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Benguigui M, Cooper TJ, Kalkar P, Schif-Zuck S, Halaban R, Bacchiocchi A, Kamer I, Deo A, Manobla B, Menachem R, Haj-Shomaly J, Vorontsova A, Raviv Z, Buxbaum C, Christopoulos P, Bar J, Lotem M, Sznol M, Ariel A, Shen-Orr SS, Shaked Y. Interferon-stimulated neutrophils as a predictor of immunotherapy response. Cancer Cell 2024; 42:253-265.e12. [PMID: 38181798 PMCID: PMC10864002 DOI: 10.1016/j.ccell.2023.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 06/02/2023] [Accepted: 12/07/2023] [Indexed: 01/07/2024]
Abstract
Despite the remarkable success of anti-cancer immunotherapy, its effectiveness remains confined to a subset of patients-emphasizing the importance of predictive biomarkers in clinical decision-making and further mechanistic understanding of treatment response. Current biomarkers, however, lack the power required to accurately stratify patients. Here, we identify interferon-stimulated, Ly6Ehi neutrophils as a blood-borne biomarker of anti-PD1 response in mice at baseline. Ly6Ehi neutrophils are induced by tumor-intrinsic activation of the STING (stimulator of interferon genes) signaling pathway and possess the ability to directly sensitize otherwise non-responsive tumors to anti-PD1 therapy, in part through IL12b-dependent activation of cytotoxic T cells. By translating our pre-clinical findings to a cohort of patients with non-small cell lung cancer and melanoma (n = 109), and to public data (n = 1440), we demonstrate the ability of Ly6Ehi neutrophils to predict immunotherapy response in humans with high accuracy (average AUC ≈ 0.9). Overall, our study identifies a functionally active biomarker for use in both mice and humans.
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Affiliation(s)
- Madeleine Benguigui
- Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel; Rappaport Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Tim J Cooper
- Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel; Rappaport Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa, Israel; Department of Immunology, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
| | - Prajakta Kalkar
- Department of Human Biology, the Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Sagie Schif-Zuck
- Department of Human Biology, the Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Ruth Halaban
- Department of Dermatology, Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Antonella Bacchiocchi
- Department of Dermatology, Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Iris Kamer
- Institute of Oncology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Abhilash Deo
- Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel; Rappaport Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Bar Manobla
- Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel; Rappaport Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Rotem Menachem
- Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel; Rappaport Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Jozafina Haj-Shomaly
- Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel; Rappaport Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Avital Vorontsova
- Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel; Rappaport Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Ziv Raviv
- Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel; Rappaport Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Chen Buxbaum
- Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel; Rappaport Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Petros Christopoulos
- Department of Thoracic Oncology, Thoraxklinik and National Center for Tumor Diseases (NCT) at Heidelberg University Hospital, 69126 Heidelberg, Germany; Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Jair Bar
- Institute of Oncology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel; Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Lotem
- Department of Melanoma and Cancer Immunotherapy, Sharett Institute of Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Mario Sznol
- Department of Medicine, Division of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Amiram Ariel
- Department of Human Biology, the Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Shai S Shen-Orr
- Rappaport Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa, Israel; Department of Immunology, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yuval Shaked
- Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel; Rappaport Technion Integrated Cancer Center, Technion - Israel Institute of Technology, Haifa, Israel.
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Li X, Liu T, Bacchiocchi A, Li M, Cheng W, Wittkop T, Mendez F, Wang Y, Tang P, Yao Q, Bosenberg MW, Sznol M, Yan Q, Faham M, Weng L, Halaban R, Jin H, Hu Z. Ultra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction. medRxiv 2024:2024.01.13.24301070. [PMID: 38260271 PMCID: PMC10802755 DOI: 10.1101/2024.01.13.24301070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
While whole genome sequencing (WGS) of cell-free DNA (cfDNA) holds enormous promise for molecular residual disease (MRD) detection, its performance is limited by WGS error rate. Here we introduce AccuScan, an efficient cfDNA WGS technology that enables genome-wide error correction at single read level, achieving an error rate of 4.2×10 -7 , which is about two orders of magnitude lower than a read-centric de-noising method. When applied to MRD detection, AccuScan demonstrated analytical sensitivity down to 10 -6 circulating tumor allele fraction at 99% sample level specificity. In colorectal cancer, AccuScan showed 90% landmark sensitivity for predicting relapse. It also showed robust MRD performance with esophageal cancer using samples collected as early as 1 week after surgery, and predictive value for immunotherapy monitoring with melanoma patients. Overall, AccuScan provides a highly accurate WGS solution for MRD, empowering circulating tumor DNA detection at parts per million range without high sample input nor personalized reagents. One Sentence Summary AccuScan showed remarkable ultra-low limit of detection with a short turnaround time, low sample requirement and a simple workflow for MRD detection.
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Chen Y, Su H, Zhao J, Na Z, Jiang K, Bacchiocchi A, Loh KH, Halaban R, Wang Z, Cao X, Slavoff SA. Unannotated microprotein EMBOW regulates the interactome and chromatin and mitotic functions of WDR5. Cell Rep 2023; 42:113145. [PMID: 37725512 PMCID: PMC10629662 DOI: 10.1016/j.celrep.2023.113145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 07/20/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023] Open
Abstract
The conserved WD40-repeat protein WDR5 interacts with multiple proteins both inside and outside the nucleus. However, it is currently unclear whether and how the distribution of WDR5 between complexes is regulated. Here, we show that an unannotated microprotein EMBOW (endogenous microprotein binder of WDR5) dually encoded in the human SCRIB gene interacts with WDR5 and regulates its binding to multiple interaction partners, including KMT2A and KIF2A. EMBOW is cell cycle regulated, with two expression maxima at late G1 phase and G2/M phase. Loss of EMBOW decreases WDR5 interaction with KIF2A, aberrantly shortens mitotic spindle length, prolongs G2/M phase, and delays cell proliferation. In contrast, loss of EMBOW increases WDR5 interaction with KMT2A, leading to WDR5 binding to off-target genes, erroneously increasing H3K4me3 levels, and activating transcription of these genes. Together, these results implicate EMBOW as a regulator of WDR5 that regulates its interactions and prevents its off-target binding in multiple contexts.
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Affiliation(s)
- Yanran Chen
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Brain Functional Genomics, Ministry of Education and Shanghai, School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Haomiao Su
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Jianing Zhao
- Frontier Innovation Center, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200433, China; Shanghai Fifth People's Hospital, Fudan University, Shanghai 200433, China
| | - Zhenkun Na
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Kevin Jiang
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Antonella Bacchiocchi
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ken H Loh
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Zhentian Wang
- Frontier Innovation Center, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200433, China; Shanghai Fifth People's Hospital, Fudan University, Shanghai 200433, China
| | - Xiongwen Cao
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Brain Functional Genomics, Ministry of Education and Shanghai, School of Life Sciences, East China Normal University, Shanghai 200062, China.
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA.
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Earland N, Zhang W, Usmani A, Nene A, Bacchiocchi A, Chen DY, Sznol M, Halaban R, Chaudhuri AA, Newman AM. CD4 T cells and toxicity from immune checkpoint blockade. Immunol Rev 2023; 318:96-109. [PMID: 37491734 PMCID: PMC10838135 DOI: 10.1111/imr.13248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/27/2023] [Indexed: 07/27/2023]
Abstract
Immune-related toxicities, otherwise known as immune-related adverse events (irAEs), occur in a substantial fraction of cancer patients treated with immune checkpoint inhibitors (ICIs). Ranging from asymptomatic to life-threatening, ICI-induced irAEs can result in hospital admission, high-dose corticosteroid treatment, ICI discontinuation, and in some cases, death. A deeper understanding of the factors underpinning severe irAE development will be essential for improved irAE prediction and prevention, toward maximizing the benefits and safety profiles of ICIs. In recent work, we applied mass cytometry, single-cell RNA sequencing, single-cell V(D)J sequencing, bulk RNA sequencing, and bulk T-cell receptor (TCR) sequencing to identify pretreatment determinants of severe irAE development in patients with advanced melanoma. Across 71 patients separated into three cohorts, we found that two baseline features in circulation-elevated activated CD4 effector memory T-cell abundance and TCR diversity-are associated with severe irAE development, independent of the affected organ system within 3 months of ICI treatment initiation. Here, we provide an extended perspective on this work, synthesize and discuss related literature, and summarize practical considerations for clinical translation. Collectively, these findings lay a foundation for data-driven and mechanistic insights into irAE development, with the potential to reduce ICI morbidity and mortality in the future.
