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Aya F, Lanuza-Gracia P, González-Pérez A, Bonnal S, Mancini E, López-Bigas N, Arance A, Valcárcel J. Genomic deletions explain the generation of alternative BRAF isoforms conferring resistance to MAPK inhibitors in melanoma. Cell Rep 2024; 43:114048. [PMID: 38614086 DOI: 10.1016/j.celrep.2024.114048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/06/2024] [Accepted: 03/19/2024] [Indexed: 04/15/2024] Open
Abstract
Resistance to MAPK inhibitors (MAPKi), the main cause of relapse in BRAF-mutant melanoma, is associated with the production of alternative BRAF mRNA isoforms (altBRAFs) in up to 30% of patients receiving BRAF inhibitor monotherapy. These altBRAFs have been described as being generated by alternative pre-mRNA splicing, and splicing modulation has been proposed as a therapeutic strategy to overcome resistance. In contrast, we report that altBRAFs are generated through genomic deletions. Using different in vitro models of altBRAF-mediated melanoma resistance, we demonstrate the production of altBRAFs exclusively from the BRAF V600E allele, correlating with corresponding genomic deletions. Genomic deletions are also detected in tumor samples from melanoma and breast cancer patients expressing altBRAFs. Along with the identification of altBRAFs in BRAF wild-type and in MAPKi-naive melanoma samples, our results represent a major shift in our understanding of mechanisms leading to the generation of BRAF transcripts variants associated with resistance in melanoma.
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Affiliation(s)
- Francisco Aya
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Medical Oncology Department, Hospital Clinic, Barcelona, Spain; Institut de Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Pablo Lanuza-Gracia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Abel González-Pérez
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Estefania Mancini
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nuria López-Bigas
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Ana Arance
- Medical Oncology Department, Hospital Clinic, Barcelona, Spain; Institut de Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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2
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Dinter L, Karitzky PC, Schulz A, Wurm AA, Mehnert MC, Sergon M, Tunger A, Lesche M, Wehner R, Müller A, Käubler T, Niessner H, Dahl A, Beissert S, Schmitz M, Meier F, Seliger B, Westphal D. BRAF and MEK inhibitor combinations induce potent molecular and immunological effects in NRAS-mutant melanoma cells: Insights into mode of action and resistance mechanisms. Int J Cancer 2024; 154:1057-1072. [PMID: 38078628 DOI: 10.1002/ijc.34807] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 10/17/2023] [Accepted: 11/03/2023] [Indexed: 01/23/2024]
Abstract
About 25% of melanoma harbor activating NRAS mutations, which are associated with aggressive disease therefore requiring a rapid antitumor intervention. However, no efficient targeted therapy options are currently available for patients with NRAS-mutant melanoma. MEK inhibitors (MEKi) appear to display a moderate antitumor activity and also immunological effects in NRAS-mutant melanoma, providing an ideal backbone for combination treatments. In our study, the MEKi binimetinib, cobimetinib and trametinib combined with the BRAF inhibitors (BRAFi) encorafenib, vemurafenib and dabrafenib were investigated for their ability to inhibit proliferation, induce apoptosis and alter the expression of immune modulatory molecules in sensitive NRAS-mutant melanoma cells using two- and three-dimensional cell culture models as well as RNA sequencing analyses. Furthermore, NRAS-mutant melanoma cells resistant to the three BRAFi/MEKi combinations were established to characterize the mechanisms contributing to their resistance. All BRAFi induced a stress response in the sensitive NRAS-mutant melanoma cells thereby significantly enhancing the antiproliferative and proapoptotic activity of the MEKi analyzed. Furthermore, BRAFi/MEKi combinations upregulated immune relevant molecules, such as ICOS-L, components of antigen-presenting machinery and the "don't eat me signal" molecule CD47 in the melanoma cells. The BRAFi/MEKi-resistant, NRAS-mutant melanoma cells counteracted the molecular and immunological effects of BRAFi/MEKi by upregulating downstream mitogen-activated protein kinase pathway molecules, inhibiting apoptosis and promoting immune escape mechanisms. Together, our study reveals potent molecular and immunological effects of BRAFi/MEKi in sensitive NRAS-mutant melanoma cells that may be exploited in new combinational treatment strategies for patients with NRAS-mutant melanoma.
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Affiliation(s)
- Lisa Dinter
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT) Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Paula C Karitzky
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, Dresden, Germany
| | - Alexander Schulz
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT) Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Alexander A Wurm
- National Center for Tumor Diseases (NCT) Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Department of Translational Medical Oncology, NCT Dresden, Dresden, Germany
- Mildred Scheel Early Career Center, NCT Dresden, Medical Faculty and University Hospital Carl Gustav Carus at TU Dresden, Dresden, Germany
| | - Marie-Christin Mehnert
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT) Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Mildred Sergon
- Institute of Pathology, University Hospital Carl Gustav Carus at TU Dresden, Dresden, Germany
| | - Antje Tunger
- National Center for Tumor Diseases (NCT) Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Mathias Lesche
- DRESDEN-Concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden, Dresden, Germany
| | - Rebekka Wehner
- National Center for Tumor Diseases (NCT) Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anja Müller
- Medical Faculty, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Theresa Käubler
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, Dresden, Germany
| | - Heike Niessner
- Department of Dermatology, Oncology, University Medical Center, Tübingen, Germany
| | - Andreas Dahl
- DRESDEN-Concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden, Dresden, Germany
| | - Stefan Beissert
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT) Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Marc Schmitz
- National Center for Tumor Diseases (NCT) Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Friedegund Meier
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT) Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Skin Cancer Center at the University Cancer Center Dresden, University Hospital Carl Gustav Carus at TU Dresden, Dresden, Germany
| | - Barbara Seliger
- Medical Faculty, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- Institute of Translational Immunology, Medical School "Theodor Fontane", Brandenburg an der Havel, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Dana Westphal
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, Dresden, Germany
- National Center for Tumor Diseases (NCT) Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
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3
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Kadamb R, Anton ML, Purwin TJ, Chua V, Seeneevassen L, Teh J, Angela Nieto M, Sato T, Terai M, Roman SR, De Koning L, Zheng D, Aplin AE, Aguirre-Ghiso J. Lineage commitment pathways epigenetically oppose oncogenic Gαq/11-YAP signaling in dormant disseminated uveal melanoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.583565. [PMID: 38496663 PMCID: PMC10942354 DOI: 10.1101/2024.03.05.583565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The mechanisms driving late relapse in uveal melanoma (UM) patients remains a medical mystery and major challenge. Clinically it is inferred that UM disseminated cancer cells (DCCs) persist asymptomatic for years-to-decades mainly in the liver before they manifest as symptomatic metastasis. Here we reveal using Gαq/11 mut /BAP wt human uveal melanoma models and human UM metastatic samples, that the neural crest lineage commitment nuclear receptor NR2F1 is a key regulator of spontaneous UM DCC dormancy in the liver. Using a quiescence reporter, RNA-seq and multiplex imaging we revealed that rare dormant UM DCCs upregulate NR2F1 expression and genes related to neural crest programs while repressing gene related to cell cycle progression. Gain and loss of function assays showed that NR2F1 silences YAP1/TEAD1 transcription downstream of Gαq/11 signaling and that NR2F1 expression can also be repressed by YAP1. YAP1 expression is repressed by NR2F1 binding to its promoter and changing the histone H3 tail activation marks to repress YAP1 transcription. In vivo CRISPR KO of NR2F1 led dormant UM DCCs to awaken and initiate relentless liver metastatic growth. Cut&Run and bulk RNA sequencing further confirmed that NR2F1 epigenetically stimulates neuron axon guidance and neural lineage programs, and it globally represses gene expression linked to G-protein signaling to drive dormancy. Pharmacological inhibition of Gαq/11 mut signaling resulted in NR2F1 upregulation and robust UM growth arrest, which was also achieved using a novel NR2F1 agonist. Our work sheds light on the molecular underpinnings of UM dormancy revealing that transcriptional programs driven by NR2F1 epigenetically short-circuit Gαq/11 signaling to its downstream target YAP1. Highlights Quiescent solitary uveal melanoma (UM) DCCs in the liver up- and down-regulate neural crest and cell cycle progression programs, respectively.NR2F1 drives solitary UM DCC dormancy by antagonizing the Gαq/11-YAP1 pathway; small molecule Gαq/11 inhibition restores NR2F1 expression and quiescence. NR2F1 short-circuits oncogenic YAP1 and G-protein signaling via a chromatin remodeling program. Loss of function of NR2F1 in dormant UM DCCs leads to aggressive liver metastasis. Graphical abstract
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Wu M, Hanly A, Gibson F, Fisher R, Rogers S, Park K, Zuger A, Kuang K, Kalin JH, Nocco S, Cole M, Xiao A, Agus F, Labadorf A, Beck S, Collard M, Cole PA, Alani RM. The CoREST repressor complex mediates phenotype switching and therapy resistance in melanoma. J Clin Invest 2024; 134:e171063. [PMID: 38300709 PMCID: PMC10940100 DOI: 10.1172/jci171063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
Virtually all patients with BRAF-mutant melanoma develop resistance to MAPK inhibitors largely through nonmutational events. Although the epigenetic landscape is shown to be altered in therapy-resistant melanomas and other cancers, a specific targetable epigenetic mechanism has not been validated. Here, we evaluated the corepressor for element 1-silencing transcription factor (CoREST) epigenetic repressor complex and the recently developed bivalent inhibitor corin within the context of melanoma phenotype plasticity and therapeutic resistance. We found that CoREST was a critical mediator of the major distinct melanoma phenotypes and that corin treatment of melanoma cells led to phenotype reprogramming. Global assessment of transcript and chromatin changes conferred by corin revealed specific effects on histone marks connected to epithelial-mesenchymal transition-associated (EMT-associated) transcription factors and the dual-specificity phosphatases (DUSPs). Remarkably, treatment of BRAF inhibitor-resistant (BRAFi-R) melanomas with corin promoted resensitization to BRAFi therapy. DUSP1 was consistently downregulated in BRAFi-R melanomas, which was reversed by corin treatment and associated with inhibition of p38 MAPK activity and resensitization to BRAFi therapies. Moreover, this activity was recapitulated by the p38 MAPK inhibitor BIRB 796. These findings identify the CoREST repressor complex as a central mediator of melanoma phenotype plasticity and resistance to targeted therapy and suggest that CoREST inhibitors may prove beneficial for patients with BRAFi-resistant melanoma.
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Affiliation(s)
- Muzhou Wu
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Ailish Hanly
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Frederick Gibson
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Robert Fisher
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Samantha Rogers
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Kihyun Park
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Angelina Zuger
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Kevin Kuang
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Jay H. Kalin
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Sarah Nocco
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Matthew Cole
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Amy Xiao
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Filisia Agus
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Adam Labadorf
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Samuel Beck
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Marianne Collard
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Philip A. Cole
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Rhoda M. Alani
- Department of Dermatology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts, USA
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5
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Arasi MB, De Luca G, Chronopoulou L, Pedini F, Petrucci E, Flego M, Stringaro A, Colone M, Pasquini L, Spada M, Lulli V, Perrotta MC, Calin GA, Palocci C, Biffoni M, Felicetti F, Felli N. MiR126-targeted-nanoparticles combined with PI3K/AKT inhibitor as a new strategy to overcome melanoma resistance. Mol Ther 2024; 32:152-167. [PMID: 37990493 PMCID: PMC10787166 DOI: 10.1016/j.ymthe.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/09/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
Metastatic melanoma poses significant challenges as a highly lethal disease. Despite the success of molecular targeting using BRAFV600E inhibitors (BRAFis) and immunotherapy, the emergence of early recurrence remains an issue and there is the need for novel therapeutic approaches. This study aimed at creating a targeted delivery system for the oncosuppressor microRNA 126 (miR126) and testing its effectiveness in combination with a phosphatidylinositol 3-kinase (PI3K)/ protein kinase B (AKT) inhibitor for treating metastatic melanoma resistant to BRAFis. To achieve this, we synthesized chitosan nanoparticles containing a chemically modified miR126 sequence. These nanoparticles were further functionalized with an antibody specific to the chondroitin sulfate proteoglycan 4 (CSPG4) melanoma marker. After evaluation in vitro, the efficacy of this treatment was evaluated through an in vivo experiment using mice bearing resistant human melanoma. The co-administration of miR126 and the PI3K/AKT inhibitor in these experiments significantly reduced tumor growth and inhibited the formation of liver and lung metastases. These results provide evidence for a strategy to target an oncosuppressive nucleic acid sequence to tumor cells while simultaneously protecting it from plasma degradation. The system described in this study exhibits encouraging potential for the effective treatment of therapy-resistant metastatic melanoma while also presenting a prospective approach for other forms of cancer.
