1
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Schillo JL, Feddersen CR, Peplinski RM, Powell LS, Varzavand A, Stipp CS, Riordan JD, Dupuy AJ. Single-cell genomics analysis reveals complex genetic interactions in an in vivo model of acquired BRAF inhibitor resistance. NAR Cancer 2024; 6:zcad061. [PMID: 38213996 PMCID: PMC10782916 DOI: 10.1093/narcan/zcad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/20/2023] [Accepted: 12/21/2023] [Indexed: 01/13/2024] Open
Abstract
The evolution of therapeutic resistance is a major obstacle to the success of targeted oncology drugs. While both inter- and intratumoral heterogeneity limit our ability to detect resistant subpopulations that pre-exist or emerge during treatment, our ability to analyze tumors with single-cell resolution is limited. Here, we utilized a cell-based transposon mutagenesis method to identify mechanisms of BRAF inhibitor resistance in a model of cutaneous melanoma. This screen identified overexpression of NEDD4L and VGLL3 as significant drivers of BRAF inhibitor resistance in vivo. In addition, we describe a novel single-cell genomics profiling method to genotype thousands of individual cells within tumors driven by transposon mutagenesis. This approach revealed a surprising genetic diversity among xenograft tumors and identified recurrent co-occurring mutations that emerge within distinct tumor subclones. Taken together, these observations reveal an unappreciated genetic complexity that drives BRAF inhibitor resistance.
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Affiliation(s)
- Jacob L Schillo
- Department of Anatomy & Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA
| | - Charlotte R Feddersen
- Department of Anatomy & Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Medical Scientist Training Program, The University of Iowa, Iowa City, IA 52242, USA
| | - Rebekah M Peplinski
- Department of Anatomy & Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA
| | - Lexy S Powell
- Department of Anatomy & Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Afshin Varzavand
- Holden Comprehensive Cancer Center, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Christopher S Stipp
- Holden Comprehensive Cancer Center, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Jesse D Riordan
- Department of Anatomy & Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
| | - Adam J Dupuy
- Department of Anatomy & Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242, USA
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA
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2
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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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3
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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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4
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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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5
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Zhu EY, Dupuy AJ. Machine learning approach informs biology of cancer drug response. BMC Bioinformatics 2022; 23:184. [PMID: 35581546 PMCID: PMC9112473 DOI: 10.1186/s12859-022-04720-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/03/2022] [Indexed: 12/12/2022] Open
Abstract
Background The mechanism of action for most cancer drugs is not clear. Large-scale pharmacogenomic cancer cell line datasets offer a rich resource to obtain this knowledge. Here, we present an analysis strategy for revealing biological pathways that contribute to drug response using publicly available pharmacogenomic cancer cell line datasets. Methods We present a custom machine-learning based approach for identifying biological pathways involved in cancer drug response. We test the utility of our approach with a pan-cancer analysis of ML210, an inhibitor of GPX4, and a melanoma-focused analysis of inhibitors of BRAFV600. We apply our approach to reveal determinants of drug resistance to microtubule inhibitors. Results Our method implicated lipid metabolism and Rac1/cytoskeleton signaling in the context of ML210 and BRAF inhibitor response, respectively. These findings are consistent with current knowledge of how these drugs work. For microtubule inhibitors, our approach implicated Notch and Akt signaling as pathways that associated with response. Conclusions Our results demonstrate the utility of combining informed feature selection and machine learning algorithms in understanding cancer drug response. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04720-z.
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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
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, The University of Iowa, Iowa City, IA, USA. .,Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA.
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6
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Tan Y, Zhong X, Wen X, Yao L, Shao Z, Sun W, Wu J, Wen G, Tang D, Zhang X, Liao Y, Liu J. Bilirubin Restrains the Anticancer Effect of Vemurafenib on BRAF-Mutant Melanoma Cells Through ERK-MNK1 Signaling. Front Oncol 2021; 11:698888. [PMID: 34222023 PMCID: PMC8250144 DOI: 10.3389/fonc.2021.698888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/02/2021] [Indexed: 01/03/2023] Open
Abstract
Melanoma, the most threatening cancer in the skin, has been considered to be driven by the carcinogenic RAF-MEK1/2-ERK1/2 signaling pathway. This signaling pathway is usually mainly dysregulated by mutations in BRAF or RAS in skin melanomas. Although inhibitors targeting mutant BRAF, such as vemurafenib, have improved the clinical outcome of melanoma patients with BRAF mutations, the efficiency of vemurafenib is limited in many patients. Here, we show that blood bilirubin in patients with BRAF-mutant melanoma treated with vemurafenib is negatively correlated with clinical outcomes. In vitro and animal experiments show that bilirubin can abrogate vemurafenib-induced growth suppression of BRAF-mutant melanoma cells. Moreover, bilirubin can remarkably rescue vemurafenib-induced apoptosis. Mechanically, the activation of ERK-MNK1 axis is required for bilirubin-induced reversal effects post vemurafenib treatment. Our findings not only demonstrate that bilirubin is an unfavorable for patients with BRAF-mutant melanoma who received vemurafenib treatment, but also uncover the underlying mechanism by which bilirubin restrains the anticancer effect of vemurafenib on BRAF-mutant melanoma cells.