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Affiliation(s)
- Noah Earland
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Wubing Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Abul Usmani
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Antonella Bacchiocchi
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - David Y. Chen
- Division of Dermatology, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Mario Sznol
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Medicine, Division of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Ruth Halaban
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Aadel A. Chaudhuri
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
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Lu L, Risch E, Halaban R, Zhen P, Bacchiocchi A, Risch HA. Dynamic changes of circulating soluble PD-1/PD-L1 and its association with patient survival in immune checkpoint blockade-treated melanoma. Int Immunopharmacol 2023; 118:110092. [PMID: 37004344 DOI: 10.1016/j.intimp.2023.110092] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/10/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023]
Abstract
Immune checkpoint PD-1 and its ligand PD-L1 lead to T cell exhaustion, and a high level of circulating soluble PD-L1 at baseline indicates a poor prognosis in melanoma and other solid tumor types. Here we show that the dynamic changes of circulating soluble PD-1 and PD-L1 across the course of immune checkpoint blockades (ICBs) and their changes associate with patient survival in melanoma in a retrospective study. A high change of soluble PD-L1 level at a time-point but not PD-1 significantly increased the mortality, whereas a high change of soluble PD-1/PD-L1 ratio significantly reduced the mortality. After the initial immunotherapy, both soluble PD-1 and PD-L1 increased. However, the change pattern of soluble PD-L1 level was particularly dependent on patients' survival status. These findings indicate that the magnitudes of circulating soluble PD-L1 and PD-1/PD-L1 ratio changes over the time may reflect the patients' response to ICBs or the progression of the disease and predict the survival in melanoma patients treated with ICBs.
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Bacchiocchi A, Coma S, Chowdhury S, Sznol M, Halaban R, Pachter JA. Abstract 1179: Rational combinations with the dual RAF/MEK inhibitor VS-6766 for treatment of cutaneous melanoma harboring BRAF, NRAS, NF1 or CRAF mutations. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
VS-6766 is a unique dual RAF/MEK inhibitor which blocks MEK activity without the compensatory MEK activation that limits the efficacy of MEKi. VS-6766 produced clinical responses as a single agent in gynecological cancers and KRAS mutant non-small cell lung cancer (NSCLC) (Guo Lancet Oncology 2020). Clinical responses were also observed with VS-6766 in combination with the focal adhesion kinase (FAK) inhibitor defactinib in patients with low-grade serous ovarian cancer and KRAS mutant NSCLC. In patients with advanced cutaneous melanoma, mutations in the RAS/RAF/MEK/ERK (MAPK) pathway occur mainly in BRAF (41%), NRAS (27%), NF1 (25%) and CRAF (2.6%) (AACR Genie v10). Although several selective BRAFV600 inhibitors (BRAFi) are FDA-approved alone or in combination with MEK-only inhibitors (MEKi) for melanomas with BRAFV600E/K, there is still a need for agents to improve response rate, duration of response, and tolerability. There are no targeted therapy options for melanoma patients carrying NRAS or NF1 mutations following progression on immune checkpoint inhibitors. Using low passage cell lines derived from patients with metastatic melanoma and extensively profiled for genomic alterations together with commercially available immortalized human melanoma cell lines, all of which carried mutations in the MAPK pathway, we tested the activity of VS-6766 alone or in combination with other agents. In vitro proliferation assays showed that VS-6766 is as potent as BRAFi in BRAFV600E melanoma cell lines and is more potent than pan-RAF inhibitors in melanoma cell lines bearing NRAS, NF1 or CRAF mutations. We next tested rational combinations of VS-6766 with other agents in specific genetic backgrounds. In BRAFV600E melanoma cell lines, combination of VS-6766 with BRAFi (encorafenib, vemurafenib, dabrafenib) showed greater synergy than combination of MEKi (binimetinib, cobimetinib, trametinib) with BRAFi. Since ~65% of BRAF or NRAS mutant melanomas co-express mutations in the PI3K/AKT/mTOR pathway, we tested the combination of VS-6766 with the mTOR inhibitor everolimus. VS-6766 was synergistic with everolimus in reducing the viability of melanoma cells harboring BRAF or NRAS mutations. Because CDK4/6 pathway activation has been correlated with poor progression-free survival in melanoma patients treated with BRAFi combined with MEKi, we tested the combination of VS-6766 with the CDK4/6 inhibitor abemaciclib. We found that VS-6766 was synergistic with abemaciclib in reducing viability of melanoma cell lines. Additional combinations with VS-6766 are currently being tested and will be reported. These preclinical data support clinical testing of VS-6766 in rational combinations for treatment of cutaneous melanoma with BRAF, NRAS, NF1 or CRAF mutations. In clinical trials, a recommended phase 2 dose has been defined for the combination of VS-6766 with everolimus.
Citation Format: Antonella Bacchiocchi, Silvia Coma, Sanjib Chowdhury, Mario Sznol, Ruth Halaban, Jonathan A. Pachter. Rational combinations with the dual RAF/MEK inhibitor VS-6766 for treatment of cutaneous melanoma harboring BRAF, NRAS, NF1 or CRAF mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1179.
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Farshidfar F, Rhrissorrakrai K, Levovitz C, Peng C, Knight J, Bacchiocchi A, Su J, Yin M, Sznol M, Ariyan S, Clune J, Olino K, Parida L, Nikolaus J, Zhang M, Zhao S, Wang Y, Huang G, Wan M, Li X, Cao J, Yan Q, Chen X, Newman AM, Halaban R. Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis. Nat Commun 2022; 13:898. [PMID: 35197475 PMCID: PMC8866401 DOI: 10.1038/s41467-022-28566-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/28/2022] [Indexed: 12/11/2022] Open
Abstract
Acral melanoma, the most common melanoma subtype among non-White individuals, is associated with poor prognosis. However, its key molecular drivers remain obscure. Here, we perform integrative genomic and clinical profiling of acral melanomas from 104 patients treated in North America (n = 37) or China (n = 67). We find that recurrent, late-arising focal amplifications of cytoband 22q11.21 are a leading determinant of inferior survival, strongly associated with metastasis, and linked to downregulation of immunomodulatory genes associated with response to immune checkpoint blockade. Unexpectedly, LZTR1 - a known tumor suppressor in other cancers - is a key candidate oncogene in this cytoband. Silencing of LZTR1 in melanoma cell lines causes apoptotic cell death independent of major hotspot mutations or melanoma subtypes. Conversely, overexpression of LZTR1 in normal human melanocytes initiates processes associated with metastasis, including anchorage-independent growth, formation of spheroids, and an increase in MAPK and SRC activities. Our results provide insights into the etiology of acral melanoma and implicate LZTR1 as a key tumor promoter and therapeutic target.
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Affiliation(s)
- Farshad Farshidfar
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | | | | | - Cong Peng
- Xiangya Hospital, Central South University, Changsha, China
| | - James Knight
- Yale Center for Genome Analysis, Yale University, New Haven, CT, 06520, USA
| | | | - Juan Su
- Xiangya Hospital, Central South University, Changsha, China
| | - Mingzhu Yin
- Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Mario Sznol
- Department of Internal Medicine, Section of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephan Ariyan
- Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - James Clune
- Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Kelly Olino
- Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | | | - Joerg Nikolaus
- Department of Molecular and Cellular Physiology, Yale University School of Medicine, New Haven, CT, USA
| | - Meiling Zhang
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Shuang Zhao
- Xiangya Hospital, Central South University, Changsha, China
| | - Yan Wang
- Department of Dermatologic Surgery Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Gang Huang
- Department of Bone and Soft Tissue oncology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, Hunan, China
| | - Miaojian Wan
- Department of Dermatology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xianan Li
- Department of Bone and Soft Tissue oncology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, Hunan, China
| | - Jian Cao
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Qin Yan
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Xiang Chen
- Xiangya Hospital, Central South University, Changsha, China.
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA.
