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Gordan JD, Kennedy EB, Abou-Alfa GK, Beal E, Finn RS, Gade TP, Goff L, Gupta S, Guy J, Hoang HT, Iyer R, Jaiyesimi I, Jhawer M, Karippot A, Kaseb AO, Kelley RK, Kortmansky J, Leaf A, Remak WM, Sohal DPS, Taddei TH, Wilson Woods A, Yarchoan M, Rose MG. Systemic Therapy for Advanced Hepatocellular Carcinoma: ASCO Guideline Update. J Clin Oncol 2024:JCO2302745. [PMID: 38502889 DOI: 10.1200/jco.23.02745] [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: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 03/21/2024] Open
Abstract
PURPOSE To update an evidence-based guideline to assist in clinical decision-making for patients with advanced hepatocellular carcinoma (HCC). METHODS ASCO convened an Expert Panel to update the 2020 guideline on systemic therapy for HCC. The panel updated the systematic review to include randomized controlled trials (RCTs) published through October 2023 and updated recommendations. RESULTS Ten new RCTs met the inclusion criteria and were added to the evidence base. RECOMMENDATIONS Atezolizumab + bevacizumab (atezo + bev) or durvalumab + tremelimumab (durva + treme) may be offered first-line for patients with advanced HCC, Child-Pugh class A liver disease, and Eastern Cooperative Oncology Group performance status 0-1. Where there are contraindications to these therapies, sorafenib, lenvatinib, or durvalumab may be offered first-line. Following first-line treatment with atezo + bev, second-line therapy with a tyrosine kinase inhibitor (TKI), ramucirumab (for patients with alpha-fetoprotein [AFP] ≥400 ng/mL), durva + treme, or nivolumab + ipilimumab (nivo + ipi) may be recommended for appropriate candidates. Following first-line therapy with durva + treme, second-line therapy with a TKI is recommended. Following first-line treatment with sorafenib or lenvatinib, second-line therapy options include cabozantinib, regorafenib for patients who previously tolerated sorafenib, ramucirumab (AFP ≥400 ng/mL), nivo + ipi, or durvalumab; atezo + bev or durva + treme may be considered for patients who did not have access to these therapies in the first-line setting, and do not have contraindications. Pembrolizumab or nivolumab are also options for appropriate patients following sorafenib or lenvatinib. Third-line therapy may be considered in Child-Pugh class A patients with good PS, using one of the agents listed previously that has a nonidentical mechanism of action with previously received therapy. A cautious approach to systemic therapy is recommended for patients with Child-Pugh class B advanced HCC. Further guidance on choosing between options is included within the guideline.Additional information is available at www.asco.org/gastrointestinal-cancer-guidelines.
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Affiliation(s)
- John D Gordan
- University of California, San Francisco, San Francisco, CA
| | | | - Ghassan K Abou-Alfa
- Memorial Sloan Kettering Cancer Center and Weill Medical College at Cornell University, New York, NY
- Trinity College Dublin Medical School, Dublin, Ireland
| | | | | | | | - Laura Goff
- Vanderbilt Ingram Cancer Center, Nashville, TN
| | | | | | | | - Renuka Iyer
- Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | | | | | | | - R Kate Kelley
- University of California, San Francisco, San Francisco, CA
| | | | - Andrea Leaf
- VA New York Harbor Healthcare System, Brooklyn, NY
| | - William M Remak
- California Hepatitis C Task Force, California Chronic Care Coalition, FAIR Foundation, San Francisco, CA
| | | | - Tamar H Taddei
- Yale University School of Medicine and VA Connecticut Healthcare System, West Haven, CT
| | | | | | - Michal G Rose
- Yale Cancer Center and VA Connecticut Healthcare System, West Haven, CT
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Ma RK, Tsai PY, Farghli AR, Shumway A, Kanke M, Gordan JD, Gujral TS, Vakili K, Nukaya M, Noetzli L, Ronnekleiv-Kelly S, Broom W, Barrow J, Sethupathy P. DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and alters mitochondrial fitness in fibrolamellar carcinoma. PLoS Genet 2024; 20:e1011216. [PMID: 38512964 PMCID: PMC11020935 DOI: 10.1371/journal.pgen.1011216] [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: 09/14/2023] [Revised: 04/16/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Fibrolamellar carcinoma (FLC) is a rare liver cancer that disproportionately affects adolescents and young adults. Currently, no standard of care is available and there remains a dire need for new therapeutics. Most patients harbor the fusion oncogene DNAJB1-PRKACA (DP fusion), but clinical inhibitors are not yet developed and it is critical to identify downstream mediators of FLC pathogenesis. Here, we identify long noncoding RNA LINC00473 among the most highly upregulated genes in FLC tumors and determine that it is strongly suppressed by RNAi-mediated inhibition of the DP fusion in FLC tumor epithelial cells. We show by loss- and gain-of-function studies that LINC00473 suppresses apoptosis, increases the expression of FLC marker genes, and promotes FLC growth in cell-based and in vivo disease models. Mechanistically, LINC00473 plays an important role in promoting glycolysis and altering mitochondrial activity. Specifically, LINC00473 knockdown leads to increased spare respiratory capacity, which indicates mitochondrial fitness. Overall, we propose that LINC00473 could be a viable target for this devastating disease.
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Affiliation(s)
- Rosanna K. Ma
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Pei-Yin Tsai
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Alaa R. Farghli
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Alexandria Shumway
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - John D. Gordan
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, United States of America
| | - Taranjit S. Gujral
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Khashayar Vakili
- Department of Surgery, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Manabu Nukaya
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Leila Noetzli
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Sean Ronnekleiv-Kelly
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Wendy Broom
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Joeva Barrow
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
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Lauer SM, Omar MH, Golkowski MG, Kenerson HL, Lee KS, Pascual BC, Lim HC, Forbush K, Smith FD, Gordan JD, Ong SE, Yeung RS, Scott JD. Recruitment of BAG2 to DNAJ-PKAc scaffolds promotes cell survival and resistance to drug-induced apoptosis in fibrolamellar carcinoma. Cell Rep 2024; 43:113678. [PMID: 38236773 PMCID: PMC10964278 DOI: 10.1016/j.celrep.2024.113678] [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: 07/21/2023] [Revised: 11/23/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024] Open
Abstract
The DNAJ-PKAc fusion kinase is a defining feature of fibrolamellar carcinoma (FLC). FLC tumors are notoriously resistant to standard chemotherapies, with aberrant kinase activity assumed to be a contributing factor. By combining proximity proteomics, biochemical analyses, and live-cell photoactivation microscopy, we demonstrate that DNAJ-PKAc is not constrained by A-kinase anchoring proteins. Consequently, the fusion kinase phosphorylates a unique array of substrates, including proteins involved in translation and the anti-apoptotic factor Bcl-2-associated athanogene 2 (BAG2), a co-chaperone recruited to the fusion kinase through association with Hsp70. Tissue samples from patients with FLC exhibit increased levels of BAG2 in primary and metastatic tumors. Furthermore, drug studies implicate the DNAJ-PKAc/Hsp70/BAG2 axis in potentiating chemotherapeutic resistance. We find that the Bcl-2 inhibitor navitoclax enhances sensitivity to etoposide-induced apoptosis in cells expressing DNAJ-PKAc. Thus, our work indicates BAG2 as a marker for advanced FLC and a chemotherapeutic resistance factor in DNAJ-PKAc signaling scaffolds.
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Affiliation(s)
- Sophia M Lauer
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Mitchell H Omar
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Martin G Golkowski
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Heidi L Kenerson
- Department of Surgery, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Kyung-Soon Lee
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Bryan C Pascual
- Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Huat C Lim
- Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Katherine Forbush
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - F Donelson Smith
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - John D Gordan
- Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Raymond S Yeung
- Department of Surgery, University of Washington Medical Center, Seattle, WA 98195, USA
| | - John D Scott
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA.
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4
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Gordan JD, Keenan BP, Lim HC, Yarchoan M, Kelley RK. New Opportunities to Individualize Frontline Therapy in Advanced Stages of Hepatocellular Carcinoma. Drugs 2023; 83:1091-1109. [PMID: 37402062 DOI: 10.1007/s40265-023-01907-3] [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] [Accepted: 06/05/2023] [Indexed: 07/05/2023]
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer death globally and is rising in incidence. Until recently, treatment options for patients with advanced stages of HCC have been limited to antiangiogenic therapies with modest improvements in overall survival. The emerging role of immunotherapy with immune checkpoint inhibitors (ICI) in oncology has led to a rapid expansion in treatment options and improvements in outcomes for patients with advanced stages of HCC. Recent clinical trials have shown meaningful survival improvement in patients treated with the combination of bevacizumab and atezolizumab, as well as with the combination of tremelimumab with durvalumab, resulting in regulatory approvals of these regimens as frontline therapy. Beyond improvements in overall survival, ICI-based combination regimens achieve higher rates of durable treatment response than multikinase inhibitors and have favorable side effect profiles. With the emergence of doublet anti-angiogenic and immune checkpoint inhibitor (ICI) and dual ICI combinations, individualized therapy is now possible for patients based on co-morbidity profiles and other factors. These more potent systemic therapies are also being tested in earlier stages of disease and in combination with loco-regional therapies such as trans-arterial chemoembolization and stereotactic body radiotherapy. We summarize these advances and emerging therapeutic combinations currently in clinical trials.
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Affiliation(s)
- John D Gordan
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, UC San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, UC San Francisco, San Francisco, CA, USA.
| | - Bridget P Keenan
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, UC San Francisco, San Francisco, CA, USA
- Cancer Immunotherapy Program, Helen Diller Family Comprehensive Cancer Center, UC San Francisco, San Francisco, CA, USA
| | - Huat Chye Lim
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, UC San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, UC San Francisco, San Francisco, CA, USA
| | - Mark Yarchoan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - R Katie Kelley
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, UC San Francisco, San Francisco, CA, USA
- Cancer Immunotherapy Program, Helen Diller Family Comprehensive Cancer Center, UC San Francisco, San Francisco, CA, USA
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5
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Zack T, Losert KP, Maisel SM, Wild J, Yaqubie A, Herman M, Knox JJ, Mayer RJ, Venook AP, Butte A, O'Neill AF, Abou-Alfa GK, Gordan JD. Defining incidence and complications of fibrolamellar liver cancer through tiered computational analysis of clinical data. NPJ Precis Oncol 2023; 7:29. [PMID: 36959495 PMCID: PMC10034241 DOI: 10.1038/s41698-023-00371-2] [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: 09/19/2022] [Accepted: 03/03/2023] [Indexed: 03/25/2023] Open
Abstract
The incidence and biochemical consequences of rare tumor subtypes are often hard to study. Fibrolamellar liver cancer (FLC) is a rare malignancy affecting adolescents and young adults. To better characterize the incidence and biochemical consequences of this disease, we combined a comprehensive analysis of the electronic medical record and national payer data and found that FLC incidence is likely five to eight times higher than previous estimates. By employing unsupervised learning on clinical laboratory data from patients with hyperammonemia, we find that FLC-associated hyperammonemia mirrors metabolic dysregulation in urea cycle disorders. Our findings demonstrate that advanced computational analysis of rich clinical datasets can provide key clinical and biochemical insights into rare cancers.
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Affiliation(s)
- Travis Zack
- Helen Diller Family Comprehensive Cancer Center (HDFCCC), University of California, San Francisco (UCSF), San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | | | | | - Jennifer Wild
- Helen Diller Family Comprehensive Cancer Center (HDFCCC), University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Amin Yaqubie
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Herman
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Jennifer J Knox
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Robert J Mayer
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alan P Venook
- Helen Diller Family Comprehensive Cancer Center (HDFCCC), University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Atul Butte
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Allison F O'Neill
- Dana-Farber Cancer Institute/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Department of Pediatric Oncology, Boston, MA, USA
| | - Ghassan K Abou-Alfa
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Medical College at Cornell University, New York, NY, USA.
| | - John D Gordan
- Helen Diller Family Comprehensive Cancer Center (HDFCCC), University of California, San Francisco (UCSF), San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.
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6
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Chan GKL, Maisel S, Hwang YC, Pascual BC, Wolber RRB, Vu P, Patra KC, Bouhaddou M, Kenerson HL, Lim HC, Long D, Yeung RS, Sethupathy P, Swaney DL, Krogan NJ, Turnham RE, Riehle KJ, Scott JD, Bardeesy N, Gordan JD. Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms. eLife 2023; 12:e69521. [PMID: 36692000 PMCID: PMC9925115 DOI: 10.7554/elife.69521] [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: 04/17/2021] [Accepted: 01/22/2023] [Indexed: 01/25/2023] Open
Abstract
Genetic alterations that activate protein kinase A (PKA) are found in many tumor types. Yet, their downstream oncogenic signaling mechanisms are poorly understood. We used global phosphoproteomics and kinase activity profiling to map conserved signaling outputs driven by a range of genetic changes that activate PKA in human cancer. Two signaling networks were identified downstream of PKA: RAS/MAPK components and an Aurora Kinase A (AURKA)/glycogen synthase kinase (GSK3) sub-network with activity toward MYC oncoproteins. Findings were validated in two PKA-dependent cancer models: a novel, patient-derived fibrolamellar carcinoma (FLC) line that expresses a DNAJ-PKAc fusion and a PKA-addicted melanoma model with a mutant type I PKA regulatory subunit. We identify PKA signals that can influence both de novo translation and stability of the proto-oncogene c-MYC. However, the primary mechanism of PKA effects on MYC in our cell models was translation and could be blocked with the eIF4A inhibitor zotatifin. This compound dramatically reduced c-MYC expression and inhibited FLC cell line growth in vitro. Thus, targeting PKA effects on translation is a potential treatment strategy for FLC and other PKA-driven cancers.
