1
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Kumar V, Sabaté-Cadenas X, Soni I, Stern E, Vias C, Ginsberg D, Romá-Mateo C, Pulido R, Dodel M, Mardakheh FK, Shkumatava A, Shaulian E. The lincRNA JUNI regulates the stress-dependent induction of c-Jun, cellular migration and survival through the modulation of the DUSP14-JNK axis. Oncogene 2024; 43:1608-1619. [PMID: 38565943 PMCID: PMC11108773 DOI: 10.1038/s41388-024-03021-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/17/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Cancer cells employ adaptive mechanisms to survive various stressors, including genotoxic drugs. Understanding the factors promoting survival is crucial for developing effective treatments. In this study, we unveil a previously unexplored long non-coding RNA, JUNI (JUN-DT, LINC01135), which is upregulated by genotoxic drugs through the activation of stress-activated MAPKs, JNK, and p38 and consequently exerts positive control over the expression of its adjacent gene product c-Jun, a well-known oncoprotein, which transduces signals to multiple transcriptional outputs. JUNI regulates cellular migration and has a crucial role in conferring cellular resistance to chemotherapeutic drugs or UV radiation. Depletion of JUNI markedly increases the sensitivity of cultured cells and spheroids to chemotherapeutic agents. We identified 57 proteins interacting with JUNI. The activity of one of them the MAPK phosphatase and inhibitor, DUSP14, is counteracted by JUNI, thereby, facilitating efficient JNK phosphorylation and c-Jun induction when cells are exposed to UV radiation. The antagonistic interplay with DUSP14 contributes not only to c-Jun induction but also augments the survival of UV-exposed cells. In summary, we introduce JUNI as a novel stress-inducible regulator of c-Jun, positioning it as a potential target for enhancing the sensitivity of cancer cells to chemotherapy.
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Affiliation(s)
- Vikash Kumar
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, 9112102, Jerusalem, Israel
| | - Xavier Sabaté-Cadenas
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005, France
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Isha Soni
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, 9112102, Jerusalem, Israel
| | - Esther Stern
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, 9112102, Jerusalem, Israel
- Gene Therapy Institute, Hadassah Hebrew University Medical Center and Faculty of Medicine, Hebrew University, Jerusalem, 9112102, Israel
| | - Carine Vias
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005, France
| | - Doron Ginsberg
- The Mina and Everard Goodman, Faculty of Life Science, Bar-Ilan University, Ramat Gan, Israel
| | - Carlos Romá-Mateo
- Department of Physiology, Facultat de Medicina i Odontologia, Universitat de València & Fundación Instituto de Investigación Sanitaria INCLIVA, 46010, Valencia, Spain
| | - Rafael Pulido
- Biobizkaia Health Research Institute, Barakaldo, 48903 Spain; & Ikerbasque, The Basque Foundation for Science, 48009, Bilbao, Spain
| | - Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Alena Shkumatava
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005, France
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Eitan Shaulian
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, 9112102, Jerusalem, Israel.
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2
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Runel G, Lopez-Ramirez N, Barbollat-Boutrand L, Cario M, Durand S, Grimont M, Schartl M, Dalle S, Caramel J, Chlasta J, Masse I. Cancer Cell Biomechanical Properties Accompany Tspan8-Dependent Cutaneous Melanoma Invasion. Cancers (Basel) 2024; 16:694. [PMID: 38398085 PMCID: PMC10887418 DOI: 10.3390/cancers16040694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
The intrinsic biomechanical properties of cancer cells remain poorly understood. To decipher whether cell stiffness modulation could increase melanoma cells' invasive capacity, we performed both in vitro and in vivo experiments exploring cell stiffness by atomic force microscopy (AFM). We correlated stiffness properties with cell morphology adaptation and the molecular mechanisms underlying epithelial-to-mesenchymal (EMT)-like phenotype switching. We found that melanoma cell stiffness reduction was systematically associated with the acquisition of invasive properties in cutaneous melanoma cell lines, human skin reconstructs, and Medaka fish developing spontaneous MAP-kinase-induced melanomas. We observed a systematic correlation of stiffness modulation with cell morphological changes towards mesenchymal characteristic gains. We accordingly found that inducing melanoma EMT switching by overexpressing the ZEB1 transcription factor, a major regulator of melanoma cell plasticity, was sufficient to decrease cell stiffness and transcriptionally induce tetraspanin-8-mediated dermal invasion. Moreover, ZEB1 expression correlated with Tspan8 expression in patient melanoma lesions. Our data suggest that intrinsic cell stiffness could be a highly relevant marker for human cutaneous melanoma development.
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Affiliation(s)
- Gaël Runel
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
- BioMeca, 60F, Bioserra 2, Av. Rockefeller, 69008 Lyon, France
| | - Noémie Lopez-Ramirez
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Laetitia Barbollat-Boutrand
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Muriel Cario
- National Reference Center for Rare Skin Disease, Department of Dermatology, University Hospital, INSERM 1035, 33000 Bordeaux, France
- AquiDerm, University Bordeaux, 33076 Bordeaux, France
| | - Simon Durand
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Maxime Grimont
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Manfred Schartl
- Developmental Biochemistry, University of Würzburg, 97074 Würzburg, Germany
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX 78666, USA
| | - Stéphane Dalle
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
- Dermatology Department, Hôpital Universitaire Lyon Sud, Hospices Civils de Lyon, 69495 Pierre-Bénite, France
| | - Julie Caramel
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
| | - Julien Chlasta
- BioMeca, 60F, Bioserra 2, Av. Rockefeller, 69008 Lyon, France
| | - Ingrid Masse
- Cancer Research Center of Lyon, CNRS UMR5286, Inserm U1052, University of Lyon, University Lyon 1, 69000 Lyon, France; (G.R.); (N.L.-R.)
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3
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Florent L, Saby C, Slimano F, Morjani H. BRAF V600-Mutated Metastatic Melanoma and Targeted Therapy Resistance: An Update of the Current Knowledge. Cancers (Basel) 2023; 15:cancers15092607. [PMID: 37174072 PMCID: PMC10177463 DOI: 10.3390/cancers15092607] [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: 03/31/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Melanoma is the most common cause of death in skin cancer due to its high metastatic potential. While targeted therapies have improved the care of patients with metastatic melanoma harboring the BRAFV600E mutation, these treatments are associated with a high frequency of resistance. Resistance factors are related to cellular adaptation as well as to changes in the tumor microenvironment. At the cellular level, resistance involves mutations, overexpression, activation, or inhibition of effectors involved in cell signaling pathways such as MAPK, PI3K/AKT, MITF, and epigenetic factors (miRNAs). In addition, several components of the melanoma microenvironment, such as soluble factors, collagen, and stromal cells also play a crucial role in this resistance. In fact, extracellular matrix remodeling impacts the physical and chemical properties with changes in the stiffness and acidity, respectively of the microenvironment. The cellular and immune components of the stroma are also affected, including immune cells and CAF. The aim of this manuscript is to review the mechanisms responsible for resistance to targeted therapies in BRAFV600E-mutated metastatic melanoma.
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Affiliation(s)
- Laetitia Florent
- Université de Reims Champagne-Ardenne, UFR de Pharmacie, BioSpecT EA 7506, 51097 Reims, France
| | - Charles Saby
- Université de Reims Champagne-Ardenne, UFR de Pharmacie, BioSpecT EA 7506, 51097 Reims, France
| | - Florian Slimano
- Université de Reims Champagne-Ardenne, UFR de Pharmacie, BioSpecT EA 7506, 51097 Reims, France
- CHU Reims, Department of Pharmacy, 51097 Reims, France
| | - Hamid Morjani
- Université de Reims Champagne-Ardenne, UFR de Pharmacie, BioSpecT EA 7506, 51097 Reims, France
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4
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Patel RP, Somasundram PM, Smith LK, Sheppard KE, McArthur GA. The therapeutic potential of targeting minimal residual disease in melanoma. Clin Transl Med 2023; 13:e1197. [PMID: 36967556 PMCID: PMC10040726 DOI: 10.1002/ctm2.1197] [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: 10/17/2022] [Revised: 01/18/2023] [Accepted: 01/29/2023] [Indexed: 03/28/2023] Open
Abstract
Background Cutaneous melanoma is a lethal form of skin cancer with morbidity and mortality rates highest amongst European, North American and Australasian populations. The developments of targeted therapies (TTs) directed at the oncogene BRAF and its downstream mediator MEK, and immune checkpoint inhibitors (ICI), have revolutionized the treatment of metastatic melanoma, improving patient outcomes. However, both TT and ICI have their limitations. Although TTs are associated with high initial response rates, these are typically short‐lived due to resistance. Conversely, although ICIs provide more durable responses, they have lower initial response rates. Due to these distinct yet complementary response profiles, it has been proposed that sequencing ICI with TT could lead to a high frequency of durable responses whilst circumventing the toxicity associated with combined ICI + TT treatment. However, several questions remain unanswered, including the mechanisms underpinning this synergy and the optimal sequencing strategy. The key to determining this is to uncover the biology of each phase of the therapeutic response. Aims and methods In this review, we show that melanoma responds to TT and ICI in three phases: early response, minimal residual disease (MRD) and disease progression. We explore the effects of ICI and TT on melanoma cells and the tumour immune microenvironment, with a particular focus on MRD which is predicted to underpin the development of acquired resistance in the third phase of response. Conclusion In doing so, we provide a new framework which may inform novel therapeutic approaches for melanoma, including optimal sequencing strategies and agents that target MRD, thereby ultimately improving clinical outcomes for patients.
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Affiliation(s)
- Riyaben P Patel
- Cancer Research DivisionPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Pretashini M Somasundram
- Faculty of MedicineDentistry and Health Sciences, University of MelbourneParkvilleVictoriaAustralia
| | - Lorey K. Smith
- Cancer Research DivisionPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Karen E. Sheppard
- Cancer Research DivisionPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Grant A. McArthur
- Cancer Research DivisionPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyUniversity of MelbourneParkvilleVictoriaAustralia
- Department of Medical OncologyPeter MacCallum Cancer CentreMelbourneVictoriaAustralia
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5
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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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6
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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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7
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Diazzi S, Baeri A, Fassy J, Lecacheur M, Marin-Bejar O, Girard CA, Lefevre L, Lacoux C, Irondelle M, Mounier C, Truchi M, Couralet M, Ohanna M, Carminati A, Berestjuk I, Larbret F, Gilot D, Vassaux G, Marine JC, Deckert M, Mari B, Tartare-Deckert S. Blockade of the pro-fibrotic reaction mediated by the miR-143/-145 cluster enhances the responses to targeted therapy in melanoma. EMBO Mol Med 2022; 14:e15295. [PMID: 35156321 PMCID: PMC8899916 DOI: 10.15252/emmm.202115295] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 12/20/2022] Open
Abstract
Lineage dedifferentiation toward a mesenchymal‐like state displaying myofibroblast and fibrotic features is a common mechanism of adaptive and acquired resistance to targeted therapy in melanoma. Here, we show that the anti‐fibrotic drug nintedanib is active to normalize the fibrous ECM network, enhance the efficacy of MAPK‐targeted therapy, and delay tumor relapse in a preclinical model of melanoma. Acquisition of this resistant phenotype and its reversion by nintedanib pointed to miR‐143/‐145 pro‐fibrotic cluster as a driver of this mesenchymal‐like phenotype. Upregulation of the miR‐143/‐145 cluster under BRAFi/MAPKi therapy was observed in melanoma cells in vitro and in vivo and was associated with an invasive/undifferentiated profile. The 2 mature miRNAs generated from this cluster, miR‐143‐3p and miR‐145‐5p, collaborated to mediate transition toward a drug‐resistant undifferentiated mesenchymal‐like state by targeting Fascin actin‐bundling protein 1 (FSCN1), modulating the dynamic crosstalk between the actin cytoskeleton and the ECM through the regulation of focal adhesion dynamics and mechanotransduction pathways. Our study brings insights into a novel miRNA‐mediated regulatory network that contributes to non‐genetic adaptive drug resistance and provides proof of principle that preventing MAPKi‐induced pro‐fibrotic stromal response is a viable therapeutic opportunity for patients on targeted therapy.
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Affiliation(s)
- Serena Diazzi
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Sophia Antipolis, France.,Equipe labellisée Ligue Contre le Cancer, Nice, France
| | - Alberto Baeri
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Sophia Antipolis, France
| | - Julien Fassy
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Sophia Antipolis, France
| | - Margaux Lecacheur
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer, Nice, France
| | - Oskar Marin-Bejar
- Laboratory For Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | - Christophe A Girard
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer, Nice, France
| | - Lauren Lefevre
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer, Nice, France
| | - Caroline Lacoux
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Sophia Antipolis, France
| | | | - Carine Mounier
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Sophia Antipolis, France.,CYU Université, ERRMECe (EA1391), Neuville-sur-Oise, France
| | - Marin Truchi
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Sophia Antipolis, France
| | - Marie Couralet
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Sophia Antipolis, France
| | - Mickael Ohanna
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer, Nice, France
| | - Alexandrine Carminati
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer, Nice, France
| | - Ilona Berestjuk
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer, Nice, France
| | - Frederic Larbret
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer, Nice, France
| | - David Gilot
- INSERM U1242, University of Rennes, Rennes, France
| | - Georges Vassaux
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Sophia Antipolis, France
| | - Jean-Christophe Marine
- Laboratory For Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | - Marcel Deckert
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer, Nice, France
| | - Bernard Mari
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Sophia Antipolis, France.,FHU-OncoAge, Nice, France
| | - Sophie Tartare-Deckert
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer, Nice, France.,FHU-OncoAge, Nice, France
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8
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Barreno A, Orgaz JL. Cytoskeletal Remodelling as an Achilles’ Heel for Therapy Resistance in Melanoma. Cells 2022; 11:cells11030518. [PMID: 35159327 PMCID: PMC8834185 DOI: 10.3390/cells11030518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 12/10/2022] Open
Abstract
Melanoma is an aggressive skin cancer with a poor prognosis when diagnosed late. MAPK-targeted therapies and immune checkpoint blockers benefit a subset of melanoma patients; however, acquired therapy resistance inevitably arises within a year. In addition, some patients display intrinsic (primary) resistance and never respond to therapy. There is mounting evidence that resistant cells adapt to therapy through the rewiring of cytoskeleton regulators, leading to a profound remodelling of the actomyosin cytoskeleton. Importantly, this renders therapy-resistant cells highly dependent on cytoskeletal signalling pathways for sustaining their survival under drug pressure, which becomes a vulnerability that can be exploited therapeutically. Here, we discuss the current knowledge on cytoskeletal pathways involved in mainly targeted therapy resistance and future avenues, as well as potential clinical interventions.
