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Zheng XQ, Guo JP, Yang H, Kanai M, He LL, Li YY, Koomen JM, Minton S, Gao M, Ren XB, Coppola D, Cheng JQ. Retraction Note: Aurora-A is a determinant of tamoxifen sensitivity through phosphorylation of ERα in breast cancer. Oncogene 2024; 43:1160. [PMID: 38396296 PMCID: PMC11036404 DOI: 10.1038/s41388-024-02983-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Affiliation(s)
- X Q Zheng
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
- Departments of Thyroid and Neck Tumour, Tianjin Medical University Cancer Institute and Hospital, Oncology Key Laboratory of cancer prevention and therapy, National Clinical Research Center of Cancer, Tianjin, PR China
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Oncology Key Laboratory of cancer prevention and therapy, National Clinical Research Center of Cancer, Tianjin, PR China
| | - J P Guo
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - H Yang
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - M Kanai
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - L L He
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Y Y Li
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - J M Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - S Minton
- Departments of Women's Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - M Gao
- Departments of Thyroid and Neck Tumour, Tianjin Medical University Cancer Institute and Hospital, Oncology Key Laboratory of cancer prevention and therapy, National Clinical Research Center of Cancer, Tianjin, PR China
| | - X B Ren
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Oncology Key Laboratory of cancer prevention and therapy, National Clinical Research Center of Cancer, Tianjin, PR China
| | - D Coppola
- Departments of Women's Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - J Q Cheng
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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2
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Liao Y, Remsing Rix LL, Li X, Fang B, Izumi V, Welsh EA, Monastyrskyi A, Haura EB, Koomen JM, Doebele RC, Rix U. Differential network analysis of ROS1 inhibitors reveals lorlatinib polypharmacology through co-targeting PYK2. Cell Chem Biol 2024; 31:284-297.e10. [PMID: 37848034 PMCID: PMC10922442 DOI: 10.1016/j.chembiol.2023.09.011] [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: 01/30/2023] [Revised: 08/02/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]
Abstract
Multiple tyrosine kinase inhibitors (TKIs) are often developed for the same indication. However, their relative overall efficacy is frequently incompletely understood and they may harbor unrecognized targets that cooperate with the intended target. We compared several ROS1 TKIs for inhibition of ROS1-fusion-positive lung cancer cell viability, ROS1 autophosphorylation and kinase activity, which indicated disproportionately higher cellular potency of one TKI, lorlatinib. Quantitative chemical and phosphoproteomics across four ROS1 TKIs and differential network analysis revealed that lorlatinib uniquely impacted focal adhesion signaling. Functional validation using pharmacological probes, RNA interference, and CRISPR-Cas9 knockout uncovered a polypharmacology mechanism of lorlatinib by dual targeting ROS1 and PYK2, which form a multiprotein complex with SRC. Rational multi-targeting of this complex by combining lorlatinib with SRC inhibitors exhibited pronounced synergy. Taken together, we show that systems pharmacology-based differential network analysis can dissect mixed canonical/non-canonical polypharmacology mechanisms across multiple TKIs enabling the design of rational drug combinations.
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Affiliation(s)
- Yi Liao
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Lily L Remsing Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Xueli Li
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Victoria Izumi
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric A Welsh
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Andrii Monastyrskyi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - John M Koomen
- Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA; Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Robert C Doebele
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA.
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3
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Liu Q, Adhikari E, Lester DK, Fang B, Johnson JO, Tian Y, Mockabee-Macias AT, Izumi V, Guzman KM, White MG, Koomen JM, Wargo JA, Messina JL, Qi J, Lau EK. Androgen drives melanoma invasiveness and metastatic spread by inducing tumorigenic fucosylation. Nat Commun 2024; 15:1148. [PMID: 38326303 PMCID: PMC10850104 DOI: 10.1038/s41467-024-45324-w] [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: 07/28/2023] [Accepted: 01/18/2024] [Indexed: 02/09/2024] Open
Abstract
Melanoma incidence and mortality rates are historically higher for men than women. Although emerging studies have highlighted tumorigenic roles for the male sex hormone androgen and its receptor (AR) in melanoma, cellular and molecular mechanisms underlying these sex-associated discrepancies are poorly defined. Here, we delineate a previously undisclosed mechanism by which androgen-activated AR transcriptionally upregulates fucosyltransferase 4 (FUT4) expression, which drives melanoma invasiveness by interfering with adherens junctions (AJs). Global phosphoproteomic and fucoproteomic profiling, coupled with in vitro and in vivo functional validation, further reveal that AR-induced FUT4 fucosylates L1 cell adhesion molecule (L1CAM), which is required for FUT4-increased metastatic capacity. Tumor microarray and gene expression analyses demonstrate that AR-FUT4-L1CAM-AJs signaling correlates with pathological staging in melanoma patients. By delineating key androgen-triggered signaling that enhances metastatic aggressiveness, our findings help explain sex-associated clinical outcome disparities and highlight AR/FUT4 and its effectors as potential prognostic biomarkers and therapeutic targets in melanoma.
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Affiliation(s)
- Qian Liu
- Department of Tumor Microenvironment and Metastasis, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
- Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Emma Adhikari
- Department of Tumor Microenvironment and Metastasis, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
- Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Daniel K Lester
- Department of Tumor Microenvironment and Metastasis, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
- Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Joseph O Johnson
- Analytic Microscopy Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Yijun Tian
- Department of Tumor Microenvironment and Metastasis, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Andrea T Mockabee-Macias
- Department of Tumor Microenvironment and Metastasis, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
- Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Victoria Izumi
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Kelly M Guzman
- Analytic Microscopy Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Michael G White
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - John M Koomen
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Jane L Messina
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jianfei Qi
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Eric K Lau
- Department of Tumor Microenvironment and Metastasis, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
- Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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4
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Jimenez J, Dubey P, Carter B, Koomen JM, Markowitz J. A metabolic perspective on nitric oxide function in melanoma. Biochim Biophys Acta Rev Cancer 2024; 1879:189038. [PMID: 38061664 DOI: 10.1016/j.bbcan.2023.189038] [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: 07/19/2023] [Revised: 10/17/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
Nitric oxide (NO) generated from nitric oxide synthase (NOS) exerts a dichotomous effect in melanoma, suppressing or promoting tumor progression. This dichotomy is thought to depend on the intracellular NO concentration and the cell type in which it is generated. Due to its central role in the metabolism of multiple critical constituents involved in signaling and stress, it is crucial to explore NO's contribution to the metabolic dysfunction of melanoma. This review will discuss many known metabolites linked to NO production in melanoma. We discuss the synthesis of these metabolites, their role in biochemical pathways, and how they alter the biological processes observed in the melanoma tumor microenvironment. The metabolic pathways altered by NO and the corresponding metabolites reinforce its dual role in melanoma and support investigating this effect for potential avenues of therapeutic intervention.
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Affiliation(s)
- John Jimenez
- Department of Cutaneous Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Oncologic Sciences, University of South Florida Morsani School of Medicine, Tampa, FL 33612, USA
| | - Parul Dubey
- Department of Cutaneous Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Bethany Carter
- Department of Cutaneous Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Flow Cytometry Core Facility, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - John M Koomen
- Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Joseph Markowitz
- Department of Cutaneous Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Oncologic Sciences, University of South Florida Morsani School of Medicine, Tampa, FL 33612, USA.
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5
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Adhikari E, Liu Q, Johnson J, Stewart P, Marusyk V, Fang B, Izumi V, Bowers K, Guzman KM, Koomen JM, Marusyk A, Lau EK. Brain metastasis-associated fibroblasts secrete fucosylated PVR/CD155 that induces breast cancer invasion. Cell Rep 2023; 42:113463. [PMID: 37995180 DOI: 10.1016/j.celrep.2023.113463] [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: 05/22/2023] [Revised: 09/19/2023] [Accepted: 11/03/2023] [Indexed: 11/25/2023] Open
Abstract
Brain metastasis cancer-associated fibroblasts (bmCAFs) are emerging as crucial players in the development of breast cancer brain metastasis (BCBM), but our understanding of the underlying molecular mechanisms is limited. In this study, we aim to elucidate the pathological contributions of fucosylation (the post-translational modification of proteins by the dietary sugar L-fucose) to tumor-stromal interactions that drive the development of BCBM. Here, we report that patient-derived bmCAFs secrete high levels of polio virus receptor (PVR), which enhance the invasive capacity of BC cells. Mechanistically, we find that HIF1α transcriptionally upregulates fucosyltransferase 11, which fucosylates PVR, triggering its secretion from bmCAFs. Global phosphoproteomic analysis of BC cells followed by functional verification identifies cell-cell junction and actin cytoskeletal signaling as modulated by bmCAF-secreted, -fucosylated PVR. Our findings delineate a hypoxia- and fucosylation-regulated mechanism by which bmCAFs contribute to the invasiveness of BCBM in the brain.
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Affiliation(s)
- Emma Adhikari
- Department of Tumor Microenvironment & Metastasis, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL 33612, USA; Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Qian Liu
- Department of Tumor Microenvironment & Metastasis, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL 33612, USA; Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Joseph Johnson
- Department of Analytic Microscopy, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Paul Stewart
- Biostatistics and Bioinformatics Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Viktoriya Marusyk
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Victoria Izumi
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Kiah Bowers
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Kelly M Guzman
- Department of Analytic Microscopy, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - John M Koomen
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Andriy Marusyk
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric K Lau
- Department of Tumor Microenvironment & Metastasis, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
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6
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Khaled ML, Ren Y, Kundalia R, Alhaddad H, Chen Z, Wallace GC, Evernden B, Ospina OE, Hall M, Liu M, Darville LN, Izumi V, Chen YA, Pilon-Thomas S, Stewart PA, Koomen JM, Corallo SA, Jain MD, Robinson TJ, Locke FL, Forsyth PA, Smalley I. Branched-chain keto acids promote an immune-suppressive and neurodegenerative microenvironment in leptomeningeal disease. bioRxiv 2023:2023.12.18.572239. [PMID: 38187773 PMCID: PMC10769272 DOI: 10.1101/2023.12.18.572239] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Leptomeningeal disease (LMD) occurs when tumors seed into the leptomeningeal space and cerebrospinal fluid (CSF), leading to severe neurological deterioration and poor survival outcomes. We utilized comprehensive multi-omics analyses of CSF from patients with lymphoma LMD to demonstrate an immunosuppressive cellular microenvironment and identified dysregulations in proteins and lipids indicating neurodegenerative processes. Strikingly, we found a significant accumulation of toxic branched-chain keto acids (BCKA) in the CSF of patients with LMD. The BCKA accumulation was found to be a pan-cancer occurrence, evident in lymphoma, breast cancer, and melanoma LMD patients. Functionally, BCKA disrupted the viability and function of endogenous T lymphocytes, chimeric antigen receptor (CAR) T cells, neurons, and meningeal cells. Treatment of LMD mice with BCKA-reducing sodium phenylbutyrate significantly improved neurological function, survival outcomes, and efficacy of anti-CD19 CAR T cell therapy. This is the first report of BCKA accumulation in LMD and provides preclinical evidence that targeting these toxic metabolites improves outcomes.
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Affiliation(s)
- Mariam Lotfy Khaled
- The Department of Metabolism and Physiology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Egypt
| | - Yuan Ren
- The Department of Metabolism and Physiology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Ronak Kundalia
- The Department of Metabolism and Physiology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Hasan Alhaddad
- The Department of Metabolism and Physiology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Zhihua Chen
- Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Gerald C. Wallace
- Department of Hematology/Oncology, Georgia Cancer Center at Medical College of Georgia, Augusta, GA, USA
| | - Brittany Evernden
- Department of Neuro Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Oscar E. Ospina
- Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - MacLean Hall
- Department of Immunology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Min Liu
- The Proteomics and Metabolomics Core, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Lancia N.F. Darville
- The Proteomics and Metabolomics Core, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Victoria Izumi
- The Proteomics and Metabolomics Core, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Y. Ann Chen
- Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Shari Pilon-Thomas
- Department of Immunology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Paul A. Stewart
- Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - John M. Koomen
- The Proteomics and Metabolomics Core, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
- Department of Molecular Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Salvatore A. Corallo
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Michael D. Jain
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Timothy J. Robinson
- Therapeutic Radiology, Smilow Cancer Hospital at Yale New Haven, 35 Park Street, New Haven, CT, USA
| | - Fredrick L. Locke
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Peter A. Forsyth
- Department of Neuro Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
- The Department of Tumor Biology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Inna Smalley
- The Department of Metabolism and Physiology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
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7
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Burger KL, Fernandez MR, Meads MB, Sudalagunta P, Oliveira PS, Renatino Canevarolo R, Alugubelli RR, Tungsevik A, De Avila G, Silva M, Graeter AI, Dai HA, Vincelette ND, Prabhu A, Magaletti D, Yang C, Li W, Kulkarni A, Hampton O, Koomen JM, Roush WR, Monastyrskyi A, Berglund AE, Silva AS, Cleveland JL, Shain KH. CK1δ and CK1ε Signaling Sustains Mitochondrial Metabolism and Cell Survival in Multiple Myeloma. Cancer Res 2023; 83:3901-3919. [PMID: 37702657 PMCID: PMC10690099 DOI: 10.1158/0008-5472.can-22-2350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/24/2022] [Revised: 06/09/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023]
Abstract
Multiple myeloma remains an incurable malignancy due to acquisition of intrinsic programs that drive therapy resistance. Here we report that casein kinase-1δ (CK1δ) and CK1ε are therapeutic targets in multiple myeloma that are necessary to sustain mitochondrial metabolism. Specifically, the dual CK1δ/CK1ε inhibitor SR-3029 had potent in vivo and ex vivo anti-multiple myeloma activity, including against primary multiple myeloma patient specimens. RNA sequencing (RNA-seq) and metabolic analyses revealed inhibiting CK1δ/CK1ε disables multiple myeloma metabolism by suppressing genes involved in oxidative phosphorylation (OxPhos), reducing citric acid cycle intermediates, and suppressing complexes I and IV of the electron transport chain. Finally, sensitivity of multiple myeloma patient specimens to SR-3029 correlated with elevated expression of mitochondrial genes, and RNA-seq from 687 multiple myeloma patient samples revealed that increased CSNK1D, CSNK1E, and OxPhos genes correlate with disease progression and inferior outcomes. Thus, increases in mitochondrial metabolism are a hallmark of multiple myeloma progression that can be disabled by targeting CK1δ/CK1ε. SIGNIFICANCE CK1δ and CK1ε are attractive therapeutic targets in multiple myeloma whose expression increases with disease progression and connote poor outcomes, and that are necessary to sustain expression of genes directing OxPhos.
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Affiliation(s)
- Karen L. Burger
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Mario R. Fernandez
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Mark B. Meads
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Praneeth Sudalagunta
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Paula S. Oliveira
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Rafael Renatino Canevarolo
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | | | - Alexandre Tungsevik
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Gabe De Avila
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Maria Silva
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Allison I. Graeter
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | | | - Nicole D. Vincelette
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Antony Prabhu
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Dario Magaletti
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Chunying Yang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Weimin Li
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | | | | | - John M. Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | | | - Andrii Monastyrskyi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Anders E. Berglund
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Ariosto S. Silva
- Department of Metabolism & Physiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - John L. Cleveland
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Kenneth H. Shain
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
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8
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Emmons MF, Bennett RL, Riva A, Gupta K, Carvalho LADC, Zhang C, Macaulay R, Dupéré-Richér D, Fang B, Seto E, Koomen JM, Li J, Chen YA, Forsyth PA, Licht JD, Smalley KSM. HDAC8-mediated inhibition of EP300 drives a transcriptional state that increases melanoma brain metastasis. Nat Commun 2023; 14:7759. [PMID: 38030596 PMCID: PMC10686983 DOI: 10.1038/s41467-023-43519-1] [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: 08/24/2022] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
Melanomas can adopt multiple transcriptional states. Little is known about the epigenetic drivers of these cell states, limiting our ability to regulate melanoma heterogeneity. Here, we identify stress-induced HDAC8 activity as driving melanoma brain metastasis development. Exposure of melanocytes and melanoma cells to multiple stresses increases HDAC8 activation leading to a neural crest-stem cell transcriptional state and an amoeboid, invasive phenotype that increases seeding to the brain. Using ATAC-Seq and ChIP-Seq we show that increased HDAC8 activity alters chromatin structure by increasing H3K27ac and enhancing accessibility at c-Jun binding sites. Functionally, HDAC8 deacetylates the histone acetyltransferase EP300, causing its enzymatic inactivation. This, in turn, increases binding of EP300 to Jun-transcriptional sites and decreases binding to MITF-transcriptional sites. Inhibition of EP300 increases melanoma cell invasion, resistance to stress and increases melanoma brain metastasis development. HDAC8 is identified as a mediator of transcriptional co-factor inactivation and chromatin accessibility that drives brain metastasis.