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Premi S, Han L, Mehta S, Knight J, Zhao D, Bacchiocchi A, Halaban R, Palmatier MA, Kornacker K, Brash DE. Abstract PR01: Genomic UV-hypersensitive sites as sentinels for personal UV exposure. Cancer Prev Res (Phila) 2020. [DOI: 10.1158/1940-6215.envcaprev19-pr01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The largest risk factor for skin cancers such as melanoma is past sun exposure, so an objective measurement of traces of an individual’s sun history would allow a general practitioner to identify people who should be monitored for early cancer detection. If the genome contains outlier DNA sequences hypersensitive to environmental agents such as ultraviolet light (UV), these would be genomic dosimeters for monitoring personal carcinogen exposure and would facilitate noninvasive measurements on small skin samples. Such DNA sites might also allow UV to drive direct changes in cell physiology rather than acting through rare mutations. New methods, adductSeq and freqSeq, tagged rare UV-induced cyclobutane pyrimidine dimers (CPDs) and provided statistical resolution to quantify rare lesions at single-base resolution across the genome. Primary human melanocytes, but not fibroblasts, carried spontaneous apurinic sites and TG sequence lesions more frequent than UV-induced CPDs. UV exposure revealed hyperhotspots acquiring CPDs up to 200-fold more frequently than the genomic average; these were 20-fold more prevalent in melanocytes. Hyperhotspots were disproportionately located near genes, particularly for RNA-binding proteins, with the most-recurrent hyperhotspots at a fixed position within two motifs. One motif occurred at ETS1 transcription factor binding sites, known to be UV targets, and at sites of mTOR/TOP-tract translation regulation; the second occurred at a sequence that developed delayed CPDs after UV exposure, repaired CPDs slowly, and had accumulated CPDs prior to the experiment. Melanocyte CPD hyperhotspots aligned precisely with recurrent UV signature mutations in individual gene promoters of melanomas and with known cancer drivers. At sunburn levels of UV exposure, every cell would have a hyperhotspot CPD in each of the ~20 cell pathways targeted, rendering CPD hyperhotspots epigenetic marks.
This abstract is also being presented as Poster A28.
Citation Format: Sanjay Premi, Lynn Han, Sameet Mehta, James Knight, Dejian Zhao, Antonella Bacchiocchi, Ruth Halaban, Meg A. Palmatier, Karl Kornacker, Douglas E. Brash. Genomic UV-hypersensitive sites as sentinels for personal UV exposure [abstract]. In: Proceedings of the AACR Special Conference on Environmental Carcinogenesis: Potential Pathway to Cancer Prevention; 2019 Jun 22-24; Charlotte, NC. Philadelphia (PA): AACR; Can Prev Res 2020;13(7 Suppl): Abstract nr PR01.
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Affiliation(s)
| | - Lynn Han
- 1Yale School of Medicine, New Haven, CT,
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Halaban R, Bacchiocchi A, Straub R, Cao J, Sznol M, Narayan D, Allam A, Krauthammer M, Mansour TS. A novel anti-melanoma SRC-family kinase inhibitor. Oncotarget 2019; 10:2237-2251. [PMID: 31040916 PMCID: PMC6481345 DOI: 10.18632/oncotarget.26787] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 03/04/2019] [Indexed: 12/29/2022] Open
Abstract
The major drawback of melanoma therapy with BRAF and MAPK inhibitors is the innate and acquired drug resistance. We therefore explored alternative targets and developed a new compound, SAB298, that is a SRC-family kinase (SFK) inhibitor. The drug is cytotoxic to patient-derived melanoma cells regardless of oncogene expression and inhibits tumor growth in vivo. As expected, it inhibited SRC and PI3K activity, and had the additional property of ERBB2 inhibition, that lead to inactivation of the two ERK phosphatases PP2A and SHP2. In 57% of the melanoma cell lines tested, the consequent increase in ERK activity lead to proteolytic degradation of its substrate, the lineage specific transcription factor MITF, likely contributing to growth arrest. Treatment with a combination of SAB298 and AZD6244 (selumetinib), induced a synergistic growth inhibition, suggesting that the new compound could be used in the clinic as a substitute for, or in combination with MAPK inhibitors.
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Affiliation(s)
- Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Antonella Bacchiocchi
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Robert Straub
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jian Cao
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mario Sznol
- Comprehensive Cancer Center Section of Medical Oncology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Deepak Narayan
- Department of Surgery, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ahmed Allam
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Michael Krauthammer
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Program in Computational Biology and Bioinformatics, Yale University School of Medicine, New Haven, Connecticut, USA
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10
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Sanmamed MF, Perez-Gracia JL, Schalper KA, Fusco JP, Gonzalez A, Rodriguez-Ruiz ME, Oñate C, Perez G, Alfaro C, Martín-Algarra S, Andueza MP, Gurpide A, Morgado M, Wang J, Bacchiocchi A, Halaban R, Kluger H, Chen L, Sznol M, Melero I. Changes in serum interleukin-8 (IL-8) levels reflect and predict response to anti-PD-1 treatment in melanoma and non-small-cell lung cancer patients. Ann Oncol 2018; 28:1988-1995. [PMID: 28595336 DOI: 10.1093/annonc/mdx190] [Citation(s) in RCA: 287] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background Surrogate biomarkers of efficacy are needed for anti-PD1/PD-L1 therapy, given the existence of delayed responses and pseudo-progressions. We evaluated changes in serum IL-8 levels as a biomarker of response to anti-PD-1 blockade in melanoma and non-small-cell lung cancer (NSCLC) patients. Patients and methods Metastatic melanoma and NSCLC patients treated with nivolumab or pembrolizumab alone or nivolumab plus ipilimumab were studied. Serum was collected at baseline; at 2-4 weeks after the first dose; and at the time-points of response evaluation. Serum IL-8 levels were determined by sandwich ELISA. Changes in serum IL-8 levels were compared with the Wilcoxon test and their strength of association with response was assessed with the Mann-Whitney test. Accuracy of changes in IL-8 levels to predict response was estimated using receiver operation characteristics curves. Results Twenty-nine melanoma patients treated with nivolumab or pembrolizumab were studied. In responding patients, serum IL-8 levels significantly decreased between baseline and best response (P <0.001), and significantly increased upon progression (P = 0.004). In non-responders, IL-8 levels significantly increased between baseline and progression (P = 0.013). Early changes in serum IL-8 levels (2-4 weeks after treatment initiation) were strongly associated with response (P <0.001). These observations were validated in 19 NSCLC patients treated with nivolumab or pembrolizumab (P = 0.001), and in 15 melanoma patients treated with nivolumab plus ipilimumab (P <0.001). Early decreases in serum IL-8 levels were associated with longer overall survival in melanoma (P = 0.001) and NSCLC (P = 0.015) patients. Serum IL-8 levels also correctly reflected true response in three cancer patients presenting pseudoprogression. Conclusions Changes in serum IL-8 levels could be used to monitor and predict clinical benefit from immune checkpoint blockade in melanoma and NSCLC patients.
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Affiliation(s)
- M F Sanmamed
- Department of Immunobiology, Yale University School of Medicine, New Haven, USA
| | - J L Perez-Gracia
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain.,CIBERONC (Centro de Investigación Biomedica en Red de Cáncer)
| | - K A Schalper
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.,Comprehensive Cancer Center Section of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - J P Fusco
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - A Gonzalez
- CIBERONC (Centro de Investigación Biomedica en Red de Cáncer).,Department of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain
| | - M E Rodriguez-Ruiz
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Spain
| | - C Oñate
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - G Perez
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - C Alfaro
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain.,CIBERONC (Centro de Investigación Biomedica en Red de Cáncer)
| | - S Martín-Algarra
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - M P Andueza
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - A Gurpide
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - M Morgado
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - J Wang
- Department of Immunobiology, Yale University School of Medicine, New Haven, USA
| | - A Bacchiocchi
- Department of Dermatology, Yale University School of Medicine, New Haven, USA
| | - R Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, USA
| | - H Kluger
- Comprehensive Cancer Center Section of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - L Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, USA
| | - M Sznol
- Comprehensive Cancer Center Section of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - I Melero
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain.,Department of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Spain
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11
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Das R, Bar N, Ferreira M, Newman AM, Zhang L, Bailur JK, Bacchiocchi A, Kluger H, Wei W, Halaban R, Sznol M, Dhodapkar MV, Dhodapkar KM. Early B cell changes predict autoimmunity following combination immune checkpoint blockade. J Clin Invest 2018; 128:715-720. [PMID: 29309048 DOI: 10.1172/jci96798] [Citation(s) in RCA: 260] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/07/2017] [Indexed: 12/22/2022] Open
Abstract
Combination checkpoint blockade (CCB) targeting inhibitory CTLA4 and PD1 receptors holds promise for cancer therapy. Immune-related adverse events (IRAEs) remain a major obstacle for the optimal application of CCB in cancer. Here, we analyzed B cell changes in patients with melanoma following treatment with either anti-CTLA4 or anti-PD1, or in combination. CCB therapy led to changes in circulating B cells that were detectable after the first cycle of therapy and characterized by a decline in circulating B cells and an increase in CD21lo B cells and plasmablasts. PD1 expression was higher in the CD21lo B cells, and B cell receptor sequencing of these cells demonstrated greater clonality and a higher frequency of clones compared with CD21hi cells. CCB induced proliferation in the CD21lo compartment, and single-cell RNA sequencing identified B cell activation in cells with genomic profiles of CD21lo B cells in vivo. Increased clonality of circulating B cells following CCB occurred in some patients. Treatment-induced changes in B cells preceded and correlated with both the frequency and timing of IRAEs. Patients with early B cell changes experienced higher rates of grade 3 or higher IRAEs 6 months after CCB. Thus, early changes in B cells following CCB may identify patients who are at increased risk of IRAEs, and preemptive strategies targeting B cells may reduce toxicities in these patients.