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Affiliation(s)
- Gary KL Chan
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| | - Samantha Maisel
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| | - Yeonjoo C Hwang
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| | - Bryan C Pascual
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| | - Rebecca RB Wolber
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| | - Phuong Vu
- Department of Medicine, Harvard Medical SchoolBostonUnited States
- Massachusetts General Hospital Cancer CenterBostonUnited States
| | - Krushna C Patra
- Department of Medicine, Harvard Medical SchoolBostonUnited States
- Massachusetts General Hospital Cancer CenterBostonUnited States
| | - Mehdi Bouhaddou
- Department of Cellular and Molecular Pharmacology, University of California San FranciscoSan FranciscoUnited States
- J. David Gladstone InstituteSan FranciscoUnited States
| | - Heidi L Kenerson
- Department of Surgery and Northwest Liver Research Program, University of WashingtonSeattleUnited States
| | - Huat C Lim
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| | - Donald Long
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell UniversityNew YorkUnited States
| | - Raymond S Yeung
- Department of Surgery and Northwest Liver Research Program, University of WashingtonSeattleUnited States
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell UniversityNew YorkUnited States
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California San FranciscoSan FranciscoUnited States
- J. David Gladstone InstituteSan FranciscoUnited States
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San FranciscoSan FranciscoUnited States
| | - Rigney E Turnham
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
| | - Kimberly J Riehle
- Department of Surgery and Northwest Liver Research Program, University of WashingtonSeattleUnited States
| | - John D Scott
- Department of Pharmacology, University of Washington Medical CenterSeattleUnited States
| | - Nabeel Bardeesy
- Department of Medicine, Harvard Medical SchoolBostonUnited States
- Massachusetts General Hospital Cancer CenterBostonUnited States
| | - John D Gordan
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Quantitative Biosciences Institute (QBI), University of California San FranciscoSan FranciscoUnited States
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7
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Nayak K, Hwang Y, Wang L, Swaney DL, Krogan NJ, Gordan JD. Abstract B016: Inhibition of KRASG12C in colon cancer illustrates a link between beta-catenin, WNK, and the GID complex. Cancer Res 2022. [DOI: 10.1158/1538-7445.crc22-b016] [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: 12/04/2022]
Abstract
Abstract
KRAS is mutated in 35%-45% of colorectal cancers (CRC), and KRAS mutational status determines the prognosis and therapeutic options available to patients with advanced CRC. Direct KRASG12C inhibitors have proven to be highly effective for patients with non-small cell lung cancers, but unfortunately are relatively ineffective in the treatment of CRC. Thus, we have investigated tissue-specific mechanisms of resistance to direct KRAS inhibition. We used multiplex inhibitor bead kinome profiling (MIBs) and global phosphoproteomic analysis to determine the signaling response to the KRASG12C inhibitor ARS-1620 in four human colon cancer cell lines. Analyzing the kinome revealed a profound reprogramming beyond the Ras/MAPK pathway. We used network propagation to integrate analysis across these lines and define essential signaling nodes modified by direct KRAS inhibition, including two distinct signaling nodes containing RAS/MAPK and WNT-regulating kinases. Two additional smaller nodes contained WNK kinases and their effectors, followed by Hippo and a number of cell cycle-related kinases. The WNK kinases have been identified to modulate beta-catenin, a major driver of CRC biology, via the GID E3 ubiquitin ligase complex. Thus, to understand the signaling that links KRAS and beta-catenin, we used small molecule inhibitors of these kinases along with ARS-1620, we tested how they affected the transcription of beta-catenin targets. Additionally, we assessed the correlation between WNK/GID complex, and beta-catenin transcriptional output using western blot and quantitative real time PCR and observe that inhibition of KRASG12C also modulates beta-catenin transcriptional output. Our results identify new families of possible kinase targets in CRCs expressing KRAS mutations and shed light on the relationship of KRAS, beta-catenin, and WNK/GID in CRC maintenance. By dissecting these signaling relationships, we hope to identify potential drug combinations to overcome primary resistance KRASG12C inhibition in CRC.
Citation Format: Kasturi Nayak, Yeonjoo Hwang, LeeAnn Wang, Danielle L. Swaney, Nevan J. Krogan, John D. Gordan. Inhibition of KRASG12C in colon cancer illustrates a link between beta-catenin, WNK, and the GID complex [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr B016.
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Affiliation(s)
- Kasturi Nayak
- 1University of California, San Francisco, San Francisco, CA
| | - Yeonjoo Hwang
- 1University of California, San Francisco, San Francisco, CA
| | - LeeAnn Wang
- 1University of California, San Francisco, San Francisco, CA
| | | | | | - John D. Gordan
- 1University of California, San Francisco, San Francisco, CA
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8
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Turnham RE, Lim HC, Ferret L, Lo K, Wang L, Choi A, Gordan JD. Abstract PO023: Uncovering hepatitis B virus-induced signaling changes in hepatocellular carcinoma. Clin Cancer Res 2022. [DOI: 10.1158/1557-3265.liverca22-po023] [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
Although precision medicine has revolutionized the treatment for other solid tumors, comprehensive genome profiling of hepatocellular carcinoma (HCC) has demonstrated that there are few oncogenic mutational drivers. HCC arises nearly universally in the context of co-morbid hepatitis, driven by hepatitis C virus or hepatitis B virus (HBV). Previous work has highlighted the effects of HBV protein X (HBx) on signaling and proliferation. However, it remains unclear how these signaling changes interact with the stress imposed by HBV replication. We hypothesize that HBV replication and maintenance of HBV proteins like HBx creates specific vulnerabilities that can be uncovered and exploited. We performed whole-genome clustered regularly interspaced short palindromic repeat interference (CRISPRi) screening in two engineered, patient-derived HBV+ cell models, Hep3B and SNU-368, with cellular proliferation as the readout. A conditional induction of HBx was used to overexpress HBx in each cell model for the whole genome CRISPRi screen. Genes where HBx expression was significantly associated with a more negative dependency score were classified as HBV differential dependencies. 37 genes were identified as shared HBV-induced dependencies across both cell lines. Of these, 16 were also differentially expressed in HCC specimens with ongoing HBV replication vs. non-HBV expressing tumors collected in The Cancer Genome Atlas (TCGA), suggesting in vivo selective pressure to alter the expression of these genes. We focused on Zinc Fingers and Homeoboxes 2 (ZHX2) and methionine adenosyltransferase 2A (MAT2A). ZHX2 was identified as an HCC tumor suppressor, and data from TCGA showed differential gene expression of ZHX2 in HBV+HCC. Validation of ZHX2 sgRNA knockdown confirmed that ZHX2 knockdown preferentially reduced cell proliferation in the presence of HBx, consistent with an HBV-induced dependency. ZHX2 also can activate the HIF pathway; we identified alterations of HIF targets with ZHX2 knockdown and HBx expression. Similarly, MAT2A knockdown in HBV+HCC cell lines showed decreased cell proliferation with HBx expression. MAT2A is an emerging therapeutic target, with sensitivity to MAT2A inhibitors conferred by deletions in methylthioadenosine phosphorylase (MTAP), seen in 3% of HCC. Ongoing investigations include alteration of splicing and cell cycle changes with depletion of MAT2A in the presence of HBx. With small molecule inhibitors of MAT2A in clinical development, this finding may be therapeutically actionable. Thus, using functional genomics to interrogate HBV-associated gene dependencies has illuminated the biology of HCC and identified candidate therapeutic targets for pre-clinical validation.
Citation Format: Rigney E Turnham, Huat Chye Lim, Lucille Ferret, Katherine Lo, LeeAnn Wang, Alex Choi, John D Gordan. Uncovering hepatitis B virus-induced signaling changes in hepatocellular carcinoma [abstract]. In: Proceedings of the AACR Special Conference: Advances in the Pathogenesis and Molecular Therapies of Liver Cancer; 2022 May 5-8; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(17_Suppl):Abstract nr PO023.
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9
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Qing T, Liu J, Liu F, Mitchell DC, Beresis RT, Gordan JD. Methods to assess small molecule allosteric modulators of the STRAD pseudokinase. Methods Enzymol 2022; 667:427-453. [PMID: 35525550 DOI: 10.1016/bs.mie.2022.03.041] [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: 10/18/2022]
Abstract
With the increased appreciation of the biological relevance of pseudokinase (PSK) allostery, the broadening of small molecule strategies to target PSK function is of particular importance. We and others have pursued the development of small molecule allosteric modulators of the STRAD pseudokinase by targeting its ATP binding pocket. The purpose of this effort is to modulate the function of the LKB1 tumor suppressor kinase, which exists in a trimer with the STRAD PSK and the adaptor protein MO25. Here we provide detailed guidance regarding the different methods we have used for medium throughput screening to identify STRAD ligands and measure their impact on LKB1 kinase activity. Our experience supports preferential use of direct measurements of LKB1 kinase activity, and demonstrates the limitations of indirect assessment methods in the development trans-acting allosteric modulators.
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Affiliation(s)
- Tingting Qing
- Chempartner Co, Ltd., Shanghai, China; Chempartner Co, Ltd., South San Francisco, CA, United States
| | - Jin Liu
- Chempartner Co, Ltd., Shanghai, China; Chempartner Co, Ltd., South San Francisco, CA, United States
| | - Fen Liu
- Chempartner Co, Ltd., Shanghai, China; Chempartner Co, Ltd., South San Francisco, CA, United States
| | - Dom C Mitchell
- Division of Hematology Oncology and Quantitative Biosciences Institute, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Richard T Beresis
- Chempartner Co, Ltd., Shanghai, China; Chempartner Co, Ltd., South San Francisco, CA, United States
| | - John D Gordan
- Division of Hematology Oncology and Quantitative Biosciences Institute, University of California, San Francisco (UCSF), San Francisco, CA, United States.
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10
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Dinh TA, Utria AF, Barry KC, Ma R, Abou-Alfa GK, Gordan JD, Jaffee EM, Scott JD, Zucman-Rossi J, O’Neill AF, Furth ME, Sethupathy P. A framework for fibrolamellar carcinoma research and clinical trials. Nat Rev Gastroenterol Hepatol 2022; 19:328-342. [PMID: 35190728 PMCID: PMC9516439 DOI: 10.1038/s41575-022-00580-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/13/2022] [Indexed: 12/17/2022]
Abstract
Fibrolamellar carcinoma (FLC), a rare, lethal hepatic cancer, occurs primarily in adolescents and young adults. Unlike hepatocellular carcinoma, FLC has no known association with viral, metabolic or chemical agents that cause cirrhosis. Currently, surgical resection is the only treatment demonstrated to achieve cure, and no standard of care exists for systemic therapy. Progress in FLC research illuminates a transition from an obscure cancer to one for which an interactive community seems poised to uncover fundamental mechanisms and initiate translation towards novel therapies. In this Roadmap, we review advances since the seminal discovery in 2014 that nearly all FLC tumours express a signature oncogene (DNAJB1-PRKACA) encoding a fusion protein (DNAJ-PKAc) in which the J-domain of a heat shock protein 40 (HSP40) co-chaperone replaces an amino-terminal segment of the catalytic subunit of the cyclic AMP-dependent protein kinase (PKA). Important gains include increased understanding of oncogenic pathways driven by DNAJ-PKAc; identification of potential therapeutic targets; development of research models; elucidation of immune mechanisms with potential for the development of immunotherapies; and completion of the first multicentre clinical trials of targeted therapy for FLC. In each of these key areas we propose a Roadmap for future progress.
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Affiliation(s)
- Timothy A. Dinh
- Medical Scientist Training Program, University of North Carolina, Chapel Hill, NC, USA.,Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA.,These authors contributed equally: Timothy A. Dinh, Alan F. Utria, Kevin C. Barry
| | - Alan F. Utria
- Department of Surgery, University of Washington, Seattle, WA, USA.,These authors contributed equally: Timothy A. Dinh, Alan F. Utria, Kevin C. Barry
| | - Kevin C. Barry
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,These authors contributed equally: Timothy A. Dinh, Alan F. Utria, Kevin C. Barry
| | - Rosanna Ma
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Ghassan K. Abou-Alfa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Weill Medical College at Cornell University, New York, NY, USA
| | - John D. Gordan
- Gastrointestinal oncology, University of California at San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
| | - Elizabeth M. Jaffee
- Department of oncology, Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - John D. Scott
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne université, Inserm, Université de Paris, Functional Genomics of Solid Tumors, Paris, France
| | - Allison F. O’Neill
- Department of Paediatric Hematology/oncology, Dana-Farber Cancer Institute, Harvard University, Boston, MA, USA
| | - Mark E. Furth
- Fibrolamellar Cancer Foundation, Greenwich, CT, USA.,;
| | - Praveen Sethupathy
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA.,;
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11
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Wu Q, Zhen Y, Shi L, Vu P, Greninger P, Adil R, Merritt J, Egan R, Wu MJ, Yin X, Ferrone CR, Deshpande V, Baiev I, Pinto CJ, McLoughlin DE, Walmsley CS, Stone JR, Gordan JD, Zhu AX, Juric D, Goyal L, Benes CH, Bardeesy N. EGFR Inhibition Potentiates FGFR Inhibitor Therapy and Overcomes Resistance in FGFR2 Fusion-Positive Cholangiocarcinoma. Cancer Discov 2022; 12:1378-1395. [PMID: 35420673 PMCID: PMC9064956 DOI: 10.1158/2159-8290.cd-21-1168] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/10/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022]
Abstract
FGFR inhibitors are approved for the treatment of advanced cholangiocarcinoma harboring FGFR2 fusions. However, the response rate is moderate, and resistance emerges rapidly due to acquired secondary FGFR2 mutations or due to other less-defined mechanisms. Here, we conducted high-throughput combination drug screens, biochemical analysis, and therapeutic studies using patient-derived models of FGFR2 fusion-positive cholangiocarcinoma to gain insight into these clinical profiles and uncover improved treatment strategies. We found that feedback activation of EGFR signaling limits FGFR inhibitor efficacy, restricting cell death induction in sensitive models and causing resistance in insensitive models lacking secondary FGFR2 mutations. Inhibition of wild-type EGFR potentiated responses to FGFR inhibitors in both contexts, durably suppressing MEK/ERK and mTOR signaling, increasing apoptosis, and causing marked tumor regressions in vivo. Our findings reveal EGFR-dependent adaptive signaling as an important mechanism limiting FGFR inhibitor efficacy and driving resistance and support clinical testing of FGFR/EGFR inhibitor therapy for FGFR2 fusion-positive cholangiocarcinoma. SIGNIFICANCE We demonstrate that feedback activation of EGFR signaling limits the effectiveness of FGFR inhibitor therapy and drives adaptive resistance in patient-derived models of FGFR2 fusion-positive cholangiocarcinoma. These studies support the potential of combination treatment with FGFR and EGFR inhibitors as an improved treatment for patients with FGFR2-driven cholangiocarcinoma.