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Affiliation(s)
- Maria Beatrice Arasi
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Gabriele De Luca
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Laura Chronopoulou
- Department of Chemistry, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Research Center for Applied Sciences to the safeguard of Environment and Cultural Heritage (CIABC) Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Francesca Pedini
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Eleonora Petrucci
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Michela Flego
- National Center for Global Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Annarita Stringaro
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Marisa Colone
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Luca Pasquini
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Massimo Spada
- Center of Animal Research and Welfare, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Valentina Lulli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Maria Chiara Perrotta
- Department of Chemistry, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - George Adrian Calin
- Translational Molecular Pathology, MD Anderson Cancer Center, Texas State University, 1515 Holcombe Blvd, Houston, TX 77030, USA; The RNA Interference and Non-coding RNA Center, MD Anderson Cancer Center, Texas State University, Houston, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Cleofe Palocci
- Department of Chemistry, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Research Center for Applied Sciences to the safeguard of Environment and Cultural Heritage (CIABC) Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Mauro Biffoni
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Federica Felicetti
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Nadia Felli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
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Pu Y, Li L, Peng H, Liu L, Heymann D, Robert C, Vallette F, Shen S. Drug-tolerant persister cells in cancer: the cutting edges and future directions. Nat Rev Clin Oncol 2023; 20:799-813. [PMID: 37749382 DOI: 10.1038/s41571-023-00815-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 09/27/2023]
Abstract
Drug-tolerant persister (DTP) cell populations were originally discovered in antibiotic-resistant bacterial biofilms. Similar populations with comparable features have since been identified among cancer cells and have been linked with treatment resistance that lacks an underlying genomic alteration. Research over the past decade has improved our understanding of the biological roles of DTP cells in cancer, although clinical knowledge of the role of these cells in treatment resistance remains limited. Nonetheless, targeting this population is anticipated to provide new treatment opportunities. In this Perspective, we aim to provide a clear definition of the DTP phenotype, discuss the underlying characteristics of these cells, their biomarkers and vulnerabilities, and encourage further research on DTP cells that might improve our understanding and enable the development of more effective anticancer therapies.
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Affiliation(s)
- Yi Pu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- Department of Burn Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Lu Li
- Lung Cancer Centre, West China Hospital, Sichuan University, Chengdu, China
| | - Haoning Peng
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Lunxu Liu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Dominique Heymann
- Nantes Université, CNRS, UMR6286, US2B, Nantes, France
- Institut de Cancérologie de l'Ouest, Saint-Herblain, France
| | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France
- Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - François Vallette
- Institut de Cancérologie de l'Ouest, Saint-Herblain, France.
- Nantes Université, INSERM, U1307, CRCI2NA, Nantes, France.
| | - Shensi Shen
- Department of Thoracic Surgery and Institute of Thoracic Oncology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.
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7
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Zhu EY, Schillo JL, Murray SD, Riordan JD, Dupuy AJ. Understanding cancer drug resistance with Sleeping Beauty functional genomic screens: Application to MAPK inhibition in cutaneous melanoma. iScience 2023; 26:107805. [PMID: 37860756 PMCID: PMC10582486 DOI: 10.1016/j.isci.2023.107805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/10/2023] [Accepted: 08/29/2023] [Indexed: 10/21/2023] Open
Abstract
Combined BRAF and MEK inhibition is an effective treatment for BRAF-mutant cutaneous melanoma. However, most patients progress on this treatment due to drug resistance. Here, we applied the Sleeping Beauty transposon system to understand how melanoma evades MAPK inhibition. We found that the specific drug resistance mechanisms differed across melanomas in our genetic screens of five cutaneous melanoma cell lines. While drivers that reactivated MAPK were highly conserved, many others were cell-line specific. One such driver, VAV1, activated a de-differentiated transcriptional program like that of hyperactive RAC1, RAC1P29S. To target this mechanism, we showed that an inhibitor of SRC, saracatinib, blunts the VAV1-induced transcriptional reprogramming. Overall, we highlighted the importance of accounting for melanoma heterogeneity in treating cutaneous melanoma with MAPK inhibitors. Moreover, we demonstrated the utility of the Sleeping Beauty transposon system in understanding cancer drug resistance.
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Affiliation(s)
- Eliot Y. Zhu
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Jacob L. Schillo
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Sarina D. Murray
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Jesse D. Riordan
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Adam J. Dupuy
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA
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8
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Huang F, Cai F, Dahabieh MS, Gunawardena K, Talebi A, Dehairs J, El-Turk F, Park JY, Li M, Goncalves C, Gagnon N, Su J, LaPierre JH, Gaub P, Joyal JS, Mitchell JJ, Swinnen JV, Miller WH, del Rincón SV. Peroxisome disruption alters lipid metabolism and potentiates antitumor response with MAPK-targeted therapy in melanoma. J Clin Invest 2023; 133:e166644. [PMID: 37616051 PMCID: PMC10575734 DOI: 10.1172/jci166644] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 08/22/2023] [Indexed: 08/25/2023] Open
Abstract
Melanomas reprogram their metabolism to rapidly adapt to therapy-induced stress conditions, allowing them to persist and ultimately develop resistance. We report that a subpopulation of melanoma cells tolerate MAPK pathway inhibitors (MAPKis) through a concerted metabolic reprogramming mediated by peroxisomes and UDP-glucose ceramide glycosyltransferase (UGCG). Compromising peroxisome biogenesis, by repressing PEX3 expression, potentiated the proapoptotic effects of MAPKis via an induction of ceramides, an effect limited by UGCG-mediated ceramide metabolism. Cotargeting PEX3 and UGCG selectively eliminated a subset of metabolically active, drug-tolerant CD36+ melanoma persister cells, thereby sensitizing melanoma to MAPKis and delaying resistance. Increased levels of peroxisomal genes and UGCG were found in patient-derived MAPKi-relapsed melanomas, and simultaneously inhibiting PEX3 and UGCG restored MAPKi sensitivity in multiple models of therapy resistance. Finally, combination therapy consisting of a newly identified inhibitor of the PEX3-PEX19 interaction, a UGCG inhibitor, and MAPKis demonstrated potent antitumor activity in preclinical melanoma models, thus representing a promising approach for melanoma treatment.
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Affiliation(s)
- Fan Huang
- Lady Davis Institute
- Department of Experimental Medicine, and
| | - Feiyang Cai
- Lady Davis Institute
- Department of Experimental Medicine, and
| | | | | | - Ali Talebi
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Jonas Dehairs
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Farah El-Turk
- McGill University Health Centre, Montreal, Quebec, Canada
- Centre Hospitalier Universitaire Sainte Justine, Montreal, Quebec, Canada
| | - Jae Yeon Park
- McGill University Health Centre, Montreal, Quebec, Canada
| | - Mengqi Li
- Lady Davis Institute
- Department of Experimental Medicine, and
| | | | | | | | | | - Perrine Gaub
- Centre de Recherche, CHU St. Justine, Montréal, Quebec, Canada
| | | | | | - Johannes V. Swinnen
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Wilson H. Miller
- Lady Davis Institute
- Department of Experimental Medicine, and
- Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Sonia V. del Rincón
- Lady Davis Institute
- Department of Experimental Medicine, and
- Department of Oncology, McGill University, Montreal, Quebec, Canada
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9
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Song X, Lan Y, Zheng X, Zhu Q, Liao X, Liu K, Zhang W, Peng Q, Zhu Y, Zhao L, Chen X, Shu Y, Yang K, Hu J. Targeting drug-tolerant cells: A promising strategy for overcoming acquired drug resistance in cancer cells. MedComm (Beijing) 2023; 4:e342. [PMID: 37638338 PMCID: PMC10449058 DOI: 10.1002/mco2.342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
Drug resistance remains the greatest challenge in improving outcomes for cancer patients who receive chemotherapy and targeted therapy. Surmounting evidence suggests that a subpopulation of cancer cells could escape intense selective drug treatment by entering a drug-tolerant state without genetic variations. These drug-tolerant cells (DTCs) are characterized with a slow proliferation rate and a reversible phenotype. They reside in the tumor region and may serve as a reservoir for resistant phenotypes. The survival of DTCs is regulated by epigenetic modifications, transcriptional regulation, mRNA translation remodeling, metabolic changes, antiapoptosis, interactions with the tumor microenvironment, and activation of signaling pathways. Thus, targeting the regulators of DTCs opens a new avenue for the treatment of therapy-resistant tumors. In this review, we first provide an overview of common characteristics of DTCs and the regulating networks in DTCs development. We also discuss the potential therapeutic opportunities to target DTCs. Last, we discuss the current challenges and prospects of the DTC-targeting approach to overcome acquired drug resistance. Reviewing the latest developments in DTC research could be essential in discovering of methods to eliminate DTCs, which may represent a novel therapeutic strategy for preventing drug resistance in the future.
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Affiliation(s)
- Xiaohai Song
- Department of General SurgeryGastric Cancer CenterLaboratory of Gastric CancerState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yang Lan
- Department of General SurgeryGastric Cancer CenterLaboratory of Gastric CancerState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiuli Zheng
- Department of RadiologyHuaxi MR Research Center (HMRRC) and Critical Care MedicinePrecision Medicine Center, Frontiers Science Center for Disease‐Related Molecular Network, West China HospitalSichuan UniversityChengduChina
| | - Qianyu Zhu
- Department of General SurgeryGastric Cancer CenterLaboratory of Gastric CancerState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xuliang Liao
- Department of General SurgeryGastric Cancer CenterLaboratory of Gastric CancerState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Kai Liu
- Department of General SurgeryGastric Cancer CenterLaboratory of Gastric CancerState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Weihan Zhang
- Department of General SurgeryGastric Cancer CenterLaboratory of Gastric CancerState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - QiangBo Peng
- Department of General SurgeryGastric Cancer CenterLaboratory of Gastric CancerState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yunfeng Zhu
- Department of General SurgeryGastric Cancer CenterLaboratory of Gastric CancerState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Linyong Zhao
- Department of General SurgeryGastric Cancer CenterLaboratory of Gastric CancerState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiaolong Chen
- Department of General SurgeryGastric Cancer CenterLaboratory of Gastric CancerState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yang Shu
- Department of General SurgeryGastric Cancer CenterLaboratory of Gastric CancerState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Kun Yang
- Department of General SurgeryGastric Cancer CenterLaboratory of Gastric CancerState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jiankun Hu
- Department of General SurgeryGastric Cancer CenterLaboratory of Gastric CancerState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
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10
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Kim D, An L, Moon J, Maymi VI, McGurk AI, Rudd BD, Fowell DJ, White AC. Ccr2+ Monocyte-Derived Macrophages Influence Trajectories of Acquired Therapy Resistance in Braf-Mutant Melanoma. Cancer Res 2023; 83:2328-2344. [PMID: 37195124 PMCID: PMC10478295 DOI: 10.1158/0008-5472.can-22-2841] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 03/12/2023] [Accepted: 05/12/2023] [Indexed: 05/18/2023]
Abstract
Therapies targeting oncogene addiction have had a tremendous impact on tumor growth and patient outcome, but drug resistance continues to be problematic. One approach to deal with the challenge of resistance entails extending anticancer treatments beyond targeting cancer cells by additionally altering the tumor microenvironment. Understanding how the tumor microenvironment contributes to the evolution of diverse resistance pathways could aid in the design of sequential treatments that can elicit and take advantage of a predictable resistance trajectory. Tumor-associated macrophages often support neoplastic growth and are frequently the most abundant immune cell found in tumors. Here, we used clinically relevant in vivo Braf-mutant melanoma models with fluorescent markers to track the stage-specific changes in macrophages under targeted therapy with Braf/Mek inhibitors and assessed the dynamic evolution of the macrophage population generated by therapy pressure-induced stress. During the onset of a drug-tolerant persister state, Ccr2+ monocyte-derived macrophage infiltration rose, suggesting that macrophage influx at this point could facilitate the onset of stable drug resistance that melanoma cells show after several weeks of treatment. Comparison of melanomas that develop in a Ccr2-proficient or -deficient microenvironment demonstrated that lack of melanoma infiltrating Ccr2+ macrophages delayed onset of resistance and shifted melanoma cell evolution towards unstable resistance. Unstable resistance was characterized by sensitivity to targeted therapy when factors from the microenvironment were lost. Importantly, this phenotype was reversed by coculturing melanoma cells with Ccr2+ macrophages. Overall, this study demonstrates that the development of resistance may be directed by altering the tumor microenvironment to improve treatment timing and the probability of relapse. SIGNIFICANCE Ccr2+ melanoma macrophages that are active in tumors during the drug-tolerant persister state following targeted therapy-induced regression are key contributors directing melanoma cell reprogramming toward specific therapeutic resistance trajectories.
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Affiliation(s)
- Dahihm Kim
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853
| | - Luye An
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853
| | - Jiwon Moon
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853
| | - Viviana I Maymi
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853
| | - Alexander I McGurk
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853
| | - Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853
| | - Deborah J Fowell
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853
| | - Andrew C White
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853
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11
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Liang XW, Liu B, Chen JC, Cao Z, Chu FR, Lin X, Wang SZ, Wu JC. Characteristics and molecular mechanism of drug-tolerant cells in cancer: a review. Front Oncol 2023; 13:1177466. [PMID: 37483492 PMCID: PMC10360399 DOI: 10.3389/fonc.2023.1177466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Drug resistance in tumours has seriously hindered the therapeutic effect. Tumour drug resistance is divided into primary resistance and acquired resistance, and the recent study has found that a significant proportion of cancer cells can acquire stable drug resistance from scratch. This group of cells first enters the drug tolerance state (DT state) under drug pressure, and gradually acquires stable drug resistance through adaptive mutations in this state. Although the specific mechanisms underlying the formation of drug tolerant cells (DTCs) remain unclear, various proteins and signalling pathways have been identified as being involved in the formation of DTCs. In the current review, we summarize the characteristics, molecular mechanisms and therapeutic strategies of DTCs in detail.