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Affiliation(s)
| | | | - Michelle Ferreira
- Department of Medicine.,Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, and.,Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | | | | | | | - Wei Wei
- Yale Center for Analytic Sciences
| | | | - Mario Sznol
- Department of Medicine.,Yale Cancer Center, and
| | - Madhav V Dhodapkar
- Department of Medicine.,Yale Cancer Center, and.,Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kavita M Dhodapkar
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA.,Yale Cancer Center, and
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12
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Mackay S, Flynn B, Morse K, Paczkowski P, Bacchiocchi A, Fan R, Halaban R, Zhou J. Single-cell cytokine profiling of tumor-infiltrating T cells to measure patient responses to anti-PD-1 therapy. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.7_suppl.49] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
49 Background: Functional alteration of tumor-infiltrating T lymphocytes (TILs) may serve as a predictor for clinical outcome in cancer patients receiving immunotherapy.To evaluate TILs function unleashed by anti-PD-1 blocking, we employed a single-cell technology integrated with automated bioinformatics to simultaneously measure 17 cytokines secreted by single TILs, permitting the full spectrum delineation of anti-tumor T cell functions in patients with metastatic melanoma. Methods: TILs were enriched from biopsied melanoma tissues digested with enzymes, stimulated with anti-CD3 at 37°C, 5% CO2 for 24 hrs and loaded into a single-cell barcode chip (SCBC) containing ~12000 microchambers. Each chamber (~1.2 nl) was pre-patterned with a complete copy of a 17-plex antibody array. Cells on the SCBC were imaged and incubated for 16 hrs at 37°C, 5% CO2; single-cell cytokine signals were captured with a microarray scanner. The polyfunctional expression (2+ cytokines per cell) of single TILs was evaluated across 4 groups: Effector (Granzyme B, IFN-γ, MIP-1α, Perforin, TNF-α), Stimulatory (GM-CSF, IL-2, IL-5, IL-8, IL-9), Regulatory (IL-4, IL-10, IL-13, IL-22), and Inflammatory (IL-6, IL-17A, MCP-1). Results: Single-cell TILs analysis revealed significant increase of polyfunctional cytokines in patients who responded to anti-PD-1 therapy, compared to those resistant to therapy or in the control group. It was further revealed that the major contributions to enhanced polyfunctional strength are dominated by effector and stimulatory cytokines – both associated with anti-tumor immunity. Notably, TILs of patients responding to therapy exhibited polyfunctional secretions containing a subset of cells co-secreting Granzyme B, IFN- γ, MIP-1 α, and IL-8, which upon further validation is potentially a biomarker to predict clinical outcome of melanoma patients treated by checkpoint immunotherapy. Conclusions: Single-cell multiplexed cytokine profiling is capable of dissecting the full spectrum of immune functions associated with anti-tumor T cell immunity and more accurately measuring the function of TILs for predicting the response of patients receiving anti-PD-1 blocking therapy.
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Affiliation(s)
| | | | | | | | | | | | - Ruth Halaban
- Yale University School of Medicine, New Haven, CT
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13
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Dhodapkar KM, Boddupalli CS, Bar N, Kadaveru K, Krauthammer M, Pornputtapong N, Mai Z, Ariyan S, Narayan D, Kluger HM, Deng Y, Verma R, Das R, Bacchiocchi A, Halaban R, Sznol M, Dhodapkar MV. Distinct dominant T-cell receptors with a tissue resident memory phenotype in individual melanoma metastases. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.7_suppl.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3 Background: Expression of inhibitory immune checkpoints (ICPs) within tumors has emerged as an important barrier for effective anti-tumor immunity. Antibody-mediated blockade of ICPs can lead to durable responses in patients. Interestingly, only a small subset of tumor infiltrating lymphocytes (TILs) express these checkpoints and there is a need to better understand the characteristics of this subset. We undertook this study to understand characteristics of TILs within melanoma. Methods: We used single cell mass cytometry, gene expression profiling of purified T cell subsets, T cell receptor (TCR) sequencing as well as functional studies to understand the characteristics of TILs in melanoma patients (n=50). We also performed exome sequencing of tumor cells in some patients. Results: We find that TILs are functionally and phenotypically distinct from circulating T cells. They express higher levels of inhibitory ICPs (PD-1, TIM-3) and secrete less IL2, IFNg and TNFa than T cells in circulation. Expression of vascular endothelial growth factor within tumors correlated with reduced T cell infiltration. Expression of ICPs (PD-1, TIM-3, PD-L1) were enriched in T cells with a phenotype and expression profile of tissue resident memory T (TRM) cells with most cells expressing multiple checkpoints. Within the myeloid compartment, ICPs were predominantly expressed on CD14+CD16+ subset. TCR sequencing revealed that individual melanoma metastases revealed that the top clones within each of the lesions have distinct TCRs. Concurrent TCR and tumor exome sequencing of individual metastases in the same patient revealed that inter-lesional diversity of TCRs exceeded differences in mutation/neoantigen load in tumor cells. Conclusions: Our findings suggest that TRM cells and CD16+ myeloid cells may be the major target of ICP blockade within tumors. The ability to activate, and retain TRM cells may be an important determinant of the T cell content of the tumor microenvironment and should be a goal for future vaccines. Importantly, our study illustrates inter-lesional diversity of TCRs within individual metastases which may differentially impact the outcome of immune therapy at each site.
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Affiliation(s)
| | | | - Noffar Bar
- Yale-New Haven Smilow Cancer Hosp, New Haven, CT
| | | | | | | | | | | | | | | | - Yanhong Deng
- Yale Center for Analytical Sciences, New Haven, CT
| | | | | | | | - Ruth Halaban
- Yale University School of Medicine, New Haven, CT
| | - Mario Sznol
- Yale University School of Medicine, New Haven, CT
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14
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Boddupalli CS, Bar N, Kadaveru K, Krauthammer M, Pornputtapong N, Mai Z, Ariyan S, Narayan D, Kluger H, Deng Y, Verma R, Das R, Bacchiocchi A, Halaban R, Sznol M, Dhodapkar MV, Dhodapkar KM. Interlesional diversity of T cell receptors in melanoma with immune checkpoints enriched in tissue-resident memory T cells. JCI Insight 2016; 1:e88955. [PMID: 28018970 DOI: 10.1172/jci.insight.88955] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Heterogeneity of tumor cells and their microenvironment can affect outcome in cancer. Blockade of immune checkpoints (ICPs) expressed only on a subset of immune cells leads to durable responses in advanced melanoma. Tissue-resident memory T (TRM) cells have recently emerged as a distinct subset of memory T cells in nonlymphoid tissues. Here, we show that functional properties and expression of ICPs within tumor-infiltrating lymphocytes (TILs) differ from those of blood T cells. TILs secrete less IL-2, IFN-γ, and TNF-α compared with circulating counterparts, and expression of VEGF correlated with reduced TIL infiltration. Within tumors, ICPs are particularly enriched within T cells with phenotype and genomic features of TRM cells and the CD16+ subset of myeloid cells. Concurrent T cell receptor (TCR) and tumor exome sequencing of individual metastases in the same patient revealed that interlesional diversity of TCRs exceeded differences in mutation/neoantigen load in tumor cells. These findings suggest that the TRM subset of TILs may be the major target of ICP blockade and illustrate interlesional diversity of tissue-resident TCRs within individual metastases, which did not equilibrate between metastases and may differentially affect the outcome of immune therapy at each site.