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Affiliation(s)
- Qibiao Wu
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yuanli Zhen
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lei Shi
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Phuong Vu
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Patricia Greninger
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ramzi Adil
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Joshua Merritt
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Regina Egan
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Meng-Ju Wu
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Xunqin Yin
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Cristina R Ferrone
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Vikram Deshpande
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Islam Baiev
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Christopher J Pinto
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel E McLoughlin
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Charlotte S Walmsley
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - James R Stone
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - John D Gordan
- Helen Diller Family Comprehensive Cancer Center and Quantitative Biosciences Institute, University of California, San Francisco
| | - Andrew X Zhu
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.,Jiahui International Cancer Center, Jiahui Health, Shanghai, China
| | - Dejan Juric
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lipika Goyal
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Cyril H Benes
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nabeel Bardeesy
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
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12
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Kim M, Park J, Bouhaddou M, Kim K, Rojc A, Modak M, Soucheray M, McGregor MJ, O'Leary P, Wolf D, Stevenson E, Foo TK, Mitchell D, Herrington KA, Muñoz DP, Tutuncuoglu B, Chen KH, Zheng F, Kreisberg JF, Diolaiti ME, Gordan JD, Coppé JP, Swaney DL, Xia B, van 't Veer L, Ashworth A, Ideker T, Krogan NJ. A protein interaction landscape of breast cancer. Science 2021; 374:eabf3066. [PMID: 34591612 PMCID: PMC9040556 DOI: 10.1126/science.abf3066] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Minkyu Kim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Jisoo Park
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA
| | - Mehdi Bouhaddou
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Kyumin Kim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Ajda Rojc
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Maya Modak
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Margaret Soucheray
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Michael J McGregor
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Patrick O'Leary
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Denise Wolf
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Erica Stevenson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Tzeh Keong Foo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Dominique Mitchell
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - Kari A Herrington
- Department of Biochemistry and Biophysics, Center for Advanced Light Microscopy, University of California, San Francisco, CA, USA
| | - Denise P Muñoz
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Beril Tutuncuoglu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Kuei-Ho Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Fan Zheng
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA
| | - Jason F Kreisberg
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA
| | - Morgan E Diolaiti
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - John D Gordan
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - Jean-Philippe Coppé
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Laura van 't Veer
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Alan Ashworth
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Trey Ideker
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Department of Bioengineering, University of California, San Diego, CA, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
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13
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Kelley RK, Joseph NM, Nimeiri HS, Hwang J, Kulik LM, Ngo Z, Behr SC, Onodera C, Zhang K, Bocobo AG, Benson AB, Venook AP, Gordan JD. Phase II Trial of the Combination of Temsirolimus and Sorafenib in Advanced Hepatocellular Carcinoma with Tumor Mutation Profiling. Liver Cancer 2021; 10:561-571. [PMID: 34950179 PMCID: PMC8647100 DOI: 10.1159/000518297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 03/10/2021] [Accepted: 07/01/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The mammalian target of rapamycin (mTOR) pathway is upregulated in nearly half of hepatocellular carcinoma (HCC) tumors and is associated with poor prognosis. In preclinical models of HCC, the combination of mTOR pathway inhibition with the multikinase inhibitor sorafenib improves treatment efficacy. A prior phase I study of the allosteric mTOR inhibitor temsirolimus combined with sorafenib demonstrated acceptable safety at the recommended phase II dose. METHODS We conducted a single-arm, multicenter phase II trial of the combination of temsirolimus 10 mg intravenously weekly plus sorafenib 200 mg b.i.d. The primary endpoint was time to progression (TTP) with efficacy target of median TTP of at least 6 months; secondary endpoints included overall survival (OS), objective response rate, safety, and alpha-fetoprotein (AFP) tumor marker response. Next-generation tumor sequencing was performed as an exploratory endpoint. RESULTS Twenty-nine patients were enrolled, including 48% with hepatitis C virus infection and 28% with hepatitis B virus; 86% had Barcelona clinic liver cancer stage C disease. Among 28 patients evaluable for efficacy, the median TTP was 3.7 (95% confidence interval [CI]: 2.2, 5.3) months, with 14% of patients achieving TTP of at least 6 months. The median OS was 8.8 (95% CI: 6.8, 14.8) months. There were no complete or partial responses; 75% of patients had stable disease as best response. AFP decline by at least 50% was associated with prolonged TTP and OS. Serious adverse events occurred in 21%; the most common treatment-related adverse events of CTCAE grade 3 or higher were hypophosphatemia (36%), thrombocytopenia (14%), and rash (11%). There were no grade 5 events attributed to sorafenib or temsirolimus. Tumor next-generation sequencing (NGS) was performed in a subgroup of 24 patients with adequate tumor samples. Tumor mTOR pathway mutations were identified in 42%. There was no association between tumor mutation profile and OS or TTP. CONCLUSIONS The combination of temsirolimus and sorafenib demonstrated acceptable safety but did not achieve the target threshold for efficacy in this phase II study. Tumor NGS including the presence of mTOR pathway mutations was not associated with treatment response in an exploratory subgroup analysis.
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Affiliation(s)
- Robin K. Kelley
- Helen Diller Family Comprehensive Cancer Center (HDFCCC), University of California, San Francisco (UCSF), San Francisco, California, USA,*Robin K. Kelley,
| | - Nancy M. Joseph
- Department of Pathology, University of California, San Francisco (UCSF), San Francisco, California, USA
| | - Halla S. Nimeiri
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Jimmy Hwang
- Helen Diller Family Comprehensive Cancer Center (HDFCCC), University of California, San Francisco (UCSF), San Francisco, California, USA
| | - Laura M. Kulik
- Division of Hepatology, Department of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Zoe Ngo
- Helen Diller Family Comprehensive Cancer Center (HDFCCC), University of California, San Francisco (UCSF), San Francisco, California, USA
| | - Spencer C. Behr
- Department of Radiology, University of California, San Francisco (UCSF), San Francisco, California, USA
| | - Courtney Onodera
- Clinical Cancer Genomics Lab, UCSF Health, San Francisco, California, USA
| | - Karen Zhang
- Helen Diller Family Comprehensive Cancer Center (HDFCCC), University of California, San Francisco (UCSF), San Francisco, California, USA,*Robin K. Kelley,
| | - Andrea G. Bocobo
- Helen Diller Family Comprehensive Cancer Center (HDFCCC), University of California, San Francisco (UCSF), San Francisco, California, USA
| | - Al B. Benson
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Alan P. Venook
- Helen Diller Family Comprehensive Cancer Center (HDFCCC), University of California, San Francisco (UCSF), San Francisco, California, USA
| | - John D. Gordan
- Helen Diller Family Comprehensive Cancer Center (HDFCCC), University of California, San Francisco (UCSF), San Francisco, California, USA
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14
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Kim M, Park J, Bouhaddou M, Kim K, Rojc A, Modak M, Soucheray M, O'Leary P, Wolf D, Mitchell DC, Zheng F, Gordan JD, Coppé JP, Swaney DL, van' t Veer L, Ashworth A, Ideker T, Krogan NJ. Abstract 2308: The protein interaction landscape of breast cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2308] [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
Cancers have been associated with a diverse array of genomic alterations, many of which are rare with unknown significance. To understand the cellular mechanisms impacted by such alterations in breast invasive carcinoma, we have applied affinity-purification mass spectrometry to delineate comprehensive biophysical interaction networks for 40 frequently altered breast cancer proteins across three human breast cell lines, providing a novel resource of context-specific and shared protein-protein interaction networks in breast cancer cells. These networks interconnect and enrich for common and rare cancer mutations, and are substantially rewired by mutations. Our analysis identifies novel PIK3CA-interacting proteins which repress AKT signaling, and UBE2N emerges as a BRCA1 interactor predictive of clinical response to PARP inhibition. We also show that Spinophilin interacts with and dephosphorylates BRCA1 to promote DNA double-strand break repair. Thus, cancer protein interaction landscapes provide a framework for recognizing oncogenic drivers and drug vulnerabilities.
Citation Format: Minkyu Kim, Jisoo Park, Mehdi Bouhaddou, Kyumin Kim, Ajda Rojc, Maya Modak, Margaret Soucheray, Patrick O'Leary, Denise Wolf, Dominique C. Mitchell, Fan Zheng, John D. Gordan, Jean-Philippe Coppé, Danielle L. Swaney, Laura van' t Veer, Alan Ashworth, Trey Ideker, Nevan J. Krogan. The protein interaction landscape of breast cancer [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 2308.
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Affiliation(s)
- Minkyu Kim
- 1University of California San Francisco, San Francisco, CA
| | - Jisoo Park
- 2University of California San Diego, San Diego, CA
| | | | - Kyumin Kim
- 3University of Southern California, Los Angeles, CA
| | - Ajda Rojc
- 1University of California San Francisco, San Francisco, CA
| | - Maya Modak
- 1University of California San Francisco, San Francisco, CA
| | | | | | - Denise Wolf
- 1University of California San Francisco, San Francisco, CA
| | | | - Fan Zheng
- 2University of California San Diego, San Diego, CA
| | - John D. Gordan
- 1University of California San Francisco, San Francisco, CA
| | | | | | | | - Alan Ashworth
- 1University of California San Francisco, San Francisco, CA
| | - Trey Ideker
- 2University of California San Diego, San Diego, CA
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15
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Lim HC, Gordan JD. Tumor hepatitis B virus RNA identifies a clinically and molecularly distinct subset of hepatocellular carcinoma. PLoS Comput Biol 2021; 17:e1008699. [PMID: 33561166 PMCID: PMC7909678 DOI: 10.1371/journal.pcbi.1008699] [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] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 02/26/2021] [Accepted: 01/13/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatitis B virus (HBV) infection contributes to hepatocellular carcinoma (HCC) initiation and is associated with worse outcomes. Many prior studies of HBV-related HCC have not accounted for potential heterogeneity among HBV-related tumors by assessing whether HBV activity is present in tumor tissue. Here, we measured tumor HBV RNA, a proxy for viral activity, and investigated the association between HBV RNA status and several clinicogenomic characteristics. We obtained clinical, mutation, RNA-Seq and survival data for 439 HCC tumors from The Cancer Genome Atlas and International Cancer Genome Consortium. Tumors were classified as HBV RNA positive if they harbored >1 HBV RNA read per million human reads. We investigated the association between HBV RNA status and nonsynonymous somatic mutations, gene set expression, homologous recombination deficiency (HRD) score and mutation-specific survival. HBV RNA positive status was associated with higher nonsynonymous mutation rates of multiple genes, including TP53 and CDKN2A, while HBV RNA negative status was associated with higher nonsynonymous BAP1 mutation rate. HBV RNA positive status was also associated with increased transcription of genes involved in multiple DNA damage repair pathways, genes upregulated by MYC and mTORC1, and genes overexpressed in several HCC subclasses associated with a proliferative phenotype. Further, HBV RNA positive status was associated with increased three-biomarker HRD score (22.2 for HBV RNA+ vs. 16.0 for HBV RNA-). Finally, HBV RNA status was associated with multiple mutation-specific survival differences, including decreased survival for HBV RNA positive patients with nonsynonymous KEAP1 mutations compared to those without (hazard ratio 4.26). HCC tumors harboring genomic evidence of HBV activity therefore constitute a distinct HCC subset characterized by specific differences in nonsynonymous mutations, gene set expression, three-biomarker HRD score and mutation-specific survival. Hepatocellular carcinoma, the most common type of liver cancer, is the second leading cause of cancer death worldwide and is most commonly caused by hepatitis B virus infection. Currently, scientists have an incomplete understanding of the genomic basis of hepatocellular carcinoma associated with hepatitis B virus infection, because prior studies have been limited by imprecision in assessing hepatitis B virus infection status and heterogeneity in hepatitis B virus activity levels in liver tumors. This has limited scientists’ ability to devise new diagnostic and therapeutic options for hepatocellular carcinoma. In this study, we used computational genomics to directly measure hepatitis B virus RNA levels in a large dataset of hepatocellular carcinoma tumors, and found that tumors with measurable hepatitis B virus RNA levels are associated with a specific set of clinical and genomic characteristics. These characteristics have not previously been reported and harbor implications for future clinical and genomics research in hepatocellular carcinoma, as well as computational genomics efforts in other cancer types.
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Affiliation(s)
- Huat Chye Lim
- Division of Hematology and Oncology, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (HCL); (JDG)
| | - John D. Gordan
- Division of Hematology and Oncology, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (HCL); (JDG)
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16
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Gordan JD, Kennedy EB, Abou-Alfa GK, Beg MS, Brower ST, Gade TP, Goff L, Gupta S, Guy J, Harris WP, Iyer R, Jaiyesimi I, Jhawer M, Karippot A, Kaseb AO, Kelley RK, Knox JJ, Kortmansky J, Leaf A, Remak WM, Shroff RT, Sohal DPS, Taddei TH, Venepalli NK, Wilson A, Zhu AX, Rose MG. Systemic Therapy for Advanced Hepatocellular Carcinoma: ASCO Guideline. J Clin Oncol 2020; 38:4317-4345. [PMID: 33197225 DOI: 10.1200/jco.20.02672] [Citation(s) in RCA: 319] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
PURPOSE To develop an evidence-based clinical practice guideline to assist in clinical decision making for patients with advanced hepatocellular carcinoma (HCC). METHODS ASCO convened an Expert Panel to conduct a systematic review of published phase III randomized controlled trials (2007-2020) on systemic therapy for advanced HCC and provide recommended care options for this patient population. RESULTS Nine phase III randomized controlled trials met the inclusion criteria. RECOMMENDATIONS Atezolizumab + bevacizumab (atezo + bev) may be offered as first-line treatment of most patients with advanced HCC, Child-Pugh class A liver disease, Eastern Cooperative Oncology Group Performance Status (ECOG PS) 0-1, and following management of esophageal varices, when present, according to institutional guidelines. Where there are contraindications to atezolizumab and/or bevacizumab, tyrosine kinase inhibitors sorafenib or lenvatinib may be offered as first-line treatment of patients with advanced HCC, Child-Pugh class A liver disease, and ECOG PS 0-1. Following first-line treatment with atezo + bev, and until better data are available, second-line therapy with a tyrosine kinase inhibitor may be recommended for appropriate candidates. Following first-line therapy with sorafenib or lenvatinib, second-line therapy options for appropriate candidates include cabozantinib, regorafenib for patients who previously tolerated sorafenib, or ramucirumab (for patients with α-fetoprotein ≥ 400 ng/mL), or atezo + bev where patients did not have access to this option as first-line therapy. Pembrolizumab or nivolumab are also reasonable options for appropriate patients following sorafenib or lenvatinib. Consideration of nivolumab + ipilimumab as an option for second-line therapy and third-line therapy is discussed. Further guidance on choosing between therapy options is included within the guideline. Additional information is available at www.asco.org/gastrointestinal-cancer-guidelines.