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Affiliation(s)
- Yufan Tan
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xiaoyu Zhong
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China.,Institute of Digestive Disease of Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Xizhi Wen
- Biotherapy Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Leyi Yao
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Zhenlong Shao
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Wenshuang Sun
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Jiawen Wu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Guanmei Wen
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Daolin Tang
- Department of Surgery, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Xiaoshi Zhang
- Biotherapy Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yuning Liao
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China.,Institute of Digestive Disease of Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Jinbao Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China.,Institute of Digestive Disease of Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
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7
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Hartman ML, Gajos-Michniewicz A, Talaj JA, Mielczarek-Lewandowska A, Czyz M. BH3 mimetics potentiate pro-apoptotic activity of encorafenib in BRAF V600E melanoma cells. Cancer Lett 2020; 499:122-136. [PMID: 33259900 DOI: 10.1016/j.canlet.2020.11.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 12/29/2022]
Abstract
BRAFV600- and MEK1/2-targeting therapies rarely produce durable response in melanoma patients. We investigated five BRAFV600E melanoma cell lines derived from drug-naïve tumor specimens to assess cell death response to encorafenib (Braftovi), a recently FDA-approved BRAFV600 inhibitor. Drug-naïve cell lines (i) did not harbor damaging alterations in genes encoding core apoptotic machinery, but they differed in (ii) mitochondrial priming as demonstrated by whole-cell BH3 profiling, and (iii) levels of selected anti-apoptotic proteins. Encorafenib modulated the balance between apoptosis-regulating proteins as it upregulated BIM and BMF, and attenuated NOXA, but did not affect the levels of pro-survival proteins except for MCL-1 and BCL-XL in selected cell lines. Induction of apoptosis could be predicted using Dynamic BH3 profiling. The extent of apoptosis was dependent on both (i) cell-intrinsic proximity to the apoptotic threshold (initial mitochondrial priming) and (ii) the abundance of encorafenib-induced BIM (iBIM; drug-induced change in priming). While co-inhibition of MCL-1 and BCL-XL/BCL-2 was indispensable for apoptosis in drug-naïve cells, encorafenib altered cell dependence to MCL-1, and reliance on BCL-XL/BCL-2 was additionally found in cell lines that were highly primed to apoptosis by encorafenib. This translated into robust apoptosis when encorafenib was combined with selective BH3 mimetics. Our study provides a mechanistic insight into the role of proteins from the BCL-2 family in melanoma cell response to targeted therapy, and presents preclinical evidence that (i) MCL-1 is a druggable target to potentiate encorafenib activity, whereas (ii) pharmacological inhibition of BCL-XL/BCL-2 might be relevant but only for a narrow group of encorafenib-treated patients.
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Affiliation(s)
- Mariusz L Hartman
- Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92-215, Lodz, Poland.
| | - Anna Gajos-Michniewicz
- Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92-215, Lodz, Poland
| | - Julita A Talaj
- Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92-215, Lodz, Poland
| | | | - Malgorzata Czyz
- Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92-215, Lodz, Poland
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8
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Proietti I, Skroza N, Bernardini N, Tolino E, Balduzzi V, Marchesiello A, Michelini S, Volpe S, Mambrin A, Mangino G, Romeo G, Maddalena P, Rees C, Potenza C. Mechanisms of Acquired BRAF Inhibitor Resistance in Melanoma: A Systematic Review. Cancers (Basel) 2020; 12:E2801. [PMID: 33003483 PMCID: PMC7600801 DOI: 10.3390/cancers12102801] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/21/2020] [Accepted: 09/25/2020] [Indexed: 12/18/2022] Open
Abstract
This systematic review investigated the literature on acquired v-raf murine sarcoma viral oncogene homolog B1 (BRAF) inhibitor resistance in patients with melanoma. We searched MEDLINE for articles on BRAF inhibitor resistance in patients with melanoma published since January 2010 in the following areas: (1) genetic basis of resistance; (2) epigenetic and transcriptomic mechanisms; (3) influence of the immune system on resistance development; and (4) combination therapy to overcome resistance. Common resistance mutations in melanoma are BRAF splice variants, BRAF amplification, neuroblastoma RAS viral oncogene homolog (NRAS) mutations and mitogen-activated protein kinase kinase 1/2 (MEK1/2) mutations. Genetic and epigenetic changes reactivate previously blocked mitogen-activated protein kinase (MAPK) pathways, activate alternative signaling pathways, and cause epithelial-to-mesenchymal transition. Once BRAF inhibitor resistance develops, the tumor microenvironment reverts to a low immunogenic state secondary to the induction of programmed cell death ligand-1. Combining a BRAF inhibitor with a MEK inhibitor delays resistance development and increases duration of response. Multiple other combinations based on known mechanisms of resistance are being investigated. BRAF inhibitor-resistant cells develop a range of 'escape routes', so multiple different treatment targets will probably be required to overcome resistance. In the future, it may be possible to personalize combination therapy towards the specific resistance pathway in individual patients.