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Affiliation(s)
- Michael F Emmons
- Department of Tumor Biology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Richard L Bennett
- UF Health Cancer Center, 2033 Mowry Road, University of Florida, Gainesville, FL, 32610, USA
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, 2033 Mowry Road, Gainesville, FL, 32610, USA
| | - Kanchan Gupta
- UF Health Cancer Center, 2033 Mowry Road, University of Florida, Gainesville, FL, 32610, USA
| | | | - Chao Zhang
- Department of Tumor Biology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Robert Macaulay
- Department of Neuro-Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Daphne Dupéré-Richér
- UF Health Cancer Center, 2033 Mowry Road, University of Florida, Gainesville, FL, 32610, USA
| | - Bin Fang
- Proteomics & Metabolomics Core, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Edward Seto
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, George Washington Cancer Center, George Washington University, 2300 Eye Street, Washington, DC, 20037, USA
| | - John M Koomen
- Department of Molecular Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Jiannong Li
- Department of Bioinformatics and Biostatistics, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Y Ann Chen
- Department of Bioinformatics and Biostatistics, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Peter A Forsyth
- Department of Neuro-Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Jonathan D Licht
- UF Health Cancer Center, 2033 Mowry Road, University of Florida, Gainesville, FL, 32610, USA
| | - Keiran S M Smalley
- Department of Tumor Biology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
- Department of Cutaneous Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
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9
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Yaghjyan L, Mai V, Darville LNF, Cline J, Wang X, Ukhanova M, Tagliamonte MS, Martinez YC, Rich SN, Koomen JM, Egan KM. Associations of gut microbiome with endogenous estrogen levels in healthy postmenopausal women. Cancer Causes Control 2023; 34:873-881. [PMID: 37286847 DOI: 10.1007/s10552-023-01728-5] [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: 01/17/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023]
Abstract
PURPOSE The gut microbiome is a potentially important contributor to endogenous estrogen levels after menopause. In healthy postmenopausal women, we examined associations of fecal microbiome composition with levels of urinary estrogens, their metabolites, and relevant metabolic pathway ratios implicated in breast cancer risk. METHODS Eligible postmenopausal women (n = 164) had a body mass index (BMI) ≤ 35 kg/m2 and no history of hormone use (previous 6 months) or cancer/metabolic disorders. Estrogens were quantified in spot urine samples with liquid chromatography-high resolution mass spectrometry (corrected for creatinine). Bacterial DNA was isolated from fecal samples and the V1-V2 hypervariable regions of 16S rRNA were sequenced on the Illumina MiSeq platform. We examined associations of gut microbiome's indices of within-sample (alpha) diversity (i.e., Shannon, Chao1, and Inverse Simpson), phylogenetic diversity, and the ratio of the two main phyla (Firmicutes and Bacteroidetes; F/B ratio) with individual estrogens and metabolic ratios, adjusted for age and BMI. RESULTS In this sample of 164 healthy postmenopausal women, the mean age was 62.9 years (range 47.0-86.0). We found significant inverse associations of observed species with 4-pathway:total estrogens (p = 0.04) and 4-pathway:2-pathway (p = 0.01). Shannon index was positively associated with 2-catechols: methylated 2-catechols (p = 0.04). Chao1 was inversely associated with E1:total estrogens (p = 0.04), and 4-pathway:2-pathway (p = 0.02) and positively associated with 2-pathway:parent estrogens (p = 0.01). Phylogenetic diversity was inversely associated with 4-pathway:total estrogens (p = 0.02), 4-pathway:parent estrogens (p = 0.03), 4-pathway:2-pathway (p = 0.01), and 4-pathway:16-pathway (p = 0.03) and positively associated with 2-pathway:parent estrogens (p = 0.01). F/B ratio was not associated with any of the estrogen measures. CONCLUSION Microbial diversity was associated with several estrogen metabolism ratios implicated in breast cancer risk. Further studies are warranted to confirm these findings in a larger and more representative sample of postmenopausal women, particularly with enrichment of minority participants.
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Affiliation(s)
- Lusine Yaghjyan
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA.
| | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | | | | | | | - Maria Ukhanova
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Massimiliano S Tagliamonte
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | | | - Shannan N Rich
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA
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10
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Elmarsafawi AG, Hesterberg RS, Fernandez MR, Yang C, Darville LN, Liu M, Koomen JM, Phanstiel O, Atkins R, Mullinax JE, Pilon-Thomas SA, Locke FL, Epling-Burnette PK, Cleveland JL. Modulating the polyamine/hypusine axis controls generation of CD8+ tissue-resident memory T cells. JCI Insight 2023; 8:e169308. [PMID: 37581943 PMCID: PMC10561731 DOI: 10.1172/jci.insight.169308] [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: 03/22/2023] [Accepted: 08/08/2023] [Indexed: 08/17/2023] Open
Abstract
Glutaminolysis is a hallmark of the activation and metabolic reprogramming of T cells. Isotopic tracer analyses of antigen-activated effector CD8+ T cells revealed that glutamine is the principal carbon source for the biosynthesis of polyamines putrescine, spermidine, and spermine. These metabolites play critical roles in activation-induced T cell proliferation, as well as for the production of hypusine, which is derived from spermidine and is covalently linked to the translation elongation factor eukaryotic translation initiation factor 5A (eIF5A). Here, we demonstrated that the glutamine/polyamine/hypusine axis controlled the expression of CD69, an important regulator of tissue-resident memory T cells (Trm). Inhibition of this circuit augmented the development of Trm cells ex vivo and in vivo in the BM, a well-established niche for Trm cells. Furthermore, blocking the polyamine/hypusine axis augmented CD69 expression as well as IFN-γ and TNF-α production in (a) human CD8+ T cells from peripheral blood and sarcoma tumor infiltrating lymphocytes and (b) human CD8+ CAR-T cells. Collectively, these findings support the notion that the polyamine-hypusine circuit can be exploited to modulate Trm cells for therapeutic benefit.
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Affiliation(s)
- Aya G. Elmarsafawi
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
- Department of Tumor Biology and
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Rebecca S. Hesterberg
- Department of Tumor Biology and
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
- Cancer Biology PhD Program, University of South Florida, Tampa, Florida, USA
| | | | | | - Lancia N.F. Darville
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Min Liu
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - John M. Koomen
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Otto Phanstiel
- Department of Medical Education, University of Central Florida College of Medicine, Orlando, Florida, USA
| | | | | | - Shari A. Pilon-Thomas
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Frederick L. Locke
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
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11
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Mooradian MJ, Cleary JM, Giobbie-Hurder A, Darville LNF, Parikh A, Buchbinder EI, Cohen JV, Lawrence DP, Shapiro GI, Keer H, Chen HX, Ivy SP, Smalley KSM, Koomen JM, Sullivan RJ. Dose-escalation trial of combination dabrafenib, trametinib, and AT13387 in patients with BRAF-mutant solid tumors. Cancer 2023; 129:1904-1918. [PMID: 37042037 PMCID: PMC10793106 DOI: 10.1002/cncr.34730] [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: 08/04/2022] [Revised: 12/27/2022] [Accepted: 01/04/2023] [Indexed: 04/13/2023]
Abstract
BACKGROUND Combination BRAF and MEK inhibitor therapy is an active regimen in patients who have BRAF V600E-mutated tumors; however, the clinical efficacy of this therapy is limited by resistance. Preclinically, the addition of heat shock protein 90 (HSP90) inhibition improves the efficacy of BRAF inhibitor therapy in both BRAF inhibitor-sensitive and BRAF inhibitor-resistant mutant cell lines. METHODS Cancer Therapy Evaluation Program study 9557 (ClinicalTrials.gov identifier NCT02097225) is a phase 1 study that was designed to assess the safety and efficacy of the small-molecule HSP90 inhibitor, AT13387, in combination with dabrafenib and trametinib in BRAF V600E/K-mutant solid tumors. Correlative analyses evaluated the expression of HSP90 client proteins and chaperones. RESULTS Twenty-two patients with metastatic, BRAF V600E-mutant solid tumors were enrolled using a 3 + 3 design at four dose levels, and 21 patients were evaluable for efficacy assessment. The most common tumor type was colorectal cancer (N = 12). Dose-limiting toxicities occurred in one patient at dose level 3 and in one patient at dose level 4; specifically, myelosuppression and fatigue, respectively. The maximum tolerated dose was oral dabafenib 150 mg twice daily, oral trametinib 2 mg once daily, and intravenous AT13387 260 mg/m2 on days 1, 8, and 15. The best response was a partial response in two patients and stable disease in eight patients, with an overall response rate of 9.5% (90% exact confidence interval [CI], 2%-27%), a disease control rate of 47.6% (90% CI, 29%-67%), and a median overall survival of 5.1 months (90% CI, 3.4-7.6 months). There were no consistent proteomic changes associated with response or resistance, although responders did have reductions in BRAF expression, and epidermal growth factor receptor downregulation using HSP90 inhibition was observed in one patient who had colorectal cancer. CONCLUSIONS HSP90 inhibition combined with BRAF/MEK inhibition was safe and produced evidence of modest disease control in a heavily pretreated population. Additional translational work may identify tumor types and resistance mechanisms that are most sensitive to this approach.
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Affiliation(s)
- Meghan J. Mooradian
- Division of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - James M. Cleary
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Anita Giobbie-Hurder
- Division of Biostatistics, Departments of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Lancia N. F. Darville
- Department of Proteomics and Metabolomics Core, Moffitt Cancer Center, Tampa, Florida, USA
| | - Aparna Parikh
- Division of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Elizabeth I. Buchbinder
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Justine V. Cohen
- Division of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Donald P. Lawrence
- Division of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Geoffrey I. Shapiro
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Harold Keer
- Astex Pharmaceuticals Inc., Pleasanton, California, USA
| | - Helen X. Chen
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, USA
| | - Susan Percy Ivy
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, USA
| | | | - John M. Koomen
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Ryan J. Sullivan
- Division of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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12
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Hu Q, Liao Y, Cao J, Fang B, Yun SY, Kinose F, Haura EB, Lawrence HR, Doebele RC, Koomen JM, Rix U. Differential Chemoproteomics Reveals MARK2/3 as Cell Migration-Relevant Targets of the ALK Inhibitor Brigatinib. Chembiochem 2023; 24:e202200766. [PMID: 36922348 PMCID: PMC10413441 DOI: 10.1002/cbic.202200766] [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: 12/22/2022] [Revised: 03/15/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023]
Abstract
Metastasis poses a major challenge in cancer management, including EML4-ALK-rearranged non-small cell lung cancer (NSCLC). As cell migration is a critical step during metastasis, we assessed the anti-migratory activities of several clinical ALK inhibitors in NSCLC cells and observed differential anti-migratory capabilities despite similar ALK inhibition, with brigatinib displaying superior anti-migratory effects over other ALK inhibitors. Applying an unbiased in situ mass spectrometry-based chemoproteomics approach, we determined the proteome-wide target profile of brigatinib in EML4-ALK+ NSCLC cells. Dose-dependent and cross-competitive chemoproteomics suggested MARK2 and MARK3 as relevant brigatinib kinase targets. Functional validation showed that combined pharmacological inhibition or genetic modulation of MARK2/3 inhibited cell migration. Consistently, brigatinib treatment induced inhibitory YAP1 phosphorylation downstream of MARK2/3. Collectively, our data suggest that brigatinib exhibits unusual cross-phenotype polypharmacology as, despite similar efficacy for inhibiting EML4-ALK-dependent cell proliferation as other ALK inhibitors, it more effectively prevented migration of NSCLC cells due to co-targeting of MARK2/3.
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Affiliation(s)
- Qianqian Hu
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL 33620, USA
| | - Yi Liao
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
| | - Jessica Cao
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
| | - Sang Y. Yun
- Chemical Biology Core (Chemistry Unit), H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
| | - Fumi Kinose
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
| | - Harshani R. Lawrence
- Chemical Biology Core (Chemistry Unit), H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
- Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Robert C. Doebele
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - John M. Koomen
- Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
- Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
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13
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Putty Reddy S, Alontaga AY, Welsh EA, Haura EB, Boyle TA, Eschrich SA, Koomen JM. Deciphering Phenotypes from Protein Biomarkers for Translational Research with PIPER. J Proteome Res 2023. [PMID: 37171072 DOI: 10.1021/acs.jproteome.3c00137] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM) has widespread clinical use for detection of inborn errors of metabolism, therapeutic drug monitoring, and numerous other applications. This technique detects proteolytic peptides as surrogates for protein biomarker expression, mutation, and post-translational modification in individual clinical assays and in cancer research with highly multiplexed quantitation across biological pathways. LC-MRM for protein biomarkers must be translated from multiplexed research-grade panels to clinical use. LC-MRM panels provide the capability to quantify clinical biomarkers and emerging protein markers to establish the context of tumor phenotypes that provide highly relevant supporting information. An application to visualize and communicate targeted proteomics data will empower translational researchers to move protein biomarker panels from discovery to clinical use. Therefore, we have developed a web-based tool for targeted proteomics that provides pathway-level evaluations of key biological drivers (e.g., EGFR signaling), signature scores (representing phenotypes) (e.g., EMT), and the ability to quantify specific drug targets across a sample cohort. This tool represents a framework for integrating summary information, decision algorithms, and risk scores to support Physician-Interpretable Phenotypic Evaluation in R (PIPER) that can be reused or repurposed by other labs to communicate and interpret their own biomarker panels.
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Affiliation(s)
- Sudhir Putty Reddy
- Molecular Oncology, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Aileen Y Alontaga
- Pathology, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Eric A Welsh
- Bioinformatics and Biostatistics, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Eric B Haura
- Thoracic Oncology, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Theresa A Boyle
- Pathology, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - Steven A Eschrich
- Bioinformatics and Biostatistics, Moffitt Cancer Center, Tampa, Florida 33612, United States
| | - John M Koomen
- Molecular Oncology, Moffitt Cancer Center, Tampa, Florida 33612, United States
- Pathology, Moffitt Cancer Center, Tampa, Florida 33612, United States
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14
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Liao Y, Chan SC, Welsh EA, Fang B, Sun L, Schönbrunn E, Koomen JM, Duckett DR, Haura EB, Monastyrskyi A, Rix U. Abstract 3839: Discovery of GSTZ1 as a novel target for drug refractory non-small cell lung cancer by using fragment-based chemical proteomics. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3839] [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: 04/07/2023]
Abstract
Abstract
A subset of non-small cell lung cancer (NSCLC) patients respond poorly to clinical drugs targeting defined oncogenic driver mutations. To improve the efficacy of these drugs in drug refractory NSCLC, the identification of supporting therapeutic targets and discovery of the binding molecules are urgently needed. Photoreactive fragment-like probes can discover target proteins that constitute novel cellular vulnerabilities and provide the chemical basis for drug discovery. However, the rational design of the fragment probe library, target prioritization, and sample throughput are still challenging. We applied a structurally diverse panel of BioCore fragments fully functionalized with orthogonal diazirine and alkyne moieties. These probes were used for protein crosslinking in live cells and subsequent target identification through label-free quantitative LC-MS/MS analysis. High-confidence targets were queried against a pharmacogenomic database (DepMap) and prioritized through multiple cross-comparison with other probes. The top-ranked probe-binding target was validated using a competitive affinity assay, an enzymatic activity assay, and RNA interference. Proteome-wide tyrosine reactivity was profiled using sulfur-triazole exchange chemistry (SuTEx). The tyrosine phosphorylation of proteins was investigated using a pY-100 antibody and western blotting. Using sotorasib-refractory KRAS G12C H1792 lung cancer cells, we identified 932 probe-enriched proteins from panel-wide cross-comparisons suggesting the high potential of exploring the ligandable proteome. We also performed intensive cross-comparison analysis and identified 31 unique high-confidence targets, with glutathione S-transferase zeta 1 (GSTZ1) identified as a unique target of probe 17. We found that high expression of GSTZ1 was significantly associated with poorer NSCLC patient survival. Probe 17 was validated to physically bind to GSTZ1 and inhibit the enzymatic activity of GSTZ1. In addition, GSTZ1 gene knockdown sensitized drug-refractory NSCLC cells with KRAS G12C, FGFR1 amplification, and DDR2 mutation to clinical targeted drugs and induced more cell apoptosis in combination with these targeted drugs. SuTEx proteomics suggests modulation of drug resistance pathways leading to the identification of altered KRAS and FGFR1 tyrosine phosphorylation by GSTZ1, which provides a functional insight into the mechanism of drug sensitization. We developed a chemical biology workflow for the simultaneous discovery of high-confidence targets and their binding probe molecules, such as probe 17 and GSTZ1. GSTZ1 was found to cooperate with oncogenic alterations in supporting refractory NSCLC cell survival signaling, which may form the biological basis for developing novel GSTZ1 inhibitors to improve the therapeutic efficacy of oncogene-directed targeted drugs.