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Affiliation(s)
- Xian-Wen Liang
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
| | - Bing- Liu
- Department of Gastrointestinal Surgery, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, China
| | - Jia-Cheng Chen
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
| | - Zhi Cao
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
| | - Feng-ran Chu
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
| | - Xiong Lin
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
| | - Sheng-Zhong Wang
- Department of Gastrointestinal Surgery, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, China
| | - Jin-Cai Wu
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
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12
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Ding L, Sun L, Bu MT, Zhang Y, Scott LN, Prins RM, Su MA, Lechner MG, Hugo W. Antigen presentation by clonally diverse CXCR5+ B cells to CD4 and CD8 T cells is associated with durable response to immune checkpoint inhibitors. Front Immunol 2023; 14:1176994. [PMID: 37435085 PMCID: PMC10330698 DOI: 10.3389/fimmu.2023.1176994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/22/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction Increased T cell infiltration and interferon gamma (IFNγ) pathway activation are seen in tumors of melanoma patients who respond to ICI (immune checkpoint inhibitor) or MAPK pathway inhibitor (MAPKi) therapies. Yet, the rate of durable tumor control after ICI is almost twice that of MAPKi, suggesting that additional mechanisms may be present in patients responding to ICI therapy that are beneficial for anti-tumor immunity. Methods We used transcriptional analysis and clinical outcomes from patients treated with ICI or MAPKi therapies to delineate immune mechanisms driving tumor response. Results We discovered response to ICI is associated with CXCL13-driven recruitment of CXCR5+ B cells with significantly higher clonal diversity than MAPKi. Our in vitro data indicate that CXCL13 production was increased in human peripheral blood mononuclear cells by anti-PD1, but not MAPKi, treatment. Higher B cell infiltration and B cell receptor (BCR) diversity allows presentation of diverse tumor antigens by B cells, resulting in activation of follicular helper CD4 T cells (Tfh) and tumor reactive CD8 T cells after ICI therapy. Higher BCR diversity and IFNγ pathway score post-ICI are associated with significantly longer patient survival compared to those with either one or none. Conclusions Response to ICI, but not to MAPKi, depends on the recruitment of CXCR5+ B cells into the tumor microenvironment and their productive tumor antigen presentation to follicular helper and cytotoxic, tumor reactive T cells. Our study highlights the potential of CXCL13 and B cell based strategies to enhance the rate of durable response in melanoma patients treated with ICI.
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Affiliation(s)
- Lizhong Ding
- Department of Medicine, Division of Dermatology, University of California, Los Angeles, Los Angeles, CA, United States
- Parker Institute for Cancer Immunotherapy, University of California, Los Angeles, Los Angeles, CA, United States
| | - Lu Sun
- Parker Institute for Cancer Immunotherapy, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Neurosurgery, University of California, Los Angeles, Los Angeles, CA, United States
| | - Melissa T. Bu
- Department of Medicine, Division of Dermatology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Yanjun Zhang
- Department of Medicine, Division of Dermatology, University of California, Los Angeles, Los Angeles, CA, United States
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lauren N. Scott
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of California, Los Angeles, Los Angeles, CA, United States
| | - Robert M. Prins
- Parker Institute for Cancer Immunotherapy, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Neurosurgery, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, United States
| | - Maureen A. Su
- Parker Institute for Cancer Immunotherapy, University of California, Los Angeles, Los Angeles, CA, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Pediatrics, Division of Pediatric Endocrinology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Melissa G. Lechner
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Willy Hugo
- Department of Medicine, Division of Dermatology, University of California, Los Angeles, Los Angeles, CA, United States
- Parker Institute for Cancer Immunotherapy, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
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13
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Haist M, Stege H, Kuske M, Bauer J, Klumpp A, Grabbe S, Bros M. Combination of immune-checkpoint inhibitors and targeted therapies for melanoma therapy: The more, the better? Cancer Metastasis Rev 2023; 42:481-505. [PMID: 37022618 PMCID: PMC10348973 DOI: 10.1007/s10555-023-10097-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/27/2023] [Indexed: 04/07/2023]
Abstract
The approval of immune-checkpoint inhibitors (CPI) and mitogen activated protein kinase inhibitors (MAPKi) in recent years significantly improved the treatment management and survival of patients with advanced malignant melanoma. CPI aim to counter-act receptor-mediated inhibitory effects of tumor cells and immunomodulatory cell types on effector T cells, whereas MAPKi are intended to inhibit tumor cell survival. In agreement with these complementary modes of action preclinical data indicated that the combined application of CPI and MAPKi or their optimal sequencing might provide additional clinical benefit. In this review the rationale and preclinical evidence that support the combined application of MAPKi and CPI either in concurrent or consecutive regimens are presented. Further, we will discuss the results from clinical trials investigating the sequential or combined application of MAPKi and CPI for advanced melanoma patients and their implications for clinical practice. Finally, we outline mechanisms of MAPKi and CPI cross-resistance which limit the efficacy of currently available treatments, as well as combination regimens.
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Affiliation(s)
- Maximilian Haist
- Department of Dermatology, University Medical Center Mainz, Langenbeckstraße 1, 55131, Mainz, Germany.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Henner Stege
- Department of Dermatology, University Medical Center Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Michael Kuske
- Department of Dermatology, University Medical Center Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Julia Bauer
- Department of Dermatology, University Medical Center Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Annika Klumpp
- Department of Dermatology, University Medical Center Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Stephan Grabbe
- Department of Dermatology, University Medical Center Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Matthias Bros
- Department of Dermatology, University Medical Center Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
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14
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Dharanipragada P, Zhang X, Liu S, Lomeli SH, Hong A, Wang Y, Yang Z, Lo KZ, Vega-Crespo A, Ribas A, Moschos SJ, Moriceau G, Lo RS. Blocking Genomic Instability Prevents Acquired Resistance to MAPK Inhibitor Therapy in Melanoma. Cancer Discov 2023; 13:880-909. [PMID: 36700848 PMCID: PMC10068459 DOI: 10.1158/2159-8290.cd-22-0787] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/27/2022] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
Blocking cancer genomic instability may prevent tumor diversification and escape from therapies. We show that, after MAPK inhibitor (MAPKi) therapy in patients and mice bearing patient-derived xenografts (PDX), acquired resistant genomes of metastatic cutaneous melanoma specifically amplify resistance-driver, nonhomologous end-joining (NHEJ), and homologous recombination repair (HRR) genes via complex genomic rearrangements (CGR) and extrachromosomal DNAs (ecDNA). Almost all sensitive and acquired-resistant genomes harbor pervasive chromothriptic regions with disproportionately high mutational burdens and significant overlaps with ecDNA and CGR spans. Recurrently, somatic mutations within ecDNA and CGR amplicons enrich for HRR signatures, particularly within acquired resistant tumors. Regardless of sensitivity or resistance, breakpoint-junctional sequence analysis suggests NHEJ as critical to double-stranded DNA break repair underlying CGR and ecDNA formation. In human melanoma cell lines and PDXs, NHEJ targeting by a DNA-PKCS inhibitor prevents/delays acquired MAPKi resistance by reducing the size of ecDNAs and CGRs early on combination treatment. Thus, targeting the causes of genomic instability prevents acquired resistance. SIGNIFICANCE Acquired resistance often results in heterogeneous, redundant survival mechanisms, which challenge strategies aimed at reversing resistance. Acquired-resistant melanomas recurrently evolve resistance-driving and resistance-specific amplicons via ecDNAs and CGRs, thereby nominating chromothripsis-ecDNA-CGR biogenesis as a resistance-preventive target. Specifically, targeting DNA-PKCS/NHEJ prevents resistance by suppressing ecDNA/CGR rearrangements in MAPKi-treated melanomas. This article is highlighted in the In This Issue feature, p. 799.
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Affiliation(s)
- Prashanthi Dharanipragada
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Xiao Zhang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Sixue Liu
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Shirley H. Lomeli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Aayoung Hong
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Yan Wang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Zhentao Yang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Kara Z. Lo
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Agustin Vega-Crespo
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Antoni Ribas
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Stergios J. Moschos
- Division of Medical Oncology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Roger S. Lo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
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15
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The mechanical phenotypic plasticity of melanoma cell: an emerging driver of therapy cross-resistance. Oncogenesis 2023; 12:7. [PMID: 36774337 PMCID: PMC9922263 DOI: 10.1038/s41389-023-00452-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/13/2023] Open
Abstract
Advanced cutaneous melanoma is the deadliest form of skin cancer and one of the most aggressive human cancers. Targeted therapies (TT) against BRAF mutated melanoma and immune checkpoints blockade therapies (ICB) have been a breakthrough in the treatment of metastatic melanoma. However, therapy-driven resistance remains a major hurdle in the clinical management of the metastatic disease. Besides shaping the tumor microenvironment, current treatments impact transition states to promote melanoma cell phenotypic plasticity and intratumor heterogeneity, which compromise treatment efficacy and clinical outcomes. In this context, mesenchymal-like dedifferentiated melanoma cells exhibit a remarkable ability to autonomously assemble their own extracellular matrix (ECM) and to biomechanically adapt in response to therapeutic insults, thereby fueling tumor relapse. Here, we review recent studies that highlight mechanical phenotypic plasticity of melanoma cells as a hallmark of adaptive and non-genetic resistance to treatment and emerging driver in cross-resistance to TT and ICB. We also discuss how targeting BRAF-mutant dedifferentiated cells and ECM-based mechanotransduction pathways may overcome melanoma cross-resistance.
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16
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BET inhibitors synergize with sunitinib in melanoma through GDF15 suppression. Exp Mol Med 2023; 55:364-376. [PMID: 36720918 PMCID: PMC9981764 DOI: 10.1038/s12276-023-00936-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/26/2022] [Accepted: 12/02/2022] [Indexed: 02/02/2023] Open
Abstract
Targeting bromodomain and extra-terminal domain (BET) proteins has shown a promising therapeutic effect on melanoma. The development of strategies to better kill melanoma cells with BET inhibitor treatment may provide new clinical applications. Here, we used a drug synergy screening approach to combine JQ1 with 240 antitumor drugs from the Food and Drug Administration (FDA)-approved drug library and found that sunitinib synergizes with BET inhibitors in melanoma cells. We further demonstrated that BET inhibitors synergize with sunitinib in melanoma by inducing apoptosis and cell cycle arrest. Mechanistically, BET inhibitors sensitize melanoma cells to sunitinib by inhibiting GDF15 expression. Strikingly, GDF15 is transcriptionally regulated directly by BRD4 or indirectly by the BRD4/IL6/STAT3 axis. Xenograft assays revealed that the combination of BET inhibitors with sunitinib causes melanoma suppression in vivo. Altogether, these findings suggest that BET inhibitor-mediated GDF15 inhibition plays a critical role in enhancing sunitinib sensitivity in melanoma, indicating that BET inhibitors synergize with sunitinib in melanoma.
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17
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Ziogas DC, Theocharopoulos C, Koutouratsas T, Haanen J, Gogas H. Mechanisms of resistance to immune checkpoint inhibitors in melanoma: What we have to overcome? Cancer Treat Rev 2023; 113:102499. [PMID: 36542945 DOI: 10.1016/j.ctrv.2022.102499] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
Marching into the second decade after the approval of ipilimumab, it is clear that immune checkpoint inhibitors (ICIs) have dramatically improved the prognosis of melanoma. Although the current edge is already high, with a 4-year OS% of 77.9% for adjuvant nivolumab and a 6.5-year OS% of 49% for nivolumab/ipilimumab combination in the metastatic setting, a high proportion of patients with advanced melanoma have no benefit from immunotherapy, or experience an early disease relapse/progression in the first few months of treatment, surviving much less. Reasonably, the primary and acquired resistance to ICIs has entered into the focus of clinical research with positive (e.g., nivolumab and relatlimab combination) and negative feedbacks (e.g., nivolumab with pegylated-IL2, pembrolizumab with T-VEC, nivolumab with epacadostat, and combinatorial triplets of BRAF/MEK inhibitors with immunotherapy). Many intrinsic (intracellular or intra-tumoral) but also extrinsic (systematic) events are considered to be involved in the development of this resistance to ICIs: i) melanoma cell immunogenicity (e.g., tumor mutational burden, antigen-processing machinery and immunogenic cell death, neoantigen affinity and heterogeneity, genomic instability, melanoma dedifferentiation and phenotypic plasticity), ii) immune cell trafficking, T-cell priming, and cell death evasion, iii) melanoma neovascularization, cellular TME components(e.g., Tregs, CAFs) and extracellular matrix modulation, iv) metabolic antagonism in the TME(highly glycolytic status, upregulated CD39/CD73/adenosine pathway, iDO-dependent tryptophan catabolism), v) T-cell exhaustion and negative immune checkpoints, and vi) gut microbiota. In the present overview, we discuss how these parameters compromise the efficacy of ICIs, with an emphasis on the lessons learned by the latest melanoma studies; and in parallel, we describe the main ongoing approaches to overcome the resistance to immunotherapy. Summarizing this information will improve the understanding of how these complicated dynamics contribute to immune escape and will help to develop more effective strategies on how anti-tumor immunity can surpass existing barriers of ICI-refractory melanoma.
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Affiliation(s)
- Dimitrios C Ziogas
- First Department of Medicine, National and Kapodistrian University of Athens School of Medicine, Athens, Greece.
| | - Charalampos Theocharopoulos
- First Department of Medicine, National and Kapodistrian University of Athens School of Medicine, Athens, Greece.
| | - Tilemachos Koutouratsas
- First Department of Medicine, National and Kapodistrian University of Athens School of Medicine, Athens, Greece.
| | - John Haanen
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Helen Gogas
- First Department of Medicine, National and Kapodistrian University of Athens School of Medicine, Athens, Greece.
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18
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Oncosuppressive miRNAs loaded in lipid nanoparticles potentiate targeted therapies in BRAF-mutant melanoma by inhibiting core escape pathways of resistance. Oncogene 2023; 42:293-307. [PMID: 36418472 PMCID: PMC9684877 DOI: 10.1038/s41388-022-02547-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022]
Abstract
BRAF-mutated melanoma relapsing after targeted therapies is an aggressive disease with unmet clinical need. Hence the need to identify novel combination therapies able to overcome drug resistance. miRNAs have emerged as orchestrators of non-genetic mechanisms adopted by melanoma cells to challenge therapies. In this context we previously identified a subset of oncosuppressor miRNAs downregulated in drug-resistant melanomas. Here we demonstrate that lipid nanoparticles co-encapsulating two of them, miR-199-5p and miR-204-5p, inhibit tumor growth both in vitro and in vivo in combination with target therapy and block the development of drug resistance. Mechanistically they act by directly reducing melanoma cell growth and also indirectly by hampering the recruitment and reprogramming of pro-tumoral macrophages. Molecularly, we demonstrate that the effects on macrophages are mediated by the dysregulation of a newly identified miR-204-5p-miR-199b-5p/CCL5 axis. Finally, we unveiled that M2 macrophages programs are molecular signatures of resistance and predict response to therapy in patients. Overall, these findings have strong translational implications to propose new combination therapies making use of RNA therapeutics for metastatic melanoma patients.