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Affiliation(s)
- John D Gordan
- University of California, San Francisco, San Francisco, CA
| | | | - Ghassan K Abou-Alfa
- Memorial Sloan Kettering Cancer Center, Weill Medical College at Cornell University, New York, NY
| | | | - Steven T Brower
- Lefcourt Family Cancer Treatment and Wellness Center, Englewood, NJ
| | | | - Laura Goff
- Vanderbilt Ingram Cancer Center, Nashville, TN
| | | | | | | | - Renuka Iyer
- Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | | | | | | | - R Kate Kelley
- University of California, San Francisco, San Francisco, CA
| | | | | | - Andrea Leaf
- VA New York Harbor Healthcare System, Brooklyn, NY
| | - William M Remak
- California Hepatitis C Task Force, California Chronic Care Coalition, FAIR Foundation, San Francisco, CA
| | | | | | - Tamar H Taddei
- Yale University School of Medicine and VA Connecticut Healthcare System, West Haven, CT
| | | | - Andrea Wilson
- Blue Faery: The Adrienne Wilson Liver Cancer Association, Birmingham, AL
| | - Andrew X Zhu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
| | - Michal G Rose
- Yale Cancer Center and VA Connecticut Healthcare System, West Haven, CT
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El Dika I, Mayer RJ, Venook AP, Capanu M, LaQuaglia MP, Kobos R, O'Neill AF, Chou JF, Ly M, Ang C, O'Reilly EM, Gordan JD, Abou‐Alfa GK. A Multicenter Randomized Three-Arm Phase II Study of (1) Everolimus, (2) Estrogen Deprivation Therapy (EDT) with Leuprolide + Letrozole, and (3) Everolimus + EDT in Patients with Unresectable Fibrolamellar Carcinoma. Oncologist 2020; 25:925-e1603. [PMID: 32400000 PMCID: PMC7648371 DOI: 10.1634/theoncologist.2020-0367] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 04/28/2020] [Indexed: 12/11/2022] Open
Abstract
LESSONS LEARNED FLC is a complex cancer with many implicated oncogenic pathways. Single or dual targeting does not appear to alter the natural history of the cancer, and novel therapeutics are needed. Estrogen deprivation therapy with letrozole and leuprolide, alone or in combination with the mTOR inhibitor, everolimus, did not demonstrate clinical activity in advanced fibrolamellar carcinoma. The study drugs were well tolerated when administered as single agents or in combination in this patient population. This study demonstrates that, despite the rarity of FLC, multicenter therapeutic clinical trials are feasible and support the value of this consortium. BACKGROUND Fibrolamellar carcinoma (FLC) is an uncommon malignancy in young people and is sometimes associated with pregnancy and oral contraceptive use. Immunohistochemical staining and genetic profiling of FLC tumor specimens have revealed aromatase overexpression. The overexpression of mTOR and S6 kinase has been noted in 25% of FLC. On the basis of interaction between estrogen and the PI3K/Akt/mTOR pathway, we hypothesized that suppression of estrogen and mTOR signaling could have antineoplastic activity in FLC. METHODS Patients were randomized to arm A (everolimus), arm B (letrozole/leuprolide; estrogen deprivation therapy [EDT]), or arm C (everolimus/letrozole/leuprolide). Upon disease progression, patients in arm A or B could proceed to part 2 (everolimus/letrozole/leuprolide). The primary endpoint was progression-free survival (PFS) at 6 months (PFS6) assessed using a Simon's minimax two-stage design, hypothesizing an improvement in PFS6 from 40% to 64% with the study regimen. RESULTS Twenty-eight patients were enrolled. An unplanned analysis was performed because of perceived concern for lack of efficacy. Stable disease was observed in 9 of 26 evaluable patients (35%). PFS6 was 0%. Median overall survival (OS) was 12.4 months (95% confidence interval [CI], 7.4-20.9) for the whole study cohort. Grade 3 adverse events in ≥10% of patients were nausea (11%), vomiting (11%), anemia (11%), elevated aspartate transaminase (AST; 32%), alanine transaminase (ALT; 36%), and alkaline phosphatase (14%). All 28 patients experienced an event for PFS outcome, and four deaths were due to disease progression. CONCLUSION Neither EDT nor mTOR inhibition improved outcomes in FLC. Other treatment strategies are needed.
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Affiliation(s)
- Imane El Dika
- Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
- Weill Cornell College of MedicineNew YorkNew YorkUSA
| | - Robert J. Mayer
- Dana‐Farber Cancer Institute, Harvard Medical SchoolBostonMassachusettsUSA
| | - Alan P. Venook
- University of California San FranciscoSan FranciscoCaliforniaUSA
| | | | - Michael P. LaQuaglia
- Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
- Weill Cornell College of MedicineNew YorkNew YorkUSA
| | - Rachel Kobos
- Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
- Weill Cornell College of MedicineNew YorkNew YorkUSA
| | - Allison F. O'Neill
- Dana‐Farber Cancer Institute, Harvard Medical SchoolBostonMassachusettsUSA
| | - Joanne F. Chou
- Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | - Michele Ly
- Sidney Kimmel Medical College of Thomas Jefferson UniversityPhiladelphiaPennsylvaniaUSA
| | - Celina Ang
- Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Eileen M. O'Reilly
- Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
- Weill Cornell College of MedicineNew YorkNew YorkUSA
| | - John D. Gordan
- University of California San FranciscoSan FranciscoCaliforniaUSA
| | - Ghassan K. Abou‐Alfa
- Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
- Weill Cornell College of MedicineNew YorkNew YorkUSA
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Hwang Y, Swaney DL, Bardeesy N, Gordan JD. Abstract 6572: Integrative network propagation to uncover potential drug resistance mechanisms in FGFR2 fusion-positive cholangiocarcinoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-6572] [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
Drug resistance emerges in response to most targeted therapies and is a common mechanism of treatment failure in patients with advanced cancer. We have studied resistance in intrahepatic cholangiocarcinoma (ICC) with oncogenic FGFR2 fusions. FGFR2 fusions are seen in 10-15% of ICC patients, and FGFR inhibition (FGFRi) is associated with relatively rapid emergence of resistance. While some FGFRi resistance results from mutations that block drug from binding, previous analysis has revealed polyclonal mechanisms relying on multiple pathways. Given this complexity of treatment-emergent resistance, we have employed computational strategies to integrate the phenotypic response to FGFRi with essential growth mechanisms in FGFR2 fusion-driven ICC. We applied network propagation approaches to the results of multiple -omics platforms to develop an integrated network map of the response of a patient-derived FGFR2 fusion-positive ICC line to the FGFR inhibitor TAS-120. For this analysis, multiple distinct -omics datasets (RNASEQ, global phosphoproteomics) were propagated across the ReactomeFI network, based on experimentally proven physical interactions. We propagated each dataset across the network separately and multiplied the propagation scores for each gene to generate a combined p-value, allowing us to uncover significant pathways in the network that may not have been apparent in the individual datasets. We have identified numerous groups of nodes of functional importance, including a large cluster of proteins involved in Rho family GTPase signaling. To pursue a potentially druggable target, we evaluated the Rho effector Protein Kinase N2 (PKN2). Follow-up biochemical analysis suggests that PKN2 modulates signaling feedback to AKT following FGFRi and results in altered phosphorylation of the apoptotic regulator BAD. Consistent with this, we have found that PKN2 is required for sensitivity to FGFRi in the patient-derived line using a cell viability assay. Furthermore, synergy assays with TAS-120 and the AKT inhibitor MK2206, SGK inhibitor GSK650934, and Bcl-2 inhibitor ABT-263 each resulted in significant synergistic activity, suggesting that AKT is a key effector in PKN2-mediated FGFRi resistance. We are in the process of validating these results in different cell lines and further characterizing the mechanism by which PKN2 is contributing to the FGFR/AKT signaling. In addition to identifying PKN2 as a key mediator of pathway feedback, multiple other candidate resistance mechanisms have emerged, including well established and relatively understudied pathways. These results allow multiple further avenues of investigation, and demonstrate the value of systems approaches in identifying new targets to counter drug resistance.
Citation Format: Yeonjoo Hwang, Danielle L. Swaney, Nabeel Bardeesy, John D. Gordan. Integrative network propagation to uncover potential drug resistance mechanisms in FGFR2 fusion-positive cholangiocarcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6572.
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Chan GKL, Maisel SM, Hwang YC, Wolber R, Swaney DL, Bardeesy N, Gordan JD. Abstract 309: Mapping oncogenic signal transduction in PKA-driven cancers. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-309] [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
Protein Kinase A (PKA) is a major effector of cyclic-AMP (cAMP) signaling and has recently been appreciated to play a role in multiple malignancies. Mutations of its catalytic subunit (PRKACA) have been identified in a substantial proportion of adrenocortical tumors, and are also detected in a wide spectrum of tumor types in the TCGA dataset, although at a low frequency. A unique fusion protein of PRKACA and DNAJB1 is seen in the majority of fibrolamellar liver cancers (FLC), a rare malignancy of young adults, where it is suspected to be the primary oncogenic driver. However, the key effectors of oncogenic signaling in FLC and other PRKACA driven cancers remain unknown. To understand PKA's downstream targets, we generated genetic cell models with doxycycline-inducible PRKACA or its dominant negative counterpart, a mutant form of the PRKAR1A regulatory subunit. These cell models were then subjected to mass spectrometry for kinome profiling in order to detect kinases with significant altered activity following PKA modulation. This was integrated with small molecule inhibition and siRNA knockdown to identify PKA-regulated kinases that impact cell proliferation. Our analysis revealed activation of the aurora-family kinase AURKA, with preferential sensitivity to the confirmation-disrupting AURKA inhibitor (CD-AURKAi) CD532 compared to other AURKA inhibitors. CD-AURKAi not only selectively inhibit AURKA's kinase activity, but also disrupt its interaction with MYC-family transcription factors. These key oncogenic mediators are necessary to drive the proliferation of multiple tumor types, although they have not yet been connected with oncogenic PKA signaling. Our follow up quantitative PCR experiments confirm that CD-532 treatment results in reduced expression of MYC family members and their transcriptional targets. We next confirmed that MYC family members support the proliferation of PKA-driven cell models with live cell imaging. Finally, we have begun to investigate other kinases identified in our siRNA screen for potential effects on MYC, and have identified several potential combination partners to augment the activity of CD-532 and other CD-AURKAi. These data suggest that CD-AURKAi, either alone or in combination, have the potential to serve as therapeutic agents for PKA-driven cancers.
Citation Format: Gary Kwan Leung Chan, Samantha M. Maisel, Y. Christina Hwang, Rebecca Wolber, Danielle L. Swaney, Nabeel Bardeesy, John D. Gordan. Mapping oncogenic signal transduction in PKA-driven cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 309.
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Mitchell DC, Liu J, Wang Z, He C, Ding L, Adler M, Wang LL, Keith A, Hwang YC, Tsui TKM, Ramamoorthi R, Lively S, Drakas RA, Ramani V, Verba KA, Qing T, Beresis RT, Gordan JD. Abstract 5228: Small molecule activation of the LKB1 tumor suppressor. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5228] [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
Cancer treatment has been considerably advanced by the relatively recent development of small molecules capable of inhibiting oncogenic kinase signaling, but exogenous enhancement of tumor suppressive signaling remains elusive. Here, we sought to design small molecules capable of activating the tumor suppressor kinase LKB1. Designing compounds capable of increasing kinase activity has been more structurally challenging than those aimed at inhibiting them: apart from the ATP-binding pocket, there is rarely a site that would be conducive to binding a small molecule. Unlike most protein kinases, LKB1 signals as part of an obligate trimer consisting of itself, a scaffolding protein (MO25), and a pseudokinase (STRAD). As part of its mechanism of activation, LKB1 must bind to an ATP-bound STRAD to take on its active kinase conformation. Targeting STRAD provides a unique opportunity to allosterically stabilize and enhance LKB1 kinase activity. Using a structure-based drug design, we developed compounds that are able to selectively bind STRAD's ATP-binding pocket. We confirmed that our STRAD targeting small molecules are able to enhance the activity of recombinant LKB1 in a kinase assay. The observed increase in LKB1's kinase activity corresponds to increased association of complex components after drug treatment, as suggested by immunoprecipitation of the trimer. To understand the clinical contexts in which our compounds might be most effective, we performed a viability screen across multiple histologies to determine which cancer cells could be sensitive to LKB1 activation. Sensitive cells were used to investigate the mechanism of action of exogenous LKB1 stimulation. LKB1 signals through members of the AMPK-related kinase family to carry out its tumor suppressive functions in the cell. Thus, we used western blot analysis of LKB1 proximal and distal mediators to assess changes in downstream signaling. We found that activation of multiple LKB1 effectors was dose dependent and occurred rapidly, with signal enhancement seen in more tumor-relevant low adherence cell culture conditions. Real-time microscopy confirmed that our compounds slowed cell proliferation in a dose-dependent manner. This work demonstrates that targeting a pseudokinase with a small molecule to allosterically activate of a tumor suppressor kinase is possible, therapeutically effective in vitro, and triggers multiple downstream signaling pathways to decrease cancer cell proliferation.
Citation Format: Dominique C. Mitchell, Jin Liu, Zheng Wang, Changliang He, Luo Ding, Marc Adler, LeeAnn L. Wang, Aidan Keith, Y. Christina Hwang, Tsz Kin M. Tsui, Roopa Ramamoorthi, Sarah Lively, Robert A. Drakas, Vijay Ramani, Kliment A. Verba, Tingting Qing, Richard T. Beresis, John D. Gordan. Small molecule activation of the LKB1 tumor suppressor [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5228.
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Gordan JD, Pitea A, Eckhardt M, Jang G, Turnham RE, Choi ALM, Von Dollen J, Lim HC, Thayer EF, Kelley RK, Swaney DL, Zhang W, Theis FJ, Ideker T, Krogan NJ. Abstract 4891: Hepatitis B virus remodels host protein interaction networks to generate distinct cellular dependencies. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-4891] [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
Hepatocellular carcinoma (HCC) is the second leading cause of cancer death worldwide. Advanced HCC has proven particularly difficult to treat because of a scarcity of clear genetic drivers of cancer progression; thus, there are currently no predictive markers that guide HCC therapy. HCC arises in the context of co-morbid hepatitis due to hepatitis B virus (HBV), hepatitis C (HCV) or fatty liver disease. We hypothesize that protein-protein interactions (PPIs) between viral proteins and HCC genes may contribute to tumor initiation and maintenance. In order to characterize these PPIs, we performed affinity purification - mass spectrometry (APMS), defining 145 HBV/host PPIs including known and novel interacting partners. We next used a network propagation algorithm to identify host genes and protein complexes that were preferentially mutated in the absence of HBV infection. HBV is a small DNA virus, with 4 genes of which only one has enzymatic activity, raising a question as to how HBV interaction modifies host behavior. Using AP-MS of host proteins, we found that the HBV X protein (HBx) remodels multiple host protein complexes through direct interaction. These physical effects on complex components result in distinct biochemical behavior from the CRL4 E3 ubiquitin ligase complex as well as the phosphatase PP2A, as determined through global phosphoproteomics and ubiquitin analysis. We show that this remodeling driven by HBx substantially changes cellular protein turnover and downstream signaling dynamics. We followed this up with assessments of cellular viability and proliferation in response to pharmacological inhibition or CRISPRi-based knockdown of HBx effectors. Our data support a model where HBV proteins alter the components and behavior of key regulatory protein complexes in the cell, altering tumor behavior and raising the possibility of precision therapeutics for HCC.