Citation Format: Yi Liao, Sean Chin Chan, Eric A. Welsh, Bin Fang, Luxin Sun, Ernst Schönbrunn, John M. Koomen, Derek R. Duckett, Eric B. Haura, Andrii Monastyrskyi, Uwe Rix. Discovery of GSTZ1 as a novel target for drug refractory non-small cell lung cancer by using fragment-based chemical proteomics. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3839.
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Affiliation(s)
- Yi Liao
- 1Moffitt Cancer Center, Tampa, FL
| | | | | | - Bin Fang
- 1Moffitt Cancer Center, Tampa, FL
| | | | | | | | | | | | | | - Uwe Rix
- 1Moffitt Cancer Center, Tampa, FL
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15
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Liao Y, Chin Chan S, Welsh EA, Fang B, Sun L, Schönbrunn E, Koomen JM, Duckett DR, Haura EB, Monastyrskyi A, Rix U. Chemical Proteomics with Novel Fully Functionalized Fragments and Stringent Target Prioritization Identifies the Glutathione-Dependent Isomerase GSTZ1 as a Lung Cancer Target. ACS Chem Biol 2023; 18:251-264. [PMID: 36630201 DOI: 10.1021/acschembio.2c00587] [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: 01/12/2023]
Abstract
Photoreactive fragment-like probes have been applied to discover target proteins that constitute novel cellular vulnerabilities and to identify viable chemical hits for drug discovery. Through forming covalent bonds, functionalized probes can achieve stronger target engagement and require less effort for on-target mechanism validation. However, the design of probe libraries, which directly affects the biological target space that is interrogated, and effective target prioritization remain critical challenges of such a chemical proteomic platform. In this study, we designed and synthesized a diverse panel of 20 fragment-based probes containing natural product-based privileged structural motifs for small-molecule lead discovery. These probes were fully functionalized with orthogonal diazirine and alkyne moieties and used for protein crosslinking in live lung cancer cells, target enrichment via "click chemistry," and subsequent target identification through label-free quantitative liquid chromatography-tandem mass spectrometry analysis. Pair-wise comparison with a blunted negative control probe and stringent prioritization via individual cross-comparisons against the entire panel identified glutathione S-transferase zeta 1 (GSTZ1) as a specific and unique target candidate. DepMap database query, RNA interference-based gene silencing, and proteome-wide tyrosine reactivity profiling suggested that GSTZ1 cooperated with different oncogenic alterations by supporting survival signaling in refractory non-small cell lung cancer cells. This finding may form the basis for developing novel GSTZ1 inhibitors to improve the therapeutic efficacy of oncogene-directed targeted drugs. In summary, we designed a novel fragment-based probe panel and developed a target prioritization scheme with improved stringency, which allows for the identification of unique target candidates, such as GSTZ1 in refractory lung cancer.
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Affiliation(s)
- Yi Liao
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States
| | - Sean Chin Chan
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States.,Cancer Chemical Biology Ph.D. Program, University of South Florida, Tampa, Florida 33620, United States
| | - Eric A Welsh
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States
| | - Bin Fang
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States
| | - Luxin Sun
- Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States
| | - Ernst Schönbrunn
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States.,Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States
| | - John M Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States.,Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States
| | - Derek R Duckett
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States.,Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States
| | - Andrii Monastyrskyi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States.,Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States.,Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States.,Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States
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16
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Lester DK, Burton C, Gardner A, Innamarato P, Kodumudi K, Liu Q, Adhikari E, Ming Q, Williamson DB, Frederick DT, Sharova T, White MG, Markowitz J, Cao B, Nguyen J, Johnson J, Beatty M, Mockabee-Macias A, Mercurio M, Watson G, Chen PL, McCarthy S, MoranSegura C, Messina J, Thomas KL, Darville L, Izumi V, Koomen JM, Pilon-Thomas SA, Ruffell B, Luca VC, Haltiwanger RS, Wang X, Wargo JA, Boland GM, Lau EK. Fucosylation of HLA-DRB1 regulates CD4 + T cell-mediated anti-melanoma immunity and enhances immunotherapy efficacy. Nat Cancer 2023; 4:222-239. [PMID: 36690875 PMCID: PMC9970875 DOI: 10.1038/s43018-022-00506-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/14/2022] [Indexed: 01/24/2023]
Abstract
Immunotherapy efficacy is limited in melanoma, and combinations of immunotherapies with other modalities have yielded limited improvements but also adverse events requiring cessation of treatment. In addition to ineffective patient stratification, efficacy is impaired by paucity of intratumoral immune cells (itICs); thus, effective strategies to safely increase itICs are needed. We report that dietary administration of L-fucose induces fucosylation and cell surface enrichment of the major histocompatibility complex (MHC)-II protein HLA-DRB1 in melanoma cells, triggering CD4+ T cell-mediated increases in itICs and anti-tumor immunity, enhancing immune checkpoint blockade responses. Melanoma fucosylation and fucosylated HLA-DRB1 associate with intratumoral T cell abundance and anti-programmed cell death protein 1 (PD1) responder status in patient melanoma specimens, suggesting the potential use of melanoma fucosylation as a strategy for stratifying patients for immunotherapies. Our findings demonstrate that fucosylation is a key mediator of anti-tumor immunity and, importantly, suggest that L-fucose is a powerful agent for safely increasing itICs and immunotherapy efficacy in melanoma.
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Affiliation(s)
- Daniel K Lester
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
- Molecular Medicine Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Chase Burton
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
- Molecular Medicine Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alycia Gardner
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Patrick Innamarato
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Krithika Kodumudi
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Qian Liu
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
- Molecular Medicine Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Emma Adhikari
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL, USA
- Molecular Medicine Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Qianqian Ming
- Molecular Medicine Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Daniel B Williamson
- Complex Carbohydrate Research Center, the University of Georgia, Athens, GA, USA
| | | | - Tatyana Sharova
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Michael G White
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph Markowitz
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Biwei Cao
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jonathan Nguyen
- Advanced Analytical and Digital Laboratory, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Joseph Johnson
- Department of Analytic Microscopy, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Matthew Beatty
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Andrea Mockabee-Macias
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Molecular Medicine Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Matthew Mercurio
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Molecular Medicine Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Gregory Watson
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Molecular Medicine Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Pei-Ling Chen
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Susan McCarthy
- Advanced Analytical and Digital Laboratory, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Carlos MoranSegura
- Advanced Analytical and Digital Laboratory, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jane Messina
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Kerry L Thomas
- Department of Diagnostic Imaging, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Lancia Darville
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Victoria Izumi
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - John M Koomen
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Shari A Pilon-Thomas
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Brian Ruffell
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Vincent C Luca
- Molecular Medicine Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Robert S Haltiwanger
- Complex Carbohydrate Research Center, the University of Georgia, Athens, GA, USA
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Genevieve M Boland
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Massachusetts General Hospital, Boston, MA, USA
| | - Eric K Lau
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
- Molecular Medicine Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
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Soupir AC, Tian Y, Stewart PA, Nunez-Lopez YO, Manley BJ, Pellini B, Bloomer AM, Zhang J, Mo Q, Marchion DC, Liu M, Koomen JM, Siegel EM, Wang L. Detectable Lipidomes and Metabolomes by Different Plasma Exosome Isolation Methods in Healthy Controls and Patients with Advanced Prostate and Lung Cancer. Int J Mol Sci 2023; 24:1830. [PMID: 36768152 PMCID: PMC9916336 DOI: 10.3390/ijms24031830] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Circulating exosomes in the blood are promising tools for biomarker discovery in cancer. Due to their heterogeneity, different isolation methods may enrich distinct exosome cargos generating different omic profiles. In this study, we evaluated the effects of plasma exosome isolation methods on detectable multi-omic profiles in patients with non-small cell lung cancer (NSCLC), castration-resistant prostate cancer (CRPC), and healthy controls, and developed an algorithm to quantify exosome enrichment. Plasma exosomes were isolated from CRPC (n = 10), NSCLC (n = 14), and healthy controls (n = 10) using three different methods: size exclusion chromatography (SEC), lectin binding, and T-cell immunoglobulin domain and mucin domain-containing protein 4 (TIM4) binding. Molecular profiles were determined by mass spectrometry of extracted exosome fractions. Enrichment analysis of uniquely detected molecules was performed for each method with MetaboAnalyst. The exosome enrichment index (EEI) scores methods based on top differential molecules between patient groups. The lipidomic analysis detected 949 lipids using exosomes from SEC, followed by 246 from lectin binding and 226 from TIM4 binding. The detectable metabolites showed SEC identifying 191 while lectin binding and TIM4 binding identified 100 and 107, respectively. When comparing uniquely detected molecules, different methods showed preferential enrichment of different sets of molecules with SEC enriching the greatest diversity. Compared to controls, SEC identified 28 lipids showing significant difference in NSCLC, while only 1 metabolite in NSCLC and 5 metabolites in CRPC were considered statistically significant (FDR < 0.1). Neither lectin-binding- nor TIM4-binding-derived exosome lipids or metabolites demonstrated significant differences between patient groups. We observed the highest EEI from SEC in lipids (NSCLC: 871.33) which was also noted in metabolites. These results support that the size exclusion method of exosome extraction implemented by SBI captures more heterogeneous exosome populations. In contrast, lectin-binding and TIM4-binding methods bind surface glycans or phosphatidylserine moieties of the exosomes. Overall, these findings suggest that specific isolation methods select subpopulations which may significantly impact cancer biomarker discovery.
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Affiliation(s)
- Alex C. Soupir
- Department of Tumor Biology, Moffitt Cancer Center, Tampa, FL 33612, USA
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Yijun Tian
- Department of Tumor Biology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Paul A. Stewart
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Yury O. Nunez-Lopez
- Advent Health, Translational Research Institute for Metabolism and Diabetes, Orlando, FL 32804, USA
| | - Brandon J. Manley
- Department of Genitourinary Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Bruna Pellini
- Department of Thoracic Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Amanda M. Bloomer
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Jingsong Zhang
- Department of Genitourinary Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Qianxing Mo
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL 33612, USA
| | | | - Min Liu
- Proteomics & Metabolomics Core, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - John M. Koomen
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Erin M. Siegel
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Liang Wang
- Department of Tumor Biology, Moffitt Cancer Center, Tampa, FL 33612, USA
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18
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Adhikari E, Liu Q, Marusyk V, Lzumi V, Koomen JM, Marusyk A, Lau E. Abstract B003: Hypoxia-induced secretion of fucosylated PVR/CD155 from brain met-associated fibroblasts drives breast cancer invasive capacity by altering cell-cell contacts & focal adhesion. Cancer Res 2023. [DOI: 10.1158/1538-7445.metastasis22-b003] [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: 01/19/2023]
Abstract
Abstract
Background: Brain metastasis (BM) develops in ~10-30% of breast cancer (BC) patients; triple negative breast cancer (TNBC), the most aggressive subtype of BC, exhibits the highest incidence of BM. Treatment options for BCBM are extremely limited due to the poor biological understanding. Hence, there is an urgent need to elucidate molecular mechanisms driving BCBM. We aim to study BCBM pathogenesis by dissecting the role of tumorigenic fucosylated proteins secreted by BM-associated fibroblasts (bmCAFs). Methods: We assessed global fucosylation (post-translational protein modification by L-fucose) patterns by fucose-binding lectin pulldown and immunoblot (IB) analysis. Conditioned media (CM) derived from CAFs that were depleted or not of fucosylated proteins were used to treat BC cells to assess motility and invasion. Fuco-proteomics and phosphoproteomic profiling identified bmCAF-secreted fucosylated (sf) proteins in bmCAF-derived CM and associated global signaling changes induced in BC cells, respectively. qRT-PCR was performed to analyze FUT11 levels under normoxia and hypoxia. Immunofluorescence and IB analyses of BC cells treated ± with bmCAF-derived CM was performed to validate PVR downstream signaling changes. Stereotactic intracranial implantation of BC cells alone or with ctrl/PVR knocked-down- bmCAFs was used for the BCBM mouse model. Results: We discovered that fucosylated proteins secreted uniquely by bmCAFs but not by normal-breast fibroblasts (NBF) or primary tumor-CAFs (tCAF), potently drives BC proliferation and invasiveness. Fucosylated proteomic profiling of the bmCAF secretome identified a soluble Polio Virus Receptor (PVR) isoform as uniquely upregulated, fucosylated, and secreted by bmCAFs. Of the 13 fucosyltransferases (FUTs), we found that bmCAFs upregulate FUT11, a key hypoxia-related gene. FUT11 and secreted fucosylated PVR (sfPVR) are significantly increased in bmCAFs exposed to hypoxia, consistent with the hypoxic environment of the brain. PVR can exist as transmembrane and secreted isoforms. Whereas transmembrane PVR is known to contribute to poor prognosis in a number of cancers by facilitating tumorigenic cell:matrix interactions and attenuating anti-tumor immunity, roles of secreted fucosylated PVR (sfPVR) in cancer are unknown. Our phosphoproteomics analyses of BC cells identified cellular adhesion/cytoskeletal and EPHA2 signaling as significantly modulated by bmCAF sfPVR to drive BC cell motility and invasiveness. Indeed, PVR knockdown abrogates the ability of bmCAFs to enhance BC growth/spread in the brain in a mouse model. Conclusion: Our data demonstrate that pathological hypoxia drives FUT11-mediated fucosylation and secretion of PVR by bmCAFs, which potently drives BC cells motility and invasiveness, representing a mechanism by which bmCAFs can promote BCBM. We expect our ongoing and further studies to advance our understanding of how sfPVR from bmCAFs promotes BCBM and to establish a basis for therapeutic targeting of PVR and/or use of fucosylated PVR and its signaling effectors as biomarkers.
Citation Format: Emma Adhikari, Qian Liu, Viktoriya Marusyk, Victoria Lzumi, John M. Koomen, Andriy Marusyk, Eric Lau. Hypoxia-induced secretion of fucosylated PVR/CD155 from brain met-associated fibroblasts drives breast cancer invasive capacity by altering cell-cell contacts & focal adhesion [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr B003.
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Affiliation(s)
| | - Qian Liu
- 1Moffitt Cancer Center, Tampa, FL
| | | | | | | | | | - Eric Lau
- 1Moffitt Cancer Center, Tampa, FL
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19
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Sarcar B, Fang B, Izumi V, O Nunez Lopez Y, Tassielli A, Pratley R, Jeong D, Permuth JB, Koomen JM, Fleming JB, Stewart PA. A comparative Proteomics Analysis Identified Differentially Expressed Proteins in Pancreatic Cancer-Associated Stellate Cell Small Extracellular Vesicles. Mol Cell Proteomics 2022; 21:100438. [PMID: 36332889 PMCID: PMC9792568 DOI: 10.1016/j.mcpro.2022.100438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 10/03/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
Human pancreatic stellate cells (HPSCs) are an essential stromal component and mediators of pancreatic ductal adenocarcinoma (PDAC) progression. Small extracellular vesicles (sEVs) are membrane-enclosed nanoparticles involved in cell-to-cell communications and are released from stromal cells within PDAC. A detailed comparison of sEVs from normal pancreatic stellate cells (HPaStec) and from PDAC-associated stellate cells (HPSCs) remains a gap in our current knowledge regarding stellate cells and PDAC. We hypothesized there would be differences in sEVs secretion and protein expression that might contribute to PDAC biology. To test this hypothesis, we isolated sEVs using ultracentrifugation followed by characterization by electron microscopy and Nanoparticle Tracking Analysis. We report here our initial observations. First, HPSC cells derived from PDAC tumors secrete a higher volume of sEVs when compared to normal pancreatic stellate cells (HPaStec). Although our data revealed that both normal and tumor-derived sEVs demonstrated no significant biological effect on cancer cells, we observed efficient uptake of sEVs by both normal and cancer epithelial cells. Additionally, intact membrane-associated proteins on sEVs were essential for efficient uptake. We then compared sEV proteins isolated from HPSCs and HPaStecs cells using liquid chromatography-tandem mass spectrometry. Most of the 1481 protein groups identified were shared with the exosome database, ExoCarta. Eighty-seven protein groups were differentially expressed (selected by 2-fold difference and adjusted p value ≤0.05) between HPSC and HPaStec sEVs. Of note, HPSC sEVs contained dramatically more CSE1L (chromosome segregation 1-like protein), a described marker of poor prognosis in patients with pancreatic cancer. Based on our results, we have demonstrated unique populations of sEVs originating from stromal cells with PDAC and suggest that these are significant to cancer biology. Further studies should be undertaken to gain a deeper understanding that could drive novel therapy.
