. Targeting the RAS/RAF/MAPK pathway for cancer therapy: from mechanism to clinical studies. Signal Transduct Target Ther 2023; 8:455. [PMID: 38105263 PMCID: PMC10725898 DOI: 10.1038/s41392-023-01705-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/03/2023] [Accepted: 11/12/2023] [Indexed: 12/19/2023] Open
Abstract
Metastatic dissemination of solid tumors, a leading cause of cancer-related mortality, underscores the urgent need for enhanced insights into the molecular and cellular mechanisms underlying metastasis, chemoresistance, and the mechanistic backgrounds of individuals whose cancers are prone to migration. The most prevalent signaling cascade governed by multi-kinase inhibitors is the mitogen-activated protein kinase (MAPK) pathway, encompassing the RAS-RAF-MAPK kinase (MEK)-extracellular signal-related kinase (ERK) pathway. RAF kinase is a primary mediator of the MAPK pathway, responsible for the sequential activation of downstream targets, such as MEK and the transcription factor ERK, which control numerous cellular and physiological processes, including organism development, cell cycle control, cell proliferation and differentiation, cell survival, and death. Defects in this signaling cascade are associated with diseases such as cancer. RAF inhibitors (RAFi) combined with MEK blockers represent an FDA-approved therapeutic strategy for numerous RAF-mutant cancers, including melanoma, non-small cell lung carcinoma, and thyroid cancer. However, the development of therapy resistance by cancer cells remains an important barrier. Autophagy, an intracellular lysosome-dependent catabolic recycling process, plays a critical role in the development of RAFi resistance in cancer. Thus, targeting RAF and autophagy could be novel treatment strategies for RAF-mutant cancers. In this review, we delve deeper into the mechanistic insights surrounding RAF kinase signaling in tumorigenesis and RAFi-resistance. Furthermore, we explore and discuss the ongoing development of next-generation RAF inhibitors with enhanced therapeutic profiles. Additionally, this review sheds light on the functional interplay between RAF-targeted therapies and autophagy in cancer.
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Affiliation(s)
- Md Entaz Bahar
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Hyun Joon Kim
- Department of Anatomy and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea
| | - Deok Ryong Kim
- Department of Biochemistry and Convergence Medical Sciences and Institute of Medical Science, Gyeongsang National University, College of Medicine, Jinju, South Korea.
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16
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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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17
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Emmons MF, Bennett RL, Riva A, Gupta K, Carvalho LADC, Zhang C, Macaulay R, Dupéré-Richér D, Fang B, Seto E, Koomen JM, Li J, Chen YA, Forsyth PA, Licht JD, Smalley KSM. HDAC8-mediated inhibition of EP300 drives a transcriptional state that increases melanoma brain metastasis. Nat Commun 2023; 14:7759. [PMID: 38030596 PMCID: PMC10686983 DOI: 10.1038/s41467-023-43519-1] [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: 08/24/2022] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
Melanomas can adopt multiple transcriptional states. Little is known about the epigenetic drivers of these cell states, limiting our ability to regulate melanoma heterogeneity. Here, we identify stress-induced HDAC8 activity as driving melanoma brain metastasis development. Exposure of melanocytes and melanoma cells to multiple stresses increases HDAC8 activation leading to a neural crest-stem cell transcriptional state and an amoeboid, invasive phenotype that increases seeding to the brain. Using ATAC-Seq and ChIP-Seq we show that increased HDAC8 activity alters chromatin structure by increasing H3K27ac and enhancing accessibility at c-Jun binding sites. Functionally, HDAC8 deacetylates the histone acetyltransferase EP300, causing its enzymatic inactivation. This, in turn, increases binding of EP300 to Jun-transcriptional sites and decreases binding to MITF-transcriptional sites. Inhibition of EP300 increases melanoma cell invasion, resistance to stress and increases melanoma brain metastasis development. HDAC8 is identified as a mediator of transcriptional co-factor inactivation and chromatin accessibility that drives brain metastasis.
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Affiliation(s)
- Michael F Emmons
- Department of Tumor Biology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Richard L Bennett
- UF Health Cancer Center, 2033 Mowry Road, University of Florida, Gainesville, FL, 32610, USA
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, 2033 Mowry Road, Gainesville, FL, 32610, USA
| | - Kanchan Gupta
- UF Health Cancer Center, 2033 Mowry Road, University of Florida, Gainesville, FL, 32610, USA
| | | | - Chao Zhang
- Department of Tumor Biology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Robert Macaulay
- Department of Neuro-Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Daphne Dupéré-Richér
- UF Health Cancer Center, 2033 Mowry Road, University of Florida, Gainesville, FL, 32610, USA
| | - Bin Fang
- Proteomics & Metabolomics Core, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Edward Seto
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, George Washington Cancer Center, George Washington University, 2300 Eye Street, Washington, DC, 20037, USA
| | - John M Koomen
- Department of Molecular Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Jiannong Li
- Department of Bioinformatics and Biostatistics, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Y Ann Chen
- Department of Bioinformatics and Biostatistics, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Peter A Forsyth
- Department of Neuro-Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Jonathan D Licht
- UF Health Cancer Center, 2033 Mowry Road, University of Florida, Gainesville, FL, 32610, USA
| | - Keiran S M Smalley
- Department of Tumor Biology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
- Department of Cutaneous Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
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18
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Harmange G, Hueros RAR, Schaff DL, Emert B, Saint-Antoine M, Kim LC, Niu Z, Nellore S, Fane ME, Alicea GM, Weeraratna AT, Simon MC, Singh A, Shaffer SM. Disrupting cellular memory to overcome drug resistance. Nat Commun 2023; 14:7130. [PMID: 37932277 PMCID: PMC10628298 DOI: 10.1038/s41467-023-41811-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/15/2023] [Indexed: 11/08/2023] Open
Abstract
Gene expression states persist for varying lengths of time at the single-cell level, a phenomenon known as gene expression memory. When cells switch states, losing memory of their prior state, this transition can occur in the absence of genetic changes. However, we lack robust methods to find regulators of memory or track state switching. Here, we develop a lineage tracing-based technique to quantify memory and identify cells that switch states. Applied to melanoma cells without therapy, we quantify long-lived fluctuations in gene expression that are predictive of later resistance to targeted therapy. We also identify the PI3K and TGF-β pathways as state switching modulators. We propose a pretreatment model, first applying a PI3K inhibitor to modulate gene expression states, then applying targeted therapy, which leads to less resistance than targeted therapy alone. Together, we present a method for finding modulators of gene expression memory and their associated cell fates.
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Affiliation(s)
- Guillaume Harmange
- Cellular and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Raúl A Reyes Hueros
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dylan L Schaff
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin Emert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Michael Saint-Antoine
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Laura C Kim
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zijian Niu
- Department of Chemistry, College of the Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physics, College of the Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Shivani Nellore
- Department of Biology, College of the Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Mitchell E Fane
- Cancer Signaling and Microenvironment Research Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Gretchen M Alicea
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Ashani T Weeraratna
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, USA
- Sidney Kimmel Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Sydney M Shaffer
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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19
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Martin-Vega A, Cobb MH. Navigating the ERK1/2 MAPK Cascade. Biomolecules 2023; 13:1555. [PMID: 37892237 PMCID: PMC10605237 DOI: 10.3390/biom13101555] [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: 09/30/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
The RAS-ERK pathway is a fundamental signaling cascade crucial for many biological processes including proliferation, cell cycle control, growth, and survival; common across all cell types. Notably, ERK1/2 are implicated in specific processes in a context-dependent manner as in stem cells and pancreatic β-cells. Alterations in the different components of this cascade result in dysregulation of the effector kinases ERK1/2 which communicate with hundreds of substrates. Aberrant activation of the pathway contributes to a range of disorders, including cancer. This review provides an overview of the structure, activation, regulation, and mutational frequency of the different tiers of the cascade; with a particular focus on ERK1/2. We highlight the importance of scaffold proteins that contribute to kinase localization and coordinate interaction dynamics of the kinases with substrates, activators, and inhibitors. Additionally, we explore innovative therapeutic approaches emphasizing promising avenues in this field.
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Affiliation(s)
- Ana Martin-Vega
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
| | - Melanie H. Cobb
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA
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20
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Zhu EY, Schillo JL, Murray SD, Riordan JD, Dupuy AJ. Understanding cancer drug resistance with Sleeping Beauty functional genomic screens: Application to MAPK inhibition in cutaneous melanoma. iScience 2023; 26:107805. [PMID: 37860756 PMCID: PMC10582486 DOI: 10.1016/j.isci.2023.107805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/10/2023] [Accepted: 08/29/2023] [Indexed: 10/21/2023] Open
Abstract
Combined BRAF and MEK inhibition is an effective treatment for BRAF-mutant cutaneous melanoma. However, most patients progress on this treatment due to drug resistance. Here, we applied the Sleeping Beauty transposon system to understand how melanoma evades MAPK inhibition. We found that the specific drug resistance mechanisms differed across melanomas in our genetic screens of five cutaneous melanoma cell lines. While drivers that reactivated MAPK were highly conserved, many others were cell-line specific. One such driver, VAV1, activated a de-differentiated transcriptional program like that of hyperactive RAC1, RAC1P29S. To target this mechanism, we showed that an inhibitor of SRC, saracatinib, blunts the VAV1-induced transcriptional reprogramming. Overall, we highlighted the importance of accounting for melanoma heterogeneity in treating cutaneous melanoma with MAPK inhibitors. Moreover, we demonstrated the utility of the Sleeping Beauty transposon system in understanding cancer drug resistance.