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Affiliation(s)
| | | | | | - Michael Krauthammer
- Program for Computational Biology and Bioinformatics.,Department of Pathology
| | | | | | | | | | | | | | | | | | | | | | | | - Madhav V Dhodapkar
- Department of Medicine.,Yale Cancer Center.,Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
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15
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Sanmamed M, Perez-Gracia J, Fusco J, Oñate C, Perez G, Alfaro C, Martín-Algarra S, González A, Rodriguez-Ruiz M, Andueza M, Wang J, Bacchiocchi A, Halaban R, Kluger H, Sznol M, Melero I. Changes in serum IL8 levels reflect and predict response to anti-PD-1 treatment in melanoma and non-small cell lung cancer patients. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw378.03] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Lim YH, Bacchiocchi A, Qiu J, Straub R, Bruckner A, Bercovitch L, Narayan D, McNiff J, Ko C, Robinson-Bostom L, Antaya R, Halaban R, Choate KA. GNA14 Somatic Mutation Causes Congenital and Sporadic Vascular Tumors by MAPK Activation. Am J Hum Genet 2016; 99:443-50. [PMID: 27476652 PMCID: PMC4974082 DOI: 10.1016/j.ajhg.2016.06.010] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 06/13/2016] [Indexed: 12/20/2022] Open
Abstract
Vascular tumors are among the most common neoplasms in infants and children; 5%-10% of newborns present with or develop lesions within the first 3 months of life. Most are benign infantile hemangiomas that typically regress by 5 years of age; other vascular tumors include congenital tufted angiomas (TAs), kaposiform hemangioendotheliomas (KHEs), and childhood lobular capillary hemangiomas (LCHs). Some of these lesions can become locally invasive and unresponsive to pharmacologic intervention, leading to significant complications. Recent investigation has revealed that activating mutations in HRAS, KRAS, NRAS, GNAQ, and GNA11 can cause certain types of rare childhood vascular tumors, and we have now identified causal recurrent somatic activating mutations in GNA14 by whole-exome and targeted sequencing. We found somatic activating GNA14 c.614A>T (p.Gln205Leu) mutations in one KHE, one TA, and one LCH and a GNA11 c.547C>T (p.Arg183Cys) mutation in two LCH lesions. We examined mutation pathobiology via expression of mutant GNA14 or GNA11 in primary human endothelial cells and melanocytes. GNA14 and GNA11 mutations induced changes in cellular morphology and rendered cells growth-factor independent by upregulating the MAPK pathway. Our findings identify GNA14 mutations as a cause of childhood vascular tumors, offer insight into mechanisms of oncogenic transformation by mutations affecting Gaq family members, and identify potential targets for therapeutic intervention.
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Affiliation(s)
- Young H Lim
- Department of Dermatology, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Pathology, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Genetics, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Antonella Bacchiocchi
- Department of Dermatology, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Jingyao Qiu
- Department of Genetics, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Robert Straub
- Department of Dermatology, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Anna Bruckner
- Departments of Dermatology and Pediatrics, School of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Lionel Bercovitch
- Department of Dermatology, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Deepak Narayan
- Section of Plastic Surgery, Department of Surgery, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Jennifer McNiff
- Department of Dermatology, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Pathology, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Christine Ko
- Department of Dermatology, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Pathology, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Leslie Robinson-Bostom
- Department of Dermatology, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Richard Antaya
- Department of Dermatology, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Pediatrics, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Ruth Halaban
- Department of Dermatology, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Keith A Choate
- Department of Dermatology, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Pathology, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Genetics, School of Medicine, Yale University, New Haven, CT 06510, USA.
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17
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Zhou D, Halaban R, Bacchiocchi A, Nardin C, Zippin J. 606 The pH sensor soluble adenylyl cyclase regulates melanogenesis. J Invest Dermatol 2016. [DOI: 10.1016/j.jid.2016.02.646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Premi S, Wallisch S, Mano C, Weiner A, Bacchiocchi A, Wakamatsu K, Bechara E, Halaban R, Douki T, Brash DE. Abstract LB-104: Excited electrons in melanin induce cyclobutane dimers in the dark. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-lb-104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Sunlight-induced melanomas contain UV-signature mutations, which are caused by cyclobutane pyrimidine dimers (CPD). These photoproducts are typically created picoseconds after a UV photon is absorbed at adjacent thymines or cytosines. However, using immunohistochemistry, mass spectrometry, and RNAi, we find that melanocytes generate CPD for >3 hours after exposure to UVA or UVB, wavelengths found in sunlight and in tanning beds; these “dark CPD” constitute the majority of CPD induced. Using pharmacologic inhibitors, single-photon counting, and specific energy acceptors, we elucidated the mechanism. The process begins when UV-induced superoxide and nitric oxide combine to form peroxynitrite, one of the few biological molecules capable of exciting an electron. Excitation creates a quantum triplet state in the skin pigment melanin that has the energy of a UV photon but induces CPD by transferring its energy to DNA in a radiation-independent manner. Melanin is evidently carcinogenic as well as protective. These findings may underlie the dependence of UV-induced and spontaneous skin cancers on melanin type. The results also validate the long-standing suggestion that chemical generation of excited electronic states - the source of bioluminescence in lower organisms - is important in mammalian biology.
Citation Format: Sanjay Premi, Silvia Wallisch, Camila Mano, Adam Weiner, Antonella Bacchiocchi, Kazumasa Wakamatsu, Etelvino Bechara, Ruth Halaban, Thierry Douki, Douglas E. Brash. Excited electrons in melanin induce cyclobutane dimers in the dark. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-104. doi:10.1158/1538-7445.AM2015-LB-104
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Affiliation(s)
| | | | | | | | | | | | | | | | - Thierry Douki
- 4Commissariat à l'Energie Atomique, Grenoble, France
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19
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Krauthammer M, Kong Y, Bacchiocchi A, Evans P, Pornputtapong N, Wu C, McCusker JP, Ma S, Cheng E, Straub R, Serin M, Bosenberg M, Ariyan S, Narayan D, Sznol M, Kluger HM, Mane S, Schlessinger J, Lifton RP, Halaban R. Exome sequencing identifies recurrent mutations in NF1 and RASopathy genes in sun-exposed melanomas. Nat Genet 2015. [PMID: 26214590 DOI: 10.1038/ng.3361] [Citation(s) in RCA: 276] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We report on whole-exome sequencing (WES) of 213 melanomas. Our analysis established NF1, encoding a negative regulator of RAS, as the third most frequently mutated gene in melanoma, after BRAF and NRAS. Inactivating NF1 mutations were present in 46% of melanomas expressing wild-type BRAF and RAS, occurred in older patients and showed a distinct pattern of co-mutation with other RASopathy genes, particularly RASA2. Functional studies showed that NF1 suppression led to increased RAS activation in most, but not all, melanoma cases. In addition, loss of NF1 did not predict sensitivity to MEK or ERK inhibitors. The rebound pathway, as seen by the induction of phosphorylated MEK, occurred in cells both sensitive and resistant to the studied drugs. We conclude that NF1 is a key tumor suppressor lost in melanomas, and that concurrent RASopathy gene mutations may enhance its role in melanomagenesis.
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Affiliation(s)
- Michael Krauthammer
- Program in Computational Biology and Bioinformatics, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yong Kong
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Antonella Bacchiocchi
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Perry Evans
- Program in Computational Biology and Bioinformatics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Natapol Pornputtapong
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Cen Wu
- School of Public Health, Yale University School of Medicine, New Haven, Connecticut, USA
| | - James P McCusker
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Shuangge Ma
- School of Public Health, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Elaine Cheng
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Robert Straub
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Merdan Serin
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Marcus Bosenberg
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Stephan Ariyan
- Department of Surgery, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Deepak Narayan
- Department of Surgery, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mario Sznol
- Comprehensive Cancer Center Section of Medical Oncology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Harriet M Kluger
- Comprehensive Cancer Center Section of Medical Oncology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Shrikant Mane
- Yale Center for Genome Analysis, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
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20
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Nardin C, Park M, Bacchiocchi A, Halaban R. Rôle de l’adénylate cyclase soluble dans la mélanomagenèse. Ann Dermatol Venereol 2015. [DOI: 10.1016/j.annder.2015.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Premi S, Wallisch S, Mano CM, Weiner AB, Bacchiocchi A, Wakamatsu K, Bechara EJH, Halaban R, Douki T, Brash DE. Photochemistry. Chemiexcitation of melanin derivatives induces DNA photoproducts long after UV exposure. Science 2015; 347:842-7. [PMID: 25700512 PMCID: PMC4432913 DOI: 10.1126/science.1256022] [Citation(s) in RCA: 314] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Mutations in sunlight-induced melanoma arise from cyclobutane pyrimidine dimers (CPDs), DNA photoproducts that are typically created picoseconds after an ultraviolet (UV) photon is absorbed at thymine or cytosine. We found that in melanocytes, CPDs are generated for >3 hours after exposure to UVA, a major component of the radiation in sunlight and in tanning beds. These "dark CPDs" constitute the majority of CPDs and include the cytosine-containing CPDs that initiate UV-signature C→T mutations. Dark CPDs arise when UV-induced reactive oxygen and nitrogen species combine to excite an electron in fragments of the pigment melanin. This creates a quantum triplet state that has the energy of a UV photon but induces CPDs by energy transfer to DNA in a radiation-independent manner. Melanin may thus be carcinogenic as well as protective against cancer. These findings also validate the long-standing suggestion that chemically generated excited electronic states are relevant to mammalian biology.