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Affiliation(s)
- Bhaswati Sarcar
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Bin Fang
- Proteomics and Metabolomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Victoria Izumi
- Proteomics and Metabolomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | | | - Alexandra Tassielli
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Richard Pratley
- Translational Research Institute, Advent Health, Orlando, Florida, USA
| | - Daniel Jeong
- Department of Diagnostic and Interventional Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jennifer B Permuth
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA; Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - John M Koomen
- Proteomics and Metabolomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jason B Fleming
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA.
| | - Paul A Stewart
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA.
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Deng O, Dash S, Nepomuceno TC, Fang B, Yun SY, Welsh EA, Lawrence HR, Marchion D, Koomen JM, Monteiro AN, Rix U. Integrated proteomics identifies PARP inhibitor-induced prosurvival signaling changes as potential vulnerabilities in ovarian cancer. J Biol Chem 2022; 298:102550. [PMID: 36183837 PMCID: PMC9636579 DOI: 10.1016/j.jbc.2022.102550] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
BRCA1/2-deficient ovarian carcinoma (OC) has been shown to be particularly sensitive to poly (ADP-ribose) polymerase inhibitors (PARPis). Furthermore, BRCA1/2 mutation status is currently used as a predictive biomarker for PARPi therapy. Despite providing a major clinical benefit to the majority of patients, a significant proportion of BRCA1/2-deficient OC tumors do not respond to PARPis for reasons that are incompletely understood. Using an integrated chemical, phospho- and ADP-ribosylation proteomics approach, we sought here to develop additional mechanism-based biomarker candidates for PARPi therapy in OC and identify new targets for combination therapy to overcome primary resistance. Using chemical proteomics with PARPi baits in a BRCA1-isogenic OC cell line pair, as well as patient-derived BRCA1-proficient and BRCA1-deficient tumor samples, and subsequent validation by coimmunoprecipitation, we showed differential PARP1 and PARP2 protein complex composition in PARPi-sensitive, BRCA1-deficient UWB1.289 (UWB) cells compared to PARPi-insensitive, BRCA1-reconstituted UWB1.289+BRCA1 (UWB+B) cells. In addition, global phosphoproteomics and ADP-ribosylation proteomics furthermore revealed that the PARPi rucaparib induced the cell cycle pathway and nonhomologous end joining (NHEJ) pathway in UWB cells but downregulated ErbB signaling in UWB+B cells. In addition, we observed AKT PARylation and prosurvival AKT-mTOR signaling in UWB+B cells after PARPi treatment. Consistently, we found the synergy of PARPis with DNAPK or AKT inhibitors was more pronounced in UWB+B cells, highlighting these pathways as actionable vulnerabilities. In conclusion, we demonstrate the combination of chemical proteomics, phosphoproteomics, and ADP-ribosylation proteomics can identify differential PARP1/2 complexes and diverse, but actionable, drug compensatory signaling in OC.
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Affiliation(s)
- Ou Deng
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Sweta Dash
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Thales C Nepomuceno
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Bin Fang
- Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Sang Y Yun
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA; Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Eric A Welsh
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Harshani R Lawrence
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA; Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Douglas Marchion
- Tissue Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - John M Koomen
- Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA.
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA.
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21
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Hesterberg RS, Liu M, Elmarsafawi AG, Koomen JM, Welsh EA, Hesterberg SG, Ranatunga S, Yang C, Li W, Lawrence HR, Rodriguez PC, Berglund AE, Cleveland JL. TCR-Independent Metabolic Reprogramming Precedes Lymphoma-Driven Changes in T-cell Fate. Cancer Immunol Res 2022; 10:1263-1279. [PMID: 35969234 PMCID: PMC9662872 DOI: 10.1158/2326-6066.cir-21-0813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/27/2021] [Revised: 05/09/2022] [Accepted: 08/03/2022] [Indexed: 01/07/2023]
Abstract
Chronic T-cell receptor (TCR) signaling in the tumor microenvironment is known to promote T-cell dysfunction. However, we reasoned that poorly immunogenic tumors may also compromise T cells by impairing their metabolism. To address this, we assessed temporal changes in T-cell metabolism, fate, and function in models of B-cell lymphoma driven by Myc, a promoter of energetics and repressor of immunogenicity. Increases in lymphoma burden most significantly impaired CD4+ T-cell function and promoted regulatory T cell (Treg) and Th1-cell differentiation. Metabolomic analyses revealed early reprogramming of CD4+ T-cell metabolism, reduced glucose uptake, and impaired mitochondrial function, which preceded changes in T-cell fate. In contrast, B-cell lymphoma metabolism remained robust during tumor progression. Finally, mitochondrial functions were impaired in CD4+ and CD8+ T cells in lymphoma-transplanted OT-II and OT-I transgenic mice, respectively. These findings support a model, whereby early, TCR-independent, metabolic interactions with developing lymphomas limits T cell-mediated immune surveillance.
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Affiliation(s)
- Rebecca S. Hesterberg
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Min Liu
- Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Aya G. Elmarsafawi
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - John M. Koomen
- Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Eric A. Welsh
- Biostatistics & Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | | | - Sujeewa Ranatunga
- Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Chunying Yang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Weimin Li
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Harshani R. Lawrence
- Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Paulo C. Rodriguez
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Anders E. Berglund
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - John L. Cleveland
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
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22
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Chang A, Chakiryan NH, Du D, Stewart PA, Zhang Y, Tian Y, Soupir AC, Bowers K, Fang B, Morganti A, Teer JK, Kim Y, Spiess PE, Chahoud J, Noble JD, Putney RM, Berglund AE, Robinson TJ, Koomen JM, Wang L, Manley BJ. Proteogenomic, Epigenetic, and Clinical Implications of Recurrent Aberrant Splice Variants in Clear Cell Renal Cell Carcinoma. Eur Urol 2022; 82:354-362. [PMID: 35718636 PMCID: PMC11075093 DOI: 10.1016/j.eururo.2022.05.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 01/13/2022] [Revised: 04/24/2022] [Accepted: 05/24/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Alternative mRNA splicing can be dysregulated in cancer, resulting in the generation of aberrant splice variants (SVs). Given the paucity of actionable genomic mutations in clear cell renal cell carcinoma (ccRCC), aberrant SVs may be an avenue to novel mechanisms of pathogenesis. OBJECTIVE To identify and characterize aberrant SVs enriched in ccRCC. DESIGN, SETTING, AND PARTICIPANTS Using RNA-seq data from the Cancer Cell Line Encyclopedia, we identified neojunctions uniquely expressed in ccRCC. Candidate SVs were then checked for expression across normal tissue in the Genotype-Tissue Expression Project and primary tumor tissue from The Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), and our institutional Total Cancer Care database. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Clinicopathologic, genomic, and survival data were available for all cohorts. Epigenetic data were available for the TCGA and CPTAC cohorts. Proteomic data were available for the CPTAC cohort. The association of aberrant SV expression with these variables was examined using the Kruskal-Wallis test, pairwise t test, Spearman correlation test, and Cox regression analysis. RESULTS AND LIMITATIONS Our pipeline identified 16 ccRCC-enriched SVs. EGFR, HPCAL1-SV and RNASET2-SV expression was negatively correlated with gene-specific CpG methylation. We derived a survival risk score based primarily on the expression of five SVs (RNASET2, FGD1, PDZD2, COBLL1, and PTPN14), which was consistent and applicable across multiple cohorts on multivariate analysis. The splicing factor RBM4, which modulates splicing of HIF-1α, exhibited significantly lower expression at the protein level in the high-risk group, as defined by our SV-based score. CONCLUSIONS We describe 16 aberrant SVs enriched in ccRCC, many of which are associated with disease biology and/or clinical outcomes. This study provides a novel strategy for identifying and characterizing disease-specific aberrant SVs. PATIENT SUMMARY We describe a method to identify disease targets and biomarkers using transcriptomic analysis beyond somatic mutations or gene expression. Kidney tumors express unique splice variants that may provide additional prognostic information following surgery.
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Affiliation(s)
- Andrew Chang
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
| | - Nicholas H Chakiryan
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Dongliang Du
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Paul A Stewart
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Yonghong Zhang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Yijun Tian
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alex C Soupir
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA; Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Kiah Bowers
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Bin Fang
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Ashley Morganti
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Youngchul Kim
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Philippe E Spiess
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jad Chahoud
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jerald D Noble
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA; Department of Radiation Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Ryan M Putney
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Anders E Berglund
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Timothy J Robinson
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - John M Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Brandon J Manley
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA; Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
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23
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Madanayake TW, Welsh EA, Darville LN, Koomen JM, Chalfant CE, Haura EB, Robinson TJ. Inhibition of Epidermal Growth Factor Receptor Signaling by Antisense Oligonucleotides as a Novel Approach to Epidermal Growth Factor Receptor Inhibition. Nucleic Acid Ther 2022; 32:391-400. [PMID: 35861718 PMCID: PMC9595651 DOI: 10.1089/nat.2021.0101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/11/2021] [Accepted: 04/21/2022] [Indexed: 11/12/2022] Open
Abstract
We report a novel method to inhibit epidermal growth factor receptor (EGFR) signaling using custom morpholino antisense oligonucleotides (ASOs) to drive expression of dominant negative mRNA isoforms of EGFR by ASO-induced exon skipping within the transmembrane (16) or tyrosine kinase domains (18 and 21). In vivo ASO formulations induced >95% exon skipping in several models of nonsmall cell lung cancer (NSCLC) and were comparable in efficacy to erlotinib in reducing colony formation, cell viability, and migration in EGFR mutant NSCLC (PC9). However, unlike erlotinib, ASOs maintained their efficacy in both erlotinib-resistant subclones (PC9-GR) and wild-type overexpressing EGFR models (H292), in which erlotinib had no significant effect. The most dramatic ASO-induced phenotype resulted from targeting the EGFR kinase domain directly, which resulted in maximal inhibition of phosphorylation of EGFR, Akt, and Erk in both PC9 and PC9GR cells. Phosphoproteomic mass spectrometry confirmed highly congruent impacts of exon 16-, 18-, and 21-directed ASOs compared with erlotinib on PC9 genome-wide cell signaling. Furthermore, EGFR-directed ASOs had no impact in EGFR-independent NSCLC models, confirming an EGFR-specific therapeutic mechanism. Further exploration of synergy of ASOs with existing tyrosine kinase inhibitors may offer novel clinical models to improve EGFR-targeted therapies for both mutant and wild-type NSCLC patients.
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Affiliation(s)
- Thushara W. Madanayake
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Eric A. Welsh
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Lancia N.F. Darville
- Department of Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - John M. Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Charles E. Chalfant
- Department of Cell Biology and Medicine, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
- Research Service, James A. Haley Veterans' Administration Hospital, Tampa, Florida, USA
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Timothy J. Robinson
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut, USA
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24
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Rix LLR, Sumi NJ, Hu Q, Desai B, Bryant AT, Li X, Welsh EA, Fang B, Kinose F, Kuenzi BM, Chen YA, Antonia SJ, Lovly CM, Koomen JM, Haura EB, Marusyk A, Rix U. IGF-binding proteins secreted by cancer-associated fibroblasts induce context-dependent drug sensitization of lung cancer cells. Sci Signal 2022; 15:eabj5879. [PMID: 35973030 PMCID: PMC9528501 DOI: 10.1126/scisignal.abj5879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cancer-associated fibroblasts (CAFs) in the tumor microenvironment are often linked to drug resistance. Here, we found that coculture with CAFs or culture in CAF-conditioned medium unexpectedly induced drug sensitivity in certain lung cancer cell lines. Gene expression and secretome analyses of CAFs and normal lung-associated fibroblasts (NAFs) revealed differential abundance of insulin-like growth factors (IGFs) and IGF-binding proteins (IGFBPs), which promoted or inhibited, respectively, signaling by the receptor IGF1R and the kinase FAK. Similar drug sensitization was seen in gefitinib-resistant, EGFR-mutant PC9GR lung cancer cells treated with recombinant IGFBPs. Conversely, drug sensitivity was decreased by recombinant IGFs or conditioned medium from CAFs in which IGFBP5 or IGFBP6 was silenced. Phosphoproteomics and receptor tyrosine kinase (RTK) array analyses indicated that exposure of PC9GR cells to CAF-conditioned medium also inhibited compensatory IGF1R and FAK signaling induced by the EGFR inhibitor osimertinib. Combined small-molecule inhibition of IGF1R and FAK phenocopied the CAF-mediated effects in culture and increased the antitumor effect of osimertinib in mice. Cells that were osimertinib resistant and had MET amplification or showed epithelial-to-mesenchymal transition also displayed residual sensitivity to IGFBPs. Thus, CAFs promote or reduce drug resistance in a context-dependent manner, and deciphering the relationship between the differential content of CAF secretomes and the signaling dependencies of the tumor may reveal effective combination treatment strategies.
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Affiliation(s)
- Lily L. Remsing Rix
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida 33612, USA
| | - Natalia J. Sumi
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida 33612, USA.,Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL 33620, USA
| | - Qianqian Hu
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida 33612, USA.,Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL 33620, USA
| | - Bina Desai
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida 33612, USA.,Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL 33620, USA
| | - Annamarie T. Bryant
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida 33612, USA
| | - Xueli Li
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida 33612, USA
| | - Eric A. Welsh
- Biostatistics and Bioinformatics Shared Resource, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Fumi Kinose
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Brent M. Kuenzi
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida 33612, USA.,Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL 33620, USA
| | - Y. Ann Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL 33612, USA,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Scott J. Antonia
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Christine M. Lovly
- Department of Medicine, Vanderbilt University Medical Center; Nashville, TN 37232, USA
| | - John M. Koomen
- Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA,Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Andriy Marusyk
- Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA,Department of Cancer Physiology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Uwe Rix
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida 33612, USA.,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA,Corresponding author.
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25
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Solanki HS, Stewart PA, Welsh EA, Izumi V, Fang B, Yoder SJ, Koomen JM, Haura EB. Abstract 3911: Proteomic and transcriptomic subtypes of KRASG12C mutant lung cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3911] [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
Sotorasib (AMG510) is the first KRASG12C covalent inhibitor (KRASG12Ci) approved by the FDA in lung cancers harboring oncogenic KRASG12C mutation. However, it remains unclear why some patients show upfront resistance to the KRASG12Ci, and the mechanisms of adaptive resistance. To enhance the efficacy of the KRASG12Ci, several combination regimens are in clinical trials which includes Sotorasib combination with MEK, PD1, SHP2, pan-HER, PD-L1, and EGFR inhibitors. However, it remains unclear how to precisely identify an appropriate cohort for analysis and predict tumor-centric combination strategies that would be effective in the clinic. We hypothesized that subsets of KRASG12C lung cancer could be identified using transcriptomics and proteomics. To test our hypothesis, we performed hierarchical clustering of the microarray dataset on 87 NSCLC KRASG12C tumors and identified three novel transcriptomic subtypes - Subtype 1 had higher expression of extracellular matrix (ECM) genes, which are related to cellular adhesion, and lower expression of EMT genes. Subtype 2 had low ECM expression, high expression in EMT and cell cycle pathway genes suggesting that this is a more invasive subtype. Subtype 2 had lowest expression of small molecule metabolism, suggesting it may be more responsive to KRASG12Ci. Subtype 3 had the lowest expression in interferon gamma/cytotoxic T-cell, T-cell, and B-cell pathways. Subtype 3 had the highest expression of small molecule metabolism, suggesting that it could be more resistant to KRASG12Ci. Having observed these unique clusters, we next hypothesized that mass spectrometry-based expression and phosphoproteomic analysis (pY and pS/T/Y) will further refine these clusters and help identifying new subsets. Our previous work by Stewart et al., demonstrated the importance of proteomics integrated with genomic and transcriptomic analyses to define molecular subtypes in a cohort of 108 squamous cell lung cancer patients. We believe that a similar integrated proteogenomic study is important in context of KRASG12C tumors to understand the signaling diversity and phenotypically categorized them to optimize patient enrichment schemes for effective combination therapy. For that purpose, we performed an integrative proteogenomic analysis of 75 KRASG12C tumors (55 lung, 12 large bowel adenocarcinomas and 8 PDXs) with full clinical follow up and pathology data. We are presently classifying the 75 KRASG12C tumors into phosphoproteomic subtypes. We also carried out targeted exome sequencing for cancer-specific genes. Next, we plan to leverage existing gene expression microarray data and add exome sequencing proteomics, and phosphoproteomics for a comprehensive, protein-centric characterization on these tumors. Importantly, the inclusion of 8 PDXs being co-processed and co-analyzed along with the tumors will enable rapid follow-up experiments to validate the findings into preclinical therapy trials.