Citation Format: John D. Gordan, Adriana Pitea, Manon Eckhardt, Gwendolyn Jang, Rigney E. Turnham, Alex L M. Choi, John Von Dollen, Huat C. Lim, Elizabeth F. Thayer, R. Katie Kelley, Danielle L. Swaney, Wei Zhang, Fabian J. Theis, Trey Ideker, Nevan J. Krogan. Hepatitis B virus remodels host protein interaction networks to generate distinct cellular dependencies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4891.
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Coles GL, Cristea S, Webber JT, Levin RS, Moss SM, He A, Sangodkar J, Hwang YC, Arand J, Drainas AP, Mooney NA, Demeter J, Spradlin JN, Mauch B, Le V, Shue YT, Ko JH, Lee MC, Kong C, Nomura DK, Ohlmeyer M, Swaney DL, Krogan NJ, Jackson PK, Narla G, Gordan JD, Shokat KM, Sage J. Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells. Cancer Cell 2020; 38:129-143.e7. [PMID: 32531271 PMCID: PMC7363571 DOI: 10.1016/j.ccell.2020.05.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 02/18/2020] [Accepted: 05/04/2020] [Indexed: 12/23/2022]
Abstract
Using unbiased kinase profiling, we identified protein kinase A (PKA) as an active kinase in small cell lung cancer (SCLC). Inhibition of PKA activity genetically, or pharmacologically by activation of the PP2A phosphatase, suppresses SCLC expansion in culture and in vivo. Conversely, GNAS (G-protein α subunit), a PKA activator that is genetically activated in a small subset of human SCLC, promotes SCLC development. Phosphoproteomic analyses identified many PKA substrates and mechanisms of action. In particular, PKA activity is required for the propagation of SCLC stem cells in transplantation studies. Broad proteomic analysis of recalcitrant cancers has the potential to uncover targetable signaling networks, such as the GNAS/PKA/PP2A axis in SCLC.
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Affiliation(s)
- Garry L Coles
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sandra Cristea
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - James T Webber
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Rebecca S Levin
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Steven M Moss
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Andy He
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jaya Sangodkar
- Division of Genetic Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Yeonjoo C Hwang
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Julia Arand
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Alexandros P Drainas
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Nancie A Mooney
- Baxter Laboratory, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brandon Mauch
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Vicky Le
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Yan Ting Shue
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julie H Ko
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Myung Chang Lee
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Christina Kong
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael Ohlmeyer
- Icahn School of Medicine at Mount Sinai, New York, NY, USA; Atux Iskay LLC, Plainsboro, New Jersey, NJ 08536, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; David J. Gladstone Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; David J. Gladstone Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Peter K Jackson
- Baxter Laboratory, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Goutham Narla
- Division of Genetic Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John D Gordan
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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Huppert LA, Gordan JD, Kelley RK. Checkpoint Inhibitors for the Treatment of Advanced Hepatocellular Carcinoma. Clin Liver Dis (Hoboken) 2020; 15:53-58. [PMID: 32226615 PMCID: PMC7098670 DOI: 10.1002/cld.879] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/25/2019] [Indexed: 02/04/2023] Open
Abstract
http://aasldpubs.onlinelibrary.wiley.com/hub/journal/10.1002/(ISSN)2046-2484/video/15-2-reading-huppert a video presentation of this article Answer questions and earn https://www.wileyhealthlearning.com/Activity/7036144/disclaimerspopup.aspx.
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Affiliation(s)
- Laura A. Huppert
- Department of MedicineUniversity of California San FranciscoSan FranciscoCA
| | - John D. Gordan
- Department of MedicineUniversity of California San FranciscoSan FranciscoCA
| | - Robin Kate Kelley
- UCSF HelenDiller Family Comprehensive Cancer CenterUniversity of California San FranciscoSan FranciscoCA
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Abou-Alfa GK, Mayer R, Venook AP, O'Neill AF, Beg MS, LaQuaglia M, Kingham PT, Kobos R, Basturk O, Brennan C, Yopp A, Harding JJ, Leong S, Crown J, Hoti E, Leonard G, Ly M, Bradley M, Valentino E, Markowitz D, Zukiwski A, Ren K, Gordan JD. Phase II Multicenter, Open-Label Study of Oral ENMD-2076 for the Treatment of Patients with Advanced Fibrolamellar Carcinoma. Oncologist 2020; 25:e1837-e1845. [PMID: 32154962 DOI: 10.1634/theoncologist.2020-0093] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/03/2020] [Indexed: 12/19/2022] Open
Abstract
LESSONS LEARNED The fibrolamellar carcinoma-associated DNAJB1-PRKACA gene fusion transcript RNA codes for the catalytic domain of protein kinase A and, thus, overexpression of Aurora kinase A. ENMD-2076 showed a favorable toxicity profile. The limited results, one patient (3%) with a partial response and 57% of patients with stable disease, do not support further evaluation of ENMD-2076 as single agent. Future studies will depend on the simultaneous targeting approach of DNAJB1-PRKACA and the critical downstream components. BACKGROUND Fibrolamellar carcinoma (FLC) represents approximately 0.85% of liver cancers. The associated DNAJB1-PRKACA gene fusion transcript RNA codes for the catalytic domain of protein kinase A and overexpression of Aurora kinase A (AURKA). ENMD-2076 is a selective anti-AURKA inhibitor. METHODS Patients aged >12 years with pathologically confirmed incurable FLC, with measurable disease, Eastern Cooperative Oncology Group performance status 0-2 or Lansky 70-100, and adequate organ function were eligible. Patients were prescribed ENMD-2076 based on body surface area. The primary endpoint was overall objective response rate by RECIST v1.1, with a null hypothesis of true response rate of 2% versus one-sided alternative of 15%. Secondary endpoints included 6-month progression-free survival (PFS) rate (Fig. 1), median PFS, time to progression (TTP), and overall survival (OS). Safety was evaluated throughout the study. RESULTS Of 35 patients who enrolled and received treatment, 1 (3%) had a partial response (PR) and 20 (57%) had stable disease (SD). Median TTP, PFS, and OS were 5, 3.9, and 19 months, respectively. The most frequently reported drug-related serious adverse event was hypertension in three patients. Three deaths were reported on-study-two due to disease progression and one due to pulmonary embolism not related to ENMD-2076. CONCLUSION The study provided no rationale for further studying ENMD-2076 as a single agent in FLC.
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Affiliation(s)
- Ghassan K Abou-Alfa
- Weill Medical College at Cornell University, New York, New York, USA
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Robert Mayer
- Dana-Farber Cancer Institute, Harvard University, Boston, Massachusetts, USA
| | - Alan P Venook
- University of California San Francisco, San Francisco, California, USA
| | - Allison F O'Neill
- Dana-Farber Cancer Institute, Harvard University, Boston, Massachusetts, USA
| | | | - Michael LaQuaglia
- Weill Medical College at Cornell University, New York, New York, USA
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Peter T Kingham
- Weill Medical College at Cornell University, New York, New York, USA
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rachel Kobos
- Weill Medical College at Cornell University, New York, New York, USA
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Olca Basturk
- Weill Medical College at Cornell University, New York, New York, USA
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Cameron Brennan
- Weill Medical College at Cornell University, New York, New York, USA
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Adam Yopp
- UT Southwestern Medical Center, Dallas, Texas, USA
| | - James J Harding
- Weill Medical College at Cornell University, New York, New York, USA
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stephen Leong
- University of Colorado Cancer Center, Aurora, Colorado, USA
| | - John Crown
- St Vincent's Private Hospital, Dublin, Ireland
| | - Emir Hoti
- St Vincent's Private Hospital, Dublin, Ireland
| | | | - Michele Ly
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mikaela Bradley
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Emily Valentino
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | | | - Ken Ren
- CASI Pharmaceuticals, Inc., Rockville, Maryland, USA
| | - John D Gordan
- University of California San Francisco, San Francisco, California, USA
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25
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McMahon M, Contreras A, Holm M, Uechi T, Forester CM, Pang X, Jackson C, Calvert ME, Chen B, Quigley DA, Luk JM, Kelley RK, Gordan JD, Gill RM, Blanchard SC, Ruggero D. A single H/ACA small nucleolar RNA mediates tumor suppression downstream of oncogenic RAS. eLife 2019; 8:48847. [PMID: 31478838 PMCID: PMC6776443 DOI: 10.7554/elife.48847] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/02/2019] [Indexed: 12/19/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are a diverse group of non-coding RNAs that direct chemical modifications at specific residues on other RNA molecules, primarily on ribosomal RNA (rRNA). SnoRNAs are altered in several cancers; however, their role in cell homeostasis as well as in cellular transformation remains poorly explored. Here, we show that specific subsets of snoRNAs are differentially regulated during the earliest cellular response to oncogenic RASG12V expression. We describe a novel function for one H/ACA snoRNA, SNORA24, which guides two pseudouridine modifications within the small ribosomal subunit, in RAS-induced senescence in vivo. We find that in mouse models, loss of Snora24 cooperates with RASG12V to promote the development of liver cancer that closely resembles human steatohepatitic hepatocellular carcinoma (HCC). From a clinical perspective, we further show that human HCCs with low SNORA24 expression display increased lipid content and are associated with poor patient survival. We next asked whether ribosomes lacking SNORA24-guided pseudouridine modifications on 18S rRNA have alterations in their biophysical properties. Single-molecule Fluorescence Resonance Energy Transfer (FRET) analyses revealed that these ribosomes exhibit perturbations in aminoacyl-transfer RNA (aa-tRNA) selection and altered pre-translocation ribosome complex dynamics. Furthermore, we find that HCC cells lacking SNORA24-guided pseudouridine modifications have increased translational miscoding and stop codon readthrough frequencies. These findings highlight a role for specific snoRNAs in safeguarding against oncogenic insult and demonstrate a functional link between H/ACA snoRNAs regulated by RAS and the biophysical properties of ribosomes in cancer.
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Affiliation(s)
- Mary McMahon
- Helen Diller Family Comprehensive Cancer Center, Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Adrian Contreras
- Helen Diller Family Comprehensive Cancer Center, Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Mikael Holm
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States
| | - Tamayo Uechi
- Helen Diller Family Comprehensive Cancer Center, Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Craig M Forester
- Helen Diller Family Comprehensive Cancer Center, Department of Urology, University of California, San Francisco, San Francisco, United States.,Division of Pediatric Allergy, Immunology & Bone Marrow Transplantation, University of California, San Francisco, San Francisco, United States
| | - Xiaming Pang
- Helen Diller Family Comprehensive Cancer Center, Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Cody Jackson
- Gladstone Histology and Light Microscopy Core, Gladstone Institutes, San Francisco, United States
| | - Meredith E Calvert
- Gladstone Histology and Light Microscopy Core, Gladstone Institutes, San Francisco, United States
| | - Bin Chen
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, United States.,Department of Pharmacology and Toxicology, Michigan State University, Grand Rapids, United States
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, United States
| | - John M Luk
- Arbele Corporation, Seattle, United States
| | - R Kate Kelley
- Helen Diller Family Comprehensive Cancer Center, Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - John D Gordan
- Helen Diller Family Comprehensive Cancer Center, Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - Ryan M Gill
- Department of Pathology, University of California, San Francisco, San Francisco, United States
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States
| | - Davide Ruggero
- Helen Diller Family Comprehensive Cancer Center, Department of Urology, University of California, San Francisco, San Francisco, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
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26
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Keenan BP, Tamaki W, Liu E, Chen B, Cheung A, Gordan JD, Sheldon B, Zhang L, Kelley RK, Fong L. Abstract 4063: Single cell immune profiling of patients with advanced biliary cancers treated with combination checkpoint inhibition and GM-CSF reveals diverse T cell and myeloid cell mechanisms of action. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4063] [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: Advanced biliary cancers (ABC) including cholangiocarcinoma and gallbladder adenocarcinoma are rising in incidence with limited standard treatment options. While checkpoint inhibition (CPI) achieves durable tumor responses in subsets of patients across many malignancies, less than 10% of ABC patients respond to single agent PD-1-targeted therapy. Combination immunotherapy aims to overcome pre-existing and adaptive resistance to immunotherapy. GM-CSF is a cytokine that activates and matures antigen-presenting cells, suggesting the potential to enhance immune responses. The exact mechanisms of action of this cytokine have not been defined in cancer patients. The combination of GM-CSF and anti-CTLA-4 CPI demonstrated safety along with inducing clinical responses in melanoma and prostate cancer. We conducted a phase II trial of the novel combination of GM-CSF and pembrolizumab (Pembro) in patients with ABC which has resulted in durable clinical responses in greater proportion than previously reported with anti-PD-1 monotherapy.
Methods: We assessed peripheral blood mononuclear cells (PBMC) from patients on Pembro monotherapy and combined Pembro/GM-CSF by mass cytometry (CyTOF) and T cell receptor (TCR) sequencing. We explored for the differences between clinical responders versus non-responders.
Results: We find that the addition of GM-CSF to Pembro leads to a higher frequency of myeloid cells overall; however, certain sub-populations of classical monocytes and conventional dendritic cells decreased in peripheral blood following upfront Pembro followed by GM-CSF. GM-CSF did not seem to change the phenotypes or relative frequencies of circulating T cell subsets. We also find that clinical responders possess specific circulating populations of classical monocyte and conventional dendritic cells prior to treatment. Responders also had higher percentages of CD8+ T cells expressing CD39 following Pembro treatment compared to non-responders. Combination therapy with Pembro/GM-CSF led to different effects on the T cell repertoire compared to Pembro alone.
Conclusions: The addition of GM-CSF to Pembro leads to dynamic shifts in myeloid cell subsets in the peripheral blood of ABC patients treated with immunotherapy, whereas Pembro alone led to changes in the activation states of T cell subsets. The TCR repertoire shifts reflect distinct mechanisms of action for Pembro monotherapy versus Pembro/GM-CSF. Future studies will explore the mechanisms driving the increased response rate seen with combination immunotherapy in comparison to Pembro alone in ABC patients, both through the study of peripheral immune responses as well as via immune-profiling of tumors from sequential biopsies of patients on Pembro monotherapy versus combined Pembro/GM-CSF.