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Affiliation(s)
- Sanjay Premi
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Silvia Wallisch
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Camila M Mano
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA. Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05513-970 SP, Brazil
| | - Adam B Weiner
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Antonella Bacchiocchi
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake, Aichi 470-1192, Japan
| | - Etelvino J H Bechara
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05513-970 SP, Brazil. Departamento de Ciências Exatas e da Terra, Universidade Federal de São Paulo, Diadema, São Paulo 09972-270 SP, Brazil
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA. Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Thierry Douki
- INAC/LCIB UMR-E3 CEA-UJF/Commissariat à l'Energie Atomique (CEA), 38054 Grenoble Cedex 9, France
| | - Douglas E Brash
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA. Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA.
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22
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Weber J, Martinez AJ, Roder H, Roder J, Meyer K, Asmellash S, Grigorieva J, Tsypin M, Oliveira C, Steingrimsson A, Sayers K, Bacchiocchi A, Sznol M, Halaban R, Kluger H. Pre-treatment patient selection for nivolumab benefit based on serum mass spectra. J Immunother Cancer 2015. [PMCID: PMC4645498 DOI: 10.1186/2051-1426-3-s2-p103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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23
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Choi J, Landrette SF, Wang T, Evans P, Bacchiocchi A, Bjornson R, Cheng E, Stiegler AL, Gathiaka S, Acevedo O, Boggon TJ, Krauthammer M, Halaban R, Xu T. Identification of PLX4032-resistance mechanisms and implications for novel RAF inhibitors. Pigment Cell Melanoma Res 2014; 27:253-62. [PMID: 24283590 PMCID: PMC4065135 DOI: 10.1111/pcmr.12197] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 11/26/2013] [Indexed: 02/02/2023]
Abstract
BRAF inhibitors improve melanoma patient survival, but resistance invariably develops. Here we report the discovery of a novel BRAF mutation that confers resistance to PLX4032 employing whole-exome sequencing of drug-resistant BRAFV600K melanoma cells. We further describe a new screening approach, a genome-wide piggyBac mutagenesis screen that revealed clinically relevant aberrations (N-terminal BRAF truncations and CRAF overexpression). The novel BRAF mutation, a Leu505 to His substitution (BRAFL505H), is the first resistance-conferring second-site mutation identified in BRAF mutant cells. The mutation replaces a small nonpolar amino acid at the BRAF-PLX4032 interface with a larger polar residue. Moreover, we show that BRAFL505H, found in human prostate cancer, is itself a MAPK-activating, PLX4032-resistant oncogenic mutation. Lastly, we demonstrate that the PLX4032-resistant melanoma cells are sensitive to novel, next-generation BRAF inhibitors, especially the ‘paradox-blocker’ PLX8394, supporting its use in clinical trials for treatment of melanoma patients with BRAF-mutations.
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Affiliation(s)
- Jaehyuk Choi
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
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24
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Zhang R, Premi S, Kilic SS, Bacchiocchi A, Halaban R, Brash DE. Clonal growth of human melanocytes using cell-free extracellular matrix. Pigment Cell Melanoma Res 2013; 26:925-7. [PMID: 24034857 PMCID: PMC4086752 DOI: 10.1111/pcmr.12159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 08/19/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Rong Zhang
- Department of Therapeutic Radiology, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Sanjay Premi
- Department of Therapeutic Radiology, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Sarah S. Kilic
- Department of Therapeutic Radiology, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Antonella Bacchiocchi
- Department of Dermatology, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Ruth Halaban
- Department of Dermatology, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Douglas E. Brash
- Department of Therapeutic Radiology, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
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25
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Tworkoski KA, Platt JT, Bacchiocchi A, Bosenberg M, Boggon TJ, Stern DF. MERTK controls melanoma cell migration and survival and differentially regulates cell behavior relative to AXL. Pigment Cell Melanoma Res 2013; 26:527-41. [PMID: 23617806 DOI: 10.1111/pcmr.12110] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/12/2013] [Indexed: 11/28/2022]
Abstract
The receptor tyrosine kinase AXL regulates melanoma cell proliferation and migration. We now demonstrate that AXL and the related kinase MERTK are alternately expressed in melanoma and are associated with different transcriptional signatures. MERTK-positive melanoma cells are more proliferative and less migratory than AXL-positive melanoma cells and overexpression of AXL increases cell motility relative to MERTK. MERTK is expressed in up to 50% of melanoma cells and shRNA-mediated knockdown of MERTK reduces colony formation and cell migration in a CDC42-dependent fashion. Targeting MERTK also decreases cell survival and proliferation in an AKT-dependent manner. Finally, we identify a novel mutation in the kinase domain of MERTK, MERTK(P) (802S) , that increases the motility of melanoma cells relative to wild-type MERTK. Together, these data demonstrate that MERTK is a possible therapeutic target in melanoma, that AXL and MERTK are associated with differential cell behaviors, and that mutations in MERTK may contribute to melanoma pathogenesis.
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Affiliation(s)
- Kathryn A Tworkoski
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
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26
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Held MA, Langdon CG, Platt JT, Graham-Steed T, Liu Z, Chakraborty A, Bacchiocchi A, Koo A, Haskins JW, Bosenberg MW, Stern DF. Genotype-selective combination therapies for melanoma identified by high-throughput drug screening. Cancer Discov 2012; 3:52-67. [PMID: 23239741 DOI: 10.1158/2159-8290.cd-12-0408] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
UNLABELLED Resistance and partial responses to targeted monotherapy are major obstacles in cancer treatment. Systematic approaches to identify efficacious drug combinations for cancer are not well established, especially in the context of genotype. To address this, we have tested pairwise combinations of an array of small-molecule inhibitors on early-passage melanoma cultures using combinatorial drug screening. Results reveal several inhibitor combinations effective for melanomas with activating RAS or BRAF mutations, including mutant BRAF melanomas with intrinsic or acquired resistance to vemurafenib. Inhibition of both EGF receptor and AKT sensitized treatment-resistant BRAF mutant melanoma cultures to vemurafenib. Melanomas with RAS mutations were more resistant to combination therapies relative to BRAF mutants, but were sensitive to combinations of statins and cyclin-dependent kinase inhibitors in vitro and in vivo. These results show the use of combinatorial drug screening for discovering unique treatment regimens that overcome resistance phenotypes of mutant BRAF- and RAS-driven melanomas. SIGNIFICANCE We have used drug combinatorial screening to identify effective combinations for mutant BRAF melanomas, including those resistant to vemurafenib, and mutant RAS melanomas that are resistant to many therapies. Mechanisms governing the interactions of the drug combinations are proposed, and in vivo xenografts show the enhanced benefit and tolerability of a mutant RAS -selective combination, which is currently lacking in the clinic.
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Affiliation(s)
- Matthew A Held
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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27
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Shi H, Moriceau G, Kong X, Koya RC, Nazarian R, Pupo GM, Bacchiocchi A, Dahlman KB, Chmielowski B, Sosman JA, Halaban R, Kefford RF, Long GV, Ribas A, Lo RS. Preexisting MEK1 exon 3 mutations in V600E/KBRAF melanomas do not confer resistance to BRAF inhibitors. Cancer Discov 2012; 2:414-24. [PMID: 22588879 DOI: 10.1158/2159-8290.cd-12-0022] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
UNLABELLED BRAF inhibitors (BRAFi) induce antitumor responses in nearly 60% of patients with advanced V600E/KBRAF melanomas. Somatic activating MEK1 mutations are thought to be rare in melanomas, but their potential concurrence with V600E/KBRAF may be selected for by BRAFi. We sequenced MEK1/2 exon 3 in melanomas at baseline and upon disease progression. Of 31 baseline V600E/KBRAF melanomas, 5 (16%) carried concurrent somatic BRAF/MEK1 activating mutations. Three of 5 patients with BRAF/MEK1 double-mutant baseline melanomas showed objective tumor responses, consistent with the overall 60% frequency. No MEK1 mutation was found in disease progression melanomas, except when it was already identified at baseline. MEK1-mutant expression in V600E/KBRAF melanoma cell lines resulted in no significant alterations in p-ERK1/2 levels or growth-inhibitory sensitivities to BRAFi, MEK1/2 inhibitor (MEKi), or their combination. Thus, activating MEK1 exon 3 mutations identified herein and concurrent with V600E/KBRAF do not cause BRAFi resistance in melanoma. SIGNIFICANCE As BRAF inhibitors gain widespread use for treatment of advanced melanoma, biomarkers for drug sensitivity or resistance are urgently needed. We identify here concurrent activating mutations in BRAF and MEK1 in melanomas and show that the presence of a downstream mutation in MEK1 does not necessarily make BRAF–mutant melanomas resistant to BRAF inhibitors.