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9
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Chakraborty S, Carnazza M, Jarboe T, DeSouza N, Li XM, Moscatello A, Geliebter J, Tiwari RK. Disruption of Cell-Cell Communication in Anaplastic Thyroid Cancer as an Immunotherapeutic Opportunity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1350:33-66. [PMID: 34888843 DOI: 10.1007/978-3-030-83282-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thyroid cancer incidence is increasing at an alarming rate, almost tripling every decade. About 44,280 new cases of thyroid cancer (12,150 in men and 32,130 in women) are estimated to be diagnosed in 2021, with an estimated death toll of around 2200. Although most thyroid tumors are treatable and associated with a favorable outcome, anaplastic thyroid cancer (ATC) is extremely aggressive with a grim prognosis of 6-9 months post-diagnosis. A large contributing factor to this aggressive nature is that ATC is completely refractory to mainstream therapies. Analysis of the tumor microenvironment (TME) associated with ATC can relay insight to the pathological realm that encompasses tumors and aids in cancer progression and proliferation. The TME is defined as a complex niche that surrounds a tumor and involves a plethora of cellular components whose secretions can modulate the environment in order to favor tumor progression. The cellular heterogeneity of the TME contributes to its dynamic function due to the presence of both immune and nonimmune resident, infiltrating, and interacting cell types. Associated immune cells discussed in this chapter include macrophages, dendritic cells (DCs), natural killer (NK) cells, and tumor-infiltrating lymphocytes (TILs). Nonimmune cells also play a role in the establishment and proliferation of the TME, including neuroendocrine (NE) cells, adipocytes, endothelial cells (ECs), mesenchymal stem cells (MSCs), and fibroblasts. The dynamic nature of the TME contributes greatly to cancer progression.Recent work has found ATC tissues to be defined by a T cell-inflamed "hot" tumor immune microenvironment (TIME) as evidenced by presence of CD3+ and CD8+ T cells. These tumor types are amenable to immune checkpoint blockade (ICB) therapy. This therapeutic avenue, as of 2021, has remained unexplored in ATC. New studies should seek to explore the therapeutic feasibility of a combination therapy, through the use of a small molecule inhibitor with ICB in ATC. Screening of in vitro model systems representative of papillary, anaplastic, and follicular thyroid cancer explored the expression of 29 immune checkpoint molecules. There are higher expressions of HVEM, BTLA, and CD160 in ATC cell lines when compared to the other TC subtypes. The expression level of HVEM was more than 30-fold higher in ATC compared to the others, on average. HVEM is a member of tumor necrosis factor (TNF) receptor superfamily, which acts as a bidirectional switch through interaction with BTLA, CD160, and LIGHT, in a cis or trans manner. Given the T cell-inflamed hot TIME in ATC, expression of HVEM on tumor cells was suggestive of a possibility for complex crosstalk of HVEM with inflammatory cytokines. Altogether, there is emerging evidence of a T cell-inflamed TIME in ATC along with the expression of immune checkpoint proteins HVEM, BTLA, and CD160 in ATC. This can open doors for combination therapies using small molecule inhibitors targeting downstream effectors of MAPK pathway and antagonistic antibodies targeting the HVEM/BTLA axis as a potentially viable therapeutic avenue for ATC patients. With this being stated, the development of adaptive resistance to targeted therapies is inevitable; therefore, using a combination therapy that targets the TIME can serve as a preemptive tactic against the characteristic therapeutic resistance that is seen in ATC. The dynamic nature of the TME, including the immune cells, nonimmune cells, and acellular components, can serve as viable targets for combination therapy in ATC. Understanding the complex interactions of these associated cells and the paradigm in which their secretions and components can serve as immunomodulators are critical points of understanding when trying to develop therapeutics specifically tailored for the anaplastic thyroid carcinoma microenvironment.
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Affiliation(s)
- Sanjukta Chakraborty
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, NY, USA.,Weill Cornell Medicine, New York, NY, USA
| | - Michelle Carnazza
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, NY, USA
| | - Tara Jarboe
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, NY, USA
| | - Nicole DeSouza
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, NY, USA
| | - Xiu-Min Li
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, NY, USA
| | | | - Jan Geliebter
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, NY, USA
| | - Raj K Tiwari
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, NY, USA.
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10
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Oxidative Stress-Related Mechanisms in Melanoma and in the Acquired Resistance to Targeted Therapies. Antioxidants (Basel) 2021; 10:antiox10121942. [PMID: 34943045 PMCID: PMC8750393 DOI: 10.3390/antiox10121942] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 02/06/2023] Open
Abstract
Melanoma is a highly aggressive cancer with the poorest prognosis, representing the deadliest form of skin cancer. Activating mutations in BRAF are the most frequent genetic alterations, present in approximately 50% of all melanoma cases. The use of specific inhibitors towards mutant BRAF variants and MEK, a downstream signaling target of BRAF in the MAPK pathway, has significantly improved progression-free and overall survival in advanced melanoma patients carrying BRAF mutations. Nevertheless, despite these improvements, resistance still develops within the first year of therapy in around 50% of patients, which is a significant problem in managing BRAF-mutated advanced melanoma. Understanding these mechanisms is one of the mainstreams of the research on BRAFi/MEKi acquired resistance. Both genetic and epigenetic mechanisms have been described. Moreover, in recent years, oxidative stress has emerged as another major force involved in all the phases of melanoma development, from initiation to progression until the onsets of the metastatic phenotype and chemoresistance, and has thus become a target for therapy. In the present review, we discuss the current knowledge on oxidative stress and its signaling in melanoma, as well as the oxidative stress-related mechanisms in the acquired resistance to targeted therapies.
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11
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Tanimura K, Yamada T, Horinaka M, Katayama Y, Fukui S, Morimoto K, Nakano T, Tokuda S, Morimoto Y, Iwasaku M, Kaneko Y, Uchino J, Yoneda K, Yano S, Sakai T, Takayama K. Inhibition of c-Jun N-terminal kinase signaling increased apoptosis and prevented the emergence of ALK-TKI-tolerant cells in ALK-rearranged non-small cell lung cancer. Cancer Lett 2021; 522:119-128. [PMID: 34534615 DOI: 10.1016/j.canlet.2021.09.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/25/2021] [Accepted: 09/10/2021] [Indexed: 10/20/2022]
Abstract
Anaplastic lymphoma kinase-tyrosine kinase inhibitors (ALK-TKIs) have improved clinical outcomes in non-small cell lung cancer (NSCLC) harboring ALK- rearrangements. However, a small population of tumor cells survives due to adaptive resistance under drug pressure and ultimately acquires drug resistance. Thus, it is necessary to elucidate the mechanisms underlying the prevention of drug resistance to improve the prognosis of patients with ALK-rearranged NSCLC. We identified novel adaptive resistance, generated through c-Jun N-terminal kinase (JNK)/c-Jun signaling, to initial ALK-TKIs-alectinib and brigatinib-in ALK-rearranged NSCLC. Inhibition of JNK/c-Jun axis showed suppression of growth and promotion of apoptosis induced by ALK-TKIs in drug-tolerant cells. JNK inhibition, in combination with the use of ALK-TKIs, increased cell apoptosis through repression of the Bcl-xL proteins, compared with ALK-TKI monotherapy. Importantly, combination therapy targeting JNK and ALK significantly delayed the regrowth following cessation of these treatments. Together, our results demonstrated that JNK pathway activation plays a pivotal role in the intrinsic resistance to ALK-TKIs and the emergence of ALK-TKI-tolerant cells in ALK-rearranged NSCLC, thus indicating that optimal inhibition of tolerant signals combined with ALK-TKIs may potentially improve the outcome of ALK-rearranged NSCLC.
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Affiliation(s)
- Keiko Tanimura
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Tadaaki Yamada
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan.
| | - Mano Horinaka
- Department of Drug Discovery Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yuki Katayama
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Sarina Fukui
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Kenji Morimoto
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Takayuki Nakano
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Shinsaku Tokuda
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yoshie Morimoto
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Masahiro Iwasaku
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yoshiko Kaneko
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Junji Uchino
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Kazue Yoneda
- Second Department of Surgery, University of Occupational and Environmental Health, Kitakyushu-shi, Fukuoka, 807-8555, Japan
| | - Seiji Yano
- Division of Medical Oncology, Cancer Research Institute, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan
| | - Toshiyuki Sakai
- Department of Drug Discovery Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Koichi Takayama
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan
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12
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Schmitt M, Sinnberg T, Bratl K, Zittlau K, Garbe C, Macek B, Nalpas NC. Proteogenomics Reveals Perturbed Signaling Networks in Malignant Melanoma Cells Resistant to BRAF Inhibition. Mol Cell Proteomics 2021; 20:100163. [PMID: 34673281 PMCID: PMC8603206 DOI: 10.1016/j.mcpro.2021.100163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/04/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Analysis of nucleotide variants is a cornerstone of cancer medicine. Although only 2% of the genomic sequence is protein coding, mutations occurring in these regions have the potential to influence protein structure or modification status and may have severe impact on disease aetiology. Proteogenomics enables the analysis of sample-specific nonsynonymous nucleotide variants with regard to their effect at the proteome and phosphoproteome levels. Here, we developed a proof-of-concept proteogenomics workflow and applied it to the malignant melanoma cell line A375. Initially, we studied the resistance to serine/threonine-protein kinase B-raf (BRAF) inhibitor (BRAFi) vemurafenib in A375 cells. This allowed identification of several oncogenic nonsynonymous nucleotide variants, including a gain-of-function variant on aurora kinase A (AURKA) at F31I. We also detected significant changes in abundance among (phospho)proteins, which led to reactivation of the MAPK signaling pathway in BRAFi-resistant A375 cells. Upon reconstruction of the multiomic integrated signaling networks, we predicted drug therapies with the potential to disrupt BRAFi resistance mechanism in A375 cells. Notably, we showed that AURKA inhibition is effective and specific against BRAFi-resistant A375 cells. Subsequently, we investigated amino acid variants that interfere with protein posttranslational modification (PTM) status and potentially influence A375 cell signaling irrespective of BRAFi resistance. Mass spectrometry (MS) measurements confirmed variant-driven PTM changes in 12 proteins. Among them was the runt-related transcription factor 1 (RUNX1) displaying a variant on a known phosphorylation site S(Ph)276L. We confirmed the loss of phosphorylation site by MS and demonstrated the impact of this variant on RUNX1 interactome.
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Affiliation(s)
- Marisa Schmitt
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany
| | - Tobias Sinnberg
- Division of Dermatooncology, University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tuebingen, Tuebingen, Germany
| | - Katrin Bratl
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany
| | - Katharina Zittlau
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany
| | - Claus Garbe
- Division of Dermatooncology, University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tuebingen, Tuebingen, Germany
| | - Boris Macek
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tuebingen, Tuebingen, Germany.
| | - Nicolas C Nalpas
- Quantitative Proteomics, University of Tuebingen, Tuebingen, Germany.
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13
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Oba J, Woodman SE. The genetic and epigenetic basis of distinct melanoma types. J Dermatol 2021; 48:925-939. [PMID: 34008215 DOI: 10.1111/1346-8138.15957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022]
Abstract
Melanoma represents the deadliest skin cancer. Recent therapeutic developments, including targeted and immune therapies have revolutionized clinical management and improved patient outcome. This progress was achieved by rigorous molecular and functional studies followed by robust clinical trials. The identification of key genomic alterations and gene expression profiles have propelled the understanding of distinct characteristics within melanoma subtypes. The aim of this review is to summarize and highlight the main genetic and epigenetic findings of melanomas and highlight their pathological and therapeutic importance.
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Affiliation(s)
- Junna Oba
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Scott E Woodman
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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14
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Gautron A, Bachelot L, Aubry M, Leclerc D, Quéméner AM, Corre S, Rambow F, Paris A, Tardif N, Leclair HM, Marin‐Bejar O, Coulouarn C, Marine J, Galibert M, Gilot D. CRISPR screens identify tumor-promoting genes conferring melanoma cell plasticity and resistance. EMBO Mol Med 2021; 13:e13466. [PMID: 33724679 PMCID: PMC8103100 DOI: 10.15252/emmm.202013466] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/14/2022] Open
Abstract
Most genetic alterations that drive melanoma development and resistance to targeted therapy have been uncovered. In contrast, and despite their increasingly recognized contribution, little is known about the non-genetic mechanisms that drive these processes. Here, we performed in vivo gain-of-function CRISPR screens and identified SMAD3, BIRC3, and SLC9A5 as key actors of BRAFi resistance. We show that their expression levels increase during acquisition of BRAFi resistance and remain high in persister cells and during relapse. The upregulation of the SMAD3 transcriptional activity (SMAD3-signature) promotes a mesenchymal-like phenotype and BRAFi resistance by acting as an upstream transcriptional regulator of potent BRAFi-resistance genes such as EGFR and AXL. This SMAD3-signature predicts resistance to both current melanoma therapies in different cohorts. Critically, chemical inhibition of SMAD3 may constitute amenable target for melanoma since it efficiently abrogates persister cells survival. Interestingly, decrease of SMAD3 activity can also be reached by inhibiting the Aryl hydrocarbon Receptor (AhR), another druggable transcription factor governing SMAD3 expression level. Our work highlights novel drug vulnerabilities that can be exploited to develop long-lasting antimelanoma therapies.