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Affiliation(s)
- Ilaria Proietti
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Nevena Skroza
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Nicoletta Bernardini
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Ersilia Tolino
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Veronica Balduzzi
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Anna Marchesiello
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Simone Michelini
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Salvatore Volpe
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Alessandra Mambrin
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | - Giorgio Mangino
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 00185 Rome, Italy; (G.M.); (G.R.)
| | - Giovanna Romeo
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 00185 Rome, Italy; (G.M.); (G.R.)
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy
| | - Patrizia Maddalena
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
| | | | - Concetta Potenza
- Dermatology Unit “Daniele Innocenzi”, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Fiorini Hospital, Polo Pontino, 04019 Terracina, Italy; (N.S.); (N.B.); (E.T.); (V.B.); (A.M.); (S.M.); (S.V.); (A.M.); (P.M.); (C.P.)
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9
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Zhang Y, Zhang TJ, Tu S, Zhang ZH, Meng FH. Identification of Novel Src Inhibitors: Pharmacophore-Based Virtual Screening, Molecular Docking and Molecular Dynamics Simulations. Molecules 2020; 25:molecules25184094. [PMID: 32911607 PMCID: PMC7571137 DOI: 10.3390/molecules25184094] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/02/2020] [Accepted: 09/05/2020] [Indexed: 02/01/2023] Open
Abstract
Src plays a crucial role in many signaling pathways and contributes to a variety of cancers. Therefore, Src has long been considered an attractive drug target in oncology. However, the development of Src inhibitors with selectivity and novelty has been challenging. In the present study, pharmacophore-based virtual screening and molecular docking were carried out to identify potential Src inhibitors. A total of 891 molecules were obtained after pharmacophore-based virtual screening, and 10 molecules with high docking scores and strong interactions were selected as potential active molecules for further study. Absorption, distribution, metabolism, elimination and toxicity (ADMET) property evaluation was used to ascertain the drug-like properties of the obtained molecules. The proposed inhibitor–protein complexes were further subjected to molecular dynamics (MD) simulations involving root-mean-square deviation and root-mean-square fluctuation to explore the binding mode stability inside active pockets. Finally, two molecules (ZINC3214460 and ZINC1380384) were obtained as potential lead compounds against Src kinase. All these analyses provide a reference for the further development of novel Src inhibitors.
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Bautista L, Knippler CM, Ringel MD. p21-Activated Kinases in Thyroid Cancer. Endocrinology 2020; 161:bqaa105. [PMID: 32609833 PMCID: PMC7417880 DOI: 10.1210/endocr/bqaa105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/24/2020] [Indexed: 02/07/2023]
Abstract
The family of p21-activated kinases (PAKs) are oncogenic proteins that regulate critical cellular functions. PAKs play central signaling roles in the integrin/CDC42/Rho, ERK/MAPK, PI3K/AKT, NF-κB, and Wnt/β-catenin pathways, functioning both as kinases and scaffolds to regulate cell motility, mitosis and proliferation, cytoskeletal rearrangement, and other cellular activities. PAKs have been implicated in both the development and progression of a wide range of cancers, including breast cancer, pancreatic melanoma, thyroid cancer, and others. Here we will discuss the current knowledge on the structure and biological functions of both group I and group II PAKs, as well as the roles that PAKs play in oncogenesis and progression, with a focus on thyroid cancer and emerging data regarding BRAF/PAK signaling.