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19
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Wang J, Liu T, Huang T, Shang M, Wang X. The mechanisms on evasion of anti-tumor immune responses in gastric cancer. Front Oncol 2022; 12:943806. [PMID: 36439472 PMCID: PMC9686275 DOI: 10.3389/fonc.2022.943806] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/02/2022] [Indexed: 10/22/2023] Open
Abstract
The immune system and the tumor have been at each other's throats for so long that the neoplasm has learned to avoid detection and avoid being attacked, which is called immune evasion. Malignant tumors, such as gastric cancer (GC), share the ability to evade the body's immune system as a defining feature. Immune evasion includes alterations to tumor-associated antigens (TAAs), antigen presentation mechanisms (APMs), and the tumor microenvironment (TME). While TAA and APM are simpler in nature, they both involve mutations or epigenetic regulation of genes. The TME is comprised of numerous cell types, cytokines, chemokines and extracellular matrix, any one of which might be altered to have an effect on the surrounding ecosystem. The NF-kB, MAPK, PI3K/AKT, JAK/STAT, Wnt/β-catenin, Notch, Hippo and TGF-β/Smad signaling pathways are all associated with gastric cancer tumor immune evasion. In this review, we will delineate the functions of these pathways in immune evasion.
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Affiliation(s)
| | | | | | | | - Xudong Wang
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, Jilin, China
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20
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Paris A, Tardif N, Baietti FM, Berra C, Leclair HM, Leucci E, Galibert M, Corre S. The AhR-SRC axis as a therapeutic vulnerability in BRAFi-resistant melanoma. EMBO Mol Med 2022; 14:e15677. [PMID: 36305167 PMCID: PMC9728058 DOI: 10.15252/emmm.202215677] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
Abstract
The nongenetic mechanisms required to control tumor phenotypic plasticity and shape drug-resistance remain unclear. We show here that the Aryl hydrocarbon Receptor (AhR) transcription factor directly regulates the gene expression program associated with the acquisition of resistance to BRAF inhibitor (BRAFi) in melanoma. In addition, we show in melanoma cells that canonical activation of AhR mediates the activation of the SRC pathway and promotes the acquisition of an invasive and aggressive resistant phenotype to front-line BRAFi treatment in melanoma. This nongenetic reprogramming identifies a clinically compatible approach to reverse BRAFi resistance in melanoma. Using a preclinical BRAFi-resistant PDX melanoma model, we demonstrate that SRC inhibition with dasatinib significantly re-sensitizes melanoma cells to BRAFi. Together we identify the AhR/SRC axis as a new therapeutic vulnerability to trigger resistance and warrant the introduction of SRC inhibitors during the course of the treatment in combination with front-line therapeutics to delay BRAFi resistance.
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Affiliation(s)
- Anaïs Paris
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Génétique et Développement de Rennes) – UMR6290, ERL U1305RennesFrance
| | - Nina Tardif
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Génétique et Développement de Rennes) – UMR6290, ERL U1305RennesFrance
| | - Francesca M Baietti
- Laboratory for RNA Cancer Biology, Department of OncologyLKI, KU LeuvenLeuvenBelgium,Trace PDX Platform, Department of OncologyLKI, KU LeuvenLeuvenBelgium
| | - Cyrille Berra
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Génétique et Développement de Rennes) – UMR6290, ERL U1305RennesFrance,Department of Molecular Genetics and GenomicsHospital University of Rennes (CHU Rennes)RennesFrance
| | - Héloïse M Leclair
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Génétique et Développement de Rennes) – UMR6290, ERL U1305RennesFrance
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of OncologyLKI, KU LeuvenLeuvenBelgium,Trace PDX Platform, Department of OncologyLKI, KU LeuvenLeuvenBelgium
| | - Marie‐Dominique Galibert
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Génétique et Développement de Rennes) – UMR6290, ERL U1305RennesFrance,Department of Molecular Genetics and GenomicsHospital University of Rennes (CHU Rennes)RennesFrance
| | - Sébastien Corre
- Univ Rennes, CNRS, INSERM, IGDR (Institut de Génétique et Développement de Rennes) – UMR6290, ERL U1305RennesFrance
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21
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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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22
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Karami Fath M, Azargoonjahromi A, Soofi A, Almasi F, Hosseinzadeh S, Khalili S, Sheikhi K, Ferdousmakan S, Owrangi S, Fahimi M, Zalpoor H, Nabi Afjadi M, Payandeh Z, Pourzardosht N. Current understanding of epigenetics role in melanoma treatment and resistance. Cancer Cell Int 2022; 22:313. [PMID: 36224606 PMCID: PMC9555085 DOI: 10.1186/s12935-022-02738-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/19/2022] [Indexed: 11/30/2022] Open
Abstract
Melanoma is the most aggressive form of skin cancer resulting from genetic mutations in melanocytes. Several factors have been considered to be involved in melanoma progression, including genetic alteration, processes of damaged DNA repair, and changes in mechanisms of cell growth and proliferation. Epigenetics is the other factor with a crucial role in melanoma development. Epigenetic changes have become novel targets for treating patients suffering from melanoma. These changes can alter the expression of microRNAs and their interaction with target genes, which involves cell growth, differentiation, or even death. Given these circumstances, we conducted the present review to discuss the melanoma risk factors and represent the current knowledge about the factors related to its etiopathogenesis. Moreover, various epigenetic pathways, which are involved in melanoma progression, treatment, and chemo-resistance, as well as employed epigenetic factors as a solution to the problems, will be discussed in detail.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | | | - Asma Soofi
- Department of Physical Chemistry, School of Chemistry, College of Sciences, University of Tehran, Tehran, Iran
| | - Faezeh Almasi
- Pharmaceutical Biotechnology Lab, Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Shahnaz Hosseinzadeh
- Department of Microbiology, Parasitology and Immunology, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Kamran Sheikhi
- School of Medicine, Kurdistan University of Medical Sciences, Kurdistan, Iran
| | - Saeid Ferdousmakan
- Department of Pharmacy Practice, Nargund College of Pharmacy, Bangalore, 560085, India
| | - Soroor Owrangi
- Student Research Committe, Fasa University of Medical Sciences, Fasa, Iran
| | | | - Hamidreza Zalpoor
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran
| | - Mohsen Nabi Afjadi
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.
| | - Zahra Payandeh
- Department Medical Biochemistry and Biophysics, Division Medical Inflammation Research, Karolinska Institute, Stockholm, Sweden.
| | - Navid Pourzardosht
- Biochemistry Department, Guilan University of Medical Sciences, Rasht, Iran.
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23
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Zhang ZY, Ding Y, Ezhilarasan R, Lhakhang T, Wang Q, Yang J, Modrek AS, Zhang H, Tsirigos A, Futreal A, Draetta GF, Verhaak RGW, Sulman EP. Lineage-coupled clonal capture identifies clonal evolution mechanisms and vulnerabilities of BRAF V600E inhibition resistance in melanoma. Cell Discov 2022; 8:102. [PMID: 36202798 PMCID: PMC9537441 DOI: 10.1038/s41421-022-00462-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Targeted cancer therapies have revolutionized treatment but their efficacies are limited by the development of resistance driven by clonal evolution within tumors. We developed "CAPTURE", a single-cell barcoding approach to comprehensively trace clonal dynamics and capture live lineage-coupled resistant cells for in-depth multi-omics analysis and functional exploration. We demonstrate that heterogeneous clones, either preexisting or emerging from drug-tolerant persister cells, dominated resistance to vemurafenib in BRAFV600E melanoma. Further integrative studies uncovered diverse resistance mechanisms. This includes a previously unrecognized and clinically relevant mechanism, chromosome 18q21 gain, which leads to vulnerability of the cells to BCL2 inhibitor. We also identified targetable common dependencies of captured resistant clones, such as oxidative phosphorylation and E2F pathways. Our study provides new therapeutic insights into overcoming therapy resistance in BRAFV600E melanoma and presents a platform for exploring clonal evolution dynamics and vulnerabilities that can be applied to study treatment resistance in other cancers.
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Affiliation(s)
- Ze-Yan Zhang
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA.
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
| | - Yingwen Ding
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Ravesanker Ezhilarasan
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Tenzin Lhakhang
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA
| | - Qianghu Wang
- Department of Bioinformatics, Nanjing Medical University, Nanjing, Jiangsu, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing, Jiangsu, China
| | - Jie Yang
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aram S Modrek
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Hua Zhang
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roel G W Verhaak
- Department of Computational Biology, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Erik P Sulman
- Department of Radiation Oncology, New York University (NYU) Grossman School of Medicine, New York, NY, USA.
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
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24
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Yu J, Wu X, Song J, Zhao Y, Li H, Luo M, Liu X. Loss of MHC-I antigen presentation correlated with immune checkpoint blockade tolerance in MAPK inhibitor-resistant melanoma. Front Pharmacol 2022; 13:928226. [PMID: 36091815 PMCID: PMC9459091 DOI: 10.3389/fphar.2022.928226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/27/2022] [Indexed: 11/20/2022] Open
Abstract
Immune checkpoint blockade and MAPK-targeted combined therapy is a promising regimen for advanced melanoma patients. However, the clinical benefit from this combo regimen remains limited, especially in patients who acquired resistance to MAPK-targeted therapy. Here, we systematically characterized the immune landscape during MAPK-targeted therapy in patients and mouse melanoma models. We observed that both the abundance of tumor-infiltrated T cells and the expression of immune-related genes were upregulated in the drug-responsive period, but downregulated in the resistance period, implying that acquired drug resistance dampens the antitumor immune response. Further transcriptomic dissection indicated that loss of MHC-I antigen presentation on tumor cells plays a critical role in the reduction of T cell infiltration during drug resistance. Survival analysis demonstrates that loss of antigen presentation and reduction of T-cell infiltration during acquired drug resistance are associated with poorer clinical response and prognosis of anti-PD-1 therapy in melanoma patients. In addition, we identified that alterations in the MAPK inhibitor resistance-related oncogenic signaling pathway closely correlated with deficiency of MHC-I antigen presentation, including activation of the PI3K-mTOR, MAPK, and Wnt pathways. In conclusion, our research illuminates that decreased infiltration of T cells is associated with acquired drug resistance during MAPK-targeted therapy, which may underlie the cross-resistance to immune checkpoint blockade.
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Affiliation(s)
- Jing Yu
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Xi Wu
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Jinen Song
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Yujie Zhao
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Huifang Li
- Research Core Facility, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Min Luo
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
- *Correspondence: Xiaowei Liu, ; Min Luo,
| | - Xiaowei Liu
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
- *Correspondence: Xiaowei Liu, ; Min Luo,
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25
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Peng F, Liao M, Qin R, Zhu S, Peng C, Fu L, Chen Y, Han B. Regulated cell death (RCD) in cancer: key pathways and targeted therapies. Signal Transduct Target Ther 2022; 7:286. [PMID: 35963853 PMCID: PMC9376115 DOI: 10.1038/s41392-022-01110-y] [Citation(s) in RCA: 208] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 02/07/2023] Open
Abstract
Regulated cell death (RCD), also well-known as programmed cell death (PCD), refers to the form of cell death that can be regulated by a variety of biomacromolecules, which is distinctive from accidental cell death (ACD). Accumulating evidence has revealed that RCD subroutines are the key features of tumorigenesis, which may ultimately lead to the establishment of different potential therapeutic strategies. Hitherto, targeting the subroutines of RCD with pharmacological small-molecule compounds has been emerging as a promising therapeutic avenue, which has rapidly progressed in many types of human cancers. Thus, in this review, we focus on summarizing not only the key apoptotic and autophagy-dependent cell death signaling pathways, but the crucial pathways of other RCD subroutines, including necroptosis, pyroptosis, ferroptosis, parthanatos, entosis, NETosis and lysosome-dependent cell death (LCD) in cancer. Moreover, we further discuss the current situation of several small-molecule compounds targeting the different RCD subroutines to improve cancer treatment, such as single-target, dual or multiple-target small-molecule compounds, drug combinations, and some new emerging therapeutic strategies that would together shed new light on future directions to attack cancer cell vulnerabilities with small-molecule drugs targeting RCD for therapeutic purposes.