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Affiliation(s)
- Arthur Gautron
- CNRSIGDR (Institut de génétique et développement de Rennes)‐UMR 6290Univ RennesRennesFrance
| | - Laura Bachelot
- CNRSIGDR (Institut de génétique et développement de Rennes)‐UMR 6290Univ RennesRennesFrance
| | - Marc Aubry
- CNRSIGDR (Institut de génétique et développement de Rennes)‐UMR 6290Univ RennesRennesFrance
- Plateforme GEH, CNRS, InsermBIOSIT ‐ UMS 3480, US_S 018Univ RennesRennesFrance
| | | | - Anaïs M Quéméner
- CNRSIGDR (Institut de génétique et développement de Rennes)‐UMR 6290Univ RennesRennesFrance
| | - Sébastien Corre
- CNRSIGDR (Institut de génétique et développement de Rennes)‐UMR 6290Univ RennesRennesFrance
| | - Florian Rambow
- Department of OncologyKU LeuvenLeuvenBelgium
- VIB Center for Cancer BiologyVIBLeuvenBelgium
| | - Anaïs Paris
- CNRSIGDR (Institut de génétique et développement de Rennes)‐UMR 6290Univ RennesRennesFrance
| | - Nina Tardif
- CNRSIGDR (Institut de génétique et développement de Rennes)‐UMR 6290Univ RennesRennesFrance
| | - Héloïse M Leclair
- CNRSIGDR (Institut de génétique et développement de Rennes)‐UMR 6290Univ RennesRennesFrance
| | - Oskar Marin‐Bejar
- Department of OncologyKU LeuvenLeuvenBelgium
- VIB Center for Cancer BiologyVIBLeuvenBelgium
| | | | - Jean‐Christophe Marine
- Department of OncologyKU LeuvenLeuvenBelgium
- VIB Center for Cancer BiologyVIBLeuvenBelgium
| | - Marie‐Dominique Galibert
- CNRSIGDR (Institut de génétique et développement de Rennes)‐UMR 6290Univ RennesRennesFrance
- Service de Génétique Moléculaire et GénomiqueCHU RennesRennesFrance
| | - David Gilot
- CNRSIGDR (Institut de génétique et développement de Rennes)‐UMR 6290Univ RennesRennesFrance
- Present address:
INSERM U1242Centre Eugène MarquisRennesFrance
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15
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Many Distinct Ways Lead to Drug Resistance in BRAF- and NRAS-Mutated Melanomas. Life (Basel) 2021; 11:life11050424. [PMID: 34063141 PMCID: PMC8148104 DOI: 10.3390/life11050424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/23/2021] [Accepted: 04/30/2021] [Indexed: 11/17/2022] Open
Abstract
Advanced melanoma is a relentless tumor with a high metastatic potential. The combat of melanoma by using the targeted therapy is impeded because several major driver mutations fuel its growth (predominantly BRAF and NRAS). Both these mutated oncogenes strongly activate the MAPK (MEK/ERK) pathway. Therefore, specific inhibitors of these oncoproteins or MAPK pathway components or their combination have been used for tumor eradication. After a good initial response, resistant cells develop almost universally and need the drug for further expansion. Multiple mechanisms, sometimes very distant from the MAPK pathway, are responsible for the development of resistance. Here, we review many of the mechanisms causing resistance and leading to the dismal final outcome of mutated BRAF and NRAS therapy. Very heterogeneous events lead to drug resistance. Due to this, each individual mechanism would be in fact needed to be determined for a personalized therapy to treat patients more efficiently and causally according to molecular findings. This procedure is practically impossible in the clinic. Other approaches are therefore needed, such as combined treatment with more drugs simultaneously from the beginning of the therapy. This could eradicate tumor cells more rapidly and greatly diminish the possibility of emerging mechanisms that allow the evolution of drug resistance.
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16
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Haugh AM, Salama AKS, Johnson DB. Advanced Melanoma: Resistance Mechanisms to Current Therapies. Hematol Oncol Clin North Am 2021; 35:111-128. [PMID: 33759769 PMCID: PMC7991196 DOI: 10.1016/j.hoc.2020.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Novel therapeutic agents introduced over the past decade, including immune checkpoint inhibitors and targeted therapies, have revolutionized the management of metastatic melanoma and significantly improved patient outcomes. Although robust and durable responses have been noted in some cases, treatment is often limited by innate or acquired resistance to these agents. This article provides an overview of known and suspected mechanisms involved with acquired resistance to BRAF/MEK inhibitors as well as developing insights into innate and acquired resistance to checkpoint inhibitors in patients with melanoma.
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Affiliation(s)
- Alexandra M Haugh
- Department of Medicine, Vanderbilt University Medical Center, 719 Thompson Lane, Suite 20400, Nashville, TN 37204, USA
| | - April K S Salama
- Department of Medicine, Duke University Medical Center, 20 Duke Medicine Cir, Durham, NC 27710, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt University Medical Center, Vanderbilt Ingram Cancer Center, 777 PRB, 2220 Pierce Avenue, Nashville, TN 37232, USA.
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17
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Proietti I, Skroza N, Bernardini N, Tolino E, Balduzzi V, Marchesiello A, Michelini S, Volpe S, Mambrin A, Mangino G, Romeo G, Maddalena P, Rees C, Potenza C. Mechanisms of Acquired BRAF Inhibitor Resistance in Melanoma: A Systematic Review. Cancers (Basel) 2020; 12:E2801. [PMID: 33003483 PMCID: PMC7600801 DOI: 10.3390/cancers12102801] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/21/2020] [Accepted: 09/25/2020] [Indexed: 12/18/2022] Open
Abstract
This systematic review investigated the literature on acquired v-raf murine sarcoma viral oncogene homolog B1 (BRAF) inhibitor resistance in patients with melanoma. We searched MEDLINE for articles on BRAF inhibitor resistance in patients with melanoma published since January 2010 in the following areas: (1) genetic basis of resistance; (2) epigenetic and transcriptomic mechanisms; (3) influence of the immune system on resistance development; and (4) combination therapy to overcome resistance. Common resistance mutations in melanoma are BRAF splice variants, BRAF amplification, neuroblastoma RAS viral oncogene homolog (NRAS) mutations and mitogen-activated protein kinase kinase 1/2 (MEK1/2) mutations. Genetic and epigenetic changes reactivate previously blocked mitogen-activated protein kinase (MAPK) pathways, activate alternative signaling pathways, and cause epithelial-to-mesenchymal transition. Once BRAF inhibitor resistance develops, the tumor microenvironment reverts to a low immunogenic state secondary to the induction of programmed cell death ligand-1. Combining a BRAF inhibitor with a MEK inhibitor delays resistance development and increases duration of response. Multiple other combinations based on known mechanisms of resistance are being investigated. BRAF inhibitor-resistant cells develop a range of 'escape routes', so multiple different treatment targets will probably be required to overcome resistance. In the future, it may be possible to personalize combination therapy towards the specific resistance pathway in individual patients.
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Affiliation(s)
- Ilaria Proietti
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Nevena Skroza
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Nicoletta Bernardini
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Ersilia Tolino
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Veronica Balduzzi
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Anna Marchesiello
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Simone Michelini
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Salvatore Volpe
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Alessandra Mambrin
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Giorgio Mangino
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 00185 Rome, Italy; (G.M.); (G.R.)
| | - Giovanna Romeo
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 00185 Rome, Italy; (G.M.); (G.R.)
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy
| | - Patrizia Maddalena
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | | | - Concetta Potenza
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
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18
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Bai X, Flaherty KT. Targeted and immunotherapies in BRAF mutant melanoma: where we stand and what to expect. Br J Dermatol 2020; 185:253-262. [PMID: 32652567 DOI: 10.1111/bjd.19394] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2020] [Indexed: 01/01/2023]
Abstract
The therapeutic landscape for melanoma has evolved drastically in the past decade. Currently, immune checkpoint inhibitors and small-molecule inhibitors targeting the mitogen-activated protein kinase (MAPK) pathway are the two mainstay therapies for BRAFV600 mutant advanced melanoma. Although MAPK dependence has been variably demonstrated in melanomas lacking BRAFV600 mutations, definitive evidence of benefit with MAPK inhibitors has not been demonstrated. Thus, in the BRAFV600 'wild-type' setting, immune checkpoint inhibitors are the standalone option(s). In the BRAFV600 mutant setting, there is no definitive evidence prioritizing one therapeutic modality over another. Herein, we review the updated data of the pivotal phase III randomized controlled trials that established the standard-of-care first-line treatment for advanced melanoma, as it provides insights into long-term benefit, which is a major factor in therapy selection. We discuss the clinical considerations for choosing between these therapies in the front-line setting and beyond, specifically for patients with BRAFV600 mutant melanoma based on currently available evidence. We have previously proposed a time-dependent resistance paradigm in which future therapeutic development strategies can be rooted. We also discuss how these Food and Drug Administration (FDA)-approved therapeutic modalities are being pursued earlier in the course of disease management, namely in adjuvant and neoadjuvant settings. FDA-approved interlesional oncolytic virotherapy in the modern era is also briefly discussed.
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Affiliation(s)
- X Bai
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital and Institute, Beijing, China.,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - K T Flaherty
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
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Chang X, Zhang T, Wang Q, Rathore MG, Reddy K, Chen H, Shin SH, Ma WY, Bode AM, Dong Z. HI-511 overcomes melanoma drug resistance via targeting AURKB and BRAF V600E. Am J Cancer Res 2020; 10:9721-9740. [PMID: 32863956 PMCID: PMC7449901 DOI: 10.7150/thno.44342] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/18/2020] [Indexed: 12/14/2022] Open
Abstract
Rationale: Melanoma is an aggressive tumor of the skin and drug resistance is still a major problem in melanoma therapy. Novel targets and effective agents to overcome drug resistant melanoma are urgently needed in clinical therapy. Methods: Gene Expression Omnibus (GEO) database analysis, pathway enrichment analysis, and survival rate analysis were utilized to identify a candidate target. An anchorage-independent cell growth assay, flow cytometry, Western blot, and a xenograft mouse model were used to study the function of Aurora kinase B (AURKB) in both drug-sensitive and drug-resistant melanoma. Next, HI-511, a novel dual-target inhibitor targeting both AURKB and BRAF V600E, was designed and examined by an in vitro kinase assay. Methods as indicated above in addition to a BRAF V600E/PTEN-loss melanoma mouse model were used to demonstrate the effect of HI-511 on melanoma development in vitro and in vivo. Results: AURKB is highly expressed in melanoma and especially in vemurafenib-resistant melanoma and the expression was correlated with patient survival rate. Knocking down AURKB inhibited cell growth and induced apoptosis in melanoma, which was associated with the BRAF/MEK/ERKs and PI3-K/AKT signaling pathways. Importantly, we found that HI-511, a novel dual-target inhibitor against AURKB and BRAF V600E, suppresses both vemurafenib-sensitive and vemurafenib-resistant melanoma growth in vitro and in vivo by inducing apoptosis and mediating the inhibition of the BRAF/MEK/ERKs and PI3K/AKT signaling pathways. Conclusion: AURKB is a potential target for melanoma treatment. HI-511, a novel dual-target inhibitor against both AURKB and BRAF V600E, could achieve durable suppression of melanoma growth, even drug-resistant melanoma growth.
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Becco P, Gallo S, Poletto S, Frascione MPM, Crotto L, Zaccagna A, Paruzzo L, Caravelli D, Carnevale-Schianca F, Aglietta M. Melanoma Brain Metastases in the Era of Target Therapies: An Overview. Cancers (Basel) 2020; 12:cancers12061640. [PMID: 32575838 PMCID: PMC7352598 DOI: 10.3390/cancers12061640] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/18/2022] Open
Abstract
Malignant melanoma is the third most common type of tumor that causes brain metastases. Patients with cerebral involvement have a dismal prognosis and their treatment is an unmet medical need. Brain involvement is a multistep process involving several signaling pathways such as Janus kinase/signal Transducer and Activator of Transcription (JAK/STAT), Phosphoinositide 3-kinase/Protein Kinase B (PI3K/AKT), Vascular Endothelial Growth Factor and Phosphatase and Tensin Homolog (PTEN). Recently therapy that targets the MAPK signaling (BRAF/MEK inhibitors) and immunotherapy (anti-CTLA4 and anti-PD1 agents) have changed the therapeutic approaches to stage IV melanoma. In contrast, there are no solid data about patients with brain metastases, who are usually excluded from clinical trials. Retrospective data showed that BRAF-inhibitors, alone or in combination with MEK-inhibitors have interesting clinical activity in this setting. Prospective data about the combinations of BRAF/MEK inhibitors have been recently published, showing an improved overall response rate. Short intracranial disease control is still a challenge. Several attempts have been made in order to improve it with combinations between local and systemic therapies. Immunotherapy approaches seem to retain promising activity in the treatment of melanoma brain metastasis as showed by the results of clinical trials investigating the combination of anti-CTL4 (Ipilimumab) and anti-PD1(Nivolumab). Studies about the combination or the sequential approach of target therapy and immunotherapy are ongoing, with immature results. Several clinical trials are ongoing trying to explore new approaches in order to overcome tumor resistance. At this moment the correct therapeutic choices for melanoma with intracranial involvement is still a challenge and new strategies are needed.
