1
|
Waldschmidt JM, Kloeber JA, Anand P, Frede J, Kokkalis A, Dimitrova V, Potdar S, Nair MS, Vijaykumar T, Im NG, Guillaumet-Adkins A, Chopra N, Stuart H, Budano L, Sotudeh N, Guo G, Grassberger C, Yee AJ, Laubach JP, Richardson PG, Anderson KC, Raje NS, Knoechel B, Lohr JG. Single-Cell Profiling Reveals Metabolic Reprogramming as a Resistance Mechanism in BRAF-Mutated Multiple Myeloma. Clin Cancer Res 2021; 27:6432-6444. [PMID: 34518309 PMCID: PMC8639639 DOI: 10.1158/1078-0432.ccr-21-2040] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/04/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Although remarkably effective in some patients, precision medicine typically induces only transient responses despite initial absence of resistance-conferring mutations. Using BRAF-mutated myeloma as a model for resistance to precision medicine we investigated if BRAF-mutated cancer cells have the ability to ensure their survival by rapidly adapting to BRAF inhibitor treatment. EXPERIMENTAL DESIGN Full-length single-cell RNA (scRNA) sequencing (scRNA-seq) was conducted on 3 patients with BRAF-mutated myeloma and 1 healthy donor. We sequenced 1,495 cells before, after 1 week, and at clinical relapse to BRAF/MEK inhibitor treatment. We developed an in vitro model of dabrafenib resistance using genetically homogeneous single-cell clones from two cell lines with established BRAF mutations (U266, DP6). Transcriptional and epigenetic adaptation in resistant cells were defined by RNA-seq and H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq). Mitochondrial metabolism was characterized by metabolic flux analysis. RESULTS Profiling by scRNA-seq revealed rapid cellular state changes in response to BRAF/MEK inhibition in patients with myeloma and cell lines. Transcriptional adaptation preceded detectable outgrowth of genetically discernible drug-resistant clones and was associated with widespread enhancer remodeling. As a dominant vulnerability, dependency on oxidative phosphorylation (OxPhos) was induced. In treated individuals, OxPhos was activated at the time of relapse and showed inverse correlation to MAPK activation. Metabolic flux analysis confirmed OxPhos as a preferential energetic resource of drug-persistent myeloma cells. CONCLUSIONS This study demonstrates that cancer cells have the ability to rapidly adapt to precision treatments through transcriptional state changes, epigenetic adaptation, and metabolic rewiring, thus facilitating the development of refractory disease while simultaneously exposing novel vulnerabilities.
Collapse
Affiliation(s)
- Johannes M Waldschmidt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jake A Kloeber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Praveen Anand
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Julia Frede
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Antonis Kokkalis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Valeriya Dimitrova
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Sayalee Potdar
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Monica S Nair
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Tushara Vijaykumar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Nam Gyu Im
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Amy Guillaumet-Adkins
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Nitish Chopra
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Hannah Stuart
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Lillian Budano
- Harvard Medical School, Boston, Massachusetts
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Noori Sotudeh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Guangwu Guo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Clemens Grassberger
- Harvard Medical School, Boston, Massachusetts
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andrew J Yee
- Harvard Medical School, Boston, Massachusetts
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jacob P Laubach
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Jerome Lipper Multiple Myeloma Center and LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Paul G Richardson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Jerome Lipper Multiple Myeloma Center and LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Noopur S Raje
- Harvard Medical School, Boston, Massachusetts
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Birgit Knoechel
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jens G Lohr
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| |
Collapse
|
2
|
Keller BA, Laight BJ, Varette O, Broom A, Wedge MÈ, McSweeney B, Cemeus C, Petryk J, Lo B, Burns B, Nessim C, Ong M, Chica RA, Atkins HL, Diallo JS, Ilkow CS, Bell JC. Personalized oncology and BRAF K601N melanoma: model development, drug discovery, and clinical correlation. J Cancer Res Clin Oncol 2021; 147:1365-1378. [PMID: 33555379 DOI: 10.1007/s00432-021-03545-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 01/25/2021] [Indexed: 12/13/2022]
Abstract