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Affiliation(s)
- Eliot Y. Zhu
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Jacob L. Schillo
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Sarina D. Murray
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Jesse D. Riordan
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Adam J. Dupuy
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
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21
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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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22
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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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23
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Redondo-Muñoz M, Rodriguez-Baena FJ, Aldaz P, Caballé-Mestres A, Moncho-Amor V, Otaegi-Ugartemendia M, Carrasco-Garcia E, Olias-Arjona A, Lasheras-Otero I, Santamaria E, Bocanegra A, Chocarro L, Grier A, Dzieciatkowska M M, Bigas C, Martin J, Urdiroz-Urricelqui U, Marzo F, Santamaria E, Kochan G, Escors D, Larrayoz IM, Heyn H, D'Alessandro A, Attolini CSO, Matheu A, Wellbrock C, Benitah SA, Sanchez-Laorden B, Arozarena I. Metabolic rewiring induced by ranolazine improves melanoma responses to targeted therapy and immunotherapy. Nat Metab 2023; 5:1544-1562. [PMID: 37563469 PMCID: PMC10513932 DOI: 10.1038/s42255-023-00861-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
Resistance of melanoma to targeted therapy and immunotherapy is linked to metabolic rewiring. Here, we show that increased fatty acid oxidation (FAO) during prolonged BRAF inhibitor (BRAFi) treatment contributes to acquired therapy resistance in mice. Targeting FAO using the US Food and Drug Administration-approved and European Medicines Agency-approved anti-anginal drug ranolazine (RANO) delays tumour recurrence with acquired BRAFi resistance. Single-cell RNA-sequencing analysis reveals that RANO diminishes the abundance of the therapy-resistant NGFRhi neural crest stem cell subpopulation. Moreover, by rewiring the methionine salvage pathway, RANO enhances melanoma immunogenicity through increased antigen presentation and interferon signalling. Combination of RANO with anti-PD-L1 antibodies strongly improves survival by increasing antitumour immune responses. Altogether, we show that RANO increases the efficacy of targeted melanoma therapy through its effects on FAO and the methionine salvage pathway. Importantly, our study suggests that RANO could sensitize BRAFi-resistant tumours to immunotherapy. Since RANO has very mild side-effects, it might constitute a therapeutic option to improve the two main strategies currently used to treat metastatic melanoma.
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Grants
- P30 CA046934 NCI NIH HHS
- Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)
- Departamento de Salud del Gobierno de Navarra, Spain (Grant Ref. No: GºNa 71/17)
- Marta Redondo-Muñoz is funded by a PhD studentship from the Department of Industry of the Government of Navarra, Spain. MRM acknowledges funding from the Grupo Español Multidisciplinar de Melanoma
- The University of Colorado School of Medicine Metabolomics Core is supported in part by the University of Colorado Cancer Center award from the National Cancer Institute P30CA046934
- David Escors Acknowledges funding from The Spanish Association against Cancer (AECC), PROYE16001ESCO), Biomedicine Project Grant from the Department of Health of the Government of Navarre-FEDER funds (BMED 050-2019, 51-2021) ; Strategic projects from the Department of Industry, Government of Navarre (AGATA, Ref. 0011-1411-2020-000013; LINTERNA, Ref. 0011-1411-2020-000033; DESCARTHES, 0011-1411-2019-000058).
- Research in the S.A.B. laboratory is supported partially by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 787041), the Government of Cataluña (SGR grant), the Government of Spain (MINECO), the La Marató/TV3 Foundation, the Foundation Lilliane Bettencourt, the Spanish Association for Cancer Research (AECC) and The Worldwide Cancer Research Foundation (WCRF)
- Work in B.S-L´s lab is funded by:PID2019-106852-RBI00 funded by MCIN/AEI/ 10.13039/501100011033, the Melanoma Research Alliance (https://doi.org/10.48050/pc.gr.91574 to B.S-L) and the FERO Foundation.
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Affiliation(s)
- Marta Redondo-Muñoz
- Cancer Signaling Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
- Health Research Institute of Navarre (IdiSNA), Pamplona, Spain
| | | | - Paula Aldaz
- Cancer Signaling Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
- Health Research Institute of Navarre (IdiSNA), Pamplona, Spain
| | - Adriá Caballé-Mestres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Verónica Moncho-Amor
- Cellular Oncology Group, Biodonostia Health Research Institute, San Sebastian, Spain
- CIBER de Fragilidad y Envejecimiento Saludable (CIBERfes), Madrid, Spain
| | | | - Estefania Carrasco-Garcia
- Cellular Oncology Group, Biodonostia Health Research Institute, San Sebastian, Spain
- CIBER de Fragilidad y Envejecimiento Saludable (CIBERfes), Madrid, Spain
| | - Ana Olias-Arjona
- Cancer Signaling Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
- Health Research Institute of Navarre (IdiSNA), Pamplona, Spain
| | - Irene Lasheras-Otero
- Cancer Signaling Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
- Health Research Institute of Navarre (IdiSNA), Pamplona, Spain
| | - Eva Santamaria
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Bocanegra
- Health Research Institute of Navarre (IdiSNA), Pamplona, Spain
- Oncoimmunology Group, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Luisa Chocarro
- Health Research Institute of Navarre (IdiSNA), Pamplona, Spain
- Oncoimmunology Group, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Abby Grier
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Monika Dzieciatkowska M
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Claudia Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Josefina Martin
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Uxue Urdiroz-Urricelqui
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Florencio Marzo
- Health Research Institute of Navarre (IdiSNA), Pamplona, Spain
| | - Enrique Santamaria
- Health Research Institute of Navarre (IdiSNA), Pamplona, Spain
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Grazyna Kochan
- Health Research Institute of Navarre (IdiSNA), Pamplona, Spain
- Oncoimmunology Group, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - David Escors
- Health Research Institute of Navarre (IdiSNA), Pamplona, Spain
- Oncoimmunology Group, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Ignacio Marcos Larrayoz
- Biomarkers and Molecular Signaling Group, Center for Biomedical Research of La Rioja (CIBIR), Foundation Rioja Salud, Logroño, Spain
- Unidad Predepartamental de Enfermería, Universidad de La Rioja (UR), Logroño, Spain
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Angelo D'Alessandro
- Oncoimmunology Group, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ander Matheu
- Cellular Oncology Group, Biodonostia Health Research Institute, San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Claudia Wellbrock
- Cancer Signaling Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
- Department of Health Sciences, Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | | | - Imanol Arozarena
- Cancer Signaling Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.
- Health Research Institute of Navarre (IdiSNA), Pamplona, Spain.
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24
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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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25
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Grafanaki K, Grammatikakis I, Ghosh A, Gopalan V, Olgun G, Liu H, Kyriakopoulos GC, Skeparnias I, Georgiou S, Stathopoulos C, Hannenhalli S, Merlino G, Marie KL, Day CP. Noncoding RNA circuitry in melanoma onset, plasticity, and therapeutic response. Pharmacol Ther 2023; 248:108466. [PMID: 37301330 PMCID: PMC10527631 DOI: 10.1016/j.pharmthera.2023.108466] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/24/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
Melanoma, the cancer of the melanocyte, is the deadliest form of skin cancer with an aggressive nature, propensity to metastasize and tendency to resist therapeutic intervention. Studies have identified that the re-emergence of developmental pathways in melanoma contributes to melanoma onset, plasticity, and therapeutic response. Notably, it is well known that noncoding RNAs play a critical role in the development and stress response of tissues. In this review, we focus on the noncoding RNAs, including microRNAs, long non-coding RNAs, circular RNAs, and other small RNAs, for their functions in developmental mechanisms and plasticity, which drive onset, progression, therapeutic response and resistance in melanoma. Going forward, elucidation of noncoding RNA-mediated mechanisms may provide insights that accelerate development of novel melanoma therapies.
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Affiliation(s)
- Katerina Grafanaki
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Ioannis Grammatikakis
- Cancer Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arin Ghosh
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vishaka Gopalan
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gulden Olgun
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Huaitian Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - George C Kyriakopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Ilias Skeparnias
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Sophia Georgiou
- Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
| | | | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kerrie L Marie
- Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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26
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Priantti JN, Vilbert M, Madeira T, Moraes FCA, Hein ECK, Saeed A, Cavalcante L. Efficacy and Safety of Rechallenge with BRAF/MEK Inhibitors in Advanced Melanoma Patients: A Systematic Review and Meta-Analysis. Cancers (Basel) 2023; 15:3754. [PMID: 37568570 PMCID: PMC10417341 DOI: 10.3390/cancers15153754] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 08/13/2023] Open
Abstract
This systematic review and meta-analysis aims to evaluate the efficacy and safety of rechallenging advanced melanoma patients with BRAFi/MEKi. Seven studies, accounting for 400 patients, were included. Most patients received immunotherapy before the rechallenge, and 79% underwent rechallenge with the combination of BRAFi/MEKi. We found a median progression-free survival of 5 months and overall survival of 9.8 months. The one-year survival rate was 42.63%. Regarding response, ORR was 34% and DCR 65%. There were no new or unexpected safety concerns. Rechallenge with BRAFi/MEKi can improve outcomes in advanced melanoma patients with refractory disease. These findings have significant implications for clinical practice, particularly in the setting of progressive disease in later lines and limited treatment options.