Citation Format: Bridget P. Keenan, Whitney Tamaki, Eric Liu, Brandon Chen, Alexander Cheung, John D. Gordan, Brenna Sheldon, Li Zhang, Robin K. Kelley, Lawrence Fong. Single cell immune profiling of patients with advanced biliary cancers treated with combination checkpoint inhibition and GM-CSF reveals diverse T cell and myeloid cell mechanisms of action [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4063.
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Affiliation(s)
| | - Whitney Tamaki
- University of California San Francisco, San Francisco, CA
| | - Eric Liu
- University of California San Francisco, San Francisco, CA
| | - Brandon Chen
- University of California San Francisco, San Francisco, CA
| | | | - John D. Gordan
- University of California San Francisco, San Francisco, CA
| | - Brenna Sheldon
- University of California San Francisco, San Francisco, CA
| | - Li Zhang
- University of California San Francisco, San Francisco, CA
| | | | - Lawrence Fong
- University of California San Francisco, San Francisco, CA
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Kambhampati S, Bauer KE, Bracci PM, Keenan BP, Behr SC, Gordan JD, Kelley RK. Nivolumab in patients with advanced hepatocellular carcinoma and Child‐Pugh class B cirrhosis: Safety and clinical outcomes in a retrospective case series. Cancer 2019; 125:3234-3241. [DOI: 10.1002/cncr.32206] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/10/2019] [Accepted: 04/28/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Swetha Kambhampati
- Division of Hematology and Oncology, Department of Medicine University of California at San Francisco Medical Center San Francisco California
- Division of Hematology and Oncology, Department of MedicineUniversity of California at San Francisco Helen Diller Family Comprehensive Cancer Center San Francisco California
| | - Kelly E. Bauer
- Division of Hematology and Oncology, Department of MedicineUniversity of California at San Francisco Helen Diller Family Comprehensive Cancer Center San Francisco California
| | - Paige M. Bracci
- Department of Epidemiology and Biostatistics University of California at San Francisco San Francisco California
| | - Bridget P. Keenan
- Division of Hematology and Oncology, Department of Medicine University of California at San Francisco Medical Center San Francisco California
- Division of Hematology and Oncology, Department of MedicineUniversity of California at San Francisco Helen Diller Family Comprehensive Cancer Center San Francisco California
| | - Spencer C. Behr
- Department of Radiology University of California at San Francisco Medical Center San Francisco California
| | - John D. Gordan
- Division of Hematology and Oncology, Department of Medicine University of California at San Francisco Medical Center San Francisco California
- Division of Hematology and Oncology, Department of MedicineUniversity of California at San Francisco Helen Diller Family Comprehensive Cancer Center San Francisco California
- Quantitative Biosciences Institute University of California at San Francisco San Francisco California
| | - Robin K. Kelley
- Division of Hematology and Oncology, Department of Medicine University of California at San Francisco Medical Center San Francisco California
- Division of Hematology and Oncology, Department of MedicineUniversity of California at San Francisco Helen Diller Family Comprehensive Cancer Center San Francisco California
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28
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Lou K, Steri V, Ge AY, Hwang YC, Yogodzinski CH, Shkedi AR, Choi ALM, Mitchell DC, Swaney DL, Hann B, Gordan JD, Shokat KM, Gilbert LA. KRAS G12C inhibition produces a driver-limited state revealing collateral dependencies. Sci Signal 2019; 12:12/583/eaaw9450. [PMID: 31138768 DOI: 10.1126/scisignal.aaw9450] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Inhibitors targeting KRASG12C, a mutant form of the guanosine triphosphatase (GTPase) KRAS, are a promising new class of oncogene-specific therapeutics for the treatment of tumors driven by the mutant protein. These inhibitors react with the mutant cysteine residue by binding covalently to the switch-II pocket (S-IIP) that is present only in the inactive guanosine diphosphate (GDP)-bound form of KRASG12C, sparing the wild-type protein. We used a genome-scale CRISPR interference (CRISPRi) functional genomics platform to systematically identify genetic interactions with a KRASG12C inhibitor in cellular models of KRASG12C mutant lung and pancreatic cancer. Our data revealed genes that were selectively essential in this oncogenic driver-limited cell state, meaning that their loss enhanced cellular susceptibility to direct KRASG12C inhibition. We termed such genes "collateral dependencies" (CDs) and identified two classes of combination therapies targeting these CDs that increased KRASG12C target engagement or blocked residual survival pathways in cells and in vivo. From our findings, we propose a framework for assessing genetic dependencies induced by oncogene inhibition.
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Affiliation(s)
- Kevin Lou
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Veronica Steri
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Preclinical Therapeutics Core, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alex Y Ge
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Y Christina Hwang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Medicine and Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christopher H Yogodzinski
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Arielle R Shkedi
- Institute for Neurodegenerative Diseases and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alex L M Choi
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Medicine and Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Dominique C Mitchell
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Medicine and Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.,Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Byron Hann
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Preclinical Therapeutics Core, University of California, San Francisco, San Francisco, CA 94158, USA
| | - John D Gordan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Medicine and Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. .,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA. .,Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA.,Innovative Genomics Institute, University of California, San Francisco, San Francisco, CA 94158, USA
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29
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Kastenhuber ER, Craig J, Ramsey J, Sullivan KM, Sage J, de Oliveira S, Riehle KJ, Scott JD, Gordan JD, Bardeesy N, Abou-Alfa GK. Road map for fibrolamellar carcinoma: progress and goals of a diversified approach. J Hepatocell Carcinoma 2019; 6:41-48. [PMID: 30951568 PMCID: PMC6362920 DOI: 10.2147/jhc.s194764] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fibrolamellar carcinoma is a rare liver cancer, which primarily afflicts adolescents and young adults worldwide and is frequently lethal. Given the rarity of this disease, patient recruitment for clinical trials remains a challenge. In November 2017, the Second Fibrolamellar Cancer Foundation Scientific Summit (Stamford, CT, USA) provided an opportunity for investigators to discuss recent advances in the characterization of the disease and its surrounding liver and immune context. The Fibrolamellar Cancer Foundation has thus set out a road map to identify and test therapeutic targets in the most efficient possible manner.
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Affiliation(s)
- Edward R Kastenhuber
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA, .,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Craig
- Fibrolamellar Cancer Foundation, Greenwich, CT, USA
| | - Jon Ramsey
- Department of Biochemistry, University of Vermont Cancer Center, Burlington, VT, USA
| | - Kevin M Sullivan
- Northwest Liver Research Program, University of Washington, Seattle, WA, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, Stanford, CA, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Sofia de Oliveira
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Kimberly J Riehle
- Northwest Liver Research Program, University of Washington, Seattle, WA, USA
| | - John D Scott
- Northwest Liver Research Program, University of Washington, Seattle, WA, USA
| | - John D Gordan
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nabeel Bardeesy
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ghassan K Abou-Alfa
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA, .,Department of Medicine, Weill Cornell School of Medicine, New York, NY, USA,
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30
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Frazier NM, Brand T, Gordan JD, Grandis J, Jura N. Overexpression-mediated activation of MET in the Golgi promotes HER3/ERBB3 phosphorylation. Oncogene 2018; 38:1936-1950. [PMID: 30390071 PMCID: PMC6417953 DOI: 10.1038/s41388-018-0537-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 01/14/2018] [Revised: 09/07/2018] [Accepted: 09/25/2018] [Indexed: 12/16/2022]
Abstract
Ligand-dependent oligomerization of receptor tyrosine kinases (RTKs) results in their activation through highly specific conformational changes in the extracellular and intracellular receptor domains. These conformational changes are unique for each RTK sub-family, limiting cross-activation between unrelated RTKs. The proto-oncogene MET receptor tyrosine kinase overcomes these structural constraints and phosphorylates unrelated RTKs in numerous cancer cell lines. The molecular basis for these interactions is unknown. We investigated the mechanism by which MET phosphorylates the human epidermal growth factor receptor-3 (HER3 or ERBB3), a catalytically impaired RTK whose phosphorylation by MET has been described as an essential component of drug resistance to inhibitors targeting EGFR and HER2. We find that in untransformed cells, HER3 is not phosphorylated by MET in response to ligand stimulation, but rather to increasing levels of MET expression, which results in MET activation in a ligand-independent manner. Phosphorylation of HER3 by its canonical dimerization partners, EGFR and HER2, is achieved by engaging an allosteric site on the HER3 kinase domain, but this site is not required when HER3 is phosphorylated by MET. We also observe that HER3 preferentially interacts with MET during its maturation along the secretory pathway, before MET is post-translationally processed by cleavage within its extracellular domain. This results in accumulation of phosphorylated HER3 in the Golgi apparatus. We further show that in addition to HER3, MET phosphorylates other RTKs in the Golgi, suggesting that this mechanism is not limited to HER3 phosphorylation. These data demonstrate a link between MET overexpression and its aberrant activation in the Golgi endomembranes and suggest that non-canonical interactions between MET and unrelated RTKs occur during maturation of receptors. Our study highlights a novel aspect of MET signaling in cancer that would not be accessible to inhibition by therapeutic antibodies.
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Affiliation(s)
- Nicole Michael Frazier
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Toni Brand
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Francisco, CA, 94113, USA
| | - John D Gordan
- Division of Hematology and Oncology - University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Jennifer Grandis
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Francisco, CA, 94113, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA. .,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA.
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31
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Song X, Liu X, Wang H, Wang J, Qiao Y, Cigliano A, Utpatel K, Ribback S, Pilo MG, Serra M, Gordan JD, Che L, Zhang S, Cossu A, Porcu A, Pascale RM, Dombrowski F, Hu H, Calvisi DF, Evert M, Chen X. Combined CDK4/6 and Pan-mTOR Inhibition Is Synergistic Against Intrahepatic Cholangiocarcinoma. Clin Cancer Res 2018; 25:403-413. [PMID: 30084835 DOI: 10.1158/1078-0432.ccr-18-0284] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 04/02/2018] [Accepted: 06/25/2018] [Indexed: 02/06/2023]
Abstract
PURPOSE Intrahepatic cholangiocarcinoma (ICC) is an aggressive cancer type, lacking effective therapies and associated with a dismal prognosis. Palbociclib is a selective CDK4/6 inhibitor, which has been shown to suppress cell proliferation in many experimental cancer models. Recently, we demonstrated that pan-mTOR inhibitors, such as MLN0128, effectively induce apoptosis, although have limited efficacy in restraining proliferation of ICC cells. Here, we tested the hypothesis that palbociclib, due to its antproliferative properties in many cancer types, might synergize with MLN0128 to impair ICC growth. EXPERIMENTAL DESIGN Human ICC cell lines and the AKT/YapS127A ICC mouse model were used to test the therapeutic efficacy of palbociclib and MLN0128, either alone or in combination. RESULTS Administration of palbociclib suppressed in vitro ICC cell growth by inhibiting cell-cycle progression. Concomitant administration of palbociclib and MLN0128 led to a pronounced, synergistic growth constraint of ICC cell lines. Furthermore, while treatment with palbociclib or MLN0128 alone resulted in tumor growth reduction in AKT/YapS127A mice, a remarkable tumor regression was achieved when the two drugs were administered simultaneously. Mechanistically, palbociclib was found to potentiate MLN0128 mTOR inhibition activity, whereas MLN0128 prevented the upregulation of cyclin D1 induced by palbociclib treatment. CONCLUSIONS Our study indicates the synergistic activity of palbociclib and MLN0128 in inhibiting ICC cell proliferation. Thus, combination of CDK4/6 and mTOR inhibitors might represent a novel, promising, and effective therapeutic approach against human ICC.See related commentary by Malumbres, p. 6.
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Affiliation(s)
- Xinhua Song
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California
| | - Xianqiong Liu
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California.,School of Pharmacy, Hubei University of Chinese Medicine Wuhan, Hubei, China
| | - Haichuan Wang
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California.,Liver Transplantation Division, Department of Liver Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Jingxiao Wang
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California.,Beijing University of Chinese Medicine, Beijing, China
| | - Yu Qiao
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California.,Department of Oncology, Beijing Hospital, Beijing, China
| | - Antonio Cigliano
- Institute of Pathology, University of Greifswald, Greifswald, Germany
| | - Kirsten Utpatel
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Silvia Ribback
- Institute of Pathology, University of Greifswald, Greifswald, Germany
| | - Maria G Pilo
- Institute of Pathology, University of Greifswald, Greifswald, Germany
| | - Marina Serra
- Institute of Pathology, University of Greifswald, Greifswald, Germany
| | - John D Gordan
- Department of Medicine, University of California, San Francisco, California
| | - Li Che
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California
| | - Shanshan Zhang
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California
| | - Antonio Cossu
- Unit of Pathology, Azienda Ospedaliero Universitaria Sassari, Sassari, Italy
| | - Alberto Porcu
- Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Rosa M Pascale
- Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Frank Dombrowski
- Institute of Pathology, University of Greifswald, Greifswald, Germany
| | - Hongbo Hu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.
| | - Diego F Calvisi
- Institute of Pathology, University of Greifswald, Greifswald, Germany
| | - Matthias Evert
- Institute of Pathology, University of Regensburg, Regensburg, Germany.
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, California.
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32
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Lim HC, Montesion M, Botton T, Collisson EA, Umetsu SE, Behr SC, Gordan JD, Stephens PJ, Kelley RK. Hybrid Capture-Based Tumor Sequencing and Copy Number Analysis to Confirm Origin of Metachronous Metastases in BRCA1-Mutant Cholangiocarcinoma Harboring a Novel YWHAZ-BRAF Fusion. Oncologist 2018; 23:998-1003. [PMID: 29622700 DOI: 10.1634/theoncologist.2017-0645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/12/2018] [Indexed: 01/07/2023] Open
Abstract
Biliary tract cancers such as cholangiocarcinoma represent a heterogeneous group of cancers that can be difficult to diagnose. Recent comprehensive genomic analyses in large cholangiocarcinoma cohorts have defined important molecular subgroups within cholangiocarcinoma that may relate to anatomic location and etiology [1], [2], [3], [4] and may predict responsiveness to targeted therapies in development [5], [6], [7]. These emerging data highlight the potential for tumor genomics to inform diagnosis and treatment options in this challenging tumor type. We report the case of a patient with a germline BRCA1 mutation who presented with a cholangiocarcinoma driven by the novel YWHAZ-BRAF fusion. Hybrid capture-based DNA sequencing and copy number analysis performed as part of clinical care demonstrated that two later-occurring tumors were clonally derived from the primary cholangiocarcinoma rather than distinct new primaries, revealing an unusual pattern of late metachronous metastasis. We discuss the clinical significance of these genetic alterations and their relevance to therapeutic strategies. KEY POINTS Hybrid capture-based next-generation DNA sequencing assays can provide diagnostic clarity in patients with unusual patterns of metastasis and recurrence in which the pathologic diagnosis is ambiguous.To our knowledge, this is the first reported case of a YWHAZ-BRAF fusion in pancreaticobiliary cancer, and a very rare case of cholangiocarcinoma in the setting of a germline BRCA1 mutation.The patient's BRCA1 mutation and YWHAZ-BRAF fusion constitute potential targets for future therapy.