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Affiliation(s)
- Paolo Becco
- Istituto di Candiolo, FPO - IRCCS - Str. Prov.le 142, km 3,95, 10060 Candiolo, Italy; (P.B.); (S.P.); (M.P.M.F.); (L.C.); (A.Z.); (L.P.); (D.C.); (F.C.-S.); (M.A.)
| | - Susanna Gallo
- Ospedale Mauriziano Umberto I-Largo Turati 62, 10128 Torino, Italy
- Correspondence:
| | - Stefano Poletto
- Istituto di Candiolo, FPO - IRCCS - Str. Prov.le 142, km 3,95, 10060 Candiolo, Italy; (P.B.); (S.P.); (M.P.M.F.); (L.C.); (A.Z.); (L.P.); (D.C.); (F.C.-S.); (M.A.)
- Department of Oncology, University of Turin, 10124 Torino, Italy
| | - Mirko Pio Manlio Frascione
- Istituto di Candiolo, FPO - IRCCS - Str. Prov.le 142, km 3,95, 10060 Candiolo, Italy; (P.B.); (S.P.); (M.P.M.F.); (L.C.); (A.Z.); (L.P.); (D.C.); (F.C.-S.); (M.A.)
- Department of Oncology, University of Turin, 10124 Torino, Italy
| | - Luca Crotto
- Istituto di Candiolo, FPO - IRCCS - Str. Prov.le 142, km 3,95, 10060 Candiolo, Italy; (P.B.); (S.P.); (M.P.M.F.); (L.C.); (A.Z.); (L.P.); (D.C.); (F.C.-S.); (M.A.)
| | - Alessandro Zaccagna
- Istituto di Candiolo, FPO - IRCCS - Str. Prov.le 142, km 3,95, 10060 Candiolo, Italy; (P.B.); (S.P.); (M.P.M.F.); (L.C.); (A.Z.); (L.P.); (D.C.); (F.C.-S.); (M.A.)
| | - Luca Paruzzo
- Istituto di Candiolo, FPO - IRCCS - Str. Prov.le 142, km 3,95, 10060 Candiolo, Italy; (P.B.); (S.P.); (M.P.M.F.); (L.C.); (A.Z.); (L.P.); (D.C.); (F.C.-S.); (M.A.)
- Department of Oncology, University of Turin, 10124 Torino, Italy
| | - Daniela Caravelli
- Istituto di Candiolo, FPO - IRCCS - Str. Prov.le 142, km 3,95, 10060 Candiolo, Italy; (P.B.); (S.P.); (M.P.M.F.); (L.C.); (A.Z.); (L.P.); (D.C.); (F.C.-S.); (M.A.)
| | - Fabrizio Carnevale-Schianca
- Istituto di Candiolo, FPO - IRCCS - Str. Prov.le 142, km 3,95, 10060 Candiolo, Italy; (P.B.); (S.P.); (M.P.M.F.); (L.C.); (A.Z.); (L.P.); (D.C.); (F.C.-S.); (M.A.)
| | - Massimo Aglietta
- Istituto di Candiolo, FPO - IRCCS - Str. Prov.le 142, km 3,95, 10060 Candiolo, Italy; (P.B.); (S.P.); (M.P.M.F.); (L.C.); (A.Z.); (L.P.); (D.C.); (F.C.-S.); (M.A.)
- Department of Oncology, University of Turin, 10124 Torino, Italy
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21
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The Hippo pathway oncoprotein YAP promotes melanoma cell invasion and spontaneous metastasis. Oncogene 2020; 39:5267-5281. [PMID: 32561850 DOI: 10.1038/s41388-020-1362-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 05/31/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022]
Abstract
Melanoma is a deadly form of skin cancer that accounts for a disproportionally large proportion of cancer-related deaths in younger people. Compared with most other skin cancers, a feature of melanoma is its high metastatic capacity, although the mechanisms that confer this are not well understood. The Hippo pathway is a key regulator of organ growth and cell fate that is deregulated in many cancers. To analyse the Hippo pathway in cutaneous melanoma, we generated a transcriptional signature of melanoma cells that overexpressed YAP, the key downstream Hippo pathway oncoprotein. YAP-mediated transcriptional activity varied in melanoma cell lines but did not cluster with known genetic drivers of melanomagenesis such as BRAF and NRAS mutations. Instead, it correlated strongly with published gene expression profiles linked to melanoma cell invasiveness and varied throughout the metastatic cascade in melanoma patient tumours. Consistent with this, YAP was both necessary and sufficient for melanoma cell invasion in vitro. In vivo, YAP promoted spontaneous melanoma metastasis, whilst the growth of YAP-expressing primary tumours was impeded. Finally, we identified the YAP target genes AXL, THBS1 and CYR61 as key mediators of YAP-induced melanoma cell invasion. These data suggest that YAP is a critical regulator of melanoma metastasis.
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Lee HW, Chung W, Lee HO, Jeong DE, Jo A, Lim JE, Hong JH, Nam DH, Jeong BC, Park SH, Joo KM, Park WY. Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient. Genome Med 2020; 12:47. [PMID: 32460812 PMCID: PMC7251908 DOI: 10.1186/s13073-020-00741-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/24/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Tumor cell-intrinsic mechanisms and complex interactions with the tumor microenvironment contribute to therapeutic failure via tumor evolution. It may be possible to overcome treatment resistance by developing a personalized approach against relapsing cancers based on a comprehensive analysis of cell type-specific transcriptomic changes over the clinical course of the disease using single-cell RNA sequencing (scRNA-seq). METHODS Here, we used scRNA-seq to depict the tumor landscape of a single case of chemo-resistant metastatic, muscle-invasive urothelial bladder cancer (MIUBC) addicted to an activating Harvey rat sarcoma viral oncogene homolog (HRAS) mutation. In order to analyze tumor evolution and microenvironmental changes upon treatment, we also applied scRNA-seq to the corresponding patient-derived xenograft (PDX) before and after treatment with tipifarnib, a HRAS-targeting agent under clinical evaluation. RESULTS In the parallel analysis of the human MIUBC and the PDX, diverse stromal and immune cell populations recapitulated the cellular composition in the human and mouse tumor microenvironment. Treatment with tipifarnib showed dramatic anticancer effects but was unable to achieve a complete response. Importantly, the comparative scRNA-seq analysis between pre- and post-tipifarnib-treated PDX revealed the nature of tipifarnib-refractory tumor cells and the tumor-supporting microenvironment. Based on the upregulation of programmed death-ligand 1 (PD-L1) in surviving tumor cells, and the accumulation of multiple immune-suppressive subsets from post-tipifarnib-treated PDX, a PD-L1 inhibitor, atezolizumab, was clinically applied; this resulted in a favorable response from the patient with acquired resistance to tipifarnib. CONCLUSION We presented a single case report demonstrating the power of scRNA-seq for visualizing the tumor microenvironment and identifying molecular and cellular therapeutic targets in a treatment-refractory cancer patient.
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Affiliation(s)
- Hye Won Lee
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
- Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
- Department of Hospital Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Woosung Chung
- Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea
- DCGen Co., Ltd, Seoul, 03170, Republic of Korea
| | - Hae-Ock Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea
| | - Da Eun Jeong
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Areum Jo
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea
| | - Joung Eun Lim
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Jeong Hee Hong
- Department of Urology, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea
| | - Do-Hyun Nam
- Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Byong Chang Jeong
- Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea.
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.
| | - Se Hoon Park
- Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.
| | - Kyeung-Min Joo
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea.
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea.
- Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea.
- Stem Cell and Regenerative Medicine Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul, 06351, Republic of Korea.
| | - Woong-Yang Park
- Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea.
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea.
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea.
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23
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Diazzi S, Tartare-Deckert S, Deckert M. Bad Neighborhood: Fibrotic Stroma as a New Player in Melanoma Resistance to Targeted Therapies. Cancers (Basel) 2020; 12:cancers12061364. [PMID: 32466585 PMCID: PMC7352197 DOI: 10.3390/cancers12061364] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 12/18/2022] Open
Abstract
Current treatments for metastatic cutaneous melanoma include immunotherapies and drugs targeting key molecules of the mitogen-activated protein kinase (MAPK) pathway, which is often activated by BRAF driver mutations. Overall responses from patients with metastatic BRAF mutant melanoma are better with therapies combining BRAF and mitogen-activated protein kinase kinase (MEK) inhibitors. However, most patients that initially respond to therapies develop drug resistance within months. Acquired resistance to targeted therapies can be due to additional genetic alterations in melanoma cells and to non-genetic events frequently associated with transcriptional reprogramming and a dedifferentiated cell state. In this second scenario, it is possible to identify pro-fibrotic responses induced by targeted therapies that contribute to the alteration of the melanoma tumor microenvironment. A close interrelationship between chronic fibrosis and cancer has been established for several malignancies including breast and pancreatic cancers. In this context, the contribution of fibrosis to drug adaptation and therapy resistance in melanoma is rapidly emerging. In this review, we summarize recent evidence underlining the hallmarks of fibrotic diseases in drug-exposed and resistant melanoma, including increased remodeling of the extracellular matrix, enhanced actin cytoskeleton plasticity, high sensitivity to mechanical cues, and the establishment of an inflammatory microenvironment. We also discuss several potential therapeutic options for manipulating this fibrotic-like response to combat drug-resistant and invasive melanoma.
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Affiliation(s)
- Serena Diazzi
- C3M, Université Côte d’Azur, INSERM, 06204 Nice, France;
- Equipe labellisée Ligue Contre le Cancer 2016, 06204 Nice, France
| | - Sophie Tartare-Deckert
- C3M, Université Côte d’Azur, INSERM, 06204 Nice, France;
- Equipe labellisée Ligue Contre le Cancer 2016, 06204 Nice, France
- Correspondence: (S.T.-D.); (M.D.); Tel.: +33-(0)-489064310 (S.T.-D. & M.D.)
| | - Marcel Deckert
- C3M, Université Côte d’Azur, INSERM, 06204 Nice, France;
- Equipe labellisée Ligue Contre le Cancer 2016, 06204 Nice, France
- Correspondence: (S.T.-D.); (M.D.); Tel.: +33-(0)-489064310 (S.T.-D. & M.D.)
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24
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Su Y, Ko ME, Cheng H, Zhu R, Xue M, Wang J, Lee JW, Frankiw L, Xu A, Wong S, Robert L, Takata K, Yuan D, Lu Y, Huang S, Ribas A, Levine R, Nolan GP, Wei W, Plevritis SK, Li G, Baltimore D, Heath JR. Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line. Nat Commun 2020; 11:2345. [PMID: 32393797 PMCID: PMC7214418 DOI: 10.1038/s41467-020-15956-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/02/2020] [Indexed: 12/12/2022] Open
Abstract
The determination of individual cell trajectories through a high-dimensional cell-state space is an outstanding challenge for understanding biological changes ranging from cellular differentiation to epigenetic responses of diseased cells upon drugging. We integrate experiments and theory to determine the trajectories that single BRAFV600E mutant melanoma cancer cells take between drug-naive and drug-tolerant states. Although single-cell omics tools can yield snapshots of the cell-state landscape, the determination of individual cell trajectories through that space can be confounded by stochastic cell-state switching. We assayed for a panel of signaling, phenotypic, and metabolic regulators at points across 5 days of drug treatment to uncover a cell-state landscape with two paths connecting drug-naive and drug-tolerant states. The trajectory a given cell takes depends upon the drug-naive level of a lineage-restricted transcription factor. Each trajectory exhibits unique druggable susceptibilities, thus updating the paradigm of adaptive resistance development in an isogenic cell population.
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Affiliation(s)
- Yapeng Su
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Institute for Systems Biology, Seattle, Washington, USA
| | - Melissa E Ko
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California, USA
| | - Hanjun Cheng
- Institute for Systems Biology, Seattle, Washington, USA
| | - Ronghui Zhu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Min Xue
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
- Department of Chemistry, University of California, Riverside, Riverside, California, USA
| | - Jessica Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Jihoon W Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Luke Frankiw
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Alexander Xu
- Institute for Systems Biology, Seattle, Washington, USA
| | - Stephanie Wong
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Lidia Robert
- Department of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Kaitlyn Takata
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Dan Yuan
- Institute for Systems Biology, Seattle, Washington, USA
| | - Yue Lu
- Institute for Systems Biology, Seattle, Washington, USA
| | - Sui Huang
- Institute for Systems Biology, Seattle, Washington, USA
| | - Antoni Ribas
- Department of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, California, USA
- Department of Surgery, UCLA, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA
| | - Raphael Levine
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA
- The Fritz Haber Research Center, The Hebrew University, Jerusalem, Israel
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Wei Wei
- Institute for Systems Biology, Seattle, Washington, USA
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA
| | | | - Guideng Li
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Suzhou Institute of Systems Medicine, Suzhou, China.
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.
- Institute for Systems Biology, Seattle, Washington, USA.
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, California, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA.