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Affiliation(s)
- Jonathan N Priantti
- School of Medicine, Federal University of Amazonas-UFAM, Manaus 69020-160, AM, Brazil
| | - Maysa Vilbert
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
- Division of Medical Oncology, Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Thiago Madeira
- School of Medicine, Federal University of Minas Gerais-UFMG, Belo Horizonte 30130-100, MG, Brazil
| | | | - Erica C Koch Hein
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
- Division of Medical Oncology, Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Hematology and Oncology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Anwaar Saeed
- Department of Medicine, Division of Hematology and Oncology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ludimila Cavalcante
- Department of Medical Oncology, Novant Health Cancer Institute, Charlotte, NC 28204, USA
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27
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Wang J, Zheng X, Fu X, Jiang A, Yao Y, He W. A de novo dual-targeting supramolecular self-assembly peptide against pulmonary metastasis of melanoma. Theranostics 2023; 13:3844-3855. [PMID: 37441586 PMCID: PMC10334834 DOI: 10.7150/thno.83819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/18/2023] [Indexed: 07/15/2023] Open
Abstract
Despite recent advances in treatment, overall survival rates for metastatic melanoma, especially those that invade the lungs, continue to be low, with 5-year survival rates of only 3% to 5%. It was recently discovered that Wnt/β-catenin signaling pathways and MAPK/ERK signaling pathways are involved in melanoma metastasis. Methods: Herein, a bifunctional supramolecular peptide termed HBBplus@CA was constructed by a self-assembling RGD-modified MAPK/ERK peptide inhibitor (HBBplus) and a small molecule catenin inhibitor (carnosic acid (CA)). Results: Expectedly, the HBBplus@CA could internalize melanoma cells, accumulate in the tumor-bearing lung, and be biosafe. As designed, HBBplus@CA simultaneously suppressed both Wnt/β-catenin and MAPK/ERK signaling pathways and suppressed melanoma cell proliferation, migration, and invasion in more action than CA or HBBplus monotherapy. More importantly, HBBplus@CA demonstrated potent inhibition of lung metastasis in mice bearing metastatic melanoma of B16F10 and significantly prolonged their survival. Conclusion: In summary, a supramolecular peptide-based strategy was not only developed to suppress pulmonary metastasis of melanoma, but it also renewed efforts to identify cocktail drugs that act on intracellular targets in various human diseases, including cancer.
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Affiliation(s)
- Jingjing Wang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Xiaoqiang Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
- Institute for Stem Cell & Regenerative Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Xiao Fu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Aimin Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yu Yao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Wangxiao He
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
- Institute for Stem Cell & Regenerative Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
- Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an 710061, China
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28
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Merat R. The human antigen R as an actionable super-hub within the network of cancer cell persistency and plasticity. Transl Oncol 2023; 35:101722. [PMID: 37352624 DOI: 10.1016/j.tranon.2023.101722] [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: 04/07/2023] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 06/25/2023] Open
Abstract
In this perspective article, a clinically inspired phenotype-driven experimental approach is put forward to address the challenge of the adaptive response of solid cancers to small-molecule targeted therapies. A list of conditions is derived, including an experimental quantitative assessment of cell plasticity and an information theory-based detection of in vivo dependencies, for the discovery of post-transcriptional druggable mechanisms capable of preventing at multiple levels the emergence of plastic dedifferentiated slow-proliferating cells. The approach is illustrated by the author's own work in the example case of the adaptive response of BRAFV600-melanoma to BRAF inhibition. A bench-to-bedside and back to bench effort leads to a therapeutic strategy in which the inhibition of the baseline activity of the interferon-γ-activated inhibitor of translation (GAIT) complex, incriminated in the expression insufficiency of the RNA-binding protein HuR in a minority of cells, results in the suppression of the plastic, intermittently slow-proliferating cells involved in the adaptive response. A similar approach is recommended for the validation of other classes of mechanisms that we seek to modulate to overcome this complex challenge of modern cancer therapy.
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Affiliation(s)
- Rastine Merat
- Dermato-Oncology Unit, Division of Dermatology, Geneva University Hospitals, Switzerland; Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Switzerland.
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29
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Kharouf N, Flanagan TW, Hassan SY, Shalaby H, Khabaz M, Hassan SL, Megahed M, Haikel Y, Santourlidis S, Hassan M. Tumor Microenvironment as a Therapeutic Target in Melanoma Treatment. Cancers (Basel) 2023; 15:3147. [PMID: 37370757 DOI: 10.3390/cancers15123147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The role of the tumor microenvironment in tumor growth and therapy has recently attracted more attention in research and drug development. The ability of the microenvironment to trigger tumor maintenance, progression, and resistance is the main cause for treatment failure and tumor relapse. Accumulated evidence indicates that the maintenance and progression of tumor cells is determined by components of the microenvironment, which include stromal cells (endothelial cells, fibroblasts, mesenchymal stem cells, and immune cells), extracellular matrix (ECM), and soluble molecules (chemokines, cytokines, growth factors, and extracellular vesicles). As a solid tumor, melanoma is not only a tumor mass of monolithic tumor cells, but it also contains supporting stroma, ECM, and soluble molecules. Melanoma cells are continuously in interaction with the components of the microenvironment. In the present review, we focus on the role of the tumor microenvironment components in the modulation of tumor progression and treatment resistance as well as the impact of the tumor microenvironment as a therapeutic target in melanoma.
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Affiliation(s)
- Naji Kharouf
- Biomaterials and Bioengineering, Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, Unité Mixte de Recherche 1121, 67000 Strasbourg, France
- Department of Endodontics and Conservative Dentistry, Faculty of Dental Medicine, University of Strasbourg, 67000 Strasbourg, France
| | - Thomas W Flanagan
- Department of Pharmacology and Experimental Therapeutics, LSU Health Sciences Center, New Orleans, LA 70112, USA
| | - Sofie-Yasmin Hassan
- Department of Chemistry, 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
| | - Marla Khabaz
- Department of Production, Beta Factory for Veterinary Pharmaceutical Industries, Damascus 0100, Syria
| | - Sarah-Lilly Hassan
- Department of Chemistry, Faculty of Science, Heinrich-Heine University Duesseldorf, 40225 Dusseldorf, Germany
| | - Mosaad Megahed
- Clinic of Dermatology, University Hospital of Aachen, 52074 Aachen, Germany
| | - Youssef Haikel
- Biomaterials and Bioengineering, Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, Unité Mixte de Recherche 1121, 67000 Strasbourg, France
- Department of Endodontics and Conservative Dentistry, Faculty of Dental Medicine, University of Strasbourg, 67000 Strasbourg, France
- Pôle de Médecine et Chirurgie Bucco-Dentaire, Hôpital Civil, Hôpitaux Universitaire de Strasbourg, 67000 Strasbourg, France
| | - Simeon Santourlidis
- Epigenetics Core Laboratory, Institute of Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich-Heine University Duesseldorf, 40225 Duesseldorf, Germany
| | - Mohamed Hassan
- Biomaterials and Bioengineering, Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, Unité Mixte de Recherche 1121, 67000 Strasbourg, France
- Department of Endodontics and Conservative Dentistry, Faculty of Dental Medicine, University of Strasbourg, 67000 Strasbourg, France
- Research Laboratory of Surgery-Oncology, Department of Surgery, School of Medicine, Tulane University, New Orleans, LA 70112, USA
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30
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Venkadakrishnan VB, Yamada Y, Weng K, Idahor O, Beltran H. Significance of RB Loss in Unlocking Phenotypic Plasticity in Advanced Cancers. Mol Cancer Res 2023; 21:497-510. [PMID: 37052520 PMCID: PMC10239360 DOI: 10.1158/1541-7786.mcr-23-0045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/27/2023] [Accepted: 03/09/2023] [Indexed: 04/14/2023]
Abstract
Cancer cells can undergo plasticity in response to environmental stimuli or under selective therapeutic pressures that result in changes in phenotype. This complex phenomenon of phenotypic plasticity is now recognized as a hallmark of cancer. Lineage plasticity is often associated with loss of dependence on the original oncogenic driver and is facilitated, in part, by underlying genomic and epigenetic alterations. Understanding the molecular drivers of cancer plasticity is critical for the development of novel therapeutic strategies. The retinoblastoma gene RB1 (encoding RB) is the first tumor suppressor gene to be discovered and has a well-described role in cell-cycle regulation. RB is also involved in diverse cellular functions beyond cell cycle including differentiation. Here, we describe the emerging role of RB loss in unlocking cancer phenotypic plasticity and driving therapy resistance across cancer types. We highlight parallels in cancer with the noncanonical role of RB that is critical for normal development and lineage specification, and the downstream consequences of RB loss including epigenetic reprogramming and chromatin reorganization that can lead to changes in lineage program. Finally, we discuss potential therapeutic approaches geared toward RB loss cancers undergoing lineage reprogramming.