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Affiliation(s)
- Huat C Lim
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | | | - Thomas Botton
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Eric A Collisson
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Sarah E Umetsu
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Spencer C Behr
- Department of Radiology, University of California, San Francisco, San Francisco, California, USA
| | - John D Gordan
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | | | - Robin K Kelley
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
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33
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Urisman A, Levin RS, Gordan JD, Webber JT, Hernandez H, Ishihama Y, Shokat KM, Burlingame AL. An Optimized Chromatographic Strategy for Multiplexing In Parallel Reaction Monitoring Mass Spectrometry: Insights from Quantitation of Activated Kinases. Mol Cell Proteomics 2016; 16:265-277. [PMID: 27940637 DOI: 10.1074/mcp.m116.058172] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 12/01/2016] [Indexed: 01/06/2023] Open
Abstract
Reliable quantitation of protein abundances in defined sets of cellular proteins is critical to numerous biological applications. Traditional immunodetection-based methods are limited by the quality and availability of specific antibodies, especially for site-specific post-translational modifications. Targeted proteomic methods, including the recently developed parallel reaction monitoring (PRM) mass spectrometry, have enabled accurate quantitative measurements of up to a few hundred specific target peptides. However, the degree of practical multiplexing in label-free PRM workflows remains a significant limitation for the technique. Here we present a strategy for significantly increasing multiplexing in label-free PRM that takes advantage of the superior separation characteristics and retention time stability of meter-scale monolithic silica-C18 column-based chromatography. We show the utility of the approach in quantifying kinase abundances downstream of previously developed active kinase enrichment methodology based on multidrug inhibitor beads. We examine kinase activation dynamics in response to three different MAP kinase inhibitors in colorectal carcinoma cells and demonstrate reliable quantitation of over 800 target peptides from over 150 kinases in a single label-free PRM run. The kinase activity profiles obtained from these analyses reveal compensatory activation of TGF-β family receptors as a response to MAPK blockade. The gains achieved using this label-free PRM multiplexing strategy will benefit a wide array of biological applications.
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Affiliation(s)
- Anatoly Urisman
- From the ‡Department of Pathology, University of California San Francisco, San Francisco, California; .,§Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Rebecca S Levin
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California.,¶Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California
| | - John D Gordan
- ¶Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California.,‖Department of Medicine, University of California San Francisco, San Francisco, California
| | - James T Webber
- **Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California
| | - Hilda Hernandez
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Yasushi Ishihama
- ‡‡Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kevan M Shokat
- ¶Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California.,§§Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California
| | - Alma L Burlingame
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
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Miller RE, Brough R, Bajrami I, Williamson CT, McDade S, Campbell J, Kigozi A, Rafiq R, Pemberton H, Natrajan R, Joel J, Astley H, Mahoney C, Moore JD, Torrance C, Gordan JD, Webber JT, Levin RS, Shokat KM, Bandyopadhyay S, Lord CJ, Ashworth A. Synthetic Lethal Targeting of ARID1A-Mutant Ovarian Clear Cell Tumors with Dasatinib. Mol Cancer Ther 2016; 15:1472-84. [PMID: 27364904 DOI: 10.1158/1535-7163.mct-15-0554] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [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: 07/06/2015] [Accepted: 04/06/2016] [Indexed: 11/16/2022]
Abstract
New targeted approaches to ovarian clear cell carcinomas (OCCC) are needed, given the limited treatment options in this disease and the poor response to standard chemotherapy. Using a series of high-throughput cell-based drug screens in OCCC tumor cell models, we have identified a synthetic lethal (SL) interaction between the kinase inhibitor dasatinib and a key driver in OCCC, ARID1A mutation. Imposing ARID1A deficiency upon a variety of human or mouse cells induced dasatinib sensitivity, both in vitro and in vivo, suggesting that this is a robust synthetic lethal interaction. The sensitivity of ARID1A-deficient cells to dasatinib was associated with G1-S cell-cycle arrest and was dependent upon both p21 and Rb. Using focused siRNA screens and kinase profiling, we showed that ARID1A-mutant OCCC tumor cells are addicted to the dasatinib target YES1. This suggests that dasatinib merits investigation for the treatment of patients with ARID1A-mutant OCCC. Mol Cancer Ther; 15(7); 1472-84. ©2016 AACR.
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Affiliation(s)
- Rowan E Miller
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rachel Brough
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Chris T Williamson
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Simon McDade
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
| | - James Campbell
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Asha Kigozi
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rumana Rafiq
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Helen Pemberton
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rachel Natrajan
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Josephine Joel
- Horizon Discovery, Waterbeach, Cambridge, United Kingdom
| | - Holly Astley
- Horizon Discovery, Waterbeach, Cambridge, United Kingdom
| | - Claire Mahoney
- Horizon Discovery, Waterbeach, Cambridge, United Kingdom
| | | | - Chris Torrance
- Horizon Discovery, Waterbeach, Cambridge, United Kingdom
| | - John D Gordan
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - James T Webber
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Rebecca S Levin
- Cellular and Molecular Pharmacology University of California, San Francisco, San Francisco, California
| | - Kevan M Shokat
- Cellular and Molecular Pharmacology University of California, San Francisco, San Francisco, California. Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California
| | - Sourav Bandyopadhyay
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Christopher J Lord
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom.
| | - Alan Ashworth
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom. Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom.
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35
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Saha SK, Gordan JD, Kleinstiver BP, Vu P, Najem MS, Yeo JC, Shi L, Kato Y, Levin RS, Webber JT, Damon LJ, Egan RK, Greninger P, McDermott U, Garnett MJ, Jenkins RL, Rieger-Christ KM, Sullivan TB, Hezel AF, Liss AS, Mizukami Y, Goyal L, Ferrone CR, Zhu AX, Joung JK, Shokat KM, Benes CH, Bardeesy N. Isocitrate Dehydrogenase Mutations Confer Dasatinib Hypersensitivity and SRC Dependence in Intrahepatic Cholangiocarcinoma. Cancer Discov 2016; 6:727-39. [PMID: 27231123 DOI: 10.1158/2159-8290.cd-15-1442] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/16/2016] [Indexed: 01/06/2023]
Abstract
UNLABELLED Intrahepatic cholangiocarcinoma (ICC) is an aggressive liver bile duct malignancy exhibiting frequent isocitrate dehydrogenase (IDH1/IDH2) mutations. Through a high-throughput drug screen of a large panel of cancer cell lines, including 17 biliary tract cancers, we found that IDH mutant (IDHm) ICC cells demonstrate a striking response to the multikinase inhibitor dasatinib, with the highest sensitivity among 682 solid tumor cell lines. Using unbiased proteomics to capture the activated kinome and CRISPR/Cas9-based genome editing to introduce dasatinib-resistant "gatekeeper" mutant kinases, we identified SRC as a critical dasatinib target in IDHm ICC. Importantly, dasatinib-treated IDHm xenografts exhibited pronounced apoptosis and tumor regression. Our results show that IDHm ICC cells have a unique dependency on SRC and suggest that dasatinib may have therapeutic benefit against IDHm ICC. Moreover, these proteomic and genome-editing strategies provide a systematic and broadly applicable approach to define targets of kinase inhibitors underlying drug responsiveness. SIGNIFICANCE IDH mutations define a distinct subtype of ICC, a malignancy that is largely refractory to current therapies. Our work demonstrates that IDHm ICC cells are hypersensitive to dasatinib and critically dependent on SRC activity for survival and proliferation, pointing to new therapeutic strategies against these cancers. Cancer Discov; 6(7); 727-39. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 681.
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Affiliation(s)
- Supriya K Saha
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - John D Gordan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Benjamin P Kleinstiver
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts. Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Phuong Vu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Mortada S Najem
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jia-Chi Yeo
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Lei Shi
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Yasutaka Kato
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Rebecca S Levin
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California
| | - James T Webber
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Leah J Damon
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Regina K Egan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Patricia Greninger
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | | | | | - Roger L Jenkins
- Department of Transplantation, Lahey Hospital and Medical Center, Burlington, Massachusetts
| | - Kimberly M Rieger-Christ
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, Massachusetts
| | - Travis B Sullivan
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, Massachusetts
| | - Aram F Hezel
- University of Rochester School of Medicine, Rochester, New York
| | - Andrew S Liss
- Department of Surgery and the Andrew L. Warshaw, MD, Institute for Pancreatic Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Yusuke Mizukami
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts. Center for Clinical and Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Hokkaido, Japan
| | - Lipika Goyal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Cristina R Ferrone
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Andrew X Zhu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts. Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California. Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
| | - Nabeel Bardeesy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
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Martins MM, Zhou AY, Corella A, Horiuchi D, Yau C, Rakshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons PA, Shamji A, Schreiber S, Schreiber S, Krogan NJ, Shokat KM, Shokat KM, McCormick F, Nomura D, Bandyopadhyay S, Goga A. Abstract PR15: Functional analysis of diverse oncogenic driver mutations using an isogenic cell line library identifies novel drug responses and alterations in metabolism. Cancer Res 2015. [DOI: 10.1158/1538-7445.transcagen-pr15] [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
There is an urgent need in oncology to link molecular aberrations in tumors with altered cellular behaviors, such as metabolic derangements, and to identify novel therapeutics for cancer treatment. We have sought to identify synthetic-lethal genetic interactions that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated an unbiased and quantitative chemical-genetic interaction map that measures the influence of 51 aberrant cancer genes on 90 drug responses. The dataset strongly predicts drug responses found in cancer cell line collections, indicating that isogenic cells can model more complex cellular contexts. Applied to triple-negative breast cancer, we report clinically actionable interactions with the MYC oncogene including resistance to PI3K/AKT pathway inhibitors and an unexpected sensitivity to dasatinib through LYN inhibition in a synthetic-lethal manner. These studies provide new drug and biomarker pairs for clinical investigation. We have also performed global metabolomics analysis in a subset of the isogenic cell lines demonstrating alterations in metabolic pathways that are shared across multiple oncogenes, as well as those that are distinct to specific oncogenic drivers. This scalable approach enables the prediction of drug responses from patient data and can be used to accelerate the development of new genotype-directed therapies.
Citation Format: Maria M. Martins, Alicia Y. Zhou, Alexandra Corella, Dai Horiuchi, Christina Yau, Taha Rakshandehroo, John D. Gordan, Rebecca S. Levin, Jeff Johnson, John Jascur, Mike Shales, Antonio Sorrentino, Jaime Cheah, Paul A. Clemons, Alykhan Shamji, Stuart Schreiber, Stuart Schreiber, Nevan J. Krogan, Kevan M. Shokat, Kevan M. Shokat, Frank McCormick, Daniel Nomura, Sourav Bandyopadhyay, Andrei Goga. Functional analysis of diverse oncogenic driver mutations using an isogenic cell line library identifies novel drug responses and alterations in metabolism. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr PR15.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - John Jascur
- 1University of California, San Francisco, CA,
| | - Mike Shales
- 1University of California, San Francisco, CA,
| | | | | | | | | | | | | | | | | | | | | | | | | | - Andrei Goga
- 1University of California, San Francisco, CA,
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37
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Martins MM, Zhou AY, Corella A, Horiuchi D, Yau C, Rakshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons PA, Shamji A, Schreiber S, Schreiber S, Krogan NJ, Shokat KM, Shokat KM, McCormick F, Nomura D, Bandyopadhyay S, Goga A. Abstract PR07: Functional analysis of diverse oncogenic driver mutations using an isogenic cell line library identifies novel drug responses and alterations in metabolism. Cancer Res 2015. [DOI: 10.1158/1538-7445.compsysbio-pr07] [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
There is an urgent need in oncology to link molecular aberrations in tumors with altered cellular behaviors, such as metabolic derangements, and to identify novel therapeutics for cancer treatment. We have sought to identify synthetic-lethal genetic interactions that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated an unbiased and quantitative chemical-genetic interaction map that measures the influence of 51 aberrant cancer genes on 90 drug responses. The dataset strongly predicts drug responses found in cancer cell line collections, indicating that isogenic cells can model more complex cellular contexts. Applied to triple-negative breast cancer, we report clinically actionable interactions with the MYC oncogene including resistance to PI3K/AKT pathway inhibitors and an unexpected sensitivity to dasatinib through LYN inhibition in a synthetic-lethal manner. These studies provide new drug and biomarker pairs for clinical investigation. We have also performed global metabolomics analysis in a subset of the isogenic cell lines demonstrating alterations in metabolic pathways that are shared across multiple oncogenes, as well as those that are distinct to specific oncogenic drivers. This scalable approach enables the prediction of drug responses from patient data and can be used to accelerate the development of new genotype-directed therapies.
This abstract is also presented as a poster at the Translation of the Cancer Genome conference.
Citation Format: Maria M. Martins, Alicia Y. Zhou, Alexandra Corella, Dai Horiuchi, Christina Yau, Taha Rakshandehroo, John D. Gordan, Rebecca S. Levin, Jeff Johnson, John Jascur, Mike Shales, Antonio Sorrentino, Jaime Cheah, Paul A. Clemons, Alykhan Shamji, Stuart Schreiber, Stuart Schreiber, Nevan J. Krogan, Kevan M. Shokat, Kevan M. Shokat, Frank McCormick, Daniel Nomura, Sourav Bandyopadhyay, Andrei Goga. Functional analysis of diverse oncogenic driver mutations using an isogenic cell line library identifies novel drug responses and alterations in metabolism. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr PR07.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - John Jascur
- 1University of California, San Francisco, CA,
| | - Mike Shales
- 1University of California, San Francisco, CA,
| | | | | | | | | | | | | | | | | | | | | | | | | | - Andrei Goga
- 1University of California, San Francisco, CA,
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38
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Zhou AY, Martins MM, Corella A, Horiuchi D, Yau C, Rakshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons PA, Shamji A, Schreiber SL, Krogan NJ, Shokat KM, McCormick F, Goga A, Bandyopadhyay S. Abstract B48: Identification of novel drug interactions with MYC via a quantitative chemical-genetic interaction map. Mol Cancer Res 2015. [DOI: 10.1158/1557-3125.myc15-b48] [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
There is an urgent need in oncology to link molecular aberrations in tumors with therapeutics that can be administered in a personalized fashion. One approach identifies synthetic-lethal genetic interactions or emergent dependencies that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated an unbiased and quantitative chemical-genetic interaction map that measures the influence of 51 aberrant cancer genes on 90 drug responses. The dataset strongly predicts drug responses found in cancer cell line collections, indicating that isogenic cells can model more complex cellular contexts. Applied to triple-negative breast cancer, we report clinically actionable interactions with the MYC oncogene including resistance to AKT/PI3K pathway inhibitors and an unexpected sensitivity to dasatinib through LYN inhibition in a synthetic-lethal manner, providing new drug and biomarker pairs for clinical investigation. This scalable approach enables the prediction of drug responses from patient data and can be used to accelerate the development of new genotype-directed therapies.