Citation Format: Hitendra Singh Solanki, Paul A. Stewart, Eric A. Welsh, Victoria Izumi, Bin Fang, Sean J. Yoder, John M. Koomen, Eric B. Haura. Proteomic and transcriptomic subtypes of KRASG12C mutant lung cancer [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 3911.
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Affiliation(s)
| | | | | | | | - Bin Fang
- 1Moffitt Cancer Center, Tampa, FL
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26
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Soupir AC, Stewart PA, Lopez YN, Manley BJ, Pellini B, Zhang J, Mo Q, Marchion DC, Lui M, Koomen JM, Siegel EM, Wang L. Abstract 3417: Effects of plasma exosome isolation methods on detectable multiomic profiles in cancer patients and healthy controls. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3417] [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
Introduction: Circulating exosomes in blood have been considered as a treasure chest for biomarker discovery in cancer. Due to their heterogeneity, different isolation methods may enrich distinct exosome cargos generating different omic profiles. In this study, we evaluated the effects of plasma exosome isolation methods on detectable multiomic profiles in cancer patients and healthy controls.
Methods: Plasma exosomes were isolated from prostate cancer patients (PC; N = 11), lung cancer patients (LC; N = 13), and matched healthy controls (HC; N = 10) using three methods [SBI (size exclusion), Takara (lectin binding), and Wako (Tim4 binding)]. Mass spectrometry was performed to determine exosome lipidome and metabolome profiles. To evaluate group-specific exosome enrichment, we developed an exosome enrichment index (EEI) by summing 50 smallest p-values after log2 transformation. Higher EEI indicates prefrential capture of significant exosome cargos from patients over controls.
Results: Our data showed that the SBI method generated the most identified lipids from exosome across all groups (LC = 935, PC = 939, and HC = 943), followed by Takara (245, 245 and 245) and Wako (205, 208 and 213). Compared to controls, LC patients had 31 higher and 5 lower lipid levels (FDR < 0.1) using the SBI and 3 higher and 1 lower level (FDR < 0.1) using Takara. We did not observe any differences between cancer and normal samples using Wako. The most detectable known metabolites were found in exosomes from SBI (LC = 188, PC = 191, and HC = 100), followed by Wako (LC = 107, PC = 107, and HC = 107) and Takara (LC = 99, PC = 100, and HC = 100). Of the metabolites from SBI, 5 were significantly higher (FDR<0.1) in PC patients than in controls. The most significant metabolite in PC was L-Cystathionine, which has been shown to be upregulated in bone-metastatic PC3 cells. Neither Takara nor Wako exosome fractions showed differently expressed metabolites between any groups. Our EEI analysis showed the highest lipid EEI from SBI in PC (474.4) and LC (906.74), while a lower lipid EEI from Takara in PC (359.9), LC (495.58), and Wako in PC (307.5) and LC (148.1). Metabolite EEI showed an EEI range from 590.3 in SBI PC to 185.6 in Takara LC. SBI, again, achieved the highest EEI for both PC and LC (357.3).
Conclusion: These results support that the SBI method can capture more heterogeneous exosome populations, possibly because this size exclusion-based method does not discriminate exosomes with different protein components. In contrast, Takara and Wako methods target exosome surface proteins, enriching specific exosome subpopulations resulting in less diversity of detectable lipids and metabolites. Overall, these findings suggest that exosome isolation methods can select subpopulations and determine the exosome content, which will significantly impact exosome-based biomarker discovery.
Citation Format: Alex C. Soupir, Paul A. Stewart, Yury Nunez Lopez, Brandon J. Manley, Bruna Pellini, Jingsong Zhang, Qianxing Mo, Douglas C. Marchion, Min Lui, John M. Koomen, Erin M. Siegel, Liang Wang. Effects of plasma exosome isolation methods on detectable multiomic profiles in cancer patients and healthy controls [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 3417.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Min Lui
- 1Moffitt Cancer Center, Tampa, FL
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27
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Li J, Smalley I, Chen Z, Wu JY, Phadke MS, Teer JK, Nguyen T, Karreth FA, Koomen JM, Sarnaik AA, Zager JS, Khushalani NI, Tarhini AA, Sondak VK, Rodriguez PC, Messina JL, Chen YA, Smalley KSM. Single-cell Characterization of the Cellular Landscape of Acral Melanoma Identifies Novel Targets for Immunotherapy. Clin Cancer Res 2022; 28:2131-2146. [PMID: 35247927 PMCID: PMC9106889 DOI: 10.1158/1078-0432.ccr-21-3145] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 08/31/2021] [Revised: 12/10/2021] [Accepted: 03/01/2022] [Indexed: 12/21/2022]
Abstract
PURPOSE Acral melanoma is a rare subtype of melanoma that arises on the non-hair-bearing skin of the palms, soles, and nail beds. In this study, we used single-cell RNA sequencing (scRNA-seq) to map the transcriptional landscape of acral melanoma and identify novel immunotherapeutic targets. EXPERIMENTAL DESIGN We performed scRNA-seq on nine clinical specimens (five primary, four metastases) of acral melanoma. Detailed cell type curation was performed, the immune landscapes were mapped, and key results were validated by analysis of The Cancer Genome Atlas (TCGA) and single-cell datasets. Cell-cell interactions were inferred and compared with those in nonacral cutaneous melanoma. RESULTS Multiple phenotypic subsets of T cells, natural killer (NK) cells, B cells, macrophages, and dendritic cells with varying levels of activation/exhaustion were identified. A comparison between primary and metastatic acral melanoma identified gene signatures associated with changes in immune responses and metabolism. Acral melanoma was characterized by a lower overall immune infiltrate, fewer effector CD8 T cells and NK cells, and a near-complete absence of γδ T cells compared with nonacral cutaneous melanomas. Immune cells associated with acral melanoma exhibited expression of multiple checkpoints including PD-1, LAG-3, CTLA-4, V-domain immunoglobin suppressor of T cell activation (VISTA), TIGIT, and the Adenosine A2A receptor (ADORA2). VISTA was expressed in 58.3% of myeloid cells and TIGIT was expressed in 22.3% of T/NK cells. CONCLUSIONS Acral melanoma has a suppressed immune environment compared with that of cutaneous melanoma from nonacral skin. Expression of multiple, therapeutically tractable immune checkpoints were observed, offering new options for clinical translation.
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Affiliation(s)
- Jiannong Li
- The Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Inna Smalley
- The Department of Tumor Biology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Zhihua Chen
- The Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Jheng-Yu Wu
- The Department of Tumor Biology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Manali S. Phadke
- The Department of Tumor Biology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Jamie K. Teer
- The Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Thanh Nguyen
- The Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Florian A. Karreth
- The Department of Molecular Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - John M. Koomen
- The Department of Molecular Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Amod A. Sarnaik
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Jonathan S. Zager
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Nikhil I. Khushalani
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Ahmad A. Tarhini
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Vernon K. Sondak
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Paulo C. Rodriguez
- The Department of Immunology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Jane L. Messina
- The Department of Immunology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Y. Ann Chen
- The Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
| | - Keiran S. M. Smalley
- The Department of Tumor Biology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, USA
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Mahajan S, Majumder A, Stewart PA, Chen YA, Adhikari E, Fang B, Yang Y, Lawrence H, Kinose F, Koomen JM, Haura EB. Deubiquitinase Vulnerabilities Identified through Activity-Based Protein Profiling in Non-Small Cell Lung Cancer. ACS Chem Biol 2022; 17:776-784. [PMID: 35311290 PMCID: PMC11071078 DOI: 10.1021/acschembio.2c00018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
To aid in the prioritization of deubiquitinases (DUBs) as anticancer targets, we developed an approach combining activity-based protein profiling (ABPP) with mass spectrometry in both non-small cell lung cancer (NSCLC) tumor tissues and cell lines along with analysis of available RNA interference and CRISPR screens. We identified 67 DUBs in NSCLC tissues, 17 of which were overexpressed in adenocarcinoma or squamous cell histologies and 12 of which scored as affecting lung cancer cell viability in RNAi or CRISPR screens. We used the CSN5 inhibitor, which targets COPS5/CSN5, as a tool to understand the biological significance of one of these 12 DUBs, COPS6, in lung cancer. Our study provides a powerful resource to interrogate the role of DUB signaling biology and nominates druggable targets for the treatment of lung cancer subtypes.
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Ampomah PB, Cai B, Sukka SR, Gerlach BD, Yurdagul A, Wang X, Kuriakose G, Darville LNF, Sun Y, Sidoli S, Koomen JM, Tall AR, Tabas I. Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution. Nat Metab 2022; 4:444-457. [PMID: 35361955 PMCID: PMC9050866 DOI: 10.1038/s42255-022-00551-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/11/2022] [Indexed: 12/19/2022]
Abstract
Efferocytosis, the clearance of apoptotic cells (ACs) by macrophages, is critical for tissue resolution, with defects driving many diseases. Mechanisms of efferocytosis-mediated resolution are incompletely understood. Here, we show that AC-derived methionine regulates resolution through epigenetic repression of the extracellular signal-regulated kinase 1/2 (ERK1/2) phosphatase Dusp4. We focus on two key efferocytosis-induced pro-resolving mediators, prostaglandin E2 (PGE2) and transforming growth factor beta 1 (TGF-β1), and show that efferocytosis induces prostaglandin-endoperoxide synthase 2/cyclooxygenase 2 (Ptgs2/COX2), leading to PGE2 synthesis and PGE2-mediated induction of TGF-β1. ERK1/2 phosphorylation/activation by AC-activated CD36 is necessary for Ptgs2 induction, but this is insufficient owing to an ERK-DUSP4 negative feedback pathway that lowers phospho-ERK. However, subsequent AC engulfment and phagolysosomal degradation lead to Dusp4 repression, enabling enhanced p-ERK and induction of the Ptgs2-PGE2-TGF-β1 pathway. Mechanistically, AC-derived methionine is converted to S-adenosylmethionine, which is used by DNA methyltransferase-3A (DNMT3A) to methylate Dusp4. Bone-marrow DNMT3A deletion in mice blocks COX2/PGE2, TGF-β1, and resolution in sterile peritonitis, apoptosis-induced thymus injury and atherosclerosis. Knowledge of how macrophages use AC-cargo and epigenetics to induce resolution provides mechanistic insight and therapeutic options for diseases driven by impaired resolution.
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Affiliation(s)
- Patrick B Ampomah
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
| | - Bishuang Cai
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Santosh R Sukka
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Arif Yurdagul
- Department of Molecular and Cellular Physiology, LSU Health Shreveport, Shreveport, LA, USA
| | - Xiaobo Wang
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - George Kuriakose
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Lancia N F Darville
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Yan Sun
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - John M Koomen
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alan R Tall
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Ira Tabas
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Physiology, Columbia University Irving Medical Center, New York, NY, USA.
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30
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Majumder A, Hosseinian S, Stroud M, Adhikari E, Saller JJ, Smith MA, Zhang G, Agarwal S, Creixell M, Meyer BS, Kinose F, Bowers K, Fang B, Stewart PA, Welsh EA, Boyle TA, Meyer AS, Koomen JM, Haura EB. Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration. Mol Cancer Res 2022; 20:542-555. [PMID: 35022314 PMCID: PMC8983558 DOI: 10.1158/1541-7786.mcr-21-0275] [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: 04/15/2021] [Revised: 09/14/2021] [Accepted: 01/07/2022] [Indexed: 11/16/2022]
Abstract
To better understand the signaling complexity of AXL, a member of the tumor-associated macrophage (TAM) receptor tyrosine kinase family, we created a physical and functional map of AXL signaling interactions, phosphorylation events, and target-engagement of three AXL tyrosine kinase inhibitors (TKI). We assessed AXL protein complexes using proximity-dependent biotinylation (BioID), effects of AXL TKI on global phosphoproteins using mass spectrometry, and target engagement of AXL TKI using activity-based protein profiling. BioID identifies AXL-interacting proteins that are mostly involved in cell adhesion/migration. Global phosphoproteomics show that AXL inhibition decreases phosphorylation of peptides involved in phosphatidylinositol-mediated signaling and cell adhesion/migration. Comparison of three AXL inhibitors reveals that TKI RXDX-106 inhibits pAXL, pAKT, and migration/invasion of these cells without reducing their viability, while bemcentinib exerts AXL-independent phenotypic effects on viability. Proteomic characterization of these TKIs demonstrates that they inhibit diverse targets in addition to AXL, with bemcentinib having the most off-targets. AXL and EGFR TKI cotreatment did not reverse resistance in cell line models of erlotinib resistance. However, a unique vulnerability was identified in one resistant clone, wherein combination of bemcentinib and erlotinib inhibited cell viability and signaling. We also show that AXL is overexpressed in approximately 30% to 40% of nonsmall but rarely in small cell lung cancer. Cell lines have a wide range of AXL expression, with basal activation detected rarely. IMPLICATIONS Our study defines mechanisms of action of AXL in lung cancers which can be used to establish assays to measure drug targetable active AXL complexes in patient tissues and inform the strategy for targeting it's signaling as an anticancer therapy.
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Affiliation(s)
- Anurima Majumder
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Sina Hosseinian
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Mia Stroud
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Emma Adhikari
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - James J. Saller
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Matthew A. Smith
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Guolin Zhang
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Shruti Agarwal
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | | | - Benjamin S. Meyer
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Fumi Kinose
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Kiah Bowers
- Department of Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Bin Fang
- Department of Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Paul A. Stewart
- Department of Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Eric A. Welsh
- Department of Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Theresa A. Boyle
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | | | - John M. Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
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31
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Chang A, Stewart P, Chakiryan NH, Soupir AC, Tian Y, Du D, Teer JK, Kim Y, Spiess PE, Chahoud J, Zhang Y, Koomen JM, Berglund AE, Wang L, Robinson TJ, Manley BJ. Proteogenomic and clinical implications of unique recurrent splice variants in clear cell renal cell carcinoma. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.6_suppl.380] [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: 11/20/2022] Open
Abstract
380 Background: Alternative mRNA splicing is recognized as a key driver of proteomic diversity. In cancer, this splicing process can be altered resulting in generation of aberrant splice variants (SvPs) that can contribute to tumor pathogenesis. However, our understanding of the significance of splice variants in clear cell renal cell carcinoma (ccRCC) is currently limited. Given the lack of actionable genomic mutations in ccRCC, aberrant SpVs may be the avenue to new pathogenic mechanisms and biomarkers. Methods: We implemented a novel pipeline to screen for and select SpVs frequent in and relatively specific to ccRCC. We started with RNA-seq data from the Cancer Cell Line Encyclopedia to identify SpVs specific to ccRCC cell lines. These were then screened across normal tissue in the Genotype-Tissue Expression Project (GTEx) and excluded if expressed. We analyzed bulk RNA-seq data of ccRCC primary tumors obtained from our institutional Total Cancer Care cohort (TCC; n = 111), The Cancer Genome Atlas (TCGA; n = 484) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC; n = 110) to analyze SpV expression in these samples. Using raw proteomics files from the CPTAC portal, proteins were identified and quantified using MaxQuant. Associations of SvP with protein expression were filtered by a Spearman correlation cutoff of +/-0.3. The Enrichr R library was used for pathway enrichment. Finally, we correlated splice variant expression with overall (OS) and cancer-specific survival (CSS). Using LASSO Cox regression analysis, we derived a SpV-based risk score trained on OS from the TCGA cohort and validated on the TCC and CPTAC cohorts. Results: Our pipeline selected 16 previously uncharacterized SpVs, including variants of suspected oncogenes and tumor suppressors. Proteogenomic analysis identified interesting biological associations. Among patients with high levels of EGFR SpV, we found significantly higher expression of the protein regulatory T cell marker CD70 (padj = 0.03). MVK SvP was highly correlated with 25 proteins enriched for the mTOR pathway (padj = 0.002). We derived a survival risk score based on expression of 5 SpVs ( PDZD2, COBLL1, PTPN14, RNASET2, FGD1) in the TCGA cohort. This risk score remained significant on multivariate analysis (HR 1.4, p = 0.002) adjusting for covariates including AJCC stage. This was validated on multivariate analysis in the TCC (HR 3.56, p < 0.001) and CPTAC (HR 3.18, p = 0.019) cohorts. Conclusions: Our novel pipeline selected 16 unique SpVs frequent in and relatively specific for ccRCC. Some are associated with proteins expressed in oncogenic pathways, suggesting a potential role in disease pathogenesis. Additionally, our SpV-based risk score is strongly associated with OS and CSS across multiple cohorts. This study provides a template for identifying and characterizing disease-specific aberrant SpVs to aid discovery of new mechanisms and biomarkers.