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Affiliation(s)
- Fu Peng
- West China School of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Minru Liao
- West China School of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Rui Qin
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shiou Zhu
- West China School of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China.,Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Leilei Fu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
| | - Yi Chen
- West China School of Pharmacy, State Key Laboratory of Biotherapy and Cancer Center, Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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26
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Yang Z, Wang Y, Liu S, Deng W, Lomeli SH, Moriceau G, Wohlschlegel J, Piva M, Lo RS. Enhancing PD-L1 Degradation by ITCH during MAPK Inhibitor Therapy Suppresses Acquired Resistance. Cancer Discov 2022; 12:1942-1959. [PMID: 35638972 PMCID: PMC9357203 DOI: 10.1158/2159-8290.cd-21-1463] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/23/2022] [Accepted: 05/25/2022] [Indexed: 01/09/2023]
Abstract
MAPK inhibitor (MAPKi) therapy in melanoma leads to the accumulation of tumor-surface PD-L1/L2, which may evade antitumor immunity and accelerate acquired resistance. Here, we discover that the E3 ligase ITCH binds, ubiquitinates, and downregulates tumor-surface PD-L1/L2 in MAPKi-treated human melanoma cells, thereby promoting T-cell activation. During MAPKi therapy in vivo, melanoma cell-intrinsic ITCH knockdown induced tumor-surface PD-L1, reduced intratumoral cytolytic CD8+ T cells, and accelerated acquired resistance only in immune-competent mice. Conversely, tumor cell-intrinsic ITCH overexpression reduced MAPKi-elicited PD-L1 accumulation, augmented intratumoral cytolytic CD8+ T cells, and suppressed acquired resistance in BrafV600MUT, NrasMUT, or Nf1MUT melanoma and KrasMUT-driven cancers. CD8+ T-cell depletion and tumor cell-intrinsic PD-L1 overexpression nullified the phenotype of ITCH overexpression, thereby supporting an in vivo ITCH-PD-L1-T-cell regulatory axis. Moreover, we identify a small-molecular ITCH activator that suppresses acquired MAPKi resistance in vivo. Thus, MAPKi-induced PD-L1 accelerates resistance, and a PD-L1-degrading ITCH activator prolongs antitumor response. SIGNIFICANCE MAPKi induces tumor cell-surface PD-L1 accumulation, which promotes immune evasion and therapy resistance. ITCH degrades PD-L1, optimizing antitumor T-cell immunity. We propose degrading tumor cell-surface PD-L1 and/or activating tumor-intrinsic ITCH as strategies to overcome MAPKi resistance. This article is highlighted in the In This Issue feature, p. 1825.
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Affiliation(s)
- Zhentao Yang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Yan Wang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Sixue Liu
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Weixian Deng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Shirley H. Lomeli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Marco Piva
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Roger S. Lo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
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27
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Bari S, Muzaffar J, Eroglu Z. Combination targeted and immune therapy in the treatment of advanced melanoma: a valid treatment option for patients? Ther Adv Med Oncol 2022; 14:17588359221090306. [PMID: 35478991 PMCID: PMC9036333 DOI: 10.1177/17588359221090306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/10/2022] [Indexed: 11/16/2022] Open
Abstract
Melanomas harboring an activating BRAFV600 mutation account for 50% of all advanced melanomas. The approval of BRAF-targeted therapy revolutionized treatment of these patients with achievement of impressive responses. However, development of resistance to these drugs is a significant problem, and as such, duration of response remains low, with median progression free survival of around 11–15 months. Immune checkpoint blockers exploit the immune system to eradicate cancer and can produce durable disease control that results in long-term, treatment-free survival in some patients. These drugs have shown very impressive survival in patients with BRAF-mutated melanoma. Thus, there is a need to continue to utilize emerging data to achieve long-term disease control for patients with advanced melanoma. Combining targeted therapy with immune therapy may be one possible way to achieve this goal. In this review, the mechanisms of action of these two pathways, including the mechanistic basis of this combination, are summarized, along with results of completed and ongoing trials in triple therapy.
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Affiliation(s)
- Shahla Bari
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Jameel Muzaffar
- Department of Head and Neck Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Zeynep Eroglu
- Department of Cutaneous Oncology, Moffitt Cancer Center, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
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28
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Dixon-Douglas JR, Patel RP, Somasundram PM, McArthur GA. Triplet Therapy in Melanoma - Combined BRAF/MEK Inhibitors and Anti-PD-(L)1 Antibodies. Curr Oncol Rep 2022; 24:1071-1079. [PMID: 35366166 PMCID: PMC9249697 DOI: 10.1007/s11912-022-01243-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2021] [Indexed: 01/29/2023]
Abstract
PURPOSE OF REVIEW We provide an updated review of clinical trials evaluating the combination of BRAF/MEK inhibitors with anti-PD-(L)1 therapy (triplet therapy) for patients with advanced BRAF-mutant melanoma, accompanied by a summary of the biological evidence supporting this combination. RECENT FINDINGS Resistance to BRAF/MEK inhibition and comparatively low response rates to immune checkpoint inhibitors remain clinical challenges in the treatment of melanoma. Preclinical data demonstrates that targeted therapy is immune-modulatory and synergises with immune checkpoint inhibition. Several randomised controlled trials have evaluated the combination of targeted therapy with immune checkpoint inhibition. Triplet therapy has shown improvements in progression-free survival and durability of response compared to BRAF/MEK inhibition alone; however, questions remain regarding the best clinical scenario for implementation of this regimen in the era of front-line immunotherapy.
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Affiliation(s)
- Julia R Dixon-Douglas
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Riyaben P Patel
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Pretashini M Somasundram
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Grant A McArthur
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Department of Oncology, Sir Peter MacCallum, University of Melbourne, Parkville, VIC, Australia.
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29
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Song K, Minami JK, Huang A, Dehkordi SR, Lomeli SH, Luebeck J, Goodman MH, Moriceau G, Krijgsman O, Dharanipragada P, Ridgley T, Crosson WP, Salazar J, Pazol E, Karin G, Jayaraman R, Balanis NG, Alhani S, Sheu K, Hoeve JT, Palermo A, Motika SE, Senaratne TN, Paraiso KH, Hergenrother PJ, Rao PN, Multani AS, Peeper DS, Bafna V, Lo RS, Graeber TG. Plasticity of Extrachromosomal and Intrachromosomal BRAF Amplifications in Overcoming Targeted Therapy Dosage Challenges. Cancer Discov 2022; 12:1046-1069. [PMID: 34930786 PMCID: PMC9192483 DOI: 10.1158/2159-8290.cd-20-0936] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 11/06/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022]
Abstract
Focal amplifications (FA) can mediate targeted therapy resistance in cancer. Understanding the structure and dynamics of FAs is critical for designing treatments that overcome plasticity-mediated resistance. We developed a melanoma model of dual MAPK inhibitor (MAPKi) resistance that bears BRAFV600 amplifications through either extrachromosomal DNA (ecDNA)/double minutes (DM) or intrachromosomal homogenously staining regions (HSR). Cells harboring BRAFV600E FAs displayed mode switching between DMs and HSRs, from both de novo genetic changes and selection of preexisting subpopulations. Plasticity is not exclusive to ecDNAs, as cells harboring HSRs exhibit drug addiction-driven structural loss of BRAF amplicons upon dose reduction. FA mechanisms can couple with kinase domain duplications and alternative splicing to enhance resistance. Drug-responsive amplicon plasticity is observed in the clinic and can involve other MAPK pathway genes, such as RAF1 and NRAS. BRAF FA-mediated dual MAPKi-resistant cells are more sensitive to proferroptotic drugs, extending the spectrum of ferroptosis sensitivity in MAPKi resistance beyond cases of dedifferentiation. SIGNIFICANCE Understanding the structure and dynamics of oncogene amplifications is critical for overcoming tumor relapse. BRAF amplifications are highly plastic under MAPKi dosage challenges in melanoma, through involvement of de novo genomic alterations, even in the HSR mode. Moreover, BRAF FA-driven, dual MAPKi-resistant cells extend the spectrum of resistance-linked ferroptosis sensitivity. This article is highlighted in the In This Issue feature, p. 873.
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Affiliation(s)
- Kai Song
- Department of Bioengineering, UCLA, Los Angeles, CA 90095, USA
| | - Jenna K. Minami
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Department of Integrative Biology and Physiology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Arthur Huang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Siavash R. Dehkordi
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Shirley H. Lomeli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jens Luebeck
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Mark H. Goodman
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Oscar Krijgsman
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Prashanthi Dharanipragada
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Trevor Ridgley
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, 90095, USA
| | - William P. Crosson
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jesus Salazar
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Eli Pazol
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Gabriel Karin
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Rachana Jayaraman
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Nikolas G. Balanis
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Salwan Alhani
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Kyle Sheu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Johanna ten Hoeve
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- UCLA Metabolomics Center, Los Angeles, CA, 90095, USA
| | - Amelia Palermo
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- UCLA Metabolomics Center, Los Angeles, CA, 90095, USA
| | - Stephen E. Motika
- Department of Chemistry, Institute for Genomic Biology, Cancer Center at Illinois, University of Illinois, Urbana-Champaign, USA
| | - T. Niroshi Senaratne
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Kim H. Paraiso
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Paul J. Hergenrother
- Department of Chemistry, Institute for Genomic Biology, Cancer Center at Illinois, University of Illinois, Urbana-Champaign, USA
| | - P. Nagesh Rao
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Asha S. Multani
- Department of Genetics, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030
| | - Daniel S. Peeper
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Roger S. Lo
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, 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, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
- Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA
- UCLA Metabolomics Center, Los Angeles, CA, 90095, USA
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30
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Zhang P, Guan H, Yuan S, Cheng H, Zheng J, Zhang Z, Liu Y, Yu Y, Meng Z, Zheng X, Zhao L. Targeting myeloid derived suppressor cells reverts immune suppression and sensitizes BRAF-mutant papillary thyroid cancer to MAPK inhibitors. Nat Commun 2022; 13:1588. [PMID: 35332119 PMCID: PMC8948260 DOI: 10.1038/s41467-022-29000-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 02/22/2022] [Indexed: 02/07/2023] Open
Abstract
MAPK signaling inhibitor (MAPKi) therapies show limited efficacy for advanced thyroid cancers despite constitutive activation of the signaling correlates with disease recurrence and persistence. Understanding how BRAF pathway stimulates tumorigenesis could lead to new therapeutic targets. Here, through genetic and pathological approaches, we demonstrate that BRAFV600E promotes thyroid cancer development by increasing myeloid-derived suppressor cells (MDSCs) penetrance. This BRAFV600E-induced immune suppression involves re-activation of the developmental factor TBX3, which in turn up-regulates CXCR2 ligands in a TLR2-NFκB dependent manner, leading to MDSCs recruitment into the tumor microenvironment. CXCR2 inhibition or MDSCs repression improves MAPKi therapy effect. Clinically, high TBX3 expression correlates with BRAFV600E mutation and increased CXCR2 ligands, along with abundant MDSCs infiltration. Thus, our study uncovers a BRAFV600E-TBX3-CXCLs-MDSCs axis that guides patient stratification and could be targeted to improve the efficacy of MAPKi therapy in advanced thyroid cancer patients. BRAF-V600E mutation is common in patients with papillary thyroid carcinoma (PTC) and has been associated with an aggressive phenotype. Here the authors show that the mutation supports cancer progression by reactivating the developmental factor TBX3 and promoting the recruitment of myeloid derived suppressive cells.
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Affiliation(s)
- Peitao Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Department of Nuclear Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Haixia Guan
- Department of Endocrinology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Science, Guangzhou, Guangdong Province, China.,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Shukai Yuan
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Huili Cheng
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jian Zheng
- Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhenlei Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yifan Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yang Yu
- Department of Thyroid and Neck Oncology, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zhaowei Meng
- Department of Nuclear Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiangqian Zheng
- Department of Thyroid and Neck Oncology, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Li Zhao
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
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31
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Intermittent treatment of BRAF V600E melanoma cells delays resistance by adaptive resensitization to drug rechallenge. Proc Natl Acad Sci U S A 2022; 119:e2113535119. [PMID: 35290123 PMCID: PMC8944661 DOI: 10.1073/pnas.2113535119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Preclinical studies of metastatic melanoma treated with targeted therapeutics have suggested that alternating periods of treatment and withdrawal might delay the onset of resistance. This has been attributed to drug addiction, where cells lose fitness upon drug removal due to the resulting hyperactivation of mitogen-activated protein (MAP) kinase signaling. This study presents evidence that the intermittent treatment response can also be explained by the resensitization of cells following drug removal and enhanced cell loss upon drug rechallenge. Resensitization is accompanied by adaptive transcriptomic switching and occurs despite the sustained expression of resistance genes throughout the intermittent treatment. Patients with melanoma receiving drugs targeting BRAFV600E and mitogen-activated protein (MAP) kinase kinases 1 and 2 (MEK1/2) invariably develop resistance and face continued progression. Based on preclinical studies, intermittent treatment involving alternating periods of drug withdrawal and rechallenge has been proposed as a method to delay the onset of resistance. The beneficial effect of intermittent treatment has been attributed to drug addiction, where drug withdrawal reduces the viability of resistant cells due to MAP kinase pathway hyperactivation. However, the mechanistic basis of the intermittent effect is incompletely understood. We show that intermittent treatment with the BRAFV600E inhibitor, LGX818/encorafenib, suppresses growth compared with continuous treatment in human melanoma cells engineered to express BRAFV600E, p61-BRAFV600E, or MEK2C125 oncogenes. Analysis of the BRAFV600E-overexpressing cells shows that, while drug addiction clearly occurs, it fails to account for the advantageous effect of intermittent treatment. Instead, growth suppression is best explained by resensitization during periods of drug removal, followed by cell death after drug readdition. Continuous treatment leads to transcriptional responses prominently associated with chemoresistance in melanoma. By contrast, cells treated intermittently reveal a subset of transcripts that reverse expression between successive cycles of drug removal and rechallenge and include mediators of cell invasiveness and the epithelial-to-mesenchymal transition. These transcripts change during periods of drug removal by adaptive switching, rather than selection pressure. Resensitization occurs against a background of sustained expression of melanoma resistance genes, producing a transcriptome distinct from that of the initial drug-naive cell state. We conclude that phenotypic plasticity leading to drug resensitization can underlie the beneficial effect of intermittent treatment.