Citation Format: Alicia Y. Zhou, Maria M. Martins, Alexandra Corella, Dai Horiuchi, Christina Yau, Taha Rakshandehroo, John D. Gordan, Rebecca S. Levin, Jeff Johnson, John Jascur, Mike Shales, Antonio Sorrentino, Jaime Cheah, Paul A. Clemons, Alykhan Shamji, Stuart L. Schreiber, Nevan J. Krogan, Kevan M. Shokat, Frank McCormick, Andrei Goga, Sourav Bandyopadhyay. Identification of novel drug interactions with MYC via a quantitative chemical-genetic interaction map. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr B48.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - John Jascur
- 1University of California, San Francisco, CA,
| | - Mike Shales
- 1University of California, San Francisco, CA,
| | | | | | | | | | | | | | | | | | - Andrei Goga
- 1University of California, San Francisco, CA,
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39
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Zhou AY, Martins MM, Corella A, Horiuchi D, Yau C, Rakshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons PA, Shamji A, Schreiber S, Krogan NJ, Shokat KM, McCormick F, Samson S, Goga A, Bandyopadhyay S. Abstract B44: A systems approach combining genomics, advocacy, and emerging novel therapeutics to address triple-negative breast cancer (TNBC) outcomes disparities. Cancer Epidemiol Biomarkers Prev 2015. [DOI: 10.1158/1538-7755.disp14-b44] [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] Open
Abstract
Abstract
Background: Genomic analyses of patient tumors have unearthed an overwhelming number of recurrent somatic alterations in genes that have dramatic effects on tumor biology, patient drug responses, and clinical outcomes. In one study, high-grade triple negative breast cancer (TNBC) accounts for 34% of breast cancers in African American women versus 21% in white women. African American women have biologically more aggressive disease, independent of social determinants, and suffer the highest mortality rates. In advanced TNBC, a poor prognosis subtype, there is an urgent need to translate this emerging patient genomic data into new therapeutic paradigms.
Objectives: Our study focuses on emerging compounds that are already approved (i.e., Dasatinib) or in testing for human use and we expect that this work will serve as a prelude to one or more clinical trials in TNBC. We seek to determine if the treatment of metastatic TNBC recurrence with more targeted genotype-specific agents could improve the outcomes/survival of all women in this particularly aggressive poor prognosis subset, including African American women.
Methods: To guide the development of genotype-specific therapies in TNBC, we have established an isogenic cell-line drug screen that measures the impact of gene activation on a panel of emerging, clinically relevant compounds targeting a variety of cancer pathways. Using engineered isogenic cells, we generated an unbiased and quantitative chemical-genetic interaction map that measures the influence of 51 aberrant cancer genes on 90 drug responses. We believe that this approach can identify core synthetic lethal interactions, which underlie drug sensitivity and can be used as a foundation to identify patient populations that will selectively respond to drug treatments.
Results: Using our systems approach, our interaction map highlights both known and novel connections between oncogene activation and drug responses and provides a modular roadmap for the exploration of synthetic lethal relationships. Applied to triple-negative breast cancer, we report clinically actionable interactions with the MYC oncogene including resistance to AKT/PI3K pathway inhibitors and an unexpected sensitivity to dasatinib through LYN inhibition in a synthetic-lethal manner. Ensuring that the voice of the patient is represented in our scientific inquiry, advocacy has played a significant role in the development and realization of this project. Aligning experiential and professionalized expertise, trained advocates explore relentless challenges and opportunities for moving the science forward.
Conclusion: A novel systems biology approach that uses module maps of oncogenes and emerging therapeutics can define synthetic-lethal interactions and actionable therapeutics to help decrease TNBC outcomes/survival disparities in African American women.
Citation Format: Alicia Y. Zhou, Maria M. Martins, Alexandra Corella, Dai Horiuchi, Christina Yau, Taha Rakshandehroo, John D. Gordan, Rebecca S. Levin, Jeff Johnson, John Jascur, Mike Shales, Antonio Sorrentino, Jaime Cheah, Paul A. Clemons, Alykhan Shamji, Stuart Schreiber, Nevan J. Krogan, Kevan M. Shokat, Frank McCormick, Susan Samson, Andrei Goga, Sourav Bandyopadhyay. A systems approach combining genomics, advocacy, and emerging novel therapeutics to address triple-negative breast cancer (TNBC) outcomes disparities. [abstract]. In: Proceedings of the Seventh AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 9-12, 2014; San Antonio, TX. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2015;24(10 Suppl):Abstract nr B44.
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Affiliation(s)
- Alicia Y. Zhou
- 1University of California, San Francisco, San Francisco, CA,
- *These authors contributed equally to this work
| | - Maria M. Martins
- 1University of California, San Francisco, San Francisco, CA,
- *These authors contributed equally to this work
| | | | - Dai Horiuchi
- 1University of California, San Francisco, San Francisco, CA,
| | - Christina Yau
- 1University of California, San Francisco, San Francisco, CA,
| | | | - John D. Gordan
- 1University of California, San Francisco, San Francisco, CA,
| | | | - Jeff Johnson
- 1University of California, San Francisco, San Francisco, CA,
| | - John Jascur
- 1University of California, San Francisco, San Francisco, CA,
| | - Mike Shales
- 1University of California, San Francisco, San Francisco, CA,
| | | | - Jaime Cheah
- 2Center for the Science of Therapeutics, Broad Institute, Cambridge, MA,
| | - Paul A. Clemons
- 2Center for the Science of Therapeutics, Broad Institute, Cambridge, MA,
| | - Alykhan Shamji
- 2Center for the Science of Therapeutics, Broad Institute, Cambridge, MA,
| | - Stuart Schreiber
- 2Center for the Science of Therapeutics, Broad Institute, Cambridge, MA,
- 3Howard Hughes Medical Institute, Chevy Chase, MD
| | - Nevan J. Krogan
- 1University of California, San Francisco, San Francisco, CA,
| | - Kevan M. Shokat
- 1University of California, San Francisco, San Francisco, CA,
- 3Howard Hughes Medical Institute, Chevy Chase, MD
| | - Frank McCormick
- 1University of California, San Francisco, San Francisco, CA,
| | - Susan Samson
- 1University of California, San Francisco, San Francisco, CA,
| | - Andrei Goga
- 1University of California, San Francisco, San Francisco, CA,
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Evason KJ, Francisco MT, Juric V, Balakrishnan S, Lopez Pazmino MDP, Gordan JD, Kakar S, Spitsbergen J, Goga A, Stainier DYR. Identification of Chemical Inhibitors of β-Catenin-Driven Liver Tumorigenesis in Zebrafish. PLoS Genet 2015; 11:e1005305. [PMID: 26134322 PMCID: PMC4489858 DOI: 10.1371/journal.pgen.1005305] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [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: 12/08/2014] [Accepted: 05/28/2015] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most lethal human cancers. The search for targeted treatments has been hampered by the lack of relevant animal models for the genetically diverse subsets of HCC, including the 20-40% of HCCs that are defined by activating mutations in the gene encoding β-catenin. To address this chemotherapeutic challenge, we created and characterized transgenic zebrafish expressing hepatocyte-specific activated β-catenin. By 2 months post fertilization (mpf), 33% of transgenic zebrafish developed HCC in their livers, and 78% and 80% of transgenic zebrafish showed HCC at 6 and 12 mpf, respectively. As expected for a malignant process, transgenic zebrafish showed significantly decreased mean adult survival compared to non-transgenic control siblings. Using this novel transgenic model, we screened for druggable pathways that mediate β-catenin-induced liver growth and identified two c-Jun N-terminal kinase (JNK) inhibitors and two antidepressants (one tricyclic antidepressant, amitriptyline, and one selective serotonin reuptake inhibitor) that suppressed this phenotype. We further found that activated β-catenin was associated with JNK pathway hyperactivation in zebrafish and in human HCC. In zebrafish larvae, JNK inhibition decreased liver size specifically in the presence of activated β-catenin. The β-catenin-specific growth-inhibitory effect of targeting JNK was conserved in human liver cancer cells. Our other class of hits, antidepressants, has been used in patient treatment for decades, raising the exciting possibility that these drugs could potentially be repurposed for cancer treatment. In support of this proposal, we found that amitriptyline decreased tumor burden in a mouse HCC model. Our studies implicate JNK inhibitors and antidepressants as potential therapeutics for β-catenin-induced liver tumors. Liver cancer is a leading cause of cancer-related death. Genetic analysis of liver cancer has enabled classification of these tumors into subsets with unique genetic, clinical, and prognostic features. The search for targeted liver cancer treatments has been hampered by the lack of relevant animal models for these genetically diverse subsets, including liver cancers that are defined by activating mutations in the gene encoding β-catenin, an integral component of the Wnt signaling pathway. Here we describe the generation and characterization of genetically modified zebrafish expressing hepatocyte-specific activated β-catenin. We used this new zebrafish model to screen for drugs that suppress β-catenin-induced liver growth, and identified two classes of hits, c-Jun N-terminal kinase (JNK) inhibitors and antidepressants, that suppressed this phenotype. Our findings provide insights into the mechanisms by which β-catenin promotes liver tumor formation and implicate JNK inhibitors and antidepressants as potential treatments for a subset of human liver cancers.
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Affiliation(s)
- Kimberley J. Evason
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, Programs in Developmental and Stem Cell Biology, Genetics and Human Genetics, Diabetes Center, Institute for Regeneration Medicine and the Liver Center, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (KJE); (AG); (DYRS)
| | - Macrina T. Francisco
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, California, United States of America
| | - Vladislava Juric
- The George Williams Hooper Research Foundation, University of California, San Francisco, San Francisco, California, United States of America
| | - Sanjeev Balakrishnan
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, California, United States of America
| | - Maria del Pilar Lopez Pazmino
- Department of Biochemistry and Biophysics, Programs in Developmental and Stem Cell Biology, Genetics and Human Genetics, Diabetes Center, Institute for Regeneration Medicine and the Liver Center, University of California, San Francisco, San Francisco, California, United States of America
| | - John D. Gordan
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Sanjay Kakar
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America
| | - Jan Spitsbergen
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Andrei Goga
- Department of Cell & Tissue Biology, University of California, San Francisco, San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (KJE); (AG); (DYRS)
| | - Didier Y. R. Stainier
- Department of Biochemistry and Biophysics, Programs in Developmental and Stem Cell Biology, Genetics and Human Genetics, Diabetes Center, Institute for Regeneration Medicine and the Liver Center, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (KJE); (AG); (DYRS)
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Martins MM, Zhou AY, Corella A, Horiuchi D, Yau C, Rakhshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons PA, Shamji AF, Schreiber SL, Krogan NJ, Shokat KM, McCormick F, Goga A, Bandyopadhyay S. Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map. Cancer Discov 2014; 5:154-67. [PMID: 25501949 DOI: 10.1158/2159-8290.cd-14-0552] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
UNLABELLED There is an urgent need in oncology to link molecular aberrations in tumors with therapeutics that can be administered in a personalized fashion. One approach identifies synthetic-lethal genetic interactions or dependencies that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated a systematic and quantitative chemical-genetic interaction map that charts the influence of 51 aberrant cancer genes on 90 drug responses. The dataset strongly predicts drug responses found in cancer cell line collections, indicating that isogenic cells can model complex cellular contexts. Applying this dataset to triple-negative breast cancer, we report clinically actionable interactions with the MYC oncogene, including resistance to AKT-PI3K pathway inhibitors and an unexpected sensitivity to dasatinib through LYN inhibition in a synthetic lethal manner, providing new drug and biomarker pairs for clinical investigation. This scalable approach enables the prediction of drug responses from patient data and can accelerate the development of new genotype-directed therapies. SIGNIFICANCE Determining how the plethora of genomic abnormalities that exist within a given tumor cell affects drug responses remains a major challenge in oncology. Here, we develop a new mapping approach to connect cancer genotypes to drug responses using engineered isogenic cell lines and demonstrate how the resulting dataset can guide clinical interrogation.
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Affiliation(s)
- Maria M Martins
- University of California, San Francisco, San Francisco, California
| | - Alicia Y Zhou
- University of California, San Francisco, San Francisco, California
| | | | - Dai Horiuchi
- University of California, San Francisco, San Francisco, California
| | - Christina Yau
- University of California, San Francisco, San Francisco, California
| | | | - John D Gordan
- University of California, San Francisco, San Francisco, California
| | - Rebecca S Levin
- University of California, San Francisco, San Francisco, California
| | - Jeff Johnson
- University of California, San Francisco, San Francisco, California
| | - John Jascur
- University of California, San Francisco, San Francisco, California
| | - Mike Shales
- University of California, San Francisco, San Francisco, California
| | | | - Jaime Cheah
- Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts
| | - Paul A Clemons
- Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts
| | - Alykhan F Shamji
- Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts
| | - Stuart L Schreiber
- Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts. Howard Hughes Medical Institute, Bethesda, Maryland
| | - Nevan J Krogan
- University of California, San Francisco, San Francisco, California
| | - Kevan M Shokat
- University of California, San Francisco, San Francisco, California. Howard Hughes Medical Institute, Bethesda, Maryland
| | - Frank McCormick
- University of California, San Francisco, San Francisco, California
| | - Andrei Goga
- University of California, San Francisco, San Francisco, California.
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Sos ML, Levin RS, Gordan JD, Oses-Prieto JA, Webber JT, Salt M, Hann B, Burlingame AL, McCormick F, Bandyopadhyay S, Shokat KM. Oncogene mimicry as a mechanism of primary resistance to BRAF inhibitors. Cell Rep 2014; 8:1037-48. [PMID: 25127139 DOI: 10.1016/j.celrep.2014.07.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/14/2014] [Accepted: 07/10/2014] [Indexed: 01/11/2023] Open
Abstract
Despite the development of potent RAF/mitogen-activated protein kinase (MAPK) pathway inhibitors, only a fraction of BRAF-mutant patients benefit from treatment with these drugs. Using a combined chemogenomics and chemoproteomics approach, we identify drug-induced RAS-RAF-MEK complex formation in a