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25
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Yue J, Vendramin R, Liu F, Lopez O, Valencia MG, Gomes Dos Santos H, Gaidosh G, Beckedorff F, Blumenthal E, Speroni L, Nimer SD, Marine JC, Shiekhattar R. Targeted chemotherapy overcomes drug resistance in melanoma. Genes Dev 2020; 34:637-649. [PMID: 32241802 PMCID: PMC7197350 DOI: 10.1101/gad.333864.119] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/13/2020] [Indexed: 12/31/2022]
Abstract
In this study, Yue et al. describe a therapeutic strategy termed “targeted chemotherapy” that involves depleting PP2A or inhibiting it using a small molecule inhibitor, phendione, in drug-resistant melanoma. The authors show phendione induces DNA damage response without causing DNA breaks or inducing cellular dormancy, therefore blocking tumor growth of BRAF mutant and NRAS mutant melanomas. The emergence of drug resistance is a major obstacle for the success of targeted therapy in melanoma. Additionally, conventional chemotherapy has not been effective as drug-resistant cells escape lethal DNA damage effects by inducing growth arrest commonly referred to as cellular dormancy. We present a therapeutic strategy termed “targeted chemotherapy” by depleting protein phosphatase 2A (PP2A) or its inhibition using a small molecule inhibitor (1,10-phenanthroline-5,6-dione [phendione]) in drug-resistant melanoma. Targeted chemotherapy induces the DNA damage response without causing DNA breaks or allowing cellular dormancy. Phendione treatment reduces tumor growth of BRAFV600E-driven melanoma patient-derived xenografts (PDX) and diminishes growth of NRASQ61R-driven melanoma, a cancer with no effective therapy. Remarkably, phendione treatment inhibits the acquisition of resistance to BRAF inhibition in BRAFV600E PDX highlighting its effectiveness in combating the advent of drug resistance.
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Affiliation(s)
- Jingyin Yue
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Roberto Vendramin
- Laboratory for Molecular Cancer Biology, Oncology Department, KULeuven, 3000 Leuven, Belgium.,Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Fan Liu
- Department of Biochemistry, University of Miami, Miami, Florida 33136, USA
| | - Omar Lopez
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Monica G Valencia
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Helena Gomes Dos Santos
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Gabriel Gaidosh
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Felipe Beckedorff
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Ezra Blumenthal
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Lucia Speroni
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Stephen D Nimer
- Department of Biochemistry, University of Miami, Miami, Florida 33136, USA.,Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Oncology Department, KULeuven, 3000 Leuven, Belgium.,Center for Cancer Biology, VIB, 3000 Leuven, Belgium
| | - Ramin Shiekhattar
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
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26
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Girard CA, Lecacheur M, Ben Jouira R, Berestjuk I, Diazzi S, Prod'homme V, Mallavialle A, Larbret F, Gesson M, Schaub S, Pisano S, Audebert S, Mari B, Gaggioli C, Leucci E, Marine JC, Deckert M, Tartare-Deckert S. A Feed-Forward Mechanosignaling Loop Confers Resistance to Therapies Targeting the MAPK Pathway in BRAF-Mutant Melanoma. Cancer Res 2020; 80:1927-1941. [PMID: 32179513 DOI: 10.1158/0008-5472.can-19-2914] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/15/2020] [Accepted: 03/06/2020] [Indexed: 11/16/2022]
Abstract
Aberrant extracellular matrix (ECM) deposition and stiffening is a physical hallmark of several solid cancers and is associated with therapy failure. BRAF-mutant melanomas treated with BRAF and MEK inhibitors almost invariably develop resistance that is frequently associated with transcriptional reprogramming and a de-differentiated cell state. Melanoma cells secrete their own ECM proteins, an event that is promoted by oncogenic BRAF inhibition. Yet, the contribution of cancer cell-derived ECM and tumor mechanics to drug adaptation and therapy resistance remains poorly understood. Here, we show that melanoma cells can adapt to targeted therapies through a mechanosignaling loop involving the autocrine remodeling of a drug-protective ECM. Analyses revealed that therapy-resistant cells associated with a mesenchymal dedifferentiated state displayed elevated responsiveness to collagen stiffening and force-mediated ECM remodeling through activation of actin-dependent mechanosensors Yes-associated protein (YAP) and myocardin-related transcription factor (MRTF). Short-term inhibition of MAPK pathway also induced mechanosignaling associated with deposition and remodeling of an aligned fibrillar matrix. This provided a favored ECM reorganization that promoted tolerance to BRAF inhibition in a YAP- and MRTF-dependent manner. Matrix remodeling and tumor stiffening were also observed in vivo upon exposure of BRAF-mutant melanoma cell lines or patient-derived xenograft models to MAPK pathway inhibition. Importantly, pharmacologic targeting of YAP reversed treatment-induced excessive collagen deposition, leading to enhancement of BRAF inhibitor efficacy. We conclude that MAPK pathway targeting therapies mechanically reprogram melanoma cells to confer a drug-protective matrix environment. Preventing melanoma cell mechanical reprogramming might be a promising therapeutic strategy for patients on targeted therapies. SIGNIFICANCE: These findings reveal a biomechanical adaptation of melanoma cells to oncogenic BRAF pathway inhibition, which fuels a YAP/MRTF-dependent feed-forward loop associated with tumor stiffening, mechanosensing, and therapy resistance. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/10/1927/F1.large.jpg.
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Affiliation(s)
- Christophe A Girard
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
| | - Margaux Lecacheur
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
| | - Rania Ben Jouira
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
| | - Ilona Berestjuk
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
| | - Serena Diazzi
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
| | - Virginie Prod'homme
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
| | - Aude Mallavialle
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
| | - Frédéric Larbret
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
| | - Maéva Gesson
- Université Côte d'Azur, INSERM, C3M, Nice, France.,Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
| | | | - Sabrina Pisano
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Stéphane Audebert
- Aix-Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Bernard Mari
- Université Côte d'Azur, CNRS, IPMC, Sophia Antipolis, France
| | | | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium.,TRACE, LKI Leuven Cancer Institute, KU Leuven
| | - Jean-Christophe Marine
- Laboratory For Molecular Cancer Biology, VIB Center for Cancer Biology, VIB, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | - Marcel Deckert
- Université Côte d'Azur, INSERM, C3M, Nice, France. .,Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
| | - Sophie Tartare-Deckert
- Université Côte d'Azur, INSERM, C3M, Nice, France. .,Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
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27
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Li Z, Wang B, Gu S, Jiang P, Sahu A, Chen CH, Han T, Shi S, Wang X, Traugh N, Liu H, Liu Y, Wu Q, Brown M, Xiao T, Boland GM, Shirley Liu X. CRISPR Screens Identify Essential Cell Growth Mediators in BRAF Inhibitor-resistant Melanoma. GENOMICS, PROTEOMICS & BIOINFORMATICS 2020; 18:26-40. [PMID: 32413516 PMCID: PMC7393575 DOI: 10.1016/j.gpb.2020.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/20/2020] [Accepted: 02/26/2020] [Indexed: 12/21/2022]
Abstract
BRAF is a serine/threonine kinase that harbors activating mutations in ∼7% of human malignancies and ∼60% of melanomas. Despite initial clinical responses to BRAF inhibitors, patients frequently develop drug resistance. To identify candidate therapeutic targets for BRAF inhibitor resistant melanoma, we conduct CRISPR screens in melanoma cells harboring an activating BRAF mutation that had also acquired resistance to BRAF inhibitors. To investigate the mechanisms and pathways enabling resistance to BRAF inhibitors in melanomas, we integrate expression, ATAC-seq, and CRISPR screen data. We identify the JUN family transcription factors and the ETS family transcription factor ETV5 as key regulators of CDK6, which together enable resistance to BRAF inhibitors in melanoma cells. Our findings reveal genes contributing to resistance to a selective BRAF inhibitor PLX4720, providing new insights into gene regulation in BRAF inhibitor resistant melanoma cells.
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Affiliation(s)
- Ziyi Li
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Binbin Wang
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Department of Data Sciences, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Shengqing Gu
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Peng Jiang
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Avinash Sahu
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Chen-Hao Chen
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Tong Han
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Sailing Shi
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaoqing Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Nicole Traugh
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Hailing Liu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yin Liu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Qiu Wu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Tengfei Xiao
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA.
| | - Genevieve M Boland
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - X Shirley Liu
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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28
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Orgaz JL, Crosas-Molist E, Sadok A, Perdrix-Rosell A, Maiques O, Rodriguez-Hernandez I, Monger J, Mele S, Georgouli M, Bridgeman V, Karagiannis P, Lee R, Pandya P, Boehme L, Wallberg F, Tape C, Karagiannis SN, Malanchi I, Sanz-Moreno V. Myosin II Reactivation and Cytoskeletal Remodeling as a Hallmark and a Vulnerability in Melanoma Therapy Resistance. Cancer Cell 2020; 37:85-103.e9. [PMID: 31935375 PMCID: PMC6958528 DOI: 10.1016/j.ccell.2019.12.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 09/04/2019] [Accepted: 12/06/2019] [Indexed: 12/30/2022]
Abstract
Despite substantial clinical benefit of targeted and immune checkpoint blockade-based therapies in melanoma, resistance inevitably develops. We show cytoskeletal remodeling and changes in expression and activity of ROCK-myosin II pathway during acquisition of resistance to MAPK inhibitors. MAPK regulates myosin II activity, but after initial therapy response, drug-resistant clones restore myosin II activity to increase survival. High ROCK-myosin II activity correlates with aggressiveness, identifying targeted therapy- and immunotherapy-resistant melanomas. Survival of resistant cells is myosin II dependent, regardless of the therapy. ROCK-myosin II ablation specifically kills resistant cells via intrinsic lethal reactive oxygen species and unresolved DNA damage and limits extrinsic myeloid and lymphoid immunosuppression. Efficacy of targeted therapies and immunotherapies can be improved by combination with ROCK inhibitors.
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Affiliation(s)
- Jose L Orgaz
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London EC1M 6BQ, UK; Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK.
| | - Eva Crosas-Molist
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London EC1M 6BQ, UK; Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Amine Sadok
- Translational Cancer Discovery Team, Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Anna Perdrix-Rosell
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London EC1M 6BQ, UK; Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK; Tumour Host Interaction, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Oscar Maiques
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London EC1M 6BQ, UK; Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Irene Rodriguez-Hernandez
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London EC1M 6BQ, UK; Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Jo Monger
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London EC1M 6BQ, UK
| | - Silvia Mele
- St. John's Institute of Dermatology, King's College London & NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, London SE1 9RT, UK
| | - Mirella Georgouli
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Victoria Bridgeman
- Tumour Host Interaction, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Panagiotis Karagiannis
- St. John's Institute of Dermatology, King's College London & NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, London SE1 9RT, UK; Department of Oncology, Haematology and Stem Cell Transplantation, University Hospital of Hamburg Eppendorf, Hamburg 20246, Germany
| | - Rebecca Lee
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester M20 4BX, UK
| | - Pahini Pandya
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Lena Boehme
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Fredrik Wallberg
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
| | - Chris Tape
- Cell Communication Lab, UCL Cancer Institute, 72 Huntley Street, London WC1E 6DD, UK
| | - Sophia N Karagiannis
- St. John's Institute of Dermatology, King's College London & NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, London SE1 9RT, UK
| | - Ilaria Malanchi
- Tumour Host Interaction, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Victoria Sanz-Moreno
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London EC1M 6BQ, UK; Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK.
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29
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Smalley I, Kim E, Li J, Spence P, Wyatt CJ, Eroglu Z, Sondak VK, Messina JL, Babacan NA, Maria-Engler SS, De Armas L, Williams SL, Gatenby RA, Chen YA, Anderson ARA, Smalley KSM. Leveraging transcriptional dynamics to improve BRAF inhibitor responses in melanoma. EBioMedicine 2019; 48:178-190. [PMID: 31594749 PMCID: PMC6838387 DOI: 10.1016/j.ebiom.2019.09.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/13/2019] [Accepted: 09/13/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Melanoma is a heterogeneous tumour, but the impact of this heterogeneity upon therapeutic response is not well understood. METHODS Single cell mRNA analysis was used to define the transcriptional heterogeneity of melanoma and its dynamic response to BRAF inhibitor therapy and treatment holidays. Discrete transcriptional states were defined in cell lines and melanoma patient specimens that predicted initial sensitivity to BRAF inhibition and the potential for effective re-challenge following resistance. A mathematical model was developed to maintain competition between the drug-sensitive and resistant states, which was validated in vivo. FINDINGS Our analyses showed melanoma cell lines and patient specimens to be composed of >3 transcriptionally distinct states. The cell state composition was dynamically regulated in response to BRAF inhibitor therapy and drug holidays. Transcriptional state composition predicted for therapy response. The differences in fitness between the different transcriptional states were leveraged to develop a mathematical model that optimized therapy schedules to retain the drug sensitive population. In vivo validation demonstrated that the personalized adaptive dosing schedules outperformed continuous or fixed intermittent BRAF inhibitor schedules. INTERPRETATION Our study provides the first evidence that transcriptional heterogeneity at the single cell level predicts for initial BRAF inhibitor sensitivity. We further demonstrate that manipulating transcriptional heterogeneity through personalized adaptive therapy schedules can delay the time to resistance. FUNDING This work was funded by the National Institutes of Health. The funder played no role in assembly of the manuscript.
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Affiliation(s)
- Inna Smalley
- The Department of Tumor Biology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Eunjung Kim
- Department of Integrated Mathematical Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Jiannong Li
- Department of Bioinformatics and Biostatistics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Paige Spence
- The Department of Tumor Biology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Clayton J Wyatt
- The Department of Tumor Biology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Zeynep Eroglu
- Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Vernon K Sondak
- Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Jane L Messina
- Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA; Department of Anatomic Pathology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Nalan Akgul Babacan
- Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Silvya Stuchi Maria-Engler
- Department of Clinical Analysis and Toxicology, School of Pharmaceutical Sciences, University of Sao Paulo, Brazil
| | - Lesley De Armas
- Sylvester Comprehensive Cancer Center, The University of Miami, Miami, FL, USA
| | - Sion L Williams
- Sylvester Comprehensive Cancer Center, The University of Miami, Miami, FL, USA
| | - Robert A Gatenby
- Department of Bioinformatics and Biostatistics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Y Ann Chen
- Department of Bioinformatics and Biostatistics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA.
| | - Alexander R A Anderson
- Department of Integrated Mathematical Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA.
| | - Keiran S M Smalley
- The Department of Tumor Biology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA; Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA.