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Affiliation(s)
| | - Yasutaka Yamada
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kenny Weng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Boston College, Chestnut Hill, Massachusetts, USA
| | - Osasenaga Idahor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard University, Cambridge, Massachusetts, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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31
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Entezari M, Yousef Abad GG, Sedghi B, Ettehadi R, Asadi S, Beiranvand R, Haratian N, Karimian SS, Jebali A, Khorrami R, Zandieh MA, Saebfar H, Hushmandi K, Salimimoghadam S, Rashidi M, Taheriazam A, Hashemi M, Ertas YN. Gold nanostructure-mediated delivery of anticancer agents: Biomedical applications, reversing drug resistance, and stimuli-responsive nanocarriers. ENVIRONMENTAL RESEARCH 2023; 225:115673. [PMID: 36906270 DOI: 10.1016/j.envres.2023.115673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
The application of nanoarchitectures in cancer therapy seems to be beneficial for the delivery of antitumor drugs. In recent years, attempts have been made to reverse drug resistance, one of the factors threatening the lives of cancer patients worldwide. Gold nanoparticles (GNPs) are metal nanostructures with a variety of advantageous properties, such as tunable size and shape, continuous release of chemicals, and simple surface modification. This review focuses on the application of GNPs for the delivery of chemotherapy agents in cancer therapy. Utilizing GNPs results in targeted delivery and increased intracellular accumulation. Besides, GNPs can provide a platform for the co-delivery of anticancer agents and genetic tools with chemotherapeutic compounds to exert a synergistic impact. Furthermore, GNPs can promote oxidative damage and apoptosis by triggering chemosensitivity. Due to their capacity for providing photothermal therapy, GNPs can enhance the cytotoxicity of chemotherapeutic agents against tumor cells. The pH-, redox-, and light-responsive GNPs are beneficial for drug release at the tumor site. For the selective targeting of cancer cells, surface modification of GNPs with ligands has been performed. In addition to improving cytotoxicity, GNPs can prevent the development of drug resistance in tumor cells by facilitating prolonged release and loading low concentrations of chemotherapeutics while maintaining their high antitumor activity. As described in this study, the clinical use of chemotherapeutic drug-loaded GNPs is contingent on enhancing their biocompatibility.
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Affiliation(s)
- Maliheh Entezari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ghazaleh Gholamiyan Yousef Abad
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Behnaz Sedghi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Reyhaneh Ettehadi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Shafagh Asadi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Razieh Beiranvand
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Negar Haratian
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Seyedeh Sara Karimian
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ali Jebali
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ramin Khorrami
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Mohammad Arad Zandieh
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Hamidreza Saebfar
- European University Association, League of European Research Universities, University of Milan, Italy
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Shokooh Salimimoghadam
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Yavuz Nuri Ertas
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey; ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri, Turkey.
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32
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Abstract
Over the past decade, melanoma has led the field in new cancer treatments, with impressive gains in on-treatment survival but more modest improvements in overall survival. Melanoma presents heterogeneity and transcriptional plasticity that recapitulates distinct melanocyte developmental states and phenotypes, allowing it to adapt to and eventually escape even the most advanced treatments. Despite remarkable advances in our understanding of melanoma biology and genetics, the melanoma cell of origin is still fiercely debated because both melanocyte stem cells and mature melanocytes can be transformed. Animal models and high-throughput single-cell sequencing approaches have opened new opportunities to address this question. Here, we discuss the melanocytic journey from the neural crest, where they emerge as melanoblasts, to the fully mature pigmented melanocytes resident in several tissues. We describe a new understanding of melanocyte biology and the different melanocyte subpopulations and microenvironments they inhabit, and how this provides unique insights into melanoma initiation and progression. We highlight recent findings on melanoma heterogeneity and transcriptional plasticity and their implications for exciting new research areas and treatment opportunities. The lessons from melanocyte biology reveal how cells that are present to protect us from the damaging effects of ultraviolet radiation reach back to their origins to become a potentially deadly cancer.
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Affiliation(s)
- Patricia P Centeno
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
| | - Valeria Pavet
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
| | - Richard Marais
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK.
- Oncodrug Ltd, Alderly Park, Macclesfield, UK.
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33
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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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Shao H, Teramae D, Wells A. Axl contributes to efficient migration and invasion of melanoma cells. PLoS One 2023; 18:e0283749. [PMID: 36989239 PMCID: PMC10057740 DOI: 10.1371/journal.pone.0283749] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Axl, a member of the TAM receptor family has been broadly suggested to play a key role in tumor metastasis. However, the function of Axl in the invasion and metastasis of melanoma, the most lethal skin cancer, remains largely unknown. In the present study, we found that melanoma cell lines present variable protein levels of Axl and Tyro3; interestingly, MerTK is not noted at detectable levels in any of tested MGP (metastatic growth phase) cell lines. Treatment with recombinant human Gas6 significantly activates Akt in the Axl-expressing WM852 and IgR3 lines but just slightly in WM1158. IgR3, WM852 and WM1158 demonstrate different autocrine signaling. Knockdown of Axl by siRNA or the treatment with Axl-specific inhibitor R428 dramatically inhibits the migration and invasion of both IgR3 and WM852 in vitro. These findings suggest that Axl enhances the invasion of melanoma cells.
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Affiliation(s)
- Hanshuang Shao
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Pittsburgh VA Health System, Pittsburgh, Pennsylvania, United States of America
| | - Diana Teramae
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Pittsburgh VA Health System, Pittsburgh, Pennsylvania, United States of America
| | - Alan Wells
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Pittsburgh VA Health System, Pittsburgh, Pennsylvania, United States of America
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Park BS, Jeon H, Chi SG, Kim T. Efficient prioritization of CRISPR screen hits by accounting for targeting efficiency of guide RNA. BMC Biol 2023; 21:45. [PMID: 36829149 PMCID: PMC9960226 DOI: 10.1186/s12915-023-01536-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/03/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND CRISPR-based screens are revolutionizing drug discovery as tools to identify genes whose ablation induces a phenotype of interest. For instance, CRISPR-Cas9 screening has been successfully used to identify novel therapeutic targets in cancer where disruption of genes leads to decreased viability of malignant cells. However, low-activity guide RNAs may give rise to variable changes in phenotype, preventing easy identification of hits and leading to false negative results. Therefore, correcting the effects of bias due to differences in guide RNA efficiency in CRISPR screening data can improve the efficiency of prioritizing hits for further validation. Here, we developed an approach to identify hits from negative CRISPR screens by correcting the fold changes (FC) in gRNA frequency by the actual, observed frequency of indel mutations generated by gRNA. RESULTS Each gRNA was coupled with the "reporter sequence" that can be targeted by the same gRNA so that the frequency of mutations in the reporter sequence can be used as a proxy for the endogenous target gene. The measured gRNA activity was used to correct the FC. We identified indel generation efficiency as the dominant factor contributing significant bias to screening results, and our method significantly removed such bias and was better at identifying essential genes when compared to conventional fold change analysis. We successfully applied our gRNA activity data to previously published gRNA screening data, and identified novel genes whose ablation could synergize with vemurafenib in the A375 melanoma cell line. Our method identified nicotinamide N-methyltransferase, lactate dehydrogenase B, and polypyrimidine tract-binding protein 1 as synergistic targets whose ablation sensitized A375 cells to vemurafenib. CONCLUSIONS We identified the variations in target cleavage efficiency, even in optimized sgRNA libraries, that pose a strong bias in phenotype and developed an analysis method that corrects phenotype score by the measured differences in the targeting efficiency among sgRNAs. Collectively, we expect that our new analysis method will more accurately identify genes that confer the phenotype of interest.
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Affiliation(s)
- Byung-Sun Park
- grid.35541.360000000121053345Medicinal Materials Research Center, Korea Institute of Science and Technology, 5 Hwarangro-14-Gil, SeongbukGu, Seoul, 02792 Republic of Korea ,grid.222754.40000 0001 0840 2678Department of Biological Sciences, Korea University, 145 AnamRo, SeongbukGu, Seoul, 02841 Republic of Korea
| | - Heeju Jeon
- grid.35541.360000000121053345Medicinal Materials Research Center, Korea Institute of Science and Technology, 5 Hwarangro-14-Gil, SeongbukGu, Seoul, 02792 Republic of Korea ,grid.222754.40000 0001 0840 2678Department of Biological Sciences, Korea University, 145 AnamRo, SeongbukGu, Seoul, 02841 Republic of Korea
| | - Sung-Gil Chi
- grid.222754.40000 0001 0840 2678Department of Biological Sciences, Korea University, 145 AnamRo, SeongbukGu, Seoul, 02841 Republic of Korea
| | - Tackhoon Kim
- Medicinal Materials Research Center, Korea Institute of Science and Technology, 5 Hwarangro-14-Gil, SeongbukGu, Seoul, 02792, Republic of Korea. .,Department of Biological Sciences, Korea University, 145 AnamRo, SeongbukGu, Seoul, 02841, Republic of Korea. .,Division of Bio-Medical Science and Technology, Korea University of Science and Technology, 217 GajeongRo YuseongGu, Daejeon, 34113, Republic of Korea.
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36
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Kenski JCN, Huang X, Vredevoogd DW, de Bruijn B, Traets JJH, Ibáñez-Molero S, Schieven SM, van Vliet A, Krijgsman O, Kuilman T, Pozniak J, Loayza-Puch F, Terry AM, Müller J, Logtenberg MEW, de Bruijn M, Levy P, Körner PR, Goding CR, Schumacher TN, Marine JC, Agami R, Peeper DS. An adverse tumor-protective effect of IDO1 inhibition. Cell Rep Med 2023; 4:100941. [PMID: 36812891 PMCID: PMC9975322 DOI: 10.1016/j.xcrm.2023.100941] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 11/19/2022] [Accepted: 01/20/2023] [Indexed: 02/23/2023]
Abstract
By restoring tryptophan, indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors aim to reactivate anti-tumor T cells. However, a phase III trial assessing their clinical benefit failed, prompting us to revisit the role of IDO1 in tumor cells under T cell attack. We show here that IDO1 inhibition leads to an adverse protection of melanoma cells to T cell-derived interferon-gamma (IFNγ). RNA sequencing and ribosome profiling shows that IFNγ shuts down general protein translation, which is reversed by IDO1 inhibition. Impaired translation is accompanied by an amino acid deprivation-dependent stress response driving activating transcription factor-4 (ATF4)high/microphtalmia-associated transcription factor (MITF)low transcriptomic signatures, also in patient melanomas. Single-cell sequencing analysis reveals that MITF downregulation upon immune checkpoint blockade treatment predicts improved patient outcome. Conversely, MITF restoration in cultured melanoma cells causes T cell resistance. These results highlight the critical role of tryptophan and MITF in the melanoma response to T cell-derived IFNγ and uncover an unexpected negative consequence of IDO1 inhibition.