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32
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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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33
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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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34
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Tripathi S, Park JH, Pudakalakatti S, Bhattacharya PK, Kaipparettu BA, Levine H. A mechanistic modeling framework reveals the key principles underlying tumor metabolism. PLoS Comput Biol 2022; 18:e1009841. [PMID: 35148308 PMCID: PMC8870510 DOI: 10.1371/journal.pcbi.1009841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 02/24/2022] [Accepted: 01/15/2022] [Indexed: 01/12/2023] Open
Abstract
While aerobic glycolysis, or the Warburg effect, has for a long time been considered a hallmark of tumor metabolism, recent studies have revealed a far more complex picture. Tumor cells exhibit widespread metabolic heterogeneity, not only in their presentation of the Warburg effect but also in the nutrients and the metabolic pathways they are dependent on. Moreover, tumor cells can switch between different metabolic phenotypes in response to environmental cues and therapeutic interventions. A framework to analyze the observed metabolic heterogeneity and plasticity is, however, lacking. Using a mechanistic model that includes the key metabolic pathways active in tumor cells, we show that the inhibition of phosphofructokinase by excess ATP in the cytoplasm can drive a preference for aerobic glycolysis in fast-proliferating tumor cells. The differing rates of ATP utilization by tumor cells can therefore drive heterogeneity with respect to the presentation of the Warburg effect. Building upon this idea, we couple the metabolic phenotype of tumor cells to their migratory phenotype, and show that our model predictions are in agreement with previous experiments. Next, we report that the reliance of proliferating cells on different anaplerotic pathways depends on the relative availability of glucose and glutamine, and can further drive metabolic heterogeneity. Finally, using treatment of melanoma cells with a BRAF inhibitor as an example, we show that our model can be used to predict the metabolic and gene expression changes in cancer cells in response to drug treatment. By making predictions that are far more generalizable and interpretable as compared to previous tumor metabolism modeling approaches, our framework identifies key principles that govern tumor cell metabolism, and the reported heterogeneity and plasticity. These principles could be key to targeting the metabolic vulnerabilities of cancer.
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Affiliation(s)
- Shubham Tripathi
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas, United States of America
- Center for Theoretical Biological Physics and Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
| | - Jun Hyoung Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shivanand Pudakalakatti
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Pratip K. Bhattacharya
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Benny Abraham Kaipparettu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Herbert Levine
- Center for Theoretical Biological Physics and Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
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Misek SA, Newbury PA, Chekalin E, Paithankar S, Doseff AI, Chen B, Gallo KA, Neubig RR. Ibrutinib Blocks YAP1 Activation and Reverses BRAF Inhibitor Resistance in Melanoma Cells. Mol Pharmacol 2022; 101:1-12. [PMID: 34732527 PMCID: PMC11037454 DOI: 10.1124/molpharm.121.000331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 10/01/2021] [Indexed: 11/22/2022] Open
Abstract
Most B-Raf proto-oncogene (BRAF)-mutant melanoma tumors respond initially to BRAF inhibitor (BRAFi)/mitogen-activated protein kinase kinase 1 inhibitor (MEKi) therapy, although few patients have durable long-term responses to these agents. The goal of this study was to use an unbiased computational approach to identify inhibitors that reverse an experimentally derived BRAFi resistance gene expression signature. Using this approach, we found that ibrutinib effectively reverses this signature, and we demonstrate experimentally that ibrutinib resensitizes a subset of BRAFi-resistant melanoma cells to vemurafenib. Ibrutinib is used clinically as an inhibitor of the Src family kinase Bruton tyrosine kinase (BTK); however, neither BTK deletion nor treatment with acalabrutinib, another BTK inhibitor with reduced off-target activity, resensitized cells to vemurafenib. These data suggest that ibrutinib acts through a BTK-independent mechanism in vemurafenib resensitization. To better understand this mechanism, we analyzed the transcriptional profile of ibrutinib-treated BRAFi-resistant melanoma cells and found that the transcriptional profile of ibrutinib was highly similar to that of multiple Src proto-oncogene kinase inhibitors. Since ibrutinib, but not acalabrutinib, has appreciable off-target activity against multiple Src family kinases, it suggests that ibrutinib may be acting through this mechanism. Furthermore, genes that are differentially expressed in ibrutinib-treated cells are enriched in Yes1-associated transcriptional regulator (YAP1) target genes, and we showed that ibrutinib, but not acalabrutinib, reduces YAP1 activity in BRAFi-resistant melanoma cells. Taken together, these data suggest that ibrutinib, or other Src family kinase inhibitors, may be useful for treating some BRAFi/MEKi-refractory melanoma tumors. SIGNIFICANCE STATEMENT: MAPK-targeted therapies provide dramatic initial responses, but resistance develops rapidly; a subset of these tumors may be rendered sensitive again by treatment with an approved Src family kinase inhibitor-ibrutinub-potentially providing improved clinical outcomes.
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Affiliation(s)
- Sean A Misek
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
| | - Patrick A Newbury
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
| | - Evgenii Chekalin
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
| | - Shreya Paithankar
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
| | - Andrea I Doseff
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
| | - Bin Chen
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
| | - Kathleen A Gallo
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
| | - Richard R Neubig
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
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Kalal BS, Modi PK, Najar MA, Behera SK, Upadhya D, Prasad TSK, Pai VR. Hyperphosphorylation of HDAC2 promotes drug resistance in a novel dual drug resistant mouse melanoma cell line model: an in vitro study. Am J Cancer Res 2021; 11:5881-5901. [PMID: 35018231 PMCID: PMC8727796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023] Open
Abstract
Drug-resistant melanoma is very difficult to treat, and a novel approach is needed to overcome resistance. The present study aims at identifying the alternate pathways utilized in the dual drug-resistant mouse melanoma cells (B16F10R) for their survival and proliferation. The dual drug-resistant mouse melanoma, B16F10R, was established by treating the cells with a combination of U0126 (MEK1/2 inhibitor) and LY294002 (PI3K-AKT kinase inhibitor) in a dose-escalating manner till they attained a resistance fold factor of ≥2. The altered phosphoproteome in the B16F10R, as compared to the parental B16F10C, was analyzed using a high-resolution Orbitrap Fusion Tribrid mass spectrometer. Histone deacetylases 2 (HDAC2) was validated for its role in drug resistance by using its inhibitor, valproic acid (VPA). In the B16F10R cells, 363 altered phosphoproteins were identified, among which 126 were hyperphosphorylated, and 137 were hypophosphorylated (1.5-fold change). Pathway analysis shows the altered phosphoproteins are from RNA metabolism and cell cycle proteins. Inhibition of HDAC2 by VPA induces apoptosis in B16F10C and B16F10R. The present study highlights the role of HDAC2, a cell cycle regulator, in the development of resistance to dual drugs in murine melanoma. Therefore, designing leads for targeting HDAC2 along with key signaling pathways may be explored in treatment strategies.
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Affiliation(s)
- Bhuvanesh Sukhlal Kalal
- Department of Biochemistry, Yenepoya Medical College, Yenepoya (Deemed to be University)Mangaluru, Karnataka, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University)Mangaluru, Karnataka, India
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University)Mangaluru, Karnataka, India
| | - Santosh Kumar Behera
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University)Mangaluru, Karnataka, India
| | - Dinesh Upadhya
- Centre for Molecular Neurosciences, Department of Anatomy, Kasturba Medical College, Manipal Academy of Higher Education ManipalUdupi 576104, Karnataka, India
| | | | - Vinitha Ramanath Pai
- Department of Biochemistry, Yenepoya Medical College, Yenepoya (Deemed to be University)Mangaluru, Karnataka, India
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Kilmister EJ, Tan ST. The Role of the Renin-Angiotensin System in the Cancer Stem Cell Niche. J Histochem Cytochem 2021; 69:835-847. [PMID: 34165363 PMCID: PMC8647629 DOI: 10.1369/00221554211026295] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/28/2021] [Indexed: 02/08/2023] Open
Abstract
Cancer stem cells (CSCs) drive metastasis, treatment resistance, and tumor recurrence. CSCs reside within a niche, an anatomically distinct site within the tumor microenvironment (TME) that consists of malignant and non-malignant cells, including immune cells. The renin-angiotensin system (RAS), a critical regulator of stem cells and key developmental processes, plays a vital role in the TME. Non-malignant cells within the CSC niche and stem cell signaling pathways such as the Wnt, Hedgehog, and Notch pathways influence CSCs. Components of the RAS and cathepsins B and D that constitute bypass loops of the RAS are expressed on CSCs in many cancer types. There is extensive in vitro and in vivo evidence showing that RAS inhibition reduces tumor growth, cell proliferation, invasion, and metastasis. However, there is inconsistent epidemiological data on the effect of RAS inhibitors on cancer incidence and survival outcomes, attributed to different patient characteristics and methodologies used between studies. Further mechanistic studies are warranted to investigate the precise effects of the RAS on CSCs directly and/or the CSC niche. Targeting the RAS, its bypass loops, and convergent signaling pathways participating in the TME and other key stem cell pathways that regulate CSCs may be a novel approach to cancer treatment.
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Affiliation(s)
| | - Swee T. Tan
- Gillies McIndoe Research Institute, Wellington,
New Zealand
- Wellington Regional Plastic, Maxillofacial and
Burns Unit, Hutt Hospital, Wellington, New Zealand
- Department of Surgery, The University of
Melbourne, Parkville, Victoria, Australia
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38
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Ahmed F, Tseng HY, Ahn A, Gunatilake D, Alavi S, Eccles M, Rizos H, Gallagher SJ, Tiffen JC, Hersey P, Emran AA. Repurposing melanoma chemotherapy to activate inflammasomes in treatment of BRAF/MAPK inhibitor resistant melanoma. J Invest Dermatol 2021; 142:1444-1455.e10. [PMID: 34695412 DOI: 10.1016/j.jid.2021.09.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/01/2021] [Accepted: 09/22/2021] [Indexed: 12/23/2022]
Abstract
The development of resistance to treatments of melanoma is commonly associated with upregulation of the MAPK pathway and development of an undifferentiated state. Prior studies have suggested that melanoma with these resistance characteristics may be susceptible to innate death mechanisms such as pyroptosis triggered by activation of inflammasomes. In the present studies we have taken cell lines from patients before and after development of resistance to BRAF V600 inhibitors and exposed the resistant melanoma to temozolomide (a commonly used chemotherapy) with and without chloroquine to inhibit autophagy. It was found that melanoma with an inflammatory undifferentiated state appeared susceptible to this combination when tested in vitro and in vivo against xenografts in NSG mice. Translation of the latter results into patients would promise durable responses in patients treated by the combination. The inflammasome and death mechanism involved appeared to vary between melanoma and involved either AIM2 or NLRP3 inflammasomes and gasdermin D or E. These preliminary studies have raised questions as to the selectivity for different inflammasomes in different melanoma and their selective targeting by chemotherapy. They also question whether the inflammatory state of melanoma may be used as biomarkers to select patients for inflammasome targeted therapy.
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Affiliation(s)
- Farzana Ahmed
- Melanoma Immunology and Oncology Group, Centenary Institute, University of Sydney, Camperdown, Australia; Melanoma Institute Australia, Sydney, Australia
| | - Hsin-Yi Tseng
- Melanoma Immunology and Oncology Group, Centenary Institute, University of Sydney, Camperdown, Australia; Melanoma Institute Australia, Sydney, Australia; Central Clinical School, The University of Sydney, Camperdown, Australia
| | - Antonio Ahn
- Peter MacCallum Cancer Centre, Melbourne, Australia; The Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Dilini Gunatilake
- Melanoma Immunology and Oncology Group, Centenary Institute, University of Sydney, Camperdown, Australia; Melanoma Institute Australia, Sydney, Australia
| | - Sara Alavi
- Melanoma Immunology and Oncology Group, Centenary Institute, University of Sydney, Camperdown, Australia; Melanoma Institute Australia, Sydney, Australia; Central Clinical School, The University of Sydney, Camperdown, Australia
| | - Michael Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Helen Rizos
- Melanoma Institute Australia, Sydney, Australia; Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Stuart J Gallagher
- Melanoma Immunology and Oncology Group, Centenary Institute, University of Sydney, Camperdown, Australia; Melanoma Institute Australia, Sydney, Australia; Central Clinical School, The University of Sydney, Camperdown, Australia
| | - Jessamy C Tiffen
- Melanoma Immunology and Oncology Group, Centenary Institute, University of Sydney, Camperdown, Australia; Melanoma Institute Australia, Sydney, Australia; Central Clinical School, The University of Sydney, Camperdown, Australia
| | - Peter Hersey
- Melanoma Immunology and Oncology Group, Centenary Institute, University of Sydney, Camperdown, Australia; Melanoma Institute Australia, Sydney, Australia; Central Clinical School, The University of Sydney, Camperdown, Australia.
| | - Abdullah Al Emran
- Melanoma Immunology and Oncology Group, Centenary Institute, University of Sydney, Camperdown, Australia; Melanoma Institute Australia, Sydney, Australia; Central Clinical School, The University of Sydney, Camperdown, Australia; Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
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Wang Y, Liu S, Yang Z, Algazi AP, Lomeli SH, Wang Y, Othus M, Hong A, Wang X, Randolph CE, Jones AM, Bosenberg MW, Byrum SD, Tackett AJ, Lopez H, Yates C, Solit DB, Ribas A, Piva M, Moriceau G, Lo RS. Anti-PD-1/L1 lead-in before MAPK inhibitor combination maximizes antitumor immunity and efficacy. Cancer Cell 2021; 39:1375-1387.e6. [PMID: 34416167 PMCID: PMC9126729 DOI: 10.1016/j.ccell.2021.07.023] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/22/2021] [Accepted: 07/29/2021] [Indexed: 12/20/2022]
Abstract
Rationally sequencing and combining PD-1/L1-and MAPK-targeted therapies may overcome innate and acquired resistance. Since increased clinical benefit of MAPK inhibitors (MAPKi) is associated with previous immune checkpoint therapy, we compare the efficacies of sequential and/or combinatorial regimens in subcutaneous murine models of melanoma driven by BrafV600, Nras, or Nf1 mutations as well as colorectal and pancreatic carcinoma driven by KrasG12C. Anti-PD-1/L1 lead-in preceding MAPKi combination optimizes response durability by promoting pro-inflammatory polarization of macrophages and clonal expansion of interferon-γhi, and CD8+ cytotoxic and proliferative (versus CD4+ regulatory) T cells that highly express activation genes. Since therapeutic resistance of melanoma brain metastasis (MBM) limits patient survival, we demonstrate that sequencing anti-PD-1/L1 therapy before MAPKi combination suppresses MBM and improves mouse survival with robust T cell clonal expansion in both intracranial and extracranial metastatic sites. We propose clinically testing brief anti-PD-1/L1 (± anti-CTLA-4) dosing before MAPKi co-treatment to suppress therapeutic resistance.