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30
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Abstract
An incomplete view of the mechanisms that drive metastasis, the primary cause of cancer-related death, has been a major barrier to development of effective therapeutics and prognostic diagnostics. Increasing evidence indicates that the interplay between microenvironment, genetic lesions, and cellular plasticity drives the metastatic cascade and resistance to therapies. Here, using melanoma as a model, we outline the diversity and trajectories of cell states during metastatic dissemination and therapy exposure, and highlight how understanding the magnitude and dynamics of nongenetic reprogramming in space and time at single-cell resolution can be exploited to develop therapeutic strategies that capitalize on nongenetic tumor evolution.
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Affiliation(s)
- Florian Rambow
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Herestraat 49, 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KULeuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Herestraat 49, 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KULeuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, United Kingdom
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31
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Bai X, Fisher DE, Flaherty KT. Cell-state dynamics and therapeutic resistance in melanoma from the perspective of MITF and IFNγ pathways. Nat Rev Clin Oncol 2019; 16:549-562. [PMID: 30967646 PMCID: PMC7185899 DOI: 10.1038/s41571-019-0204-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Targeted therapy and immunotherapy have greatly improved the prognosis of patients with metastatic melanoma, but resistance to these therapeutic modalities limits the percentage of patients with long-lasting responses. Accumulating evidence indicates that a persisting subpopulation of melanoma cells contributes to resistance to targeted therapy or immunotherapy, even in patients who initially have a therapeutic response; however, the root mechanism of resistance remains elusive. To address this problem, we propose a new model, in which dynamic fluctuations of protein expression at the single-cell level and longitudinal reshaping of the cellular state at the cell-population level explain the whole process of therapeutic resistance development. Conceptually, we focused on two different pivotal signalling pathways (mediated by microphthalmia-associated transcription factor (MITF) and IFNγ) to construct the evolving trajectories of melanoma and described each of the cell states. Accordingly, the development of therapeutic resistance could be divided into three main phases: early survival of cell populations, reversal of senescence, and the establishment of new homeostatic states and development of irreversible resistance. On the basis of existing data, we propose future directions in both translational research and the design of therapeutic strategies that incorporate this emerging understanding of resistance.
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Affiliation(s)
- Xue Bai
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital and Institute, Beijing, China
| | - David E Fisher
- Dermatology and Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Keith T Flaherty
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
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32
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Rathore M, Girard C, Ohanna M, Tichet M, Ben Jouira R, Garcia E, Larbret F, Gesson M, Audebert S, Lacour JP, Montaudié H, Prod'Homme V, Tartare-Deckert S, Deckert M. Cancer cell-derived long pentraxin 3 (PTX3) promotes melanoma migration through a toll-like receptor 4 (TLR4)/NF-κB signaling pathway. Oncogene 2019; 38:5873-5889. [PMID: 31253871 DOI: 10.1038/s41388-019-0848-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 03/30/2019] [Accepted: 04/28/2019] [Indexed: 01/23/2023]
Abstract
Cutaneous melanoma is one of the most aggressive cancers characterized by a high plasticity, a propensity for metastasis, and drug resistance. Melanomas are composed of phenotypically diverse subpopulations of tumor cells with heterogeneous molecular profiles that reflect intrinsic invasive abilities. In an attempt to identify novel factors of the melanoma invasive cell state, we previously investigated the nature of the invasive secretome by using a comparative proteomic approach. Here, we have extended this analysis to show that PTX3, an acute phase inflammatory glycoprotein, is one such factor secreted by invasive melanoma to promote tumor cell invasiveness. Elevated PTX3 production was observed in the population of MITFlow invasive cells but not in the population of MITFhigh differentiated melanoma cells. Consistently, MITF knockdown increased PTX3 expression in MITFhigh proliferative and poorly invasive cells. High levels of PTX3 were found in tissues and blood of metastatic melanoma patients, and in BRAF inhibitor-resistant melanoma cells displaying a mesenchymal invasive MITFlow phenotype. Genetic silencing of PTX3 in invasive melanoma cells dramatically impaired migration and invasion in vitro and in experimental lung extravasation assay in xenografted mice. In contrast, addition of melanoma-derived or recombinant PTX3, or expression of PTX3 enhanced motility of low migratory cells. Mechanistically, autocrine production of PTX3 by melanoma cells triggered an IKK/NFκB signaling pathway that promotes migration, invasion, and expression of the EMT factor TWIST1. Finally, we found that TLR4 and MYD88 knockdown inhibited PTX3-induced melanoma cell migration, suggesting that PTX3 functions through a TLR4-dependent pathway. Our work reveals that tumor-derived PTX3 contributes to melanoma cell invasion via targetable inflammation-related pathways. In addition to providing new insights into the biology of melanoma invasive behavior, this study underscores the notion that secreted PTX3 represents a potential biomarker and therapeutic target in a subpopulation of MITFlow invasive and/or refractory melanoma.
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Affiliation(s)
- M Rathore
- Université Côte d'Azur, INSERM, C3M, Nice, France
- Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - C Girard
- Université Côte d'Azur, INSERM, C3M, Nice, France
- Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
| | - M Ohanna
- Université Côte d'Azur, INSERM, C3M, Nice, France
- Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
| | - M Tichet
- Université Côte d'Azur, INSERM, C3M, Nice, France
- Laboratory of Translational Oncology, ISREC, EPFL, Lausanne, Switzerland
| | - R Ben Jouira
- Université Côte d'Azur, INSERM, C3M, Nice, France
| | - E Garcia
- Université Côte d'Azur, INSERM, C3M, Nice, France
| | - F Larbret
- Université Côte d'Azur, INSERM, C3M, Nice, France
- Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
| | - M Gesson
- Université Côte d'Azur, INSERM, C3M, Nice, France
| | - S Audebert
- Aix-Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - J-P Lacour
- Université Côte d'Azur, CHU Nice, Nice, France
| | - H Montaudié
- Université Côte d'Azur, CHU Nice, Nice, France
| | - V Prod'Homme
- Université Côte d'Azur, INSERM, C3M, Nice, France
- Equipe labellisée Ligue Contre le Cancer 2016, Nice, France
| | - S Tartare-Deckert
- Université Côte d'Azur, INSERM, C3M, Nice, France.
- Equipe labellisée Ligue Contre le Cancer 2016, Nice, France.
| | - M Deckert
- Université Côte d'Azur, INSERM, C3M, Nice, France.
- Equipe labellisée Ligue Contre le Cancer 2016, Nice, France.
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33
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Arozarena I, Wellbrock C. Phenotype plasticity as enabler of melanoma progression and therapy resistance. Nat Rev Cancer 2019; 19:377-391. [PMID: 31209265 DOI: 10.1038/s41568-019-0154-4] [Citation(s) in RCA: 224] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/13/2019] [Indexed: 12/31/2022]
Abstract
Malignant melanoma is notorious for its inter- and intratumour heterogeneity, based on transcriptionally distinct melanoma cell phenotypes. It is thought that these distinct phenotypes are plastic in nature and that their transcriptional reprogramming enables heterogeneous tumours both to undergo different stages of melanoma progression and to adjust to drug exposure during treatment. Recent advances in genomic technologies and the rapidly expanding availability of large gene expression datasets have allowed for a refined definition of the gene signatures that characterize these phenotypes and have revealed that phenotype plasticity plays a major role in the resistance to both targeted therapy and immunotherapy. In this Review we discuss the definition of melanoma phenotypes through particular transcriptional states and reveal the prognostic relevance of the related gene expression signatures. We review how the establishment of phenotypes is controlled and which roles phenotype plasticity plays in melanoma development and therapy. Because phenotype plasticity in melanoma bears a great resemblance to epithelial-mesenchymal transition, the lessons learned from melanoma will also benefit our understanding of other cancer types.
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Affiliation(s)
- Imanol Arozarena
- Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain.
| | - Claudia Wellbrock
- Manchester Cancer Research Centre, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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34
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Su Y, Bintz M, Yang Y, Robert L, Ng AHC, Liu V, Ribas A, Heath JR, Wei W. Phenotypic heterogeneity and evolution of melanoma cells associated with targeted therapy resistance. PLoS Comput Biol 2019; 15:e1007034. [PMID: 31166947 PMCID: PMC6576794 DOI: 10.1371/journal.pcbi.1007034] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 06/17/2019] [Accepted: 04/15/2019] [Indexed: 01/26/2023] Open
Abstract
Phenotypic plasticity is associated with non-genetic drug tolerance in several cancers. Such plasticity can arise from chromatin remodeling, transcriptomic reprogramming, and/or protein signaling rewiring, and is characterized as a cell state transition in response to molecular or physical perturbations. This, in turn, can confound interpretations of drug responses and resistance development. Using BRAF-mutant melanoma cell lines as the prototype, we report on a joint theoretical and experimental investigation of the cell-state transition dynamics associated with BRAF inhibitor drug tolerance. Thermodynamically motivated surprisal analysis of transcriptome data was used to treat the cell population as an entropy maximizing system under the influence of time-dependent constraints. This permits the extraction of an epigenetic potential landscape for drug-induced phenotypic evolution. Single-cell flow cytometry data of the same system were modeled with a modified Fokker-Planck-type kinetic model. The two approaches yield a consistent picture that accounts for the phenotypic heterogeneity observed over the course of drug tolerance development. The results reveal that, in certain plastic cancers, the population heterogeneity and evolution of cell phenotypes may be understood by accounting for the competing interactions of the epigenetic potential landscape and state-dependent cell proliferation. Accounting for such competition permits accurate, experimentally verifiable predictions that can potentially guide the design of effective treatment strategies. Cancer cells exhibit varied degrees of phenotypic heterogeneity. These phenotypes, each of them with unique molecular and functional profiles, display dynamic interconversion in response to drug perturbations, and can evolve to form new drug-tolerant phenotypes. Such phenotypic plasticity, in turn, renders tumor cells extremely difficult to treat. To get a quantitative biophysical understanding of the origins of the phenotypic equilibrium and evolution associated with drug tolerance development in highly plastic patient-derived melanoma cells, we employed joint experimental and computational approaches, using either bulk or single cell measurements as input, to interrogate the epigenetic landscape of the phenotypic evolution. We found that the observed phenotypic equilibria were established via competition between state-dependent net proliferation rates and landscape potential. The results reveal how the tumor cells maintain a phenotypic heterogeneity that facilitates appropriate responses to external cues. They implicate that, in certain phenotypically plastic tumor cells, drug targeting the driver oncogenes may not have sustained efficacy unless the phenotypic plasticity of the tumor is co-targeted.
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Affiliation(s)
- Yapeng Su
- Institute for Systems Biology, Seattle, Washington, United State of America
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United State of America
| | - Marcus Bintz
- Department of Molecular and Medical Pharmacology, University of California – Los Angeles, Los Angeles, California, United State of America
| | - Yezi Yang
- Department of Molecular and Medical Pharmacology, University of California – Los Angeles, Los Angeles, California, United State of America
| | - Lidia Robert
- Department of Medicine, University of California – Los Angeles, Los Angeles, California, United State of America
| | - Alphonsus H. C. Ng
- Institute for Systems Biology, Seattle, Washington, United State of America
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United State of America
| | - Victoria Liu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United State of America
| | - Antoni Ribas
- Department of Molecular and Medical Pharmacology, University of California – Los Angeles, Los Angeles, California, United State of America
- Department of Medicine, University of California – Los Angeles, Los Angeles, California, United State of America
- Department of Surgery, Division of Surgical-Oncology, University of California – Los Angeles, Los Angeles, California, United State of America
- Jonsson Comprehensive Cancer Center, University of California – Los Angeles, Los Angeles, California, United State of America
| | - James R. Heath
- Institute for Systems Biology, Seattle, Washington, United State of America
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United State of America
- Jonsson Comprehensive Cancer Center, University of California – Los Angeles, Los Angeles, California, United State of America
- * E-mail: (J.R.H.); (W.W.)
| | - Wei Wei
- Institute for Systems Biology, Seattle, Washington, United State of America
- Department of Molecular and Medical Pharmacology, University of California – Los Angeles, Los Angeles, California, United State of America
- Jonsson Comprehensive Cancer Center, University of California – Los Angeles, Los Angeles, California, United State of America
- * E-mail: (J.R.H.); (W.W.)
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35
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Emmons MF, Faião-Flores F, Sharma R, Thapa R, Messina JL, Becker JC, Schadendorf D, Seto E, Sondak VK, Koomen JM, Chen YA, Lau EK, Wan L, Licht JD, Smalley KSM. HDAC8 Regulates a Stress Response Pathway in Melanoma to Mediate Escape from BRAF Inhibitor Therapy. Cancer Res 2019; 79:2947-2961. [PMID: 30987999 DOI: 10.1158/0008-5472.can-19-0040] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/01/2019] [Accepted: 04/10/2019] [Indexed: 11/16/2022]
Abstract
Melanoma cells have the ability to switch to a dedifferentiated, invasive phenotype in response to multiple stimuli. Here, we show that exposure of melanomas to multiple stresses including BRAF-MEK inhibitor therapy, hypoxia, and UV irradiation leads to an increase in histone deacetylase 8 (HDAC8) activity and the adoption of a drug-resistant phenotype. Mass spectrometry-based phosphoproteomics implicated HDAC8 in the regulation of MAPK and AP-1 signaling. Introduction of HDAC8 into drug-naïve melanoma cells conveyed resistance both in vitro and in vivo. HDAC8-mediated BRAF inhibitor resistance was mediated via receptor tyrosine kinase activation, leading to MAPK signaling. Although HDACs function at the histone level, they also regulate nonhistone substrates, and introduction of HDAC8 decreased the acetylation of c-Jun, increasing its transcriptional activity and enriching for an AP-1 gene signature. Mutation of the putative c-Jun acetylation site at lysine 273 increased transcriptional activation of c-Jun in melanoma cells and conveyed resistance to BRAF inhibition. In vivo xenograft studies confirmed the key role of HDAC8 in therapeutic adaptation, with both nonselective and HDAC8-specific inhibitors enhancing the durability of BRAF inhibitor therapy. Our studies demonstrate that HDAC8-specific inhibitors limit the adaptation of melanoma cells to multiple stresses including BRAF-MEK inhibition. SIGNIFICANCE: This study provides evidence that HDAC8 drives transcriptional plasticity in melanoma cells in response to a range of stresses through direct deacetylation of c-Jun.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/11/2947/F1.large.jpg.