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Affiliation(s)
- Juliana C N Kenski
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Xinyao Huang
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - David W Vredevoogd
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Beaunelle de Bruijn
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joleen J H Traets
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Sofía Ibáñez-Molero
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Sebastiaan M Schieven
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Alex van Vliet
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Thomas Kuilman
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joanna Pozniak
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Fabricio Loayza-Puch
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Alexandra M Terry
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Judith Müller
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Meike E W Logtenberg
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Marjolein de Bruijn
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pierre Levy
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pierre-René Körner
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, OX OX3 7DQ, UK
| | - Ton N Schumacher
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
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Lasheras-Otero I, Feliu I, Maillo A, Moreno H, Redondo-Muñoz M, Aldaz P, Bocanegra A, Olias-Arjona A, Lecanda F, Fernandez-Irigoyen J, Santamaria E, Larrayoz IM, Gomez-Cabrero D, Wellbrock C, Vicent S, Arozarena I. The Regulators of Peroxisomal Acyl-Carnitine Shuttle CROT and CRAT Promote Metastasis in Melanoma. J Invest Dermatol 2023; 143:305-316.e5. [PMID: 36058299 DOI: 10.1016/j.jid.2022.08.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/26/2022] [Accepted: 08/03/2022] [Indexed: 01/25/2023]
Abstract
Circulating tumor cells are the key link between a primary tumor and distant metastases, but once in the bloodstream, loss of adhesion induces cell death. To identify the mechanisms relevant for melanoma circulating tumor cell survival, we performed RNA sequencing and discovered that detached melanoma cells and isolated melanoma circulating tumor cells rewire lipid metabolism by upregulating fatty acid (FA) transport and FA beta-oxidation‒related genes. In patients with melanoma, high expression of FA transporters and FA beta-oxidation enzymes significantly correlates with reduced progression-free and overall survival. Among the highest expressed regulators in melanoma circulating tumor cells were the carnitine transferases carnitine O-octanoyltransferase and carnitine acetyltransferase, which control the shuttle of peroxisome-derived medium-chain FAs toward mitochondria to fuel mitochondrial FA beta-oxidation. Knockdown of carnitine O-octanoyltransferase or carnitine acetyltransferase and short-term treatment with peroxisomal or mitochondrial FA beta-oxidation inhibitors thioridazine or ranolazine suppressed melanoma metastasis in mice. Carnitine O-octanoyltransferase and carnitine acetyltransferase depletion could be rescued by medium-chain FA supplementation, indicating that the peroxisomal supply of FAs is crucial for the survival of nonadherent melanoma cells. Our study identifies targeting the FA-based cross-talk between peroxisomes and mitochondria as a potential therapeutic opportunity to challenge melanoma progression. Moreover, the discovery of the antimetastatic activity of the Food and Drug Administration‒approved drug ranolazine carries translational potential.
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Affiliation(s)
- Irene Lasheras-Otero
- Cancer Signaling Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Iker Feliu
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Program in Solid Tumors, Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Alberto Maillo
- Translational Bioinformatics Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain
| | - Haritz Moreno
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Program in Solid Tumors, Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Marta Redondo-Muñoz
- Cancer Signaling Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Paula Aldaz
- Cancer Signaling Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Ana Bocanegra
- Oncoimmunology Group, Navarrabiomed, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain
| | - Ana Olias-Arjona
- Cancer Signaling Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Fernando Lecanda
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Program in Solid Tumors, Centre for Applied Medical Research, University of Navarra, Pamplona, Spain; Center for Biomedical Research Network on Cancer (CIBERONC), Madrid, Spain; Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain
| | - Joaquin Fernandez-Irigoyen
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Proteomics Platform, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain
| | - Enrique Santamaria
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Clinical Neuroproteomics Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain
| | - Ignacio M Larrayoz
- Biomarkers and Molecular Signaling Group, Center for Biomedical Research of La Rioja (CIBIR), Foundation Rioja Salud, Logroño, Spain; Pre-departmental Nursing Unit, University of La Rioja (UR), Logroño, La Rioja, Spain
| | - David Gomez-Cabrero
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Translational Bioinformatics Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Claudia Wellbrock
- Cancer Signaling Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain
| | - Silvestre Vicent
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Program in Solid Tumors, Centre for Applied Medical Research, University of Navarra, Pamplona, Spain; Center for Biomedical Research Network on Cancer (CIBERONC), Madrid, Spain
| | - Imanol Arozarena
- Cancer Signaling Unit, Navarrabiomed, University Hospital of Navarra (HUN), Public University of Navarra (UPNA), Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.
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38
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Hossain SM, Eccles MR. Phenotype Switching and the Melanoma Microenvironment; Impact on Immunotherapy and Drug Resistance. Int J Mol Sci 2023; 24:ijms24021601. [PMID: 36675114 PMCID: PMC9864717 DOI: 10.3390/ijms24021601] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Melanoma, a highly heterogeneous tumor, is comprised of a functionally diverse spectrum of cell phenotypes and subpopulations, including stromal cells in the tumor microenvironment (TME). Melanoma has been shown to dynamically shift between different transcriptional states or phenotypes. This is referred to as phenotype switching in melanoma, and it involves switching between quiescent and proliferative cell cycle states, and dramatic shifts in invasiveness, as well as changes in signaling pathways in the melanoma cells, and immune cell composition in the TME. Melanoma cell plasticity is associated with altered gene expression in immune cells and cancer-associated fibroblasts, as well as changes in extracellular matrix, which drive the metastatic cascade and therapeutic resistance. Therefore, resistance to therapy in melanoma is not only dependent on genetic evolution, but it has also been suggested to be driven by gene expression changes and adaptive phenotypic cell plasticity. This review discusses recent findings in melanoma phenotype switching, immunotherapy resistance, and the balancing of the homeostatic TME between the different melanoma cell subpopulations. We also discuss future perspectives of the biology of neural crest-like state(s) in melanoma.
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Affiliation(s)
- Sultana Mehbuba Hossain
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand
| | - Michael R. Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland 1010, New Zealand
- Correspondence:
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39
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Hattori T, Maso L, Araki KY, Koide A, Hayman J, Akkapeddi P, Bang I, Neel BG, Koide S. Creating MHC-Restricted Neoantigens with Covalent Inhibitors That Can Be Targeted by Immune Therapy. Cancer Discov 2023; 13:132-145. [PMID: 36250888 PMCID: PMC9827112 DOI: 10.1158/2159-8290.cd-22-1074] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 01/16/2023]
Abstract
Intracellular oncoproteins can be inhibited with targeted therapy, but responses are not durable. Immune therapies can be curative, but most oncogene-driven tumors are unresponsive to these agents. Fragments of intracellular oncoproteins can act as neoantigens presented by the major histocompatibility complex (MHC), but recognizing minimal differences between oncoproteins and their normal counterparts is challenging. We have established a platform technology that exploits hapten-peptide conjugates generated by covalent inhibitors to create distinct neoantigens that selectively mark cancer cells. Using the FDA-approved covalent inhibitors sotorasib and osimertinib, we developed "HapImmune" antibodies that bind to drug-peptide conjugate/MHC complexes but not to the free drugs. A HapImmune-based bispecific T-cell engager selectively and potently kills sotorasib-resistant lung cancer cells upon sotorasib treatment. Notably, it is effective against KRASG12C-mutant cells with different HLA supertypes, HLA-A*02 and A*03/11, suggesting loosening of MHC restriction. Our strategy creates targetable neoantigens by design, unifying targeted and immune therapies. SIGNIFICANCE Targeted therapies against oncoproteins often have dramatic initial efficacy but lack durability. Immunotherapies can be curative, yet most tumors fail to respond. We developed a generalizable technology platform that exploits hapten-peptides generated by covalent inhibitors as neoantigens presented on MHC to enable engineered antibodies to selectively kill drug-resistant cancer cells. See related commentary by Cox et al., p. 19. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Takamitsu Hattori
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York.,Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York
| | - Lorenzo Maso
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Kiyomi Y. Araki
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Akiko Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York.,Division of Hematology Oncology, Department of Medicine, New York University Grossman School of Medicine, New York, New York
| | - James Hayman
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Padma Akkapeddi
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Injin Bang
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Benjamin G. Neel
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York.,Division of Hematology Oncology, Department of Medicine, New York University Grossman School of Medicine, New York, New York.,Corresponding Authors: Shohei Koide, Smilow Research Center, Room 1105, 522 First Avenue, New York, NY 10016. Phone: 646-501-4601; E-mail: ; and Benjamin G. Neel, Smilow Research Center, Suite 1201, 522 First Avenue, New York, NY 10016. Phone: 212-263-3019; E-mail:
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York.,Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York.,Corresponding Authors: Shohei Koide, Smilow Research Center, Room 1105, 522 First Avenue, New York, NY 10016. Phone: 646-501-4601; E-mail: ; and Benjamin G. Neel, Smilow Research Center, Suite 1201, 522 First Avenue, New York, NY 10016. Phone: 212-263-3019; E-mail:
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40
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Moore PC, Henderson KW, Classon M. The epigenome and the many facets of cancer drug tolerance. Adv Cancer Res 2023; 158:1-39. [PMID: 36990531 DOI: 10.1016/bs.acr.2022.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The use of chemotherapeutic agents and the development of new cancer therapies over the past few decades has consequently led to the emergence of myriad therapeutic resistance mechanisms. Once thought to be explicitly driven by genetics, the coupling of reversible sensitivity and absence of pre-existing mutations in some tumors opened the way for discovery of drug-tolerant persisters (DTPs): slow-cycling subpopulations of tumor cells that exhibit reversible sensitivity to therapy. These cells confer multi-drug tolerance, to targeted and chemotherapies alike, until the residual disease can establish a stable, drug-resistant state. The DTP state can exploit a multitude of distinct, yet interlaced, mechanisms to survive otherwise lethal drug exposures. Here, we categorize these multi-faceted defense mechanisms into unique Hallmarks of Cancer Drug Tolerance. At the highest level, these are comprised of heterogeneity, signaling plasticity, differentiation, proliferation/metabolism, stress management, genomic integrity, crosstalk with the tumor microenvironment, immune escape, and epigenetic regulatory mechanisms. Of these, epigenetics was both one of the first proposed means of non-genetic resistance and one of the first discovered. As we describe in this review, epigenetic regulatory factors are involved in most facets of DTP biology, positioning this hallmark as an overarching mediator of drug tolerance and a potential avenue to novel therapies.