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Affiliation(s)
- Luis Bautista
- Division of Endocrinology, Diabetes, and Metabolism, Department of Internal Medicine, and Cancer Biology Program, The Ohio State University College of Medicine and Arthur G. James Comprehensive Cancer Center, Columbus, Ohio
| | - Christina M Knippler
- Division of Endocrinology, Diabetes, and Metabolism, Department of Internal Medicine, and Cancer Biology Program, The Ohio State University College of Medicine and Arthur G. James Comprehensive Cancer Center, Columbus, Ohio
- Department of Hematology and Medical Oncology, Emory University and Winship Cancer Institute, Atlanta, Georgia
| | - Matthew D Ringel
- Division of Endocrinology, Diabetes, and Metabolism, Department of Internal Medicine, and Cancer Biology Program, The Ohio State University College of Medicine and Arthur G. James Comprehensive Cancer Center, Columbus, Ohio
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Vanneste M, Feddersen CR, Varzavand A, Zhu EY, Foley T, Zhao L, Holt KH, Milhem M, Piper R, Stipp CS, Dupuy AJ, Henry MD. Functional Genomic Screening Independently Identifies CUL3 as a Mediator of Vemurafenib Resistance via Src-Rac1 Signaling Axis. Front Oncol 2020; 10:442. [PMID: 32346533 PMCID: PMC7169429 DOI: 10.3389/fonc.2020.00442] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/12/2020] [Indexed: 12/19/2022] Open
Abstract
Patients with malignant melanoma have a 5-year survival rate of only 15-20% once the tumor has metastasized to distant tissues. While MAP kinase pathway inhibitors (MAPKi) are initially effective for the majority of patients with melanoma harboring BRAFV600E mutation, over 90% of patients relapse within 2 years. Thus, there is a critical need for understanding MAPKi resistance mechanisms. In this manuscript, we performed a forward genetic screen using a whole genome shRNA library to identify negative regulators of vemurafenib resistance. We identified loss of NF1 and CUL3 as drivers of vemurafenib resistance. NF1 is a known driver of vemurafenib resistance in melanoma through its action as a negative regulator of RAS. However, the mechanism by which CUL3, a key protein in E3 ubiquitin ligase complexes, is involved in vemurafenib resistance was unknown. We found that loss of CUL3 was associated with an increase in RAC1 activity and MEKS298 phosphorylation. However, the addition of the Src family inhibitor saracatinib prevented resistance to vemurafenib in CUL3KD cells and reversed RAC1 activation. This finding suggests that inhibition of the Src family suppresses MAPKi resistance in CUL3KD cells by inactivation of RAC1. Our results also indicated that the loss of CUL3 does not promote the activation of RAC1 through stabilization, suggesting that CUL3 is involved in the stability of upstream regulators of RAC1. Collectively, our study identifies the loss of CUL3 as a driver of MAPKi resistance through activation of RAC1 and demonstrates that inhibition of the Src family can suppress the MAPKi resistance phenotype in CUL3KD cells by inactivating RAC1 protein.
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Affiliation(s)
- Marion Vanneste
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, United States
| | - Charlotte R. Feddersen
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Afshin Varzavand
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA, United States
| | - Elliot Y. Zhu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Tyler Foley
- Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Lei Zhao
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, United States
| | - Kathleen H. Holt
- Viral Vector Core Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Mohammed Milhem
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States
| | - Robert Piper
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, United States
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States
| | - Christopher S. Stipp
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA, United States
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States
| | - Adam J. Dupuy
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States
| | - Michael D. Henry
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, United States
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States
- Department of Radiation Oncology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, United States
- Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, United States
- Department of Urology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, United States
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Transposon Insertion Mutagenesis in Mice for Modeling Human Cancers: Critical Insights Gained and New Opportunities. Int J Mol Sci 2020; 21:ijms21031172. [PMID: 32050713 PMCID: PMC7036786 DOI: 10.3390/ijms21031172] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 02/07/2023] Open
Abstract
Transposon mutagenesis has been used to model many types of human cancer in mice, leading to the discovery of novel cancer genes and insights into the mechanism of tumorigenesis. For this review, we identified over twenty types of human cancer that have been modeled in the mouse using Sleeping Beauty and piggyBac transposon insertion mutagenesis. We examine several specific biological insights that have been gained and describe opportunities for continued research. Specifically, we review studies with a focus on understanding metastasis, therapy resistance, and tumor cell of origin. Additionally, we propose further uses of transposon-based models to identify rarely mutated driver genes across many cancers, understand additional mechanisms of drug resistance and metastasis, and define personalized therapies for cancer patients with obesity as a comorbidity.
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