PURPOSE Mutations in BRAF are the most prominent activating mutations in melanoma and are increasingly recognized in other cancers. There is currently no accepted treatment regimen for patients with mutant BRAFK601N melanoma, and the study of melanoma driven by BRAF mutations at the 601 locus is lacking due to a paucity of cellular model systems. Therefore, we sought to better understand the treatment and clinical approach to patients with mutant BRAFK601N melanoma and subsequently develop a novel personalized oncology platform for rare or treatment-refractory cancers. METHODS We developed and characterized the first patient-derived, naturally occurring BRAFK601N melanoma model, described herein as OHRI-MEL-13, and assessed efficacy using the Prestwick Chemical Library and select targeted therapeutics. RESULTS OHRI-MEL-13 exhibits loss of heterozygosity of BRAF, closely mimics the original tumor's gene expression profile, is tumorigenic in immune-deficient murine models, and is available for public accession through American Type Culture Collection. We present in silico modeling data, which illustrates the therapeutic failure of BRAFV600E-targeted therapies in BRAFK601N mutants. Our platform elucidated a unique role for MEK inhibition with cobimetinib, which resulted in short-term clinical success by reducing the metastatic burden. CONCLUSION Our model of BRAFK601N-activated melanoma was developed, thoroughly characterized, and made available for public accession. This model served to demonstrate the feasibility of a novel personalized oncology platform that could be optimized at an institutional level for rare variant or treatment-refractory cancers. We also demonstrate the clinical utility of monotherapy MEK inhibition in a case of BRAFK601N melanoma.
Collapse
Affiliation(s)
- Brian A Keller
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada.
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, K1H 8M5, Canada.
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, 501 Smyth Road, Ottawa, K1H 8L6, Canada.
| | - Brian J Laight
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Oliver Varette
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, K1H 8M5, Canada
| | - Aron Broom
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie Private, Ottawa, K1N 6N5, Canada
| | - Marie-Ève Wedge
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, K1H 8M5, Canada
| | - Benjamin McSweeney
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Catia Cemeus
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Julia Petryk
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Bryan Lo
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Molecular Oncology Diagnostics Laboratory, The Ottawa Hospital, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Bruce Burns
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Carolyn Nessim
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Division of General Surgery, The Ottawa Hospital, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Michael Ong
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Division of Medical Oncology, The Ottawa Hospital, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie Private, Ottawa, K1N 6N5, Canada
| | - Harold L Atkins
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, K1H 8M5, Canada
- The Ottawa Hospital Blood and Marrow Transplant Program, The Ottawa Hospital, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Jean-Simon Diallo
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, K1H 8M5, Canada
| | - Carolina S Ilkow
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, K1H 8M5, Canada
| | - John C Bell
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, K1H 8M5, Canada
| |
Collapse
|
3
|
The AP-1 transcription factor JunB is essential for multiple myeloma cell proliferation and drug resistance in the bone marrow microenvironment. Leukemia 2016; 31:1570-1581. [PMID: 27890927 DOI: 10.1038/leu.2016.358] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 11/08/2016] [Accepted: 11/11/2016] [Indexed: 12/13/2022]
Abstract
Despite therapeutic advances, multiple myeloma (MM) remains an incurable disease, predominantly because of the development of drug resistance. The activator protein-1 (AP-1) transcription factor family has been implicated in a multitude of physiologic processes and tumorigenesis; however, its role in MM is largely unknown. Here we demonstrate specific and rapid induction of the AP-1 family member JunB in MM cells when co-cultured with bone marrow stromal cells. Supporting a functional key role of JunB in MM pathogenesis, knockdown of JUNB significantly inhibited in vitro MM cell proliferation and survival. Consistently, induced silencing of JUNB markedly decreased tumor growth in a murine MM model of the microenvironment. Subsequent gene expression profiling revealed a role for genes associated with apoptosis, DNA replication and metabolism in driving the JunB-mediated phenotype in MM cells. Importantly, knockdown of JUNB restored the response to dexamethasone in dexamethasone-resistant MM cells. Moreover, 4-hydroxytamoxifen-induced activation of a JunB-ER fusion protein protected dexamethasone-sensitive MM cells against dexamethasone- and bortezomib-induced cytotoxicity. In summary, our results demonstrate for the first time a specific role for AP-1/JunB in MM cell proliferation, survival and drug resistance, thereby strongly supporting that this transcription factor is a promising new therapeutic target in MM.