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Corrales E, Levit-Zerdoun E, Metzger P, Mertes R, Lehmann A, Münch J, Lemke S, Kowar S, Boerries M. PI3K/AKT signaling allows for MAPK/ERK pathway independency mediating dedifferentiation-driven treatment resistance in melanoma. Cell Commun Signal 2022; 20:187. [PMID: 36434616 PMCID: PMC9700886 DOI: 10.1186/s12964-022-00989-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/08/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Current therapeutic management of advanced melanoma patients largely depends on their BRAF mutation status. However, the vast heterogeneity of the tumors hampers the success of therapies targeting the MAPK/ERK pathway alone. Dissecting this heterogeneity will contribute to identifying key players in the oncogenic progression to tailor more effective therapies. METHODS We performed a comprehensive molecular and phenotypic characterization of a panel of patient-derived BRAFV600E-positive melanoma cell lines. Transcriptional profiling was used to identify groups of coregulated genes whose expression relates to an increased migratory potential and a higher resistance. RESULTS A decrease in sensitivity to MAPK/ERK pathway inhibition with vemurafenib or trametinib corresponded with an increasing quiescence and migratory properties of the cells. This was accompanied by the loss of transcriptional signatures of melanocytic differentiation, and the gain of stem cell features that conferred highly-resistant/mesenchymal-like cells with increased xenobiotic efflux capacity. Nevertheless, targeting of the implicated ABC transporters did not improve the response to vemurafenib, indicating that incomplete BRAF inhibition due to reduced drug uptake is not a main driver of resistance. Rather, indifference to MAPK/ERK pathway inhibition arose from the activation of compensatory signaling cascades. The PI3K/AKT pathway in particular showed a higher activity in mesenchymal-like cells, conferring a lower dependency on MAPK/ERK signaling and supporting stem-like properties that could be reverted by dual PI3K/mTOR inhibition with dactolisib. CONCLUSIONS In case of MAPK/ERK independency, therapeutic focus may be shifted to the PI3K/AKT pathway to overcome late-stage resistance in melanoma tumors that have acquired a mesenchymal phenotype. Video Abstract.
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Affiliation(s)
- Eyleen Corrales
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Medicine, Medical Center-University of Freiburg, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany ,grid.5963.9Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Ella Levit-Zerdoun
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Medicine, Medical Center-University of Freiburg, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Freiburg, Germany
| | - Patrick Metzger
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Medicine, Medical Center-University of Freiburg, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
| | - Ralf Mertes
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Medicine, Medical Center-University of Freiburg, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
| | - Ariane Lehmann
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Medicine, Medical Center-University of Freiburg, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
| | - Julia Münch
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
| | - Steffen Lemke
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
| | - Silke Kowar
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Medicine, Medical Center-University of Freiburg, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
| | - Melanie Boerries
- grid.5963.9Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany ,grid.5963.9Faculty of Medicine, Medical Center-University of Freiburg, Institute of Medical Bioinformatics and Systems Medicine (IBSM), University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Freiburg, Germany
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42
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Zhu EY, Riordan JD, Vanneste M, Henry MD, Stipp CS, Dupuy AJ. SRC-RAC1 signaling drives drug resistance to BRAF inhibition in de-differentiated cutaneous melanomas. NPJ Precis Oncol 2022; 6:74. [PMID: 36271142 PMCID: PMC9587254 DOI: 10.1038/s41698-022-00310-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 08/31/2022] [Indexed: 11/09/2022] Open
Abstract
Rare gain-of-function mutations in RAC1 drive drug resistance to targeted BRAF inhibition in cutaneous melanoma. Here, we show that wildtype RAC1 is a critical driver of growth and drug resistance, but only in a subset of melanomas with elevated markers of de-differentiation. Similarly, SRC inhibition also selectively sensitized de-differentiated melanomas to BRAF inhibition. One possible mechanism may be the suppression of the de-differentiated state, as SRC and RAC1 maintained markers of de-differentiation in human melanoma cells. The functional differences between melanoma subtypes suggest that the clinical management of cutaneous melanoma can be enhanced by the knowledge of differentiation status. To simplify the task of classification, we developed a binary classification strategy based on a small set of ten genes. Using this gene set, we reliably determined the differentiation status previously defined by hundreds of genes. Overall, our study informs strategies that enhance the precision of BRAFi by discovering unique vulnerabilities of the de-differentiated cutaneous melanoma subtype and creating a practical method to resolve differentiation status.
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Affiliation(s)
- Eliot Y Zhu
- Department of Anatomy and Cell Biology, The University of Iowa, Iowa City, IA, USA.,Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA.,Cancer Biology Graduate Program, The University of Iowa, Iowa City, IA, USA.,The Medical Scientist Training Program, The University of Iowa, Iowa City, IA, USA
| | - Jesse D Riordan
- Department of Anatomy and Cell Biology, The University of Iowa, Iowa City, IA, USA.,Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA
| | - Marion Vanneste
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA.,Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA, USA
| | - Michael D Henry
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA.,Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA, USA
| | - Christopher S Stipp
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA.,Department of Biology, The University of Iowa, Iowa City, IA, USA
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, The University of Iowa, Iowa City, IA, USA. .,Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA.
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43
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Karami Fath M, Azargoonjahromi A, Soofi A, Almasi F, Hosseinzadeh S, Khalili S, Sheikhi K, Ferdousmakan S, Owrangi S, Fahimi M, Zalpoor H, Nabi Afjadi M, Payandeh Z, Pourzardosht N. Current understanding of epigenetics role in melanoma treatment and resistance. Cancer Cell Int 2022; 22:313. [PMID: 36224606 PMCID: PMC9555085 DOI: 10.1186/s12935-022-02738-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/19/2022] [Indexed: 11/30/2022] Open
Abstract
Melanoma is the most aggressive form of skin cancer resulting from genetic mutations in melanocytes. Several factors have been considered to be involved in melanoma progression, including genetic alteration, processes of damaged DNA repair, and changes in mechanisms of cell growth and proliferation. Epigenetics is the other factor with a crucial role in melanoma development. Epigenetic changes have become novel targets for treating patients suffering from melanoma. These changes can alter the expression of microRNAs and their interaction with target genes, which involves cell growth, differentiation, or even death. Given these circumstances, we conducted the present review to discuss the melanoma risk factors and represent the current knowledge about the factors related to its etiopathogenesis. Moreover, various epigenetic pathways, which are involved in melanoma progression, treatment, and chemo-resistance, as well as employed epigenetic factors as a solution to the problems, will be discussed in detail.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | | | - Asma Soofi
- Department of Physical Chemistry, School of Chemistry, College of Sciences, University of Tehran, Tehran, Iran
| | - Faezeh Almasi
- Pharmaceutical Biotechnology Lab, Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Shahnaz Hosseinzadeh
- Department of Microbiology, Parasitology and Immunology, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Kamran Sheikhi
- School of Medicine, Kurdistan University of Medical Sciences, Kurdistan, Iran
| | - Saeid Ferdousmakan
- Department of Pharmacy Practice, Nargund College of Pharmacy, Bangalore, 560085, India
| | - Soroor Owrangi
- Student Research Committe, Fasa University of Medical Sciences, Fasa, Iran
| | | | - Hamidreza Zalpoor
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran
| | - Mohsen Nabi Afjadi
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.
| | - Zahra Payandeh
- Department Medical Biochemistry and Biophysics, Division Medical Inflammation Research, Karolinska Institute, Stockholm, Sweden.
| | - Navid Pourzardosht
- Biochemistry Department, Guilan University of Medical Sciences, Rasht, Iran.