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Affiliation(s)
- Andrew Chang
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | | | | | - Alex C. Soupir
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | | | | | - Jamie K. Teer
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Youngchul Kim
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | | | - Jad Chahoud
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yonghong Zhang
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - John M Koomen
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | | | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | | | - Brandon J. Manley
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
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32
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Palve V, Knezevic CE, Bejan DS, Luo Y, Li X, Novakova S, Welsh EA, Fang B, Kinose F, Haura EB, Monteiro AN, Koomen JM, Cohen MS, Lawrence HR, Rix U. The non-canonical target PARP16 contributes to polypharmacology of the PARP inhibitor talazoparib and its synergy with WEE1 inhibitors. Cell Chem Biol 2022; 29:202-214.e7. [PMID: 34329582 PMCID: PMC8782927 DOI: 10.1016/j.chembiol.2021.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 04/08/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022]
Abstract
PARP inhibitors (PARPis) display single-agent anticancer activity in small cell lung cancer (SCLC) and other neuroendocrine tumors independent of BRCA1/2 mutations. Here, we determine the differential efficacy of multiple clinical PARPis in SCLC cells. Compared with the other PARPis rucaparib, olaparib, and niraparib, talazoparib displays the highest potency across SCLC, including SLFN11-negative cells. Chemical proteomics identifies PARP16 as a unique talazoparib target in addition to PARP1. Silencing PARP16 significantly reduces cell survival, particularly in combination with PARP1 inhibition. Drug combination screening reveals talazoparib synergy with the WEE1/PLK1 inhibitor adavosertib. Global phosphoproteomics identifies disparate effects on cell-cycle and DNA damage signaling thereby illustrating underlying mechanisms of synergy, which is more pronounced for talazoparib than olaparib. Notably, silencing PARP16 further reduces cell survival in combination with olaparib and adavosertib. Together, these data suggest that PARP16 contributes to talazoparib's overall mechanism of action and constitutes an actionable target in SCLC.
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Affiliation(s)
- Vinayak Palve
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Claire E. Knezevic
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Daniel S. Bejan
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR 97239, USA
| | - Yunting Luo
- Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Xueli Li
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Silvia Novakova
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric A. Welsh
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Bin Fang
- Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Fumi Kinose
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Alvaro N. Monteiro
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - John M. Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Michael S. Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR 97239, USA
| | - Harshani R. Lawrence
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA,Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA.
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33
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Fernandez MR, Schaub FX, Yang C, Li W, Yun S, Schaub SK, Dorsey FC, Liu M, Steeves MA, Ballabio A, Tzankov A, Chen Z, Koomen JM, Berglund AE, Cleveland JL. Disrupting the MYC-TFEB Circuit Impairs Amino Acid Homeostasis and Provokes Metabolic Anergy. Cancer Res 2022; 82:1234-1250. [PMID: 35149590 DOI: 10.1158/0008-5472.can-21-1168] [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] [Received: 04/15/2021] [Revised: 12/07/2021] [Accepted: 02/08/2022] [Indexed: 11/16/2022]
Abstract
MYC family oncoproteins are regulators of metabolic reprogramming that sustains cancer cell anabolism. Normal cells adapt to nutrient-limiting conditions by activating autophagy, which is required for amino acid (AA) homeostasis. Here we report that the autophagy pathway is suppressed by Myc in normal B cells, in premalignant and neoplastic B cells of Eμ-Myc transgenic mice, and in human MYC-driven Burkitt lymphoma. Myc suppresses autophagy by antagonizing the expression and function of transcription factor EB (TFEB), a master regulator of autophagy. Mechanisms that sustained AA pools in MYC-expressing B cells include coordinated induction of the proteasome and increases in AA transport. Reactivation of the autophagy-lysosomal pathway by TFEB disabled the malignant state by disrupting mitochondrial functions, proteasome activity, amino acid transport, and amino acid and nucleotide metabolism, leading to metabolic anergy, growth arrest and apoptosis. This phenotype provides therapeutic opportunities to disable MYC-driven malignancies, including AA restriction and treatment with proteasome inhibitors.
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Affiliation(s)
- Mario R Fernandez
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute
| | - Franz X Schaub
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute
| | - Chunying Yang
- Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute
| | - Weimin Li
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute
| | | | | | | | - Min Liu
- Proteomics Core, Moffitt Cancer Center
| | | | | | | | - Zhihua Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center
| | - John M Koomen
- Department of Molecular Oncology, Moffitt Cancer Center
| | - Anders E Berglund
- Department of Biostatistics and Bioinformatics, Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute
| | - John L Cleveland
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute
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34
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Creelan BC, Wang C, Teer JK, Toloza EM, Yao J, Kim S, Landin AM, Mullinax JE, Saller JJ, Saltos AN, Noyes DR, Montoya LB, Curry W, Pilon-Thomas SA, Chiappori AA, Tanvetyanon T, Kaye FJ, Thompson ZJ, Yoder SJ, Fang B, Koomen JM, Sarnaik AA, Chen DT, Conejo-Garcia JR, Haura EB, Antonia SJ. Tumor-infiltrating lymphocyte treatment for anti-PD-1-resistant metastatic lung cancer: a phase 1 trial. Nat Med 2021; 27:1410-1418. [PMID: 34385708 PMCID: PMC8509078 DOI: 10.1038/s41591-021-01462-y] [Citation(s) in RCA: 149] [Impact Index Per Article: 49.7] [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: 12/20/2020] [Accepted: 07/06/2021] [Indexed: 12/30/2022]
Abstract
Adoptive cell therapy using tumor-infiltrating lymphocytes (TILs) has shown activity in melanoma, but has not been previously evaluated in metastatic non-small cell lung cancer. We conducted a single-arm open-label phase 1 trial ( NCT03215810 ) of TILs administered with nivolumab in 20 patients with advanced non-small cell lung cancer following initial progression on nivolumab monotherapy. The primary end point was safety and secondary end points included objective response rate, duration of response and T cell persistence. Autologous TILs were expanded ex vivo from minced tumors cultured with interleukin-2. Patients received cyclophosphamide and fludarabine lymphodepletion, TIL infusion and interleukin-2, followed by maintenance nivolumab. The end point of safety was met according to the prespecified criteria of ≤17% rate of severe toxicity (95% confidence interval, 3-29%). Of 13 evaluable patients, 3 had confirmed responses and 11 had reduction in tumor burden, with a median best change of 35%. Two patients achieved complete responses that were ongoing 1.5 years later. In exploratory analyses, we found T cells recognizing multiple types of cancer mutations were detected after TIL treatment and were enriched in responding patients. Neoantigen-reactive T cell clonotypes increased and persisted in peripheral blood after treatment. Cell therapy with autologous TILs is generally safe and clinically active and may constitute a new treatment strategy in metastatic lung cancer.
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Affiliation(s)
- Benjamin C Creelan
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
| | - Chao Wang
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jamie K Teer
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Eric M Toloza
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jiqiang Yao
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Sungjune Kim
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Ana M Landin
- Cell Therapy Facility, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - John E Mullinax
- Department of Sarcoma, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - James J Saller
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Andreas N Saltos
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - David R Noyes
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Leighann B Montoya
- Immune and Cellular Therapy Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Wesley Curry
- Immune and Cellular Therapy Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Shari A Pilon-Thomas
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alberto A Chiappori
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Tawee Tanvetyanon
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Frederic J Kaye
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Zachary J Thompson
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Sean J Yoder
- Chemical Biology & Molecular Medicine, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Bin Fang
- Chemical Biology & Molecular Medicine, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - John M Koomen
- Chemical Biology & Molecular Medicine, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Amod A Sarnaik
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Dung-Tsa Chen
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jose R Conejo-Garcia
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Scott J Antonia
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
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35
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Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Cell Rep Methods 2021; 1:100015. [PMID: 34671754 PMCID: PMC8525888 DOI: 10.1016/j.crmeth.2021.100015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/16/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023]
Abstract
SUMMARY A primary goal of the US National Cancer Institute's Ras initiative at the Frederick National Laboratory for Cancer Research is to develop methods to quantify RAS signaling to facilitate development of novel cancer therapeutics. We use targeted proteomics technologies to develop a community resource consisting of 256 validated multiple reaction monitoring (MRM)-based, multiplexed assays for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. As proof of concept, we quantify the response of melanoma (A375 and SK-MEL-2) and colorectal cancer (HCT-116 and HT-29) cell lines to BRAF inhibition by PLX-4720. These assays replace over 60 Western blots with quantitative mass spectrometry-based assays of high molecular specificity and quantitative precision, showing the value of these methods for pharmacodynamic measurements and mechanism of action studies. Methods, fit-for-purpose validation, and results are publicly available as a resource for the community at assays.cancer.gov. MOTIVATION A lack of quantitative, multiplexable assays for phosphosignaling limits comprehensive investigation of aberrant signaling in cancer and evaluation of novel treatments. To alleviate this limitation, we sought to develop assays using targeted mass spectrometry for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. The resulting assays provide a resource for replacing over 60 Western blots in examining cancer signaling and tumor biology with high molecular specificity and quantitative rigor.
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Affiliation(s)
- Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kanika Sharma
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Melissa A. Hoffman
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric Kuhn
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alexandra R. Cocco
- Gillings School of Global Public Health, Kenan-Flagler Business School, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Regine M. Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jacob J. Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ulianna Voytovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Kiah Bowers
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Gordon Whiteley
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Simona Colantonio
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - William Bocik
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Rhonda Roberts
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Matthew Holderfield
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA 94063, USA
| | - Steven A. Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - John M. Koomen
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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El-Kenawi A, Dominguez-Viqueira W, Liu M, Awasthi S, Abraham-Miranda J, Keske A, Steiner KK, Noel L, Serna AN, Dhillon J, Gillies RJ, Yu X, Koomen JM, Yamoah K, Gatenby RA, Ruffell B. Macrophage-derived cholesterol contributes to therapeutic resistance in prostate cancer. Cancer Res 2021; 81:5477-5490. [PMID: 34301759 DOI: 10.1158/0008-5472.can-20-4028] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [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: 12/03/2020] [Revised: 06/16/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022]
Abstract
Castration-resistant prostate cancer (CRPC) is a lethal stage of disease in which androgen receptor (AR) signaling is persistent despite androgen deprivation therapy (ADT). Most studies have focused on investigating cell-autonomous alterations in CRPC, while the contributions of the tumor microenvironment are less well understood. Here we sought to determine the role of tumor-associated macrophages in CRPC, based upon their role in cancer progression and therapeutic resistance. In a syngeneic model that reflected the mutational landscape of CRPC, macrophage depletion resulted in a reduced transcriptional signature for steroid and bile acid synthesis, indicating potential perturbation of cholesterol metabolism. As cholesterol is the precursor of the five major types of steroid hormones, we hypothesized that macrophages were regulating androgen biosynthesis within the prostate tumor microenvironment. Macrophage depletion reduced androgen levels within prostate tumors and restricted androgen receptor (AR) nuclear localization in vitro and in vivo. Macrophages were also cholesterol-rich and were able to transfer cholesterol to tumor cells in vitro. AR nuclear translocation was inhibited by activation of Liver X Receptor (LXR)-β, the master regulator of cholesterol homeostasis. Consistent with these data, macrophage depletion extended survival during ADT and the presence of macrophages correlated with therapeutic resistance in patient-derived explants. Taken together, these findings support the therapeutic targeting of macrophages in CRPC.
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Affiliation(s)
- Asmaa El-Kenawi
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | | | - Min Liu
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Shivanshu Awasthi
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Julieta Abraham-Miranda
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Aysenur Keske
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - KayLee K Steiner
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Leenil Noel
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Amparo N Serna
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jasreman Dhillon
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Robert J Gillies
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - John M Koomen
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kosj Yamoah
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Robert A Gatenby
- Department of Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Brian Ruffell
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
- Department of Breast Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
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Hamaidi I, Zhang L, Kim N, Wang MH, Iclozan C, Fang B, Liu M, Koomen JM, Berglund AE, Yoder SJ, Yao J, Engelman RW, Creelan BC, Conejo-Garcia JR, Mulé JJ, Antonia SJ, Kim S. Abstract 1635: Sirt2 blockade promotes T cell metabolism and restores the anti-tumor immunity. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-1635] [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
Background: The majority of cancer patients remain refractory to existing cancer immunotherapies. Despite the growing evidence that dysregulated metabolism contributes to the exhaustion of tumor-infiltrating T lymphocytes (TILs) and the loss of their effector functions within the metabolically restricted tumor microenvironment (TME), actionable targets to rescue metabolic fitness and anti-tumor activity of TILs remain elusive. Sirt2 is an NAD+ dependent histone deacetylase and conflicting evidences suggest its tumor-suppressor and oncogenic roles. In inflammatory response, Sirt2 suppresses inflammation via negative regulation of NF-κB subunit; however, the role of Sirt2 in tumor immunity has not been described.
Method: Human TILs from non-small cell lung cancer (NSCLC) tumor samples and matched peripheral blood T cells were analyzed for Sirt2 expression by flow cytometry. The role of Sirt2 in anti-tumor immunity was studied by in vivo B16F10 tumor challenge in Wild-type (Wt) and Sirt2 knockout (Sirt2KO) mice. The role of Sirt2 in T cell effector functions was investigated ex vivo by CFSE proliferation assay, IFN-γ ELISpot assay, intracellular staining of effector markers and LDH cytotoxicity assay on Wt versus Sirt2KO T cells. Sirt2 targets were identified using mass spectrometry (MS) and Co-immunoprecipitation analyses. T cells metabolic changes were investigated using seahorse bioanalyzer and LC-MS/MS Metabolomic profiling. Sirt2 blockade in human T cells was performed using AGK2, a Sirt2 selective inhibitor.
Result: We show that Sirt2 expression is upregulated within the TME, and its upregulation in human TILs is associated with a poor clinical response to immunotherapy in a phase I clinical trial in advanced NSCLC. We also show that, Sirt2 deficiency in mice boosts T cell effector functions and tumor rejection in vivo. Our molecular and metabolomic studies revealed multiple metabolic pathways as Sirt2 targets including glycolysis, TCA-cycle, FAO and glutaminolysis. We found that Sirt2 deacetylase deficiency increased acetylation and enzymatic activity of key metabolic enzymes leading to a hyper metabolic status of T cells. Finally pharmacologic inhibition of Sirt2 in human TILs isolated from NSCLC patients enhances their metabolic fitness and effector functions.
Conclusion Our findings indicate Sirt2 as a master suppressor of T cell metabolism amenable to therapeutic targeting and Sirt2 inhibition reprograms T cell metabolic fitness to optimally sustain their effector function within the metabolically challenging TME, thus, leading to an effective anti-tumor immune response.
Citation Format: Imene Hamaidi, Lin Zhang, Nayoung Kim, Min Hsuan Wang, Cristina Iclozan, Bin Fang, Min Liu, John M. Koomen, Anders E. Berglund, Sean J. Yoder, Jiqiang Yao, Robert W. Engelman, Ben C. Creelan, Jose R. Conejo-Garcia, James J. Mulé, Scott J. Antonia, Sungjune Kim. Sirt2 blockade promotes T cell metabolism and restores the anti-tumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1635.
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Affiliation(s)
| | - Lin Zhang
- 2Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Nayoung Kim
- 3Rosetta Exosome Inc., Seoul, Democratic People's Republic of Korea
| | | | | | - Bin Fang
- 1H. Lee Moffitt Cancer Center, Tampa, FL
| | - Min Liu
- 1H. Lee Moffitt Cancer Center, Tampa, FL
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Koomen DC, Meads MB, Magaletti DM, Guingab-Cagmat JD, Oliveira PS, Fang B, Liu M, Welsh EA, Meke LE, Jiang Z, Hampton OA, Tungesvik A, De Avila G, Alugubelli RR, Nishihori T, Silva AS, Eschrich SA, Garrett TJ, Koomen JM, Shain KH. Metabolic Changes Are Associated with Melphalan Resistance in Multiple Myeloma. J Proteome Res 2021; 20:3134-3149. [PMID: 34014671 DOI: 10.1021/acs.jproteome.1c00022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multiple myeloma is an incurable hematological malignancy that impacts tens of thousands of people every year in the United States. Treatment for eligible patients involves induction, consolidation with stem cell rescue, and maintenance. High-dose therapy with a DNA alkylating agent, melphalan, remains the primary drug for consolidation therapy in conjunction with autologous stem-cell transplantation; as such, melphalan resistance remains a relevant clinical challenge. Here, we describe a proteometabolomic approach to examine mechanisms of acquired melphalan resistance in two cell line models. Drug metabolism, steady-state metabolomics, activity-based protein profiling (ABPP, data available at PRIDE: PXD019725), acute-treatment metabolomics, and western blot analyses have allowed us to further elucidate metabolic processes associated with melphalan resistance. Proteometabolomic data indicate that drug-resistant cells have higher levels of pentose phosphate pathway metabolites. Purine, pyrimidine, and glutathione metabolisms were commonly altered, and cell-line-specific changes in metabolite levels were observed, which could be linked to the differences in steady-state metabolism of naïve cells. Inhibition of selected enzymes in purine synthesis and pentose phosphate pathways was evaluated to determine their potential to improve melphalan's efficacy. The clinical relevance of these proteometabolomic leads was confirmed by comparison of tumor cell transcriptomes from newly diagnosed MM patients and patients with relapsed disease after treatment with high-dose melphalan and autologous stem-cell transplantation. The observation of common and cell-line-specific changes in metabolite levels suggests that omic approaches will be needed to fully examine melphalan resistance in patient specimens and define personalized strategies to optimize the use of high-dose melphalan.