Collapse
|
4
|
Lionetti M, Barbieri M, Todoerti K, Agnelli L, Marzorati S, Fabris S, Ciceri G, Galletti S, Milesi G, Manzoni M, Mazzoni M, Greco A, Tonon G, Musto P, Baldini L, Neri A. Molecular spectrum of BRAF, NRAS and KRAS gene mutations in plasma cell dyscrasias: implication for MEK-ERK pathway activation. Oncotarget 2016; 6:24205-17. [PMID: 26090869 PMCID: PMC4695180 DOI: 10.18632/oncotarget.4434] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/31/2015] [Indexed: 12/28/2022] Open
Abstract
Multiple myeloma (MM) is a clinically and genetically heterogeneous plasma cell (PC) malignancy. Whole-exome sequencing has identified therapeutically targetable mutations such as those in the mitogen-activated protein kinase (MAPK) pathway, which are the most prevalent MM mutations. We used deep sequencing to screen 167 representative patients with PC dyscrasias [132 with MM, 24 with primary PC leukemia (pPCL) and 11 with secondary PC leukemia (sPCL)] for mutations in BRAF, NRAS and KRAS, which were respectively found in 12%, 23.9% and 29.3% of cases. Overall, the MAPK pathway was affected in 57.5% of the patients (63.6% of those with sPCL, 59.8% of those with MM, and 41.7% of those with pPCL). The majority of BRAF variants were comparably expressed at transcript level. Additionally, gene expression profiling indicated the MAPK pathway is activated in mutated patients. Finally, we found that vemurafenib inhibition of BRAF activation in mutated U266 cells affected the expression of genes known to be associated with MM. Our data confirm and extend previous published evidence that MAPK pathway activation is recurrent in myeloma; the finding that it is mediated by BRAF mutations in a significant fraction of patients has potentially immediate clinical implications.
Collapse
Affiliation(s)
- Marta Lionetti
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Marzia Barbieri
- Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Katia Todoerti
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture, Potenza, Italy
| | - Luca Agnelli
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Simona Marzorati
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Sonia Fabris
- Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Gabriella Ciceri
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Serena Galletti
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Giulia Milesi
- Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Martina Manzoni
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Mara Mazzoni
- Molecular Mechanism Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Angela Greco
- Molecular Mechanism Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, San Raffaele Scientific Institute, Milan, Italy
| | - Pellegrino Musto
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture, Potenza, Italy
| | - Luca Baldini
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.,Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonino Neri
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.,Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| |
Collapse
|
5
|
Zhang L, Wu X, Guan P, Qiu L. [The second generation sequencing technology and its application in the field of hematologic malignancies]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2015; 36:716-20. [PMID: 26462650 PMCID: PMC7348261 DOI: 10.3760/cma.j.issn.0253-2727.2015.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Indexed: 11/05/2022]
Affiliation(s)
- Li Zhang
- Instilute of Hematology and Blood Diseases Hospital, CAMS & PUMC, Tianjin 300020, China
| | - Xiujin Wu
- Instilute of Hematology and Blood Diseases Hospital, CAMS & PUMC, Tianjin 300020, China
| | - Pujun Guan
- Instilute of Hematology and Blood Diseases Hospital, CAMS & PUMC, Tianjin 300020, China
| | - Lugui Qiu
- Instilute of Hematology and Blood Diseases Hospital, CAMS & PUMC, Tianjin 300020, China
| |
Collapse
|