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44
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Chan JM, Zaidi S, Love JR, Zhao JL, Setty M, Wadosky KM, Gopalan A, Choo ZN, Persad S, Choi J, LaClair J, Lawrence KE, Chaudhary O, Xu T, Masilionis I, Linkov I, Wang S, Lee C, Barlas A, Morris MJ, Mazutis L, Chaligne R, Chen Y, Goodrich DW, Karthaus WR, Pe’er D, Sawyers CL. Lineage plasticity in prostate cancer depends on JAK/STAT inflammatory signaling. Science 2022; 377:1180-1191. [PMID: 35981096 PMCID: PMC9653178 DOI: 10.1126/science.abn0478] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Drug resistance in cancer is often linked to changes in tumor cell state or lineage, but the molecular mechanisms driving this plasticity remain unclear. Using murine organoid and genetically engineered mouse models, we investigated the causes of lineage plasticity in prostate cancer and its relationship to antiandrogen resistance. We found that plasticity initiates in an epithelial population defined by mixed luminal-basal phenotype and that it depends on increased Janus kinase (JAK) and fibroblast growth factor receptor (FGFR) activity. Organoid cultures from patients with castration-resistant disease harboring mixed-lineage cells reproduce the dependency observed in mice by up-regulating luminal gene expression upon JAK and FGFR inhibitor treatment. Single-cell analysis confirms the presence of mixed-lineage cells with increased JAK/STAT (signal transducer and activator of transcription) and FGFR signaling in a subset of patients with metastatic disease, with implications for stratifying patients for clinical trials.
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Affiliation(s)
- Joseph M. Chan
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Samir Zaidi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Genitourinary Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jillian R. Love
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Current address: Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Lausanne, 1015 Switzerland
| | - Jimmy L. Zhao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Manu Setty
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Current address: Basic sciences division and translational data science IRC, Fred Hutchinson Cancer research center
| | - Kristine M. Wadosky
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Anuradha Gopalan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zi-Ning Choo
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sitara Persad
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Justin LaClair
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kayla E Lawrence
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ojasvi Chaudhary
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tianhao Xu
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ignas Masilionis
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Irina Linkov
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shangqian Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Cindy Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Afsar Barlas
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael J. Morris
- Department of Genitourinary Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Linas Mazutis
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Institute of Biotechnology, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Ronan Chaligne
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David W. Goodrich
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Wouter R. Karthaus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Current address: Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Lausanne, 1015 Switzerland
| | - Dana Pe’er
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Howard Hughes Medical Institute
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Howard Hughes Medical Institute
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45
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Comandante-Lou N, Baumann DG, Fallahi-Sichani M. AP-1 transcription factor network explains diverse patterns of cellular plasticity in melanoma cells. Cell Rep 2022; 40:111147. [PMID: 35926467 DOI: 10.1016/j.celrep.2022.111147] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/04/2022] [Accepted: 07/07/2022] [Indexed: 12/28/2022] Open
Abstract
Cellular plasticity associated with fluctuations in transcriptional programs allows individual cells in a tumor to adopt heterogeneous differentiation states and switch phenotype during their adaptive responses to therapies. Despite increasing knowledge of such transcriptional programs, the molecular basis of cellular plasticity remains poorly understood. Here, we combine multiplexed transcriptional and protein measurements at population and single-cell levels with multivariate statistical modeling to show that the state of AP-1 transcription factor network plays a unifying role in explaining diverse patterns of plasticity in melanoma. We find that a regulated balance among AP-1 factors cJUN, JUND, FRA2, FRA1, and cFOS determines the intrinsic diversity of differentiation states and adaptive responses to MAPK inhibitors in melanoma cells. Perturbing this balance through genetic depletion of specific AP-1 proteins, or by MAPK inhibitors, shifts cellular heterogeneity in a predictable fashion. Thus, AP-1 may serve as a critical node for manipulating cellular plasticity with potential therapeutic implications.
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Affiliation(s)
- Natacha Comandante-Lou
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Douglas G Baumann
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Mohammad Fallahi-Sichani
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; UVA Cancer Center, University of Virginia, Charlottesville, VA 22908, USA.
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46
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Falletta P, Goding CR, Vivas-García Y. Connecting Metabolic Rewiring With Phenotype Switching in Melanoma. Front Cell Dev Biol 2022; 10:930250. [PMID: 35912100 PMCID: PMC9334657 DOI: 10.3389/fcell.2022.930250] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Melanoma is a complex and aggressive cancer type that contains different cell subpopulations displaying distinct phenotypes within the same tumor. Metabolic reprogramming, a hallmark of cell transformation, is essential for melanoma cells to adopt different phenotypic states necessary for adaptation to changes arising from a dynamic milieu and oncogenic mutations. Increasing evidence demonstrates how melanoma cells can exhibit distinct metabolic profiles depending on their specific phenotype, allowing adaptation to hostile microenvironmental conditions, such as hypoxia or nutrient depletion. For instance, increased glucose consumption and lipid anabolism are associated with proliferation, while a dependency on exogenous fatty acids and an oxidative state are linked to invasion and metastatic dissemination. How these different metabolic dependencies are integrated with specific cell phenotypes is poorly understood and little is known about metabolic changes underpinning melanoma metastasis. Recent evidence suggests that metabolic rewiring engaging transitions to invasion and metastatic progression may be dependent on several factors, such as specific oncogenic programs or lineage-restricted mechanisms controlling cell metabolism, intra-tumor microenvironmental cues and anatomical location of metastasis. In this review we highlight how the main molecular events supporting melanoma metabolic rewiring and phenotype-switching are parallel and interconnected events that dictate tumor progression and metastatic dissemination through interplay with the tumor microenvironment.
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Affiliation(s)
- Paola Falletta
- Vita-Salute San Raffaele University, Milan, Italy
- Experimental Imaging Center, IRCCS Ospedale San Raffaele, Milan, Italy
- *Correspondence: Paola Falletta, ; Colin R. Goding, ; Yurena Vivas-García, ,
| | - Colin R. Goding
- Nuffield Department of Clinical Medicine, Ludwig Cancer Research, University of Oxford, Oxford, United Kingdom
- *Correspondence: Paola Falletta, ; Colin R. Goding, ; Yurena Vivas-García, ,
| | - Yurena Vivas-García
- Nuffield Department of Clinical Medicine, Ludwig Cancer Research, University of Oxford, Oxford, United Kingdom
- *Correspondence: Paola Falletta, ; Colin R. Goding, ; Yurena Vivas-García, ,
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47
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Zhu J, Yan M, Yan H, Xu L, Jiang Z, Liao G, Zhou Y, Liu W, Liang X, Li X, Xiao Y, Zhang Y. Single-Cell Transcriptomic Analysis Reveals the Crosstalk Propensity Between the Tumor Intermediate State and the CD8+ T Exhausted State to be Associated with Clinical Benefits in Melanoma. Front Immunol 2022; 13:766852. [PMID: 35903095 PMCID: PMC9314667 DOI: 10.3389/fimmu.2022.766852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 06/20/2022] [Indexed: 11/14/2022] Open
Abstract
Heterogeneous crosstalk between tumor cells and CD8+ T cells leads to substantial variation in clinical benefits from immunotherapy in melanoma. Due to spatial distribution and functional state heterogeneity, it is still unknown whether there is a crosstalk propensity between tumor cells and CD8+ T cells in melanoma, and how this crosstalk propensity affects the clinical outcome of patients. Using public single-cell transcriptome data, extensive heterogeneous functional states and ligand–receptor interactions of tumor cells and CD8+ T cells were revealed in melanoma. Furthermore, based on the association between cell–cell communication intensity and cell state activity in a single cell, we identified a crosstalk propensity between the tumor intermediate state and the CD8+ T exhausted state. This crosstalk propensity was further verified by pseudo-spatial proximity, spatial co-location, and the intra/intercellular signal transduction network. At the sample level, the tumor intermediate state and the CD8+ T exhausted state synergistically indicated better prognosis and both reduced in immunotherapy-resistant samples. The risk groups defined based on these two cell states could comprehensively reflect tumor genomic mutations and anti-tumor immunity information. The low-risk group had a higher BRAF mutation fraction as well as stronger antitumor immune response. Our findings highlighted the crosstalk propensity between the tumor intermediate state and the CD8+ T exhausted state, which may serve as a reference to guide the development of diagnostic biomarkers for risk stratification and therapeutic targets for new therapeutic strategies.