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Affiliation(s)
- David C Koomen
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Mark B Meads
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Dario M Magaletti
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Joy D Guingab-Cagmat
- University of Florida College of Medicine, Gainesville, Florida 32610, United States
| | - Paula S Oliveira
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Bin Fang
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Min Liu
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Eric A Welsh
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Laurel E Meke
- University of Florida College of Medicine, Gainesville, Florida 32610, United States
| | | | | | - Alexandre Tungesvik
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Gabriel De Avila
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | | | - Taiga Nishihori
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Ariosto S Silva
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Steven A Eschrich
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Timothy J Garrett
- University of Florida College of Medicine, Gainesville, Florida 32610, United States
| | - John M Koomen
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Kenneth H Shain
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
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Smalley KSM, Teer JK, Chen YA, Wu JY, Yao J, Koomen JM, Chen WS, Rodriguez-Waitkus P, Karreth FA, Messina JL. A Mutational Survey of Acral Nevi. JAMA Dermatol 2021; 157:831-835. [PMID: 33978681 DOI: 10.1001/jamadermatol.2021.0793] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Importance Acral skin may develop nevi, but their mutational status and association with acral melanoma is unclear. Objective To perform targeted next-generation sequencing on a cohort of acral nevi to determine their mutational spectrum. Design, Setting, and Participants Acral nevi specimens (n = 50) that had been obtained for diagnostic purposes were identified from the pathology archives of a tertiary care academic cancer center and a university dermatology clinic. Next-generation sequencing was performed on DNA extracted from the specimens, and mutations called. A subset of samples was stained immunohistochemically for the BRAF V600E mutation. Results A total of 50 nevi from 49 patients (19 males and 30 females; median [range] age, 48 [13-85] years) were examined. Analysis of the sequencing data revealed a high prevalence of BRAF mutations (n = 43), with a lower frequency of NRAS mutations (n = 5). Mutations in BRAF and NRAS were mutually exclusive. Conclusions and Relevance In this cohort study, nevi arising on mostly sun-protected acral skin showed a rate of BRAF mutation similar to that of acquired nevi on sun-exposed skin but far higher than that of acral melanoma. These findings are in contrast to the well-characterized mutational landscape of acral melanoma.
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Affiliation(s)
- Keiran S M Smalley
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, Florida.,Department of Cutaneous Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Y Ann Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jheng-Yu Wu
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jiqiang Yao
- Biostatistics and Bioinformatics Shared Resource, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - John M Koomen
- Department of Molecular Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Wei-Shen Chen
- Department of Dermatology and Cutaneous Surgery, University of South Florida Morsani College of Medicine, Tampa, Florida
| | - Paul Rodriguez-Waitkus
- Department of Dermatology and Cutaneous Surgery, University of South Florida Morsani College of Medicine, Tampa, Florida
| | - Florian A Karreth
- Department of Molecular Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jane L Messina
- Department of Cutaneous Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida
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40
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Solanki HS, Welsh EA, Fang B, Izumi V, Darville L, Stone B, Franzese R, Chavan S, Kinose F, Imbody D, Koomen JM, Rix U, Haura EB. Cell Type-specific Adaptive Signaling Responses to KRAS G12C Inhibition. Clin Cancer Res 2021; 27:2533-2548. [PMID: 33619172 PMCID: PMC9940280 DOI: 10.1158/1078-0432.ccr-20-3872] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/29/2020] [Accepted: 02/16/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Covalent inhibitors of KRASG12C specifically target tumors driven by this form of mutant KRAS, yet early studies show that bypass signaling drives adaptive resistance. Although several combination strategies have been shown to improve efficacy of KRASG12C inhibitors (KRASi), underlying mechanisms and predictive strategies for patient enrichment are less clear. EXPERIMENTAL DESIGN We performed mass spectrometry-based phosphoproteomics analysis in KRASG12C cell lines after short-term treatment with ARS-1620. To understand signaling diversity and cell type-specific markers, we compared proteome and phosphoproteomes of KRASG12C cells. Gene expression patterns of KRASG12C cell lines and lung tumor tissues were examined. RESULTS Our analysis suggests cell type-specific perturbation to ERBB2/3 signaling compensates for repressed ERK and AKT signaling following ARS-1620 treatment in epithelial cell type, and this subtype was also more responsive to coinhibition of SHP2 and SOS1. Conversely, both high basal and feedback activation of FGFR or AXL signaling were identified in mesenchymal cells. Inhibition of FGFR signaling suppressed feedback activation of ERK and mTOR, while AXL inhibition suppressed PI3K pathway. In both cell lines and human lung cancer tissues with KRASG12C, we observed high basal ERBB2/3 associated with epithelial gene signatures, while higher basal FGFR1 and AXL were observed in cells/tumors with mesenchymal gene signatures. CONCLUSIONS Our phosphoproteomic study identified cell type-adaptive responses to KRASi. Markers and targets associated with ERBB2/3 signaling in epithelial subtype and with FGFR1/AXL signaling in mesenchymal subtype should be considered in patient enrichment schemes with KRASi.
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Affiliation(s)
- Hitendra S. Solanki
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric A. Welsh
- Biostatistics and Bioinformatics Shared Resources, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Bin Fang
- Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Victoria Izumi
- Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Lancia Darville
- Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Brandon Stone
- Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Ryan Franzese
- Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Sandip Chavan
- Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Fumi Kinose
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Denis Imbody
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA,Undergraduate Studies in Chemistry, University of South Florida, Tampa, FL 33620, USA
| | - John M. Koomen
- Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA,Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA,To whom correspondence should be addressed: Eric Haura, Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, , Tel.: 813-745-6827
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Hajiran A, Chakiryan N, Aydin AM, Zemp L, Nguyen J, Laborde JM, Chahoud J, Spiess PE, Zaman S, Falasiri S, Fournier M, Teer JK, Dhillon J, McCarthy S, Moran-Segura C, Katende EN, Sexton WJ, Koomen JM, Mulé J, Kim Y, Manley B. Reconnaissance of tumor immune microenvironment spatial heterogeneity in metastatic renal cell carcinoma and correlation with immunotherapy response. Clin Exp Immunol 2021; 204:96-106. [PMID: 33346915 DOI: 10.1111/cei.13567] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/22/2020] [Accepted: 12/02/2020] [Indexed: 12/24/2022] Open
Abstract
A clearer understanding of the tumor immune microenvironment (TIME) in metastatic clear cell renal cell carcinoma (ccRCC) may help to inform precision treatment strategies. We sought to identify clinically meaningful TIME signatures in ccRCC. We studied tumors from 39 patients with metastatic ccRCC using quantitative multiplexed immunofluorescence and relevant immune marker panels. Cell densities were analyzed in three regions of interest (ROIs): tumor core, tumor-stroma interface and stroma. Patients were stratified into low- and high-marker density groups using median values as thresholds. Log-rank and Cox regression analyses while controlling for clinical variables were used to compare survival outcomes to patterns of immune cell distributions. There were significant associations with increased macrophage (CD68+ CD163+ CD206+ ) density and poor outcomes across multiple ROIs in primary and metastatic tumors. In primary tumors, T-bet+ T helper type 1 (Th1) cell density was highest at the tumor-stromal interface (P = 0·0021), and increased co-expression of CD3 and T-bet was associated with improved overall survival (P = 0·015) and survival after immunotherapy (P = 0·014). In metastatic tumor samples, decreased forkhead box protein 3 (FoxP3)+ T regulatory cell density correlated with improved survival after immunotherapy (P = 0·016). Increased macrophage markers and decreased Th1 T cell markers within the TIME correlated with poor overall survival and treatment outcomes. Immune markers such as FoxP3 showed consistent levels across the TIME, whereas others, such as T-bet, demonstrated significant variance across the distinct ROIs. These findings suggest that TIME profiling outside the tumor core may identify clinically relevant associations for patients with metastatic ccRCC.
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Affiliation(s)
- A Hajiran
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - N Chakiryan
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - A M Aydin
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - L Zemp
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - J Nguyen
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - J M Laborde
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - J Chahoud
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - P E Spiess
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - S Zaman
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - S Falasiri
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - M Fournier
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - J K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - J Dhillon
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - S McCarthy
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - C Moran-Segura
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - E N Katende
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - W J Sexton
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - J M Koomen
- Department of Proteomics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - J Mulé
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Y Kim
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - B Manley
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.,Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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42
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Fang B, Izumi V, Rix LLR, Welsh E, Pike I, Reuther GW, Haura EB, Rix U, Koomen JM. Lowering Sample Requirements to Study Tyrosine Kinase Signaling Using Phosphoproteomics with the TMT Calibrator Approach. Proteomics 2020; 20:e2000116. [PMID: 32865326 PMCID: PMC7771371 DOI: 10.1002/pmic.202000116] [Citation(s) in RCA: 8] [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] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/13/2020] [Indexed: 12/12/2022]
Abstract
Analysis of tyrosine kinase signaling is critical for the development of targeted cancer therapy. Currently, immunoprecipitation of phosphotyrosine (pY) peptides prior to liquid chromatography-tandem mass spectrometry (LC-MS/MS) is used to profile tyrosine kinase substrates. A typical protocol requests 10 mg of total protein from ≈108 cells or 50-100 mg of tissue. Large sample requirements can be cost prohibitive or not feasible for certain experiments. Sample multiplexing using chemical labeling reduces the protein amount required for each sample, and newer approaches use a material-rich reference channel as a calibrator to trigger detection and quantification for smaller samples. Here, it is demonstrated that the tandem mass tag (TMT) calibrator approach reduces the sample input for pY profiling tenfold (to ≈1 mg total protein per sample from 107 cells grown in one plate), while maintaining the depth of pY proteome sampling and the biological content of the experiment. Data are available through PRIDE (PXD019764 for label-free and PXD018952 for TMT). This strategy opens more opportunities for pY profiling of large sample cohorts and samples with limited protein quantity such as immune cells, xenograft models, and human tumors.
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Affiliation(s)
- Bin Fang
- Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Victoria Izumi
- Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | | | - Eric Welsh
- Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Ian Pike
- Proteome Sciences, Hamilton House, 4 Mabledon Place, London, WC1H 9BB, UK
| | - Gary W Reuther
- Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Eric B Haura
- Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Uwe Rix
- Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - John M Koomen
- Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL, 33612, USA
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Garg SK, Welsh EA, Fang B, Hernandez YI, Rose T, Gray J, Koomen JM, Berglund A, Mulé JJ, Markowitz J. Multi-Omics and Informatics Analysis of FFPE Tissues Derived from Melanoma Patients with Long/Short Responses to Anti-PD1 Therapy Reveals Pathways of Response. Cancers (Basel) 2020; 12:cancers12123515. [PMID: 33255891 PMCID: PMC7768436 DOI: 10.3390/cancers12123515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 11/02/2020] [Accepted: 11/21/2020] [Indexed: 01/14/2023] Open
Abstract
Simple Summary Immune based therapies have benefited many melanoma patients, but many patients still do not respond. This study analyzes biospecimens obtained from patients undergoing a type of immune based therapy called anti-PD-1 to understand mechanisms of response and resistance to this treatment. The operational definition of good response utilized in this investigation permitted us to examine the biochemical pathways that are facilitating anti-PD-1 responses independent of prior therapies received by patients. Currently, there are no clinically available tests to reliably test for the outcome of patients treated with anti-PD-1 therapy. The purpose of this study was to facilitate the development of prospective biomarker-directed trials to guide therapy, as even though the side effect profile is favorable for anti-PD-1 therapy, some patients do not respond to therapy with significant toxicity. Each patient may require testing for the pathways upregulated in the tumor to predict optimal benefit to anti-PD-1 treatment. Abstract Anti-PD-1 based immune therapies are thought to be dependent on antigen processing and presentation mechanisms. To characterize the immune-dependent mechanisms that predispose stage III/IV melanoma patients to respond to anti-PD-1 therapies, we performed a multi-omics study consisting of expression proteomics and targeted immune-oncology-based mRNA sequencing. Formalin-fixed paraffin-embedded tissue samples were obtained from stage III/IV patients with melanoma prior to anti-PD-1 therapy. The patients were first stratified into poor and good responders based on whether their tumors had or had not progressed while on anti-PD-1 therapy for 1 year. We identified 263 protein/gene candidates that displayed differential expression, of which 223 were identified via proteomics and 40 via targeted-mRNA analyses. The downstream analyses of expression profiles using MetaCore software demonstrated an enrichment of immune system pathways involved in antigen processing/presentation and cytokine production/signaling. Pathway analyses showed interferon (IFN)-γ-mediated signaling via NF-κB and JAK/STAT pathways to affect immune processes in a cell-specific manner and to interact with the inducible nitric oxide synthase. We review these findings within the context of available literature on the efficacy of anti-PD-1 therapy. The comparison of good and poor responders, using efficacy of PD-1-based therapy at 1 year, elucidated the role of antigen presentation in mediating response or resistance to anti-PD-1 blockade.
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Affiliation(s)
- Saurabh K. Garg
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (S.K.G.); (Y.I.H.)
| | - Eric A. Welsh
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA;
| | - Bin Fang
- Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (B.F.); (J.M.K.)
| | - Yuliana I. Hernandez
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (S.K.G.); (Y.I.H.)
| | - Trevor Rose
- Department of Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA;
- Department of Oncologic Sciences, University of South Florida Health Morsani College of Medicine, Tampa, FL 33620, USA; (J.G.); (A.B.); (J.J.M.)
| | - Jhanelle Gray
- Department of Oncologic Sciences, University of South Florida Health Morsani College of Medicine, Tampa, FL 33620, USA; (J.G.); (A.B.); (J.J.M.)
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - John M. Koomen
- Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (B.F.); (J.M.K.)
- Department of Oncologic Sciences, University of South Florida Health Morsani College of Medicine, Tampa, FL 33620, USA; (J.G.); (A.B.); (J.J.M.)
| | - Anders Berglund
- Department of Oncologic Sciences, University of South Florida Health Morsani College of Medicine, Tampa, FL 33620, USA; (J.G.); (A.B.); (J.J.M.)
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - James J. Mulé
- Department of Oncologic Sciences, University of South Florida Health Morsani College of Medicine, Tampa, FL 33620, USA; (J.G.); (A.B.); (J.J.M.)
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Joseph Markowitz
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; (S.K.G.); (Y.I.H.)
- Department of Oncologic Sciences, University of South Florida Health Morsani College of Medicine, Tampa, FL 33620, USA; (J.G.); (A.B.); (J.J.M.)
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-813-745-8581
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Taylor NJ, Gaynanova I, Eschrich SA, Welsh EA, Garrett TJ, Beecher C, Sharma R, Koomen JM, Smalley KSM, Messina JL, Kanetsky PA. Metabolomics of primary cutaneous melanoma and matched adjacent extratumoral microenvironment. PLoS One 2020; 15:e0240849. [PMID: 33108391 PMCID: PMC7591037 DOI: 10.1371/journal.pone.0240849] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 04/06/2020] [Accepted: 10/04/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Melanoma causes the vast majority of deaths attributable to skin cancer, largely due to its propensity for metastasis. To date, few studies have examined molecular changes between primary cutaneous melanoma and adjacent putatively normal skin. To broaden temporal inferences related to initiation of disease, we performed a metabolomics investigation of primary melanoma and matched extratumoral microenvironment (EM) tissues; and, to make inferences about progressive disease, we also compared unmatched metastatic melanoma tissues to EM tissues. METHODS Ultra-high performance liquid chromatography-mass spectrometry-based metabolic profiling was performed on frozen human tissues. RESULTS We observed 824 metabolites as differentially abundant among 33 matched tissue samples, and 1,118 metabolites as differentially abundant between metastatic melanoma (n = 46) and EM (n = 34) after false discovery rate (FDR) adjustment (p<0.01). No significant differences in metabolite abundances were noted comparing primary and metastatic melanoma tissues. CONCLUSIONS Overall, pathway-based results significantly distinguished melanoma tissues from EM in the metabolism of: ascorbate and aldarate, propanoate, tryptophan, histidine, and pyrimidine. Within pathways, the majority of individual metabolite abundances observed in comparisons of primary melanoma vs. EM and metastatic melanoma vs. EM were directionally consistent. This observed concordance suggests most identified compounds are implicated in the initiation or maintenance of melanoma.