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Affiliation(s)
- Michael F Emmons
- The Department of Tumor Biology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Fernanda Faião-Flores
- The Department of Tumor Biology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Ritin Sharma
- The Department of Molecular Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Ram Thapa
- Department of Bioinformatics and Biostatistics, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jane L Messina
- The Department of Cutaneous Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jurgen C Becker
- Department of Translational Skin Cancer Research, German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
| | - Dirk Schadendorf
- Department of Translational Skin Cancer Research, German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
| | - Edward Seto
- George Washington University, Washington, D.C
| | - Vernon K Sondak
- The Department of Cutaneous Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - John M Koomen
- The Department of Molecular Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Yian A Chen
- Department of Bioinformatics and Biostatistics, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Eric K Lau
- The Department of Tumor Biology, The Moffitt Cancer Center and Research Institute, Tampa, Florida.,The Department of Cutaneous Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Lixin Wan
- The Department of Molecular Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jonathan D Licht
- The University of Florida Health Cancer Center, Gainesville, Florida
| | - Keiran S M Smalley
- The Department of Tumor Biology, The Moffitt Cancer Center and Research Institute, Tampa, Florida. .,The Department of Cutaneous Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
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36
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Kessler BE, Mishall KM, Kellett MD, Clark EG, Pugazhenthi U, Pozdeyev N, Kim J, Tan AC, Schweppe RE. Resistance to Src inhibition alters the BRAF-mutant tumor secretome to promote an invasive phenotype and therapeutic escape through a FAK>p130Cas>c-Jun signaling axis. Oncogene 2019; 38:2565-2579. [PMID: 30531837 PMCID: PMC6450711 DOI: 10.1038/s41388-018-0617-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 11/20/2018] [Accepted: 11/23/2018] [Indexed: 01/09/2023]
Abstract
Few therapy options exist for patients with advanced papillary and anaplastic thyroid cancer. We and others have previously identified c-Src as a key mediator of thyroid cancer pro-tumorigenic processes and a promising therapeutic target for thyroid cancer. To increase the efficacy of targeting Src in the clinic, we sought to define mechanisms of resistance to the Src inhibitor, dasatinib, to identify key pathways to target in combination. Using a panel of thyroid cancer cell lines expressing clinically relevant mutations in BRAF or RAS, which were previously developed to be resistant to dasatinib, we identified a switch to a more invasive phenotype in the BRAF-mutant cells as a potential therapy escape mechanism. This phenotype switch is driven by FAK kinase activity, and signaling through the p130Cas>c-Jun signaling axis. We have further shown this more invasive phenotype is accompanied by alterations in the secretome through the increased expression of pro-inflammatory cytokines, including IL-1β, and the pro-invasive metalloprotease, MMP-9. Furthermore, IL-1β signals via a feedforward autocrine loop to promote invasion through a FAK>p130Cas>c-Jun>MMP-9 signaling axis. We further demonstrate that upfront combined inhibition of FAK and Src synergistically inhibits growth and invasion, and induces apoptosis in a panel of BRAF- and RAS-mutant thyroid cancer cell lines. Together our data demonstrate that acquired resistance to single-agent Src inhibition promotes a more invasive phenotype through an IL-1β>FAK>p130Cas>c-Jun >MMP signaling axis, and that combined inhibition of FAK and Src has the potential to block this inhibitor-induced phenotype switch.
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Affiliation(s)
- Brittelle E Kessler
- Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Katie M Mishall
- Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Meghan D Kellett
- Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Erin G Clark
- Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Umarani Pugazhenthi
- Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Nikita Pozdeyev
- Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Division of Bioinformatics and Personalized Medicine, Aurora, CO, 80045, USA
| | - Jihye Kim
- University of Colorado Cancer Center, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Aik Choon Tan
- University of Colorado Cancer Center, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Rebecca E Schweppe
- Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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37
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Almeida FV, Douglass SM, Fane ME, Weeraratna AT. Bad company: Microenvironmentally mediated resistance to targeted therapy in melanoma. Pigment Cell Melanoma Res 2019; 32:237-247. [PMID: 30216694 PMCID: PMC6727967 DOI: 10.1111/pcmr.12736] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/18/2018] [Accepted: 09/10/2018] [Indexed: 12/21/2022]
Abstract
This review will focus on the role of the tumor microenvironment (TME) in the development of drug resistance in melanoma. Resistance to mitogen-activated protein kinase inhibitors (MAPKi) in melanoma is observed months after treatment, a phenomenon that is often attributed to the incredible plasticity of melanoma cells but may also depend on the TME. The TME is unique in its cellular composition-it contains fibroblasts, immune cells, endothelial cells, adipocytes, and among others. In addition, the TME provides "non-homeostatic" levels of oxygen, nutrients (hypoxia and metabolic stress), and extracellular matrix proteins, creating a pro-tumorigenic niche that drives resistance to MAPKi treatment. In this review, we will focus on how changes in the tumor microenvironment regulate MAPKi resistance.
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Affiliation(s)
- Filipe V Almeida
- Immunology, Microenvironment & Metastasis Program, Melanoma Research Center. Wistar Institute, 3601 Spruce Street, Philadelphia PA 19104, USA
| | - Stephen M. Douglass
- Immunology, Microenvironment & Metastasis Program, Melanoma Research Center. Wistar Institute, 3601 Spruce Street, Philadelphia PA 19104, USA
| | - Mitchell E. Fane
- Immunology, Microenvironment & Metastasis Program, Melanoma Research Center. Wistar Institute, 3601 Spruce Street, Philadelphia PA 19104, USA
| | - Ashani T. Weeraratna
- Immunology, Microenvironment & Metastasis Program, Melanoma Research Center. Wistar Institute, 3601 Spruce Street, Philadelphia PA 19104, USA
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38
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Rožanc J, Sakellaropoulos T, Antoranz A, Guttà C, Podder B, Vetma V, Rufo N, Agostinis P, Pliaka V, Sauter T, Kulms D, Rehm M, Alexopoulos LG. Phosphoprotein patterns predict trametinib responsiveness and optimal trametinib sensitisation strategies in melanoma. Cell Death Differ 2018; 26:1365-1378. [PMID: 30323272 DOI: 10.1038/s41418-018-0210-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 08/19/2018] [Accepted: 09/10/2018] [Indexed: 01/02/2023] Open
Abstract
Malignant melanoma is a highly aggressive form of skin cancer responsible for the majority of skin cancer-related deaths. Recent insight into the heterogeneous nature of melanoma suggests more personalised treatments may be necessary to overcome drug resistance and improve patient care. To this end, reliable molecular signatures that can accurately predict treatment responsiveness need to be identified. In this study, we applied multiplex phosphoproteomic profiling across a panel of 24 melanoma cell lines with different disease-relevant mutations, to predict responsiveness to MEK inhibitor trametinib. Supported by multivariate statistical analysis and multidimensional pattern recognition algorithms, the responsiveness of individual cell lines to trametinib could be predicted with high accuracy (83% correct predictions), independent of mutation status. We also successfully employed this approach to case specifically predict whether individual melanoma cell lines could be sensitised to trametinib. Our predictions identified that combining MEK inhibition with selective targeting of c-JUN and/or FAK, using siRNA-based depletion or pharmacological inhibitors, sensitised resistant cell lines and significantly enhanced treatment efficacy. Our study indicates that multiplex proteomic analyses coupled with pattern recognition approaches could assist in personalising trametinib-based treatment decisions in the future.
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Affiliation(s)
- Jan Rožanc
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg.,ProtATonce Ltd, Science Park Demokritos, Athens, Greece
| | | | - Asier Antoranz
- ProtATonce Ltd, Science Park Demokritos, Athens, Greece.,Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece
| | - Cristiano Guttà
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Biswajit Podder
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Vesna Vetma
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Nicole Rufo
- Laboratory for Cell Death Research and Therapy, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Patrizia Agostinis
- Laboratory for Cell Death Research and Therapy, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Vaia Pliaka
- ProtATonce Ltd, Science Park Demokritos, Athens, Greece
| | - Thomas Sauter
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | - Dagmar Kulms
- Experimental Dermatology, Department of Dermatology, Technical University Dresden, Dresden, Germany.,Center for Regenerative Therapies, Technical University Dresden, Dresden, Germany
| | - Markus Rehm
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany.,Stuttgart Research Center Systems Biology, University of Stuttgart, Stuttgart, Germany.,Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.,Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Leonidas G Alexopoulos
- ProtATonce Ltd, Science Park Demokritos, Athens, Greece. .,Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece.
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39
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Rambow F, Rogiers A, Marin-Bejar O, Aibar S, Femel J, Dewaele M, Karras P, Brown D, Chang YH, Debiec-Rychter M, Adriaens C, Radaelli E, Wolter P, Bechter O, Dummer R, Levesque M, Piris A, Frederick DT, Boland G, Flaherty KT, van den Oord J, Voet T, Aerts S, Lund AW, Marine JC. Toward Minimal Residual Disease-Directed Therapy in Melanoma. Cell 2018; 174:843-855.e19. [PMID: 30017245 DOI: 10.1016/j.cell.2018.06.025] [Citation(s) in RCA: 418] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 04/13/2018] [Accepted: 06/12/2018] [Indexed: 01/05/2023]
Abstract
Many patients with advanced cancers achieve dramatic responses to a panoply of therapeutics yet retain minimal residual disease (MRD), which ultimately results in relapse. To gain insights into the biology of MRD, we applied single-cell RNA sequencing to malignant cells isolated from BRAF mutant patient-derived xenograft melanoma cohorts exposed to concurrent RAF/MEK-inhibition. We identified distinct drug-tolerant transcriptional states, varying combinations of which co-occurred within MRDs from PDXs and biopsies of patients on treatment. One of these exhibited a neural crest stem cell (NCSC) transcriptional program largely driven by the nuclear receptor RXRG. An RXR antagonist mitigated accumulation of NCSCs in MRD and delayed the development of resistance. These data identify NCSCs as key drivers of resistance and illustrate the therapeutic potential of MRD-directed therapy. They also highlight how gene regulatory network architecture reprogramming may be therapeutically exploited to limit cellular heterogeneity, a key driver of disease progression and therapy resistance.
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Affiliation(s)
- Florian Rambow
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Aljosja Rogiers
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Oskar Marin-Bejar
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, KU Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Julia Femel
- Department of Cell, Developmental, and Cancer Biology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Michael Dewaele
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Panagiotis Karras
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Daniel Brown
- Laboratory of reproductive genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, OR, USA
| | - Maria Debiec-Rychter
- Laboratory for Genetics of Malignant Disorders, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Carmen Adriaens
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Enrico Radaelli
- Comparative Pathology Core, University of Pennsylvania, Department of Pathobiology, Philadelphia, PA, USA
| | - Pascal Wolter
- Department of General Medical Oncology, UZ Leuven, Leuven, Belgium
| | - Oliver Bechter
- Department of General Medical Oncology, UZ Leuven, Leuven, Belgium
| | - Reinhard Dummer
- Department of Dermatology, University of Zürich Hospital, Zürich, Switzerland
| | - Mitchell Levesque
- Department of Dermatology, University of Zürich Hospital, Zürich, Switzerland
| | - Adriano Piris
- Department of Surgical Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Dennie T Frederick
- Department of Surgical Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Genevieve Boland
- Department of Surgical Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Keith T Flaherty
- Department of Medical Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Joost van den Oord
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, UZ Leuven, Leuven, Belgium
| | - Thierry Voet
- Laboratory of reproductive genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, KU Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Amanda W Lund
- Department of Cell, Developmental, and Cancer Biology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium.
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40
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Tsoi J, Robert L, Paraiso K, Galvan C, Sheu KM, Lay J, Wong DJL, Atefi M, Shirazi R, Wang X, Braas D, Grasso CS, Palaskas N, Ribas A, Graeber TG. Multi-stage Differentiation Defines Melanoma Subtypes with Differential Vulnerability to Drug-Induced Iron-Dependent Oxidative Stress. Cancer Cell 2018; 33:890-904.e5. [PMID: 29657129 PMCID: PMC5953834 DOI: 10.1016/j.ccell.2018.03.017] [Citation(s) in RCA: 500] [Impact Index Per Article: 83.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/01/2017] [Accepted: 03/16/2018] [Indexed: 01/01/2023]
Abstract
Malignant transformation can result in melanoma cells that resemble different stages of their embryonic development. Our gene expression analysis of human melanoma cell lines and patient tumors revealed that melanoma follows a two-dimensional differentiation trajectory that can be subclassified into four progressive subtypes. This differentiation model is associated with subtype-specific sensitivity to iron-dependent oxidative stress and cell death known as ferroptosis. Receptor tyrosine kinase-mediated resistance to mitogen-activated protein kinase targeted therapies and activation of the inflammatory signaling associated with immune therapy involves transitions along this differentiation trajectory, which lead to increased sensitivity to ferroptosis. Therefore, ferroptosis-inducing drugs present an orthogonal therapeutic approach to target the differentiation plasticity of melanoma cells to increase the efficacy of targeted and immune therapies.