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Affiliation(s)
- Jiali Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haoteng Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zedong Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wei Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xin Liang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of High Throughput Omics Big Data for Cold Region’s Major Diseases in Heilongjiang Province, Harbin Medical University, Harbin, China
- *Correspondence: Yunpeng Zhang, ; Yun Xiao, ; Xia Li,
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of High Throughput Omics Big Data for Cold Region’s Major Diseases in Heilongjiang Province, Harbin Medical University, Harbin, China
- *Correspondence: Yunpeng Zhang, ; Yun Xiao, ; Xia Li,
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of High Throughput Omics Big Data for Cold Region’s Major Diseases in Heilongjiang Province, Harbin Medical University, Harbin, China
- *Correspondence: Yunpeng Zhang, ; Yun Xiao, ; Xia Li,
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48
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Andrews MC, Oba J, Wu CJ, Zhu H, Karpinets T, Creasy CA, Forget MA, Yu X, Song X, Mao X, Robertson AG, Romano G, Li P, Burton EM, Lu Y, Sloane RS, Wani KM, Rai K, Lazar AJ, Haydu LE, Bustos MA, Shen J, Chen Y, Morgan MB, Wargo JA, Kwong LN, Haymaker CL, Grimm EA, Hwu P, Hoon DSB, Zhang J, Gershenwald JE, Davies MA, Futreal PA, Bernatchez C, Woodman SE. Multi-modal molecular programs regulate melanoma cell state. Nat Commun 2022; 13:4000. [PMID: 35810190 PMCID: PMC9271073 DOI: 10.1038/s41467-022-31510-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/20/2022] [Indexed: 12/12/2022] Open
Abstract
Melanoma cells display distinct intrinsic phenotypic states. Here, we seek to characterize the molecular regulation of these states using multi-omic analyses of whole exome, transcriptome, microRNA, long non-coding RNA and DNA methylation data together with reverse-phase protein array data on a panel of 68 highly annotated early passage melanoma cell lines. We demonstrate that clearly defined cancer cell intrinsic transcriptomic programs are maintained in melanoma cells ex vivo and remain highly conserved within melanoma tumors, are associated with distinct immune features within tumors, and differentially correlate with checkpoint inhibitor and adoptive T cell therapy efficacy. Through integrative analyses we demonstrate highly complex multi-omic regulation of melanoma cell intrinsic programs that provide key insights into the molecular maintenance of phenotypic states. These findings have implications for cancer biology and the identification of new therapeutic strategies. Further, these deeply characterized cell lines will serve as an invaluable resource for future research in the field.
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Affiliation(s)
- Miles C. Andrews
- grid.1002.30000 0004 1936 7857Department of Medicine, Monash University, Melbourne, VIC Australia ,grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Junna Oba
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.26091.3c0000 0004 1936 9959Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Chang-Jiun Wu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Haifeng Zhu
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Tatiana Karpinets
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Caitlin A. Creasy
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Marie-Andrée Forget
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaoxing Yu
- grid.26091.3c0000 0004 1936 9959Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Xingzhi Song
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xizeng Mao
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - A. Gordon Robertson
- grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Center, BC Cancer, Vancouver, BC Canada ,Dxige Research Inc., Courtenay, BC Canada
| | - Gabriele Romano
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Peng Li
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Elizabeth M. Burton
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Yiling Lu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Robert Szczepaniak Sloane
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Khalida M. Wani
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Kunal Rai
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Alexander J. Lazar
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Lauren E. Haydu
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Matias A. Bustos
- grid.416507.10000 0004 0450 0360Departments of Translational Molecular Medicine and Genomic Sequencing Center, St John’s Cancer Institute, Providence Saint John’s Health Center, Santa Monica, CA USA
| | - Jianjun Shen
- grid.240145.60000 0001 2291 4776Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX USA
| | - Yueping Chen
- grid.240145.60000 0001 2291 4776Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX USA
| | - Margaret B. Morgan
- grid.240145.60000 0001 2291 4776Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Jennifer A. Wargo
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Lawrence N. Kwong
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Cara L. Haymaker
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Elizabeth A. Grimm
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Patrick Hwu
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.468198.a0000 0000 9891 5233H Lee Moffitt Cancer Center, Tampa, FL USA
| | - Dave S. B. Hoon
- grid.416507.10000 0004 0450 0360Departments of Translational Molecular Medicine and Genomic Sequencing Center, St John’s Cancer Institute, Providence Saint John’s Health Center, Santa Monica, CA USA
| | - Jianhua Zhang
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Jeffrey E. Gershenwald
- grid.240145.60000 0001 2291 4776Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Michael A. Davies
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - P. Andrew Futreal
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Chantale Bernatchez
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Biologics Development, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Scott E. Woodman
- grid.240145.60000 0001 2291 4776Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
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Suppression of heparan sulfation re-sensitizes YAP1-driven melanoma to MAPK pathway inhibitors. Oncogene 2022; 41:3953-3968. [PMID: 35798875 PMCID: PMC9355870 DOI: 10.1038/s41388-022-02400-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 11/08/2022]
Abstract
Accumulating evidence identifies non-genetic mechanisms substantially contributing to drug resistance in cancer patients. Preclinical and clinical data implicate the transcriptional co-activators YAP1 and its paralog TAZ in resistance to multiple targeted therapies, highlighting the strong need for therapeutic strategies overcoming YAP1/TAZ-mediated resistance across tumor entities. Here, we show particularly high YAP1/TAZ activity in MITFlow/AXLhigh melanomas characterized by resistance to MAPK pathway inhibition and broad receptor tyrosine kinase activity. To uncover genetic dependencies of melanoma cells with high YAP1/TAZ activity, we used a genome-wide CRISPR/Cas9 functional screen and identified SLC35B2, the 3′-phosphoadenosine-5′-phosphosulfate transporter of the Golgi apparatus, as an essential gene for YAP1/TAZ-driven drug resistance. SLC35B2 expression correlates with tumor progression, and its loss decreases heparan sulfate expression, reduces receptor tyrosine kinase activity, and sensitizes resistant melanoma cells to BRAF inhibition in vitro and in vivo. Thus, targeting heparan sulfation via SLC35B2 represents a novel approach for breaking receptor tyrosine kinase-mediated resistance to MAPK pathway inhibitors.
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50
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Biermann J, Melms JC, Amin AD, Wang Y, Caprio LA, Karz A, Tagore S, Barrera I, Ibarra-Arellano MA, Andreatta M, Fullerton BT, Gretarsson KH, Sahu V, Mangipudy VS, Nguyen TTT, Nair A, Rogava M, Ho P, Koch PD, Banu M, Humala N, Mahajan A, Walsh ZH, Shah SB, Vaccaro DH, Caldwell B, Mu M, Wünnemann F, Chazotte M, Berhe S, Luoma AM, Driver J, Ingham M, Khan SA, Rapisuwon S, Slingluff CL, Eigentler T, Röcken M, Carvajal R, Atkins MB, Davies MA, Agustinus A, Bakhoum SF, Azizi E, Siegelin M, Lu C, Carmona SJ, Hibshoosh H, Ribas A, Canoll P, Bruce JN, Bi WL, Agrawal P, Schapiro D, Hernando E, Macosko EZ, Chen F, Schwartz GK, Izar B. Dissecting the treatment-naive ecosystem of human melanoma brain metastasis. Cell 2022; 185:2591-2608.e30. [PMID: 35803246 PMCID: PMC9677434 DOI: 10.1016/j.cell.2022.06.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/08/2022] [Accepted: 06/06/2022] [Indexed: 10/17/2022]
Abstract
Melanoma brain metastasis (MBM) frequently occurs in patients with advanced melanoma; yet, our understanding of the underlying salient biology is rudimentary. Here, we performed single-cell/nucleus RNA-seq in 22 treatment-naive MBMs and 10 extracranial melanoma metastases (ECMs) and matched spatial single-cell transcriptomics and T cell receptor (TCR)-seq. Cancer cells from MBM were more chromosomally unstable, adopted a neuronal-like cell state, and enriched for spatially variably expressed metabolic pathways. Key observations were validated in independent patient cohorts, patient-derived MBM/ECM xenograft models, RNA/ATAC-seq, proteomics, and multiplexed imaging. Integrated spatial analyses revealed distinct geography of putative cancer immune evasion and evidence for more abundant intra-tumoral B to plasma cell differentiation in lymphoid aggregates in MBM. MBM harbored larger fractions of monocyte-derived macrophages and dysfunctional TOX+CD8+ T cells with distinct expression of immune checkpoints. This work provides comprehensive insights into MBM biology and serves as a foundational resource for further discovery and therapeutic exploration.
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Affiliation(s)
- Jana Biermann
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA
| | - Lindsay A Caprio
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alcida Karz
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Somnath Tagore
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Irving Barrera
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Miguel A Ibarra-Arellano
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
| | - Massimo Andreatta
- Department of Oncology UNIL CHUV, Lausanne Branch, Ludwig Institute for Cancer Research Lausanne, CHUV and University of Lausanne, Lausanne, 1066 Épalinges, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Benjamin T Fullerton
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kristjan H Gretarsson
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Varun Sahu
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Vaibhav S Mangipudy
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Trang T T Nguyen
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Ajay Nair
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Patricia Ho
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter D Koch
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Matei Banu
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nelson Humala
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aayushi Mahajan
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zachary H Walsh
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Shivem B Shah
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Daniel H Vaccaro
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Blake Caldwell
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Michael Mu
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Florian Wünnemann
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
| | - Margot Chazotte
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
| | - Simon Berhe
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Adrienne M Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA
| | - Joseph Driver
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Ingham
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shaheer A Khan
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Suthee Rapisuwon
- Division of Hematology/Oncology, Medstar Washington Cancer Institute, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Craig L Slingluff
- Department of Surgery, University of Virginia, Charlottesville, VA, USA
| | - Thomas Eigentler
- Department of Dermatology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Dermatology, Venereology and Allergology, 10117, Berlin, Germany
| | - Martin Röcken
- Department of Dermatology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Richard Carvajal
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michael B Atkins
- Georgetown-Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Albert Agustinus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pharmacology, Weill Cornell Graduate School, New York, NY 10065, USA
| | - Samuel F Bakhoum
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elham Azizi
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA
| | - Markus Siegelin
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Santiago J Carmona
- Department of Oncology UNIL CHUV, Lausanne Branch, Ludwig Institute for Cancer Research Lausanne, CHUV and University of Lausanne, Lausanne, 1066 Épalinges, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Antoni Ribas
- Department of Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90024, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Jeffrey N Bruce
- Department of Neurological Surgery, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Praveen Agrawal
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Denis Schapiro
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Eva Hernando
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gary K Schwartz
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.
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