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Affiliation(s)
- Nicholas J. Taylor
- Department of Epidemiology and Biostatistics, Texas A&M University, College Station, Texas, United States of America
| | - Irina Gaynanova
- Department of Statistics, Texas A&M University, College Station, Texas, United States of America
| | - Steven A. Eschrich
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Eric A. Welsh
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Timothy J. Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Chris Beecher
- IROA Technologies, Chapel Hill, North Carolina, United States of America
| | - Ritin Sharma
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - John M. Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Keiran S. M. Smalley
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Jane L. Messina
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Peter A. Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
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Hill KS, Roberts ER, Wang X, Koomen JM, Messina JL, Teer JK, Kim Y, Wu J, Chalfant CE, Kim M. Abstract PR13: PTPN11 plays oncogenic roles and is a therapeutic target for BRAF wild-type melanomas. Cancer Res 2020. [DOI: 10.1158/1538-7445.mel2019-pr13] [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
Melanoma is one of the most highly mutated cancer types, harboring numerous alterations with unknown significance. To identify functional drivers of melanoma, we searched for cross-species conserved mutations utilizing a mouse melanoma model driven by loss of PTEN and CDKN2A, and identified mutations in Kras, Erbb3, and Ptpn11. PTPN11 encodes the SHP2 protein tyrosine phosphatase (PTP) that activates the RAS/RAF/MAPK pathway. Although PTPN11 is an oncogene in leukemia, lung, and breast cancers, its roles in melanoma are not clear. In this study, we found that PTPN11 is frequently activated in human melanoma specimens and cell lines and is required for full RAS/RAF/MAPK signaling activation in BRAF wild-type (either NRAS mutant or wild-type) melanoma cells. PTPN11 played oncogenic roles in melanoma by driving anchorage-independent colony formation and tumor growth. In Pten and Cdkn2a null mice, tet-inducible and melanocyte-specific PTPN11E76K expression significantly enhanced melanoma tumorigenesis. Melanoma cells derived from this mouse model showed doxycycline-dependent tumor growth in nude mice. Silencing PTPN11E76K expression by doxycycline withdrawal caused regression of established tumors by induction of apoptosis and senescence and suppression of proliferation. Moreover, the PTPN11 inhibitor (SHP099) also caused regression of NRASQ61K-mutant melanoma. Using a quantitative tyrosine phospho-proteomics approach, we identified GSK3α/β as one of the key substrates that were differentially tyrosine-phosphorylated in these experiments modulating PTPN11. This study demonstrates that PTPN11 plays oncogenic roles in melanoma and regulates RAS and GSK3α/β signaling pathways. This study also identifies PTPN11 as a novel and actionable therapeutic target for BRAF wild-type melanoma.
This abstract is also being presented as Poster A14.
Citation Format: Kristen S. Hill, Evan R. Roberts, Xue Wang, John M. Koomen, Jane L. Messina, Jamie K. Teer, Youngchul Kim, Jie Wu, Charles E. Chalfant, Minjung Kim. PTPN11 plays oncogenic roles and is a therapeutic target for BRAF wild-type melanomas [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr PR13.
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Affiliation(s)
| | | | - Xue Wang
- 2University of South Florida, Tampa, FL,
| | | | | | | | | | - Jie Wu
- 3University of Oklahoma Health Sciences Center, Oklahoma City, OK
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Darville LNF, Cline JK, Rozmeski C, Martinez YC, Rich S, Eschrich SA, Egan KM, Yaghjyan L, Koomen JM. LC-HRMS of derivatized urinary estrogens and estrogen metabolites in postmenopausal women. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1154:122288. [PMID: 32769047 DOI: 10.1016/j.jchromb.2020.122288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 12/13/2019] [Revised: 07/01/2020] [Accepted: 07/25/2020] [Indexed: 12/21/2022]
Abstract
In order to undertake an epidemiologic study relating levels of parent estrogens (estrone and estradiol) and estrogen metabolites (EMs) to other breast cancer risk factors, we have optimized methods for EM quantification with ultra high performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS). A two-step approach was adopted; the first step comprised method development and evaluation of the method performance. The second step consisted of applying this method to quantify estrogens in postmenopausal women and determine if the observed patterns are consistent with the existing literature and prior knowledge of estrogen metabolism. First, 1-methylimidazole-2-sulfonyl chloride (MIS) was used to derivatize endogenous estrogens and estrogen metabolites in urine from study participants. Since C18 reversed phase columns have not been able to separate all the structurally related EMs, we used a C18-pentafluorophenyl (PFP) column. The parent estrogens and EMs were baseline resolved with distinct retention times on this C18-PFP column using a 30 min gradient. This method was used to quantify the parent estrogens and 13 EMs in urine samples collected in an initial pilot study involving males as well as pre- and peri-menopausal females to assess a range of EM levels in urine samples and enable comparison to the previous literature for assay evaluation. Detection limits ranged from 1 - 20 pg/mL depending on the EM. We evaluated matrix effects and interference as well as the intra- and inter-batch reproducibility including hydrolysis, extraction, derivatization and LC-MS analysis using charcoal-stripped human urine as a matrix. Methods were then applied to the measurement of estrogens in urine samples from 169 postmenopausal women enrolled in an epidemiological study to examine relationships between breast cancer risk, the intestinal microbiome, and urinary EMs. The results from our cohort are comparable to previous reports on urinary EMs in postmenopausal women and enabled thorough evaluation of the method.
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Affiliation(s)
- Lancia N F Darville
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States.
| | - Jayden K Cline
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States
| | - Carrie Rozmeski
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States
| | - Yessica C Martinez
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States
| | - Shannan Rich
- University of Florida, Gainesville, FL, United States
| | - Steven A Eschrich
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States
| | - Kathleen M Egan
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States.
| | | | - John M Koomen
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States
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Zhang C, Smalley I, Emmons MF, Sharma R, Izumi V, Messina J, Koomen JM, Pasquale EB, Forsyth PA, Smalley KSM. Noncanonical EphA2 Signaling Is a Driver of Tumor-Endothelial Cell Interactions and Metastatic Dissemination in BRAF Inhibitor‒Resistant Melanoma. J Invest Dermatol 2020; 141:840-851.e4. [PMID: 32890629 DOI: 10.1016/j.jid.2020.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 05/08/2020] [Revised: 07/20/2020] [Accepted: 08/04/2020] [Indexed: 12/16/2022]
Abstract
Acquired BRAF/MAPK/extracellular signal‒regulated kinase inhibitor resistance in melanoma results in a new transcriptional state associated with an increased risk of metastasis. In this study, we identified noncanonical ephrin receptor (Eph) EphA2 signaling as a driver of the resistance-associated metastatic state. We used mass spectrometry‒based proteomic and phenotypic assays to demonstrate that the expression of active noncanonical EphA2-S897E in melanoma cells led to a mesenchymal-to-amoeboid transition driven by Cdc42 activation. The induction of mesenchymal-to-amoeboid transition promoted melanoma cell invasion, survival under shear stress, adhesion to endothelial cells under continuous-flow conditions, increased permeability of endothelial cell monolayers, and stimulated melanoma transendothelial cell migration. In vivo, melanoma cells expressing EphA2-S897E or active Cdc42 showed superior lung retention after tail-vain injection. Analysis of BRAF inhibitor‒sensitive and ‒resistant melanoma cells demonstrated resistance to be associated with a mesenchymal-to-amoeboid transition switch, upregulation of Cdc42 activity, increased invasion, and transendothelial migration. The drug-resistant metastatic state was dependent on histone deacetylase 8 activity. Silencing of histone deacetylase 8 led to the inhibition of EphA2 and protein kinase B phosphorylation, reduced invasion, and impaired melanoma cell-endothelial cell interactions. In summary, we have demonstrated that the metastatic state associated with acquired BRAF inhibitor resistance is dependent on noncanonical EphA2 signaling, leading to increased melanoma-endothelial cell interactions and enhanced tumor dissemination.
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Affiliation(s)
- Chao Zhang
- The Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Inna Smalley
- The Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA.
| | - Michael F Emmons
- The Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Ritin Sharma
- The Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Victoria Izumi
- The Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Jane Messina
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - John M Koomen
- The Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Elena B Pasquale
- Department of Tumor Initiation and Maintenance, Sanford Burnham Prebys Medical Discovery Institute, San Diego, California, USA
| | - Peter A Forsyth
- The Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA; The Department of Neuro-Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA; Tom Baker Cancer Center, University of Calgary, Calgary, Alberta, Canada
| | - Keiran S M Smalley
- The Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA; The Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
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Hamaidi I, Zhang L, Kim N, Wang MH, Iclozan C, Fang B, Liu M, Koomen JM, Berglund AE, Yoder SJ, Yao J, Engelman RW, Creelan BC, Conejo-Garcia JR, Antonia SJ, Mulé JJ, Kim S. Sirt2 Inhibition Enhances Metabolic Fitness and Effector Functions of Tumor-Reactive T Cells. Cell Metab 2020; 32:420-436.e12. [PMID: 32768387 PMCID: PMC7484212 DOI: 10.1016/j.cmet.2020.07.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/21/2020] [Accepted: 07/15/2020] [Indexed: 02/07/2023]
Abstract
Dysregulated metabolism is a key driver of maladaptive tumor-reactive T lymphocytes within the tumor microenvironment. Actionable targets that rescue the effector activity of antitumor T cells remain elusive. Here, we report that the Sirtuin-2 (Sirt2) NAD+-dependent deacetylase inhibits T cell metabolism and impairs T cell effector functions. Remarkably, upregulation of Sirt2 in human tumor-infiltrating lymphocytes (TILs) negatively correlates with response to TIL therapy in advanced non-small-cell lung cancer. Mechanistically, Sirt2 suppresses T cell metabolism by targeting key enzymes involved in glycolysis, tricarboxylic acid-cycle, fatty acid oxidation, and glutaminolysis. Accordingly, Sirt2-deficient murine T cells exhibit increased glycolysis and oxidative phosphorylation, resulting in enhanced proliferation and effector functions and subsequently exhibiting superior antitumor activity. Importantly, pharmacologic inhibition of Sirt2 endows human TILs with these superior metabolic fitness and effector functions. Our findings unveil Sirt2 as an unexpected actionable target for reprogramming T cell metabolism to augment a broad spectrum of cancer immunotherapies.
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Affiliation(s)
- Imene Hamaidi
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Lin Zhang
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Nayoung Kim
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Min-Hsuan Wang
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Cristina Iclozan
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Min Liu
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - John M Koomen
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; Department of Molecular Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Anders E Berglund
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Sean J Yoder
- Molecular Genomics Core, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Jiqiang Yao
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Robert W Engelman
- Pediatrics, Pathology & Cell Biology, University of South of Florida, Tampa, FL 33612, USA
| | - Ben C Creelan
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | | | - Scott J Antonia
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - James J Mulé
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Sungjune Kim
- Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; Department of Radiation Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA.
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Li Q, Fisher K, Meng W, Fang B, Welsh E, Haura EB, Koomen JM, Eschrich SA, Fridley BL, Chen YA. GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis. Bioinformatics 2020; 36:257-263. [PMID: 31199438 PMCID: PMC6956786 DOI: 10.1093/bioinformatics/btz488] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 09/14/2018] [Revised: 05/06/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022] Open
Abstract
Motivation Missingness in label-free mass spectrometry is inherent to the technology. A computational approach to recover missing values in metabolomics and proteomics datasets is important. Most existing methods are designed under a particular assumption, either missing at random or under the detection limit. If the missing pattern deviates from the assumption, it may lead to biased results. Hence, we investigate the missing patterns in free mass spectrometry data and develop an omnibus approach GMSimpute, to allow effective imputation accommodating different missing patterns. Results Three proteomics datasets and one metabolomics dataset indicate missing values could be a mixture of abundance-dependent and abundance-independent missingness. We assess the performance of GMSimpute using simulated data (with a wide range of 80 missing patterns) and metabolomics data from the Cancer Genome Atlas breast cancer and clear cell renal cell carcinoma studies. Using Pearson correlation and normalized root mean square errors between the true and imputed abundance, we compare its performance to K-nearest neighbors’ type approaches, Random Forest, GSimp, a model-based method implemented in DanteR and minimum values. The results indicate GMSimpute provides higher accuracy in imputation and exhibits stable performance across different missing patterns. In addition, GMSimpute is able to identify the features in downstream differential expression analysis with high accuracy when applied to the Cancer Genome Atlas datasets. Availability and implementation GMSimpute is on CRAN: https://cran.r-project.org/web/packages/GMSimpute/index.html. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qian Li
- Health Informatics Institute, University of South Florida, Tampa, FL, USA
| | - Kate Fisher
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA.,Department of Biostatistics, IDDI Inc., Raleigh, NC, USA
| | - Wenjun Meng
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Bin Fang
- Proteomics and Metabolomics Core Facility, Moffitt Cancer Center, Tampa, FL, USA
| | - Eric Welsh
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Eric B Haura
- Department of Thoracic Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - John M Koomen
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Steven A Eschrich
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Brooke L Fridley
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Y Ann Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
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Mooradian M, Cleary JM, Cohen JV, Lawrence DP, Buchbinder EI, Giobbie-Hurder A, Parikh AR, Shapiro G, Darville L, Smalley K, Koomen JM, Newton A, Keer HN, Ivy SP, Chen HX, Sullivan RJ. CTEP 9557: A dose-escalation trial of combination dabrafenib, trametinib, and AT13387 in patients with BRAF mutant solid tumors. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.3609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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
3609 Background: Combination BRAF and MEK inhibitor therapy is associated with response in patients (pts) with BRAF mutant (mut) solid tumors; however critical limitations for the durable activity of these agents remains. Preclinically, the addition of heat shock protein 90 (HSP90) inhibitors improves the efficacy of BRAF inhibitor (BRAFi) therapy in both BRAFi -sensitive and resistant mutant cell lines. Methods: CTEP study 9557 (NCT02097225) is a phase I study designed to determine the safety and efficacy of the small molecule HSP90inhibitor, AT13387, in combination with dabrafenib (dab) and trametinib (tram) in patients with BRAF V600E/K mut solid tumors. Prior chemotherapy, immunotherapy, BRAF and/or MEK exposure was permitted. The primary objective was to determine the maximum tolerated dose (MTD). Results: From July 2015 to June 2018, 22 patients with previously treated, metastatic BRAF V600E/K mut solid tumors were enrolled using a 3 + 3 design at four dose levels (DL) (Table). Pts were predominantly female (59%) with a median age of 57.5yrs (37 -75). The most common tumor type was BRAF V600Emut colon cancer (N=12). Dose limiting toxicities (DLTs) occurred in one patient in DL3 and one in DL4, specifically grade 3 myelosuppression and fatigue, respectively. The MTD was Dab 150mg [BID/PO], Tram 2mg [QD/PO] and AT1187 260mg/m2 [D1,8,15/IV]. Twenty-one of 22 pts were eligible for efficacy assessment. Best response, per RECIST 1.1, was partial response (PR) in 2 pts – one with colon ca (TKI-naïve), one with melanoma (TKI-resistant) - stable disease (SD) in 8 pts, and disease progression (PD) in 11 with a disease control rate (PR + SD) of 47.6% (90% CI: 29% - 67%). Median time to progression was significantly longer in DL3 (3.9 mths; 1.8-9.2) compared to DL1 (1.6mths; 0.9-1.7) or DL2 (1.5; 0.6-3.6). Median PFS and OS were 1.8mths (90% CI: 1.6 – 3.7mths) and 5.1 mths (90% CI: 2.5 -10.6mths), respectively. Median OS was not reached in DL3/4. Correlative data on the expression of the key signaling proteins relating to response will be presented at the meeting. Conclusions: HSP90 inhibition combined with BRAF/MEK inhibition was determined to be safe with evidence of disease control in a heavily pre-treated population of pts with BRAF V600E/K mut solid tumors. Clinical trial information: NCT02097225 . [Table: see text]
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Affiliation(s)
| | | | | | - Donald P. Lawrence
- Massachusetts General Hospital and Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Keiran Smalley
- Departments of Molecular Oncology and Cutaneous Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL
| | - John M Koomen
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Amber Newton
- Massachusetts General Hospital Cancer Center, Boston, MA
| | | | - S. Percy Ivy
- National Cancer Institute at the National Institutes of Health, Rockville, MD
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