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Affiliation(s)
- Yujue Wang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Sixue Liu
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Zhentao Yang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Alain P Algazi
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Shirley H Lomeli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Yan Wang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Megan Othus
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Aayoung Hong
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Xiaoyan Wang
- Division of General Internal Medicine, Department of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Chris E Randolph
- Arkansas Children's Research Institute, Little Rock, AR 72202, USA
| | - Alexis M Jones
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marcus W Bosenberg
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | | | - Clayton Yates
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL 36088, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Antoni Ribas
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Marco Piva
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
| | - Roger S Lo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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40
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Emran AA, Tseng HY, Gunatilake D, Cook SJ, Ahmed F, Wang S, Hersey P, Gallagher SJ, Tiffen JC. A Combination of Epigenetic BET and CDK9 Inhibitors for Treatment of Human Melanoma. J Invest Dermatol 2021; 141:2238-2249.e12. [DOI: 10.1016/j.jid.2020.12.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/13/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022]
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41
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Rossman P, Zabka TS, Ruple A, Tuerck D, Ramos-Vara JA, Liu L, Mohallem R, Merchant M, Franco J, Fulkerson CM, Bhide KP, Breen M, Aryal UK, Murray E, Dybdal N, Utturkar SM, Fourez LM, Enstrom AW, Dhawan D, Knapp DW. Phase I/II Trial of Vemurafenib in Dogs with Naturally Occurring, BRAF-mutated Urothelial Carcinoma. Mol Cancer Ther 2021; 20:2177-2188. [PMID: 34433660 DOI: 10.1158/1535-7163.mct-20-0893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 04/06/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022]
Abstract
BRAF-targeted therapies including vemurafenib (Zelboraf) induce dramatic cancer remission; however, drug resistance commonly emerges. The purpose was to characterize a naturally occurring canine cancer model harboring complex features of human cancer, to complement experimental models to improve BRAF-targeted therapy. A phase I/II clinical trial of vemurafenib was performed in pet dogs with naturally occurring invasive urothelial carcinoma (InvUC) harboring the canine homologue of human BRAF V600E The safety, MTD, pharmacokinetics, and antitumor activity were determined. Changes in signaling and immune gene expression were assessed by RNA sequencing and phosphoproteomic analyses of cystoscopic biopsies obtained before and during treatment, and at progression. The vemurafenib MTD was 37.5 mg/kg twice daily. Anorexia was the most common adverse event. At the MTD, partial remission occurred in 9 of 24 dogs (38%), with a median progression-free interval of 181 days (range, 53-608 days). In 18% of the dogs, new cutaneous squamous cell carcinoma and papillomas occurred, a known pharmacodynamic effect of vemurafenib in humans. Upregulation of genes in the classical and alternative MAPK-related pathways occurred in subsets of dogs at cancer progression. The most consistent transcriptomic changes were the increase in patterns of T lymphocyte infiltration during the first month of vemurafenib, and of immune failure accompanying cancer progression. In conclusion, the safety, antitumor activity, and cutaneous pharmacodynamic effects of vemurafenib, and the development of drug resistance in dogs closely mimic those reported in humans. This suggests BRAF-mutated canine InvUC offers an important complementary animal model to improve BRAF-targeted therapies in humans.
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Affiliation(s)
- Paul Rossman
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana
| | - Tanja S Zabka
- Development Sciences, Genentech Inc., South San Francisco, California
| | - Audrey Ruple
- Department of Public Health, College of Health and Human Sciences, Purdue University, West Lafayette, Indiana.,Purdue University Center for Cancer Research, West Lafayette, Indiana
| | - Dietrich Tuerck
- Department Pharmaceutical Sciences, Roche, Basel, Switzerland
| | - José A Ramos-Vara
- Purdue University Center for Cancer Research, West Lafayette, Indiana.,Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana
| | - Liling Liu
- Drug Metabolism & Pharmacokinetics, Genentech Inc., South San Francisco, California
| | - Rodrigo Mohallem
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana.,Bindley Bioscience Center, Purdue University, West Lafayette, Indiana
| | - Mark Merchant
- Translational Oncology, Genentech Inc., South San Francisco, California
| | - Jackeline Franco
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana
| | - Christopher M Fulkerson
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana.,Purdue University Center for Cancer Research, West Lafayette, Indiana
| | - Ketaki P Bhide
- Bioinformatics Core, College of Agriculture, Purdue University, West Lafayette, Indiana
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina
| | - Uma K Aryal
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana.,Bindley Bioscience Center, Purdue University, West Lafayette, Indiana
| | - Elaine Murray
- Global Safety Risk Management, Genentech Inc., South San Francisco, California
| | - Noel Dybdal
- Development Sciences, Genentech Inc., South San Francisco, California
| | - Sagar M Utturkar
- Purdue University Center for Cancer Research, West Lafayette, Indiana
| | - Lindsey M Fourez
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana
| | - Alexander W Enstrom
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana
| | - Deepika Dhawan
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana
| | - Deborah W Knapp
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana. .,Purdue University Center for Cancer Research, West Lafayette, Indiana
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Transcriptional Reprogramming and Constitutive PD-L1 Expression in Melanoma Are Associated with Dedifferentiation and Activation of Interferon and Tumour Necrosis Factor Signalling Pathways. Cancers (Basel) 2021; 13:cancers13174250. [PMID: 34503064 PMCID: PMC8428231 DOI: 10.3390/cancers13174250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/07/2021] [Accepted: 08/13/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Melanoma, an aggressive form of skin cancer, is frequently associated with drug resistance in the advanced stages. For instance, frequently resistance is observed in sequential treatment of melanoma with targeted therapy and immunotherapy. In this research, the authors investigated whether potential transcriptional mechanisms and pathways associated with PD-L1 protein expression could underlie targeted therapy drug resistance in melanoma. The authors found a PD-L1 expression transcriptional pattern underlies resistance to targeted therapy in a subgroup of melanomas. These melanomas were markedly dedifferentiated, as compared to melanomas that were not drug resistant. Understanding changes in transcription and molecular pathways that lead to drug resistance could allow researchers to develop interventions to prevent drug resistance from occurring in melanoma, which could also be relevant to other cancer types. Abstract Melanoma is the most aggressive type of skin cancer, with increasing incidence worldwide. Advances in targeted therapy and immunotherapy have improved the survival of melanoma patients experiencing recurrent disease, but unfortunately treatment resistance frequently reduces patient survival. Resistance to targeted therapy is associated with transcriptomic changes and has also been shown to be accompanied by increased expression of programmed death ligand 1 (PD-L1), a potent inhibitor of immune response. Intrinsic upregulation of PD-L1 is associated with genome-wide DNA hypomethylation and widespread alterations in gene expression in melanoma cell lines. However, an in-depth analysis of the transcriptomic landscape of melanoma cells with intrinsically upregulated PD-L1 expression is lacking. To determine the transcriptomic landscape of intrinsically upregulated PD-L1 expression in melanoma, we investigated transcriptomes in melanomas with constitutive versus inducible PD-L1 expression (referred to as PD-L1CON and PD-L1IND). RNA-Seq analysis was performed on seven PD-L1CON melanoma cell lines and ten melanoma cell lines with low inducible PD-L1IND expression. We observed that PD-L1CON melanoma cells had a reprogrammed transcriptome with a characteristic pattern of dedifferentiated gene expression, together with active interferon (IFN) and tumour necrosis factor (TNF) signalling pathways. Furthermore, we identified key transcription factors that were also differentially expressed in PD-L1CON versus PD-L1IND melanoma cell lines. Overall, our studies describe transcriptomic reprogramming of melanomas with PD-L1CON expression.
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43
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Leonce C, Saintigny P, Ortiz-Cuaran S. Cell-intrinsic mechanisms of drug tolerance to systemic therapies in cancer. Mol Cancer Res 2021; 20:11-29. [PMID: 34389691 DOI: 10.1158/1541-7786.mcr-21-0038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/11/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022]
Abstract
In cancer patients with metastatic disease, the rate of complete tumor response to systemic therapies is low, and residual lesions persist in the majority of patients due to early molecular adaptation in cancer cells. A growing body of evidence suggests that a subpopulation of drug-tolerant « persister » cells - a reversible phenotype characterized by reduced drug sensitivity and decreased cell proliferation - maintains residual disease and may serve as a reservoir for resistant phenotypes. The survival of these residual tumor cells can be caused by reactivation of specific signaling pathways, phenotypic plasticity (i.e., transdifferentiation), epigenetic or metabolic reprogramming, downregulation of apoptosis as well as transcriptional remodeling. In this review, we discuss the molecular mechanisms that enable adaptive survival in drug-tolerant cells. We describe the main characteristics and dynamic nature of this persistent state, and highlight the current therapeutic strategies that may be used to interfere with the establishment of drug-tolerant cells, as an alternative to improve objective response to systemic therapies and delay the emergence of resistance to improve long-term survival.
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Affiliation(s)
- Camille Leonce
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon
| | - Pierre Saintigny
- Department of Medical Oncology, Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon. Department of Medical Oncology, Centre Léon Bérard
| | - Sandra Ortiz-Cuaran
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon
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The evolution of acquired resistance to BRAF inhibitor is sustained by IGF1-driven tumor vascular remodeling. J Invest Dermatol 2021; 142:445-458. [PMID: 34358527 DOI: 10.1016/j.jid.2021.07.162] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 06/15/2021] [Accepted: 07/09/2021] [Indexed: 02/08/2023]
Abstract
As hallmark of cancer, angiogenesis plays a pivotal role in carcinogenesis. The correlation between angiogenesis and evolution of BRAF inhibitor acquired resistance is, however, still poorly understood. Here, we reported that the molecular signatures of angiogenesis were enriched in early on-treated biopsies but not in disease progressed biopsies. The process of drug resistance development was accompanied by remodeling of vascular morphology, which was potentially manipulated by tumor-secreted pro-angiogenic factors. Further transcriptomic dissection indicated that tumor-secreted IGF1 drove the vascular remodeling through activating IGF1/IGF1R axis on endothelial cells, and sustained the prompt re-growth of resistant tumor. Blockade of IGF1R with small molecules at early stage of response disrupted vascular reconstruction, and subsequently delayed tumor relapse. Our findings not only demonstrated the correlation between IGF1-mediated tumor vascular remodeling and the development of acquired resistance to BRAFi but also provided a potential therapeutic strategy for the prevention of tumor relapse in clinical application.
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Ngamcherdtrakul W, Reda M, Nelson MA, Wang R, Zaidan HY, Bejan DS, Hoang NH, Lane RS, Luoh SW, Leachman SA, Mills GB, Gray JW, Lund AW, Yantasee W. In Situ Tumor Vaccination with Nanoparticle Co-Delivering CpG and STAT3 siRNA to Effectively Induce Whole-Body Antitumor Immune Response. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2100628. [PMID: 34118167 PMCID: PMC8424660 DOI: 10.1002/adma.202100628] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/26/2021] [Indexed: 05/03/2023]
Abstract
The success of immunotherapy with immune checkpoint inhibitors (ICIs) in a subset of individuals has been very exciting. However, in many cancers, responses to current ICIs are modest and are seen only in a small subsets of patients. Herein, a widely applicable approach that increases the benefit of ICIs is reported. Intratumoral administration of augmenting immune response and inhibiting suppressive environment of tumors-AIRISE-02 nanotherapeutic that co-delivers CpG and STAT3 siRNA-results in not only regression of the injected tumor, but also tumors at distant sites in multiple tumor model systems. In particular, three doses of AIRISE-02 in combination with systemic ICIs completely cure both treated and untreated aggressive melanoma tumors in 63% of mice, while ICIs alone do not cure any mice. A long-term memory immune effect is also reported. AIRISE-02 is effective in breast and colon tumor models as well. Lastly, AIRISE-02 is well tolerated in mice and nonhuman primates. This approach combines multiple therapeutic agents into a single nanoconstruct to create whole-body immune responses across multiple cancer types. Being a local therapeutic, AIRISE-02 circumvents regulatory challenges of systemic nanoparticle delivery, facilitating rapid translation to the clinic. AIRISE-02 is under investigational new drug (IND)-enabling studies, and clinical trials will soon follow.