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Affiliation(s)
- Hubing Shi
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California 90095-1750, USA
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28
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Chan E, Patel R, Nallur S, Ratner E, Bacchiocchi A, Hoyt K, Szpakowski S, Godshalk S, Ariyan S, Sznol M, Halaban R, Krauthammer M, Tuck D, Slack FJ, Weidhaas JB. MicroRNA signatures differentiate melanoma subtypes. Cell Cycle 2011; 10:1845-52. [PMID: 21543894 DOI: 10.4161/cc.10.11.15777] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Melanoma is an aggressive cancer that is highly resistance to therapies once metastasized. We studied microRNA (miRNA) expression in clinical melanoma subtypes and evaluated different miRNA signatures in the background of gain of function somatic and inherited mutations associated with melanoma. Total RNA from 42 patient derived primary melanoma cell lines and three independent normal primary melanocyte cell cultures was evaluated by miRNA array. MiRNA expression was then analyzed comparing subtypes and additional clinicopathologic criteria including somatic mutations. The prevalence and association of an inherited variant in a miRNA binding site in the 3'UTR of the KRAS oncogene, referred to as the KRAS-variant, was also evaluated. We show that seven miRNAs, miR-142-3p, miR-486, miR-214, miR-218, miR-362, miR-650 and miR-31, were significantly correlated with acral as compared to non-acral melanomas (p < 0.04). In addition, we discovered that the KRAS-variant was enriched in non-acral melanoma (25%), and that miR-137 under expression was significantly associated with melanomas with the KRAS-variant. Our findings indicate that miRNAs are differentially expressed in melanoma subtypes and that their misregulation can be impacted by inherited gene variants, supporting the hypothesis that miRNA misregulation reflects biological differences in melanoma.
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Affiliation(s)
- Elcie Chan
- Yale University School of Medicine, New Haven, CT, USA
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29
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Parisi F, Ariyan S, Narayan D, Bacchiocchi A, Hoyt K, Cheng E, Xu F, Li P, Halaban R, Kluger Y. Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies. BMC Genomics 2011; 12:230. [PMID: 21569352 PMCID: PMC3114747 DOI: 10.1186/1471-2164-12-230] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 05/11/2011] [Indexed: 12/15/2022] Open
Abstract
Background Genomic aberrations can be used to determine cancer diagnosis and prognosis. Clinically relevant novel aberrations can be discovered using high-throughput assays such as Single Nucleotide Polymorphism (SNP) arrays and next-generation sequencing, which typically provide aggregate signals of many cells at once. However, heterogeneity of tumor subclones dramatically complicates the task of detecting aberrations. Results The aggregate signal of a population of subclones can be described as a linear system of equations. We employed a measure of allelic imbalance and total amount of DNA to characterize each locus by the copy number status (gain, loss or neither) of the strongest subclonal component. We designed simulated data to compare our measure to existing approaches and we analyzed SNP-arrays from 30 melanoma samples and transcriptome sequencing (RNA-Seq) from one melanoma sample. We showed that any system describing aggregate subclonal signals is underdetermined, leading to non-unique solutions for the exact copy number profile of subclones. For this reason, our illustrative measure was more robust than existing Hidden Markov Model (HMM) based tools in inferring the aberration status, as indicated by tests on simulated data. This higher robustness contributed in identifying numerous aberrations in several loci of melanoma samples. We validated the heterogeneity and aberration status within single biopsies by fluorescent in situ hybridization of four affected and transcriptionally up-regulated genes E2F8, ETV4, EZH2 and FAM84B in 11 melanoma cell lines. Heterogeneity was further demonstrated in the analysis of allelic imbalance changes along single exons from melanoma RNA-Seq. Conclusions These studies demonstrate how subclonal heterogeneity, prevalent in tumor samples, is reflected in aggregate signals measured by high-throughput techniques. Our proposed approach yields high robustness in detecting copy number alterations using high-throughput technologies and has the potential to identify specific subclonal markers from next-generation sequencing data.
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Affiliation(s)
- Fabio Parisi
- Department of Pathology and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
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30
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Tworkoski K, Singhal G, Szpakowski S, Zito CI, Bacchiocchi A, Muthusamy V, Bosenberg M, Krauthammer M, Halaban R, Stern DF. Phosphoproteomic screen identifies potential therapeutic targets in melanoma. Mol Cancer Res 2011; 9:801-12. [PMID: 21521745 DOI: 10.1158/1541-7786.mcr-10-0512] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Therapies directed against receptor tyrosine kinases are effective in many cancer subtypes, including lung and breast cancer. We used a phosphoproteomic platform to identify active receptor tyrosine kinases that might represent therapeutic targets in a panel of 25 melanoma cell strains. We detected activated receptors including TYRO3, AXL, MERTK, EPHB2, MET, IGF1R, EGFR, KIT, HER3, and HER4. Statistical analysis of receptor tyrosine kinase activation as well as ligand and receptor expression indicates that some receptors, such as FGFR3, may be activated via autocrine circuits. Short hairpin RNA knockdown targeting three of the active kinases identified in the screen, AXL, HER3, and IGF1R, inhibited the proliferation of melanoma cells and knockdown of active AXL also reduced melanoma cell migration. The changes in cellular phenotype observed on AXL knockdown seem to be modulated via the STAT3 signaling pathway, whereas the IGF1R-dependent alterations seem to be regulated by the AKT signaling pathway. Ultimately, this study identifies several novel targets for therapeutic intervention in melanoma.
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Affiliation(s)
- Kathryn Tworkoski
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
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31
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Kluger HM, Hoyt K, Bacchiocchi A, Mayer T, Kirsch J, Kluger Y, Sznol M, Ariyan S, Molinaro A, Halaban R. Plasma markers for identifying patients with metastatic melanoma. Clin Cancer Res 2011; 17:2417-25. [PMID: 21487066 DOI: 10.1158/1078-0432.ccr-10-2402] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE With the rising incidence of melanoma, more patients are undergoing surveillance for disease recurrence. Our purpose was to study levels of proteins that might be secreted in the blood of patients with metastatic melanoma that can be used for monitoring these individuals. METHODS Genome-wide gene expression data were used to identify abundantly expressed genes in melanoma cells that encode for proteins likely to be present in the blood of cancer patients, based on high expression levels in tumors. ELISA assays were employed to measure proteins in plasma of 216 individuals; 108 metastatic melanoma patients and 108 age- and gender-matched patients with resected stage I/II disease split into equal-sized training and test cohorts. RESULTS Levels of seven markers, CEACAM (carcinoembryonic antigen-related cell adhesion molecule), ICAM-1 (intercellular adhesion molecule 1), osteopontin, MIA (melanoma inhibitory activity), GDF-15 (growth differentiation factor 15), TIMP-1 (tissue inhibitor of metalloproteinase 1), and S100B, were higher in patients with unresected stage IV disease than in patients with resected stage I/II disease. About 81% of the stage I/II patients in the training set had no marker elevation, whereas 69% of the stage IV patients had elevation of at least one marker (P < 0.0001). Receiver operating characteristic curves for the markers in combination in these two patient populations had an area under curve (AUC) of 0.79 in the training set and 0.8 in the test set. A CART (Classification and Regression Trees) model developed in the training set further improved the AUC in the test set to 0.898. CONCLUSIONS Plasma markers, particularly when assessed in combination, can be used to monitor patients for disease recurrence and can compliment currently used lactate dehydrogenase and imaging studies; prospective validation is warranted.