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Affiliation(s)
- Jennifer Tsoi
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), 570 Westwood Plaza, Building 114, Los Angeles, CA 90095, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA
| | - Lidia Robert
- Department of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Kim Paraiso
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), 570 Westwood Plaza, Building 114, Los Angeles, CA 90095, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA
| | - Carlos Galvan
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), 570 Westwood Plaza, Building 114, Los Angeles, CA 90095, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA
| | - Katherine M Sheu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), 570 Westwood Plaza, Building 114, Los Angeles, CA 90095, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA
| | - Johnson Lay
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), 570 Westwood Plaza, Building 114, Los Angeles, CA 90095, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA; UCLA Metabolomics Center, Los Angeles, CA 90095, USA
| | | | - Mohammad Atefi
- Department of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Roksana Shirazi
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), 570 Westwood Plaza, Building 114, Los Angeles, CA 90095, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA
| | - Xiaoyan Wang
- Department of Medicine Statistics Core, UCLA, Los Angeles, CA 90095, USA
| | - Daniel Braas
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), 570 Westwood Plaza, Building 114, Los Angeles, CA 90095, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA; UCLA Metabolomics Center, Los Angeles, CA 90095, USA
| | | | - Nicolaos Palaskas
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), 570 Westwood Plaza, Building 114, Los Angeles, CA 90095, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA
| | - Antoni Ribas
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), 570 Westwood Plaza, Building 114, Los Angeles, CA 90095, USA; Department of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Surgery, Division of Surgical-Oncology, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), 570 Westwood Plaza, Building 114, Los Angeles, CA 90095, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA; UCLA Metabolomics Center, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA.
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41
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Konieczkowski DJ, Johannessen CM, Garraway LA. A Convergence-Based Framework for Cancer Drug Resistance. Cancer Cell 2018; 33:801-815. [PMID: 29763622 PMCID: PMC5957297 DOI: 10.1016/j.ccell.2018.03.025] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 02/02/2018] [Accepted: 03/26/2018] [Indexed: 02/07/2023]
Abstract
Despite advances in cancer biology and therapeutics, drug resistance remains problematic. Resistance is often multifactorial, heterogeneous, and prone to undersampling. Nonetheless, many individual mechanisms of targeted therapy resistance may coalesce into a smaller number of convergences, including pathway reactivation (downstream re-engagement of original effectors), pathway bypass (recruitment of a parallel pathway converging on the same downstream output), and pathway indifference (development of a cellular state independent of the initial therapeutic target). Similar convergences may also underpin immunotherapy resistance. Such parsimonious, convergence-based frameworks may help explain resistance across tumor types and therapeutic categories and may also suggest strategies to overcome it.
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42
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Martin CA, Cullinane C, Kirby L, Abuhammad S, Lelliott EJ, Waldeck K, Young RJ, Brajanovski N, Cameron DP, Walker R, Sanij E, Poortinga G, Hannan RD, Pearson RB, Hicks RJ, McArthur GA, Sheppard KE. Palbociclib synergizes with BRAF and MEK inhibitors in treatment naïve melanoma but not after the development of BRAF inhibitor resistance. Int J Cancer 2018; 142:2139-2152. [PMID: 29243224 DOI: 10.1002/ijc.31220] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 11/09/2017] [Accepted: 12/06/2017] [Indexed: 01/02/2023]
Abstract
Increased CDK4 activity occurs in the majority of melanomas and CDK4/6 inhibitors in combination with BRAF and MEK inhibitors are currently in clinical trials for the treatment of melanoma. We hypothesize that the timing of the addition of CDK4/6 inhibitors to the current BRAF and MEK inhibitor regime will impact on the efficacy of this triplet drug combination. The efficacy of BRAF, MEK and CDK4/6 inhibitors as single agents and in combination was assessed in human BRAF mutant cell lines that were treatment naïve, BRAF inhibitor tolerant or had acquired resistance to BRAF inhibitors. Xenograft studies were then performed to test the in vivo efficacy of the BRAF and CDK4/6 inhibitor combination. Melanoma cells that had developed early reversible tolerance or acquired resistance to BRAF inhibition remained sensitive to palbociclib. In drug-tolerant cells, the efficacy of the combination of palbociclib with BRAF and/or MEK inhibitors was equivalent to single agent palbociclib. Similarly, acquired BRAF inhibitor resistance cells lost efficacy to the palbociclib and BRAF combination. In contrast, upfront treatment of melanoma cells with palbociclib in combination with BRAF and/or MEK inhibitors induced either cell death or senescence and was superior to a BRAF plus MEK inhibitor combination. In vivo palbociclib plus BRAF inhibitor induced rapid and sustained tumor regression without the development of therapy resistance. In summary, upfront dual targeting of CDK4/6 and mutant BRAF signaling enables tumor cells to evade resistance to monotherapy and is required for robust and sustained tumor regression. Melanoma patients whose tumors have acquired resistance to BRAF inhibition are less likely to have favorable responses to subsequent treatment with the triplet combination of BRAF, MEK and CDK4/6 inhibitors.
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Affiliation(s)
- Claire A Martin
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia
| | - Carleen Cullinane
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic, Australia
| | - Laura Kirby
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia
| | - Shatha Abuhammad
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic, Australia
| | - Emily J Lelliott
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic, Australia
| | - Kelly Waldeck
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia
| | - Richard J Young
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia
| | - Natalie Brajanovski
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia
| | - Donald P Cameron
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia
| | - Rachael Walker
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia
| | - Elaine Sanij
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia.,Department of Pathology, University of Melbourne, Parkville, Vic, Australia
| | - Gretchen Poortinga
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic, Australia.,Department of Medicine, St. Vincent's Hospital, University of Melbourne, Parkville, Vic, Australia
| | - Ross D Hannan
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Vic, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic, Australia.,School of Biomedical Sciences, University of Queensland, Brisbane, Qld, Australia.,The John Curtin School of Medical Research, Australian National University, Acton, ACT, Australia
| | - Richard B Pearson
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Vic, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic, Australia
| | - Rodney J Hicks
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic, Australia
| | - Grant A McArthur
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic, Australia.,Department of Medicine, St. Vincent's Hospital, University of Melbourne, Parkville, Vic, Australia
| | - Karen E Sheppard
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Vic, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Vic, Australia
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43
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Single-cell analysis resolves the cell state transition and signaling dynamics associated with melanoma drug-induced resistance. Proc Natl Acad Sci U S A 2017; 114:13679-13684. [PMID: 29229836 DOI: 10.1073/pnas.1712064115] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Continuous BRAF inhibition of BRAF mutant melanomas triggers a series of cell state changes that lead to therapy resistance and escape from immune control before establishing acquired resistance genetically. We used genome-wide transcriptomics and single-cell phenotyping to explore the response kinetics to BRAF inhibition for a panel of patient-derived BRAFV600 -mutant melanoma cell lines. A subset of plastic cell lines, which followed a trajectory covering multiple known cell state transitions, provided models for more detailed biophysical investigations. Markov modeling revealed that the cell state transitions were reversible and mediated by both Lamarckian induction and nongenetic Darwinian selection of drug-tolerant states. Single-cell functional proteomics revealed activation of certain signaling networks shortly after BRAF inhibition, and before the appearance of drug-resistant phenotypes. Drug targeting those networks, in combination with BRAF inhibition, halted the adaptive transition and led to prolonged growth inhibition in multiple patient-derived cell lines.
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44
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Reinhardt J, Landsberg J, Schmid-Burgk JL, Ramis BB, Bald T, Glodde N, Lopez-Ramos D, Young A, Ngiow SF, Nettersheim D, Schorle H, Quast T, Kolanus W, Schadendorf D, Long GV, Madore J, Scolyer RA, Ribas A, Smyth MJ, Tumeh PC, Tüting T, Hölzel M. MAPK Signaling and Inflammation Link Melanoma Phenotype Switching to Induction of CD73 during Immunotherapy. Cancer Res 2017; 77:4697-4709. [PMID: 28652246 DOI: 10.1158/0008-5472.can-17-0395] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 05/13/2017] [Accepted: 06/20/2017] [Indexed: 11/16/2022]
Abstract
Evolution of tumor cell phenotypes promotes heterogeneity and therapy resistance. Here we found that induction of CD73, the enzyme that generates immunosuppressive adenosine, is linked to melanoma phenotype switching. Activating MAPK mutations and growth factors drove CD73 expression, which marked both nascent and full activation of a mesenchymal-like melanoma cell state program. Proinflammatory cytokines like TNFα cooperated with MAPK signaling through the c-Jun/AP-1 transcription factor complex to activate CD73 transcription by binding to an intronic enhancer. In a mouse model of T-cell immunotherapy, CD73 was induced in relapse melanomas, which acquired a mesenchymal-like phenotype. We also detected CD73 upregulation in melanoma patients progressing under adoptive T-cell transfer or immune checkpoint blockade, arguing for an adaptive resistance mechanism. Our work substantiates CD73 as a target to combine with current immunotherapies, but its dynamic regulation suggests limited value of CD73 pretreatment expression as a biomarker to stratify melanoma patients. Cancer Res; 77(17); 4697-709. ©2017 AACR.
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Affiliation(s)
- Julia Reinhardt
- Unit for RNA Biology, Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Jennifer Landsberg
- Laboratory of Experimental Dermatology, Department of Dermatology and Allergy, University of Bonn, Bonn, Germany.,Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
| | - Jonathan L Schmid-Burgk
- Institute of Molecular Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Bartomeu Bibiloni Ramis
- Laboratory of Experimental Dermatology, Department of Dermatology and Allergy, University of Bonn, Bonn, Germany
| | - Tobias Bald
- Laboratory of Experimental Dermatology, Department of Dermatology and Allergy, University of Bonn, Bonn, Germany.,Laboratory of Experimental Dermatology, Department of Dermatology, University of Magdeburg, Magdeburg, Germany.,Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Nicole Glodde
- Unit for RNA Biology, Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany.,Laboratory of Experimental Dermatology, Department of Dermatology and Allergy, University of Bonn, Bonn, Germany
| | - Dorys Lopez-Ramos
- Laboratory of Experimental Dermatology, Department of Dermatology and Allergy, University of Bonn, Bonn, Germany.,Laboratory of Experimental Dermatology, Department of Dermatology, University of Magdeburg, Magdeburg, Germany
| | - Arabella Young
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Shin Foong Ngiow
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Daniel Nettersheim
- Department of Developmental Pathology, Institute of Pathology, University of Bonn Medical School, Bonn, Germany
| | - Hubert Schorle
- Department of Developmental Pathology, Institute of Pathology, University of Bonn Medical School, Bonn, Germany
| | - Thomas Quast
- Molecular Immunology and Cell Biology, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Waldemar Kolanus
- Molecular Immunology and Cell Biology, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, West German Cancer Center, University Duisburg-Essen, Essen, Germany
| | - Georgina V Long
- Melanoma Institute Australia and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Jason Madore
- Melanoma Institute Australia and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Antoni Ribas
- University of California Los Angeles (UCLA), Los Angeles, California.,Jonsson Comprehensive Cancer Center, Los Angeles, California
| | - Mark J Smyth
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Paul C Tumeh
- University of California Los Angeles (UCLA), Los Angeles, California.,Jonsson Comprehensive Cancer Center, Los Angeles, California
| | - Thomas Tüting
- Laboratory of Experimental Dermatology, Department of Dermatology and Allergy, University of Bonn, Bonn, Germany.,Laboratory of Experimental Dermatology, Department of Dermatology, University of Magdeburg, Magdeburg, Germany
| | - Michael Hölzel
- Unit for RNA Biology, Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany.
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Fallahi-Sichani M, Becker V, Izar B, Baker GJ, Lin JR, Boswell SA, Shah P, Rotem A, Garraway LA, Sorger PK. Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de-differentiated state. Mol Syst Biol 2017; 13:905. [PMID: 28069687 PMCID: PMC5248573 DOI: 10.15252/msb.20166796] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Treatment of BRAF-mutant melanomas with MAP kinase pathway inhibitors is paradigmatic of the promise of precision cancer therapy but also highlights problems with drug resistance that limit patient benefit. We use live-cell imaging, single-cell analysis, and molecular profiling to show that exposure of tumor cells to RAF/MEK inhibitors elicits a heterogeneous response in which some cells die, some arrest, and the remainder adapt to drug. Drug-adapted cells up-regulate markers of the neural crest (e.g., NGFR), a melanocyte precursor, and grow slowly. This phenotype is transiently stable, reverting to the drug-naïve state within 9 days of drug withdrawal. Transcriptional profiling of cell lines and human tumors implicates a c-Jun/ECM/FAK/Src cascade in de-differentiation in about one-third of cell lines studied; drug-induced changes in c-Jun and NGFR levels are also observed in xenograft and human tumors. Drugs targeting the c-Jun/ECM/FAK/Src cascade as well as BET bromodomain inhibitors increase the maximum effect (Emax) of RAF/MEK kinase inhibitors by promoting cell killing. Thus, analysis of reversible drug resistance at a single-cell level identifies signaling pathways and inhibitory drugs missed by assays that focus on cell populations.
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Affiliation(s)
- Mohammad Fallahi-Sichani
- Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
| | - Verena Becker
- Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
| | - Benjamin Izar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gregory J Baker
- Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
| | - Jia-Ren Lin
- HMS LINCS Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sarah A Boswell
- Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA
| | - Parin Shah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Peter K Sorger
- Department of Systems Biology, Program in Therapeutic Sciences, Harvard Medical School, Boston, MA, USA .,HMS LINCS Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
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