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Affiliation(s)
| | - Moataz Reda
- PDX Pharmaceuticals, Inc., Portland, OR, 97239, USA
| | | | - Ruijie Wang
- PDX Pharmaceuticals, Inc., Portland, OR, 97239, USA
| | | | | | - Ngoc Ha Hoang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Ryan S Lane
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Shiuh-Wen Luoh
- VA Portland Health Care System, Portland, OR, 97239, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Sancy A Leachman
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Dermatology, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Gordon B Mills
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, 97239, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Joe W Gray
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, 97239, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Amanda W Lund
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Wassana Yantasee
- PDX Pharmaceuticals, Inc., Portland, OR, 97239, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, 97239, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, 97239, USA
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46
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Park R, Lopes L, Lee S, Riano I, Saeed A. The prognostic and predictive impact of BRAF mutations in deficient mismatch repair/microsatellite instability-high colorectal cancer: systematic review/meta-analysis. Future Oncol 2021; 17:4221-4231. [PMID: 34323124 DOI: 10.2217/fon-2021-0552] [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: 11/21/2022] Open
Abstract
Aims: The authors present a systematic review/meta-analysis of the impact of BRAF mutations on prognosis and immune checkpoint inhibitor (ICI) response in deficient mismatch repair/microsatellite instability-high colorectal cancer. Methods: Hazard ratios for overall survival and odds ratios for objective response rate to ICIs were calculated in BRAF-mutated versus BRAF wild-type patients. Results: After screening, nine and three studies, respectively, were included for analysis of prognosis (analysis A) and ICI response (analysis B). Analysis A showed worse overall survival in BRAF-mutated compared with BRAF wild-type stage I-IV patients (hazard ratio: 1.57; 95% CI: 1.23-1.99), and analysis B showed no difference in objective response rate (odds ratio: 1.04; 95% CI: 0.48-2.25). Conclusion: BRAF mutations are associated with worse overall survival but not differential response to ICIs in deficient mismatch repair/microsatellite instability-high colorectal cancer.
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Affiliation(s)
- Robin Park
- MetroWest Medical Center/Tufts University School of Medicine, Framingham, MA 01702, USA
| | - Laercio Lopes
- MetroWest Medical Center/Tufts University School of Medicine, Framingham, MA 01702, USA
| | - Sunggon Lee
- Department of Medicine, Korea University, Seoul 02841, Korea
| | - Ivy Riano
- MetroWest Medical Center/Tufts University School of Medicine, Framingham, MA 01702, USA
| | - Anwaar Saeed
- Department of Medicine, Division of Medical Oncology, Kansas University Cancer Center, Kansas City, KS 66205, USA
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47
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Cmero M, Kurganovs NJ, Stuchbery R, McCoy P, Grima C, Ngyuen A, Chow K, Mangiola S, Macintyre G, Howard N, Kerger M, Dundee P, Ruljancich P, Clarke D, Grummet J, Peters JS, Costello AJ, Norden S, Ryan A, Parente P, Hovens CM, Corcoran NM. Loss of SNAI2 in Prostate Cancer Correlates With Clinical Response to Androgen Deprivation Therapy. JCO Precis Oncol 2021; 5:PO.20.00337. [PMID: 34322653 PMCID: PMC8238292 DOI: 10.1200/po.20.00337] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 03/29/2021] [Accepted: 04/22/2021] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Androgen receptor (AR) signaling is important in prostate cancer progression, and therapies that target this pathway have been the mainstay of treatment for advanced disease for over 70 years. Tumors eventually progress despite castration through a number of well-characterized mechanisms; however, little is known about what determines the magnitude of response to short-term pathway inhibition. METHODS We evaluated a novel combination of AR-targeting therapies (degarelix, abiraterone, and bicalutamide) and noted that the objective patient response to therapy was highly variable. To investigate what was driving treatment resistance in poorly responding patients, as a secondary outcome we comprehensively characterized pre- and post-treatment samples using both whole-genome and RNA sequencing. RESULTS We find that resistance following short-term treatment differs molecularly from typical progressive castration-resistant disease, associated with transcriptional reprogramming, to a transitional epithelial-to-mesenchymal transition (EMT) phenotype rather than an upregulation of AR signaling. Unexpectedly, tolerance to therapy appears to be the default state, with treatment response correlating with the prevalence of tumor cells deficient for SNAI2, a key regulator of EMT reprogramming. CONCLUSION We show that EMT characterizes acutely resistant prostate tumors and that deletion of SNAI2, a key transcriptional regulator of EMT, correlates with clinical response.
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Affiliation(s)
- Marek Cmero
- Department of Surgery, University of Melbourne, Parkville, Victoria, Australia.,Division of Bioinformatics, Walter and Eliza Hall Institute, Parkville, Victoria, Australia.,Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Natalie J Kurganovs
- Department of Surgery, University of Melbourne, Parkville, Victoria, Australia
| | - Ryan Stuchbery
- Department of Surgery, University of Melbourne, Parkville, Victoria, Australia
| | - Patrick McCoy
- Department of Surgery, University of Melbourne, Parkville, Victoria, Australia
| | - Corrina Grima
- Department of Surgery, University of Melbourne, Parkville, Victoria, Australia
| | - Anne Ngyuen
- Department of Surgery, University of Melbourne, Parkville, Victoria, Australia
| | - Ken Chow
- Department of Surgery, University of Melbourne, Parkville, Victoria, Australia.,Department of Urology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Stefano Mangiola
- Department of Surgery, University of Melbourne, Parkville, Victoria, Australia.,Division of Bioinformatics, Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Geoff Macintyre
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas Howard
- Department of Urology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael Kerger
- Department of Urology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Philip Dundee
- Department of Urology, Royal Melbourne Hospital, Parkville, Victoria, Australia.,Department of Urology, Peninsula Health, Frankston, Victoria, Australia
| | - Paul Ruljancich
- Department of Urology, Box Hill Hospital, Box Hill, Victoria, Australia.,Epworth Eastern Hospital, Box Hill, Victoria, Australia
| | - David Clarke
- Department of Urology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Jeremy Grummet
- Department of Urology, Alfred Hospital, Prahan, Victoria, Australia.,Monash University, Clayton, Victoria, Australia
| | - Justin S Peters
- Department of Urology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Anthony J Costello
- Department of Surgery, University of Melbourne, Parkville, Victoria, Australia.,Department of Urology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Sam Norden
- TissuPath, Mount Waverly, Victoria, Australia
| | - Andrew Ryan
- TissuPath, Mount Waverly, Victoria, Australia
| | - Phillip Parente
- Monash University, Clayton, Victoria, Australia.,Department of Medical Oncology, Box Hill Hospital, Box Hill, Victoria, Australia
| | - Christopher M Hovens
- Department of Surgery, University of Melbourne, Parkville, Victoria, Australia.,Department of Urology, Royal Melbourne Hospital, Parkville, Victoria, Australia.,Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Niall M Corcoran
- Department of Surgery, University of Melbourne, Parkville, Victoria, Australia.,Department of Urology, Royal Melbourne Hospital, Parkville, Victoria, Australia.,Department of Urology, Peninsula Health, Frankston, Victoria, Australia.,Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
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48
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Hayford CE, Tyson DR, Robbins CJ, Frick PL, Quaranta V, Harris LA. An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability. PLoS Biol 2021; 19:e3000797. [PMID: 34061819 PMCID: PMC8195356 DOI: 10.1371/journal.pbio.3000797] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/11/2021] [Accepted: 03/16/2021] [Indexed: 12/30/2022] Open
Abstract
Tumor heterogeneity is a primary cause of treatment failure and acquired resistance in cancer patients. Even in cancers driven by a single mutated oncogene, variability in response to targeted therapies is well known. The existence of additional genomic alterations among tumor cells can only partially explain this variability. As such, nongenetic factors are increasingly seen as critical contributors to tumor relapse and acquired resistance in cancer. Here, we show that both genetic and nongenetic factors contribute to targeted drug response variability in an experimental model of tumor heterogeneity. We observe significant variability to epidermal growth factor receptor (EGFR) inhibition among and within multiple versions and clonal sublines of PC9, a commonly used EGFR mutant nonsmall cell lung cancer (NSCLC) cell line. We resolve genetic, epigenetic, and stochastic components of this variability using a theoretical framework in which distinct genetic states give rise to multiple epigenetic "basins of attraction," across which cells can transition driven by stochastic noise. Using mutational impact analysis, single-cell differential gene expression, and correlations among Gene Ontology (GO) terms to connect genomics to transcriptomics, we establish a baseline for genetic differences driving drug response variability among PC9 cell line versions. Applying the same approach to clonal sublines, we conclude that drug response variability in all but one of the sublines is due to epigenetic differences; in the other, it is due to genetic alterations. Finally, using a clonal drug response assay together with stochastic simulations, we attribute subclonal drug response variability within sublines to stochastic cell fate decisions and confirm that one subline likely contains genetic resistance mutations that emerged in the absence of drug treatment.
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Affiliation(s)
- Corey E. Hayford
- Chemical and Physical Biology Graduate Program, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Darren R. Tyson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - C. Jack Robbins
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Peter L. Frick
- Chemical and Physical Biology Graduate Program, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Vito Quaranta
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Leonard A. Harris
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas, United States of America
- Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, Arkansas, United States of America
- Cancer Biology Program, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
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49
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Lim SY, Alavi S, Ming Z, Shklovskaya E, Fung C, Stewart A, Rizos H. Melanoma Cell State-Specific Responses to TNFα. Biomedicines 2021; 9:biomedicines9060605. [PMID: 34073253 PMCID: PMC8230114 DOI: 10.3390/biomedicines9060605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
Immune checkpoint inhibitors that target the programmed cell death protein 1 (PD1) pathway have revolutionized the treatment of patients with advanced metastatic melanoma. PD1 inhibitors reinvigorate exhausted tumor-reactive T cells, thus restoring anti-tumor immunity. Tumor necrosis factor alpha (TNFα) is abundantly expressed as a consequence of T cell activation and can have pleiotropic effects on melanoma response and resistance to PD1 inhibitors. In this study, we examined the influence of TNFα on markers of melanoma dedifferentiation, antigen presentation and immune inhibition in a panel of 40 melanoma cell lines. We report that TNFα signaling is retained in all melanomas but the downstream impact of TNFα was dependent on the differentiation status of melanoma cells. We show that TNFα is a poor inducer of antigen presentation molecules HLA-ABC and HLA-DR but readily induces the PD-L2 immune checkpoint in melanoma cells. Our results suggest that TNFα promotes dynamic changes in melanoma cells that may favor immunotherapy resistance.
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Affiliation(s)
- Su Yin Lim
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (S.Y.L.); (Z.M.); (E.S.); (C.F.); (A.S.)
- Melanoma Institute Australia, Sydney, NSW 2065, Australia;
| | - Sara Alavi
- Melanoma Institute Australia, Sydney, NSW 2065, Australia;
- Melanoma Oncology and Immunology, Centenary Institute, Camperdown, NSW 2050, Australia
| | - Zizhen Ming
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (S.Y.L.); (Z.M.); (E.S.); (C.F.); (A.S.)
- Melanoma Institute Australia, Sydney, NSW 2065, Australia;
| | - Elena Shklovskaya
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (S.Y.L.); (Z.M.); (E.S.); (C.F.); (A.S.)
- Melanoma Institute Australia, Sydney, NSW 2065, Australia;
| | - Carina Fung
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (S.Y.L.); (Z.M.); (E.S.); (C.F.); (A.S.)
- Melanoma Institute Australia, Sydney, NSW 2065, Australia;
| | - Ashleigh Stewart
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (S.Y.L.); (Z.M.); (E.S.); (C.F.); (A.S.)
- Melanoma Institute Australia, Sydney, NSW 2065, Australia;
| | - Helen Rizos
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (S.Y.L.); (Z.M.); (E.S.); (C.F.); (A.S.)
- Melanoma Institute Australia, Sydney, NSW 2065, Australia;
- Correspondence: ; Tel.: +61-02-98502762
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50
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Gurule NJ, McCoach CE, Hinz TK, Merrick DT, Van Bokhoven A, Kim J, Patil T, Calhoun J, Nemenoff RA, Tan AC, Doebele RC, Heasley LE. A tyrosine kinase inhibitor-induced interferon response positively associates with clinical response in EGFR-mutant lung cancer. NPJ Precis Oncol 2021; 5:41. [PMID: 34001994 PMCID: PMC8129124 DOI: 10.1038/s41698-021-00181-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 04/21/2021] [Indexed: 02/07/2023] Open
Abstract
Tyrosine kinase inhibitors (TKIs) targeting EGFR-mutant lung cancers promote a range of tumor regression responses to yield variable residual disease, a likely incubator for acquired resistance. Herein, rapid transcriptional responses induced by TKIs early in treatment that associate with the range of patient responses were explored. RNAseq was performed on EGFR mutant cell lines treated in vitro with osimertinib and on tumor biopsies of eight EGFR mutant lung cancer patients before and after 2 weeks of TKI treatment. Data were evaluated for gene expression programs altered upon TKI treatment. Chemokine and cytokine expression were measured by ELISA and quantitative RT-PCR. IκB Kinase (IKK) and JAK-STAT pathway dependence was tested with pharmacologic and molecular inhibitors. Tumor sections were stained for the T-cell marker CD3. Osimertinib stimulated dynamic, yet wide-ranging interferon (IFN) program regulation in EGFR mutant cell lines. IL6 and CXCL10 induction varied markedly among the EGFR mutant cell lines and was sensitive to IKK and JAK-STAT inhibitors. Analysis of matched patient biopsy pairs revealed marked, yet varied enrichment of IFN transcriptional programs, effector immune cell signatures and T-cell content in treated tumors that positively correlated with time to progression in the patients. EGFR-specific TKIs induce wide-ranging IFN response program activation originating within the cancer cell. The strong association of IFN program induction and duration of clinical response indicates that the TKI-induced IFN program instructs variable recruitment and participation of immune cells in the overall therapeutic response.
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Affiliation(s)
- Natalia J Gurule
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Caroline E McCoach
- Department of Medicine and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Trista K Hinz
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Daniel T Merrick
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Adriaan Van Bokhoven
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jihye Kim
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tejas Patil
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jacob Calhoun
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Raphael A Nemenoff
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Robert C Doebele
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Lynn E Heasley
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Eastern Colorado VA Healthcare System, Rocky Mountain Regional VA Medical Center, Aurora, CO, USA.
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