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Affiliation(s)
- Harriet M Kluger
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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32
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Godshalk SE, Paranjape T, Nallur S, Speed W, Chan E, Molinaro AM, Bacchiocchi A, Hoyt K, Tworkoski K, Stern DF, Sznol M, Ariyan S, Lazova R, Halaban R, Kidd KK, Weidhaas J, Slack FJ. A Variant in a MicroRNA complementary site in the 3' UTR of the KIT oncogene increases risk of acral melanoma. Oncogene 2011; 30:1542-50. [PMID: 21119596 PMCID: PMC3069149 DOI: 10.1038/onc.2010.536] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 09/15/2010] [Accepted: 10/07/2010] [Indexed: 01/14/2023]
Abstract
MicroRNAs (miRNAs) are small ∼22nt single stranded RNAs that negatively regulate protein expression by binding to partially complementary sequences in the 3' untranslated region (3' UTRs) of target gene messenger RNAs (mRNA). Recently, mutations have been identified in both miRNAs and target genes that disrupt regulatory relationships, contribute to oncogenesis and serve as biomarkers for cancer risk. KIT, an established oncogene with a multifaceted role in melanogenesis and melanoma pathogenesis, has recently been shown to be upregulated in some melanomas, and is also a target of the miRNA miR-221. Here, we describe a genetic variant in the 3' UTR of the KIT oncogene that correlates with a greater than fourfold increased risk of acral melanoma. This KIT variant results in a mismatch in the seed region of a miR-221 complementary site and reporter data suggests that this mismatch can result in increased expression of the KIT oncogene. Consistent with the hypothesis that this is a functional variant, KIT mRNA and protein levels are both increased in the majority of samples harboring the KIT variant. This work identifies a novel genetic marker for increased heritable risk of melanoma.
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Affiliation(s)
- Sirie E. Godshalk
- Department of Molecular, Cellular and Developmental Biology, Yale University
| | - Trupti Paranjape
- Department of Therapeutic Radiology, Yale University School of Medicine
| | - Sunitha Nallur
- Department of Therapeutic Radiology, Yale University School of Medicine
| | - William Speed
- Department of Genetics, Yale University School of Medicine
| | - Elcie Chan
- Department of Therapeutic Radiology, Yale University School of Medicine
| | | | | | - Kathleen Hoyt
- Department of Dermatology, Yale University School of Medicine
| | | | - David F. Stern
- Department of Pathology, Yale University School of Medicine
| | - Mario Sznol
- Section of Medical Oncology, Yale University School of Medicine
| | - Stephan Ariyan
- Department of Surgery, Yale University School of Medicine
| | - Rossitza Lazova
- Department of Dermatology, Yale University School of Medicine
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine
| | | | - Joanne Weidhaas
- Department of Therapeutic Radiology, Yale University School of Medicine
| | - Frank J. Slack
- Department of Molecular, Cellular and Developmental Biology, Yale University
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33
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Rubinstein JC, Sznol M, Pavlick AC, Ariyan S, Cheng E, Bacchiocchi A, Kluger HM, Narayan D, Halaban R. Incidence of the V600K mutation among melanoma patients with BRAF mutations, and potential therapeutic response to the specific BRAF inhibitor PLX4032. J Transl Med 2010; 8:67. [PMID: 20630094 PMCID: PMC2917408 DOI: 10.1186/1479-5876-8-67] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 07/14/2010] [Indexed: 11/24/2022] Open
Abstract
Activating mutations in BRAF kinase are common in melanomas. Clinical trials with PLX4032, the mutant-BRAF inhibitor, show promising preliminary results in patients selected for the presence of V600E mutation. However, activating V600K mutation is the other most common mutation, yet patients with this variant are currently excluded from the PLX4032 trials. Here we present evidence that a patient bearing the BRAF V600K mutation responded remarkably to PLX4032, suggesting that clinical trials should include all patients with activating BRAF V600E/K mutations.
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Affiliation(s)
- Jill C Rubinstein
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
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34
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Halaban R, Zhang W, Bacchiocchi A, Cheng E, Parisi F, Ariyan S, Krauthammer M, McCusker JP, Kluger Y, Sznol M. PLX4032, a selective BRAF(V600E) kinase inhibitor, activates the ERK pathway and enhances cell migration and proliferation of BRAF melanoma cells. Pigment Cell Melanoma Res 2010; 23:190-200. [PMID: 20149136 PMCID: PMC2848976 DOI: 10.1111/j.1755-148x.2010.00685.x] [Citation(s) in RCA: 264] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BRAFV600E/K is a frequent mutationally active tumor-specific kinase in melanomas that is currently targeted for therapy by the specific inhibitor PLX4032. Our studies with melanoma tumor cells that are BRAFV600E/K and BRAFWT showed that, paradoxically, while PLX4032 inhibited ERK1/2 in the highly sensitive BRAFV600E/K, it activated the pathway in the resistant BRAFWT cells, via RAF1 activation, regardless of the status of mutations in NRAS or PTEN. The persistently active ERK1/2 triggered downstream effectors in BRAFWT melanoma cells and induced changes in the expression of a wide-spectrum of genes associated with cell cycle control. Furthermore, PLX4032 increased the rate of proliferation of growth factor-dependent NRAS Q61L mutant primary melanoma cells, reduced cell adherence and increased mobility of cells from advanced lesions. The results suggest that the drug can confer an advantage to BRAFWT primary and metastatic tumor cells in vivo and provide markers for monitoring clinical responses.
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Affiliation(s)
- Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA.
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Halaban R, Krauthammer M, Pelizzola M, Cheng E, Kovacs D, Sznol M, Ariyan S, Narayan D, Bacchiocchi A, Molinaro A, Kluger Y, Deng M, Tran N, Zhang W, Picardo M, Enghild JJ. Integrative analysis of epigenetic modulation in melanoma cell response to decitabine: clinical implications. PLoS One 2009; 4:e4563. [PMID: 19234609 PMCID: PMC2642998 DOI: 10.1371/journal.pone.0004563] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2008] [Accepted: 01/06/2009] [Indexed: 12/31/2022] Open
Abstract
Decitabine, an epigenetic modifier that reactivates genes otherwise suppressed by DNA promoter methylation, is effective for some, but not all cancer patients, especially those with solid tumors. It is commonly recognized that to overcome resistance and improve outcome, treatment should be guided by tumor biology, which includes genotype, epigenotype, and gene expression profile. We therefore took an integrative approach to better understand melanoma cell response to clinically relevant dose of decitabine and identify complementary targets for combined therapy. We employed eight different melanoma cell strains, determined their growth, apoptotic and DNA damage responses to increasing doses of decitabine, and chose a low, clinically relevant drug dose to perform whole-genome differential gene expression, bioinformatic analysis, and protein validation studies. The data ruled out the DNA damage response, demonstrated the involvement of p21(Cip1) in a p53-independent manner, identified the TGFbeta pathway genes CLU and TGFBI as markers of sensitivity to decitabine and revealed an effect on histone modification as part of decitabine-induced gene expression. Mutation analysis and knockdown by siRNA implicated activated beta-catenin/MITF, but not BRAF, NRAS or PTEN mutations as a source for resistance. The importance of protein stability predicted from the results was validated by the synergistic effect of Bortezomib, a proteasome inhibitor, in enhancing the growth arrest of decitabine in otherwise resistant melanoma cells. Our integrative analysis show that improved therapy can be achieved by comprehensive analysis of cancer cells, identified biomarkers for patient's selection and monitoring response, as well as targets for improved combination therapy.
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Affiliation(s)
- Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, United States of America.
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Wickens P, Kluender H, Dixon J, Brennan C, Achebe F, Bacchiocchi A, Bankston D, Bierer D, Brands M, Braun D, Brown MS, Chuang CY, Dumas J, Enyedy I, Hofilena G, Hong Z, Housley T, Jones B, Khire U, Kreiman C, Kumarasinghe E, Lowinger T, Ott-Morgan R, Perkins L, Phillips B, Schoenleber R, Scott WJ, Sheeler R, Redman A, Sun X, Taylor I, Wang L, Wilhelm S, Zhang X, Zhang M, Sullivan E, Carter C, Miglarese M, Levy J. SAR of a novel ‘Anthranilamide Like’ series of VEGFR-2, multi protein kinase inhibitors for the treatment of cancer. Bioorg Med Chem Lett 2007; 17:4378-81. [PMID: 17574417 DOI: 10.1016/j.bmcl.2007.02.075] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 02/23/2007] [Accepted: 02/26/2007] [Indexed: 11/29/2022]
Abstract
Novel anthranilamides were surprisingly found to exert additional activity on B-RAF. Corresponding thiophene, pyrazole, and thiazole core analogs were prepared as VEGFR-2 inhibitors with c-KIT, and B-RAF activity. Compounds in the phenyl, thiophene, and thiazole series are in vivo active.
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Affiliation(s)
- Philip Wickens
- Department of Chemistry Research, Bayer Research Center, 400 Morgan Lane, West Haven, CT 06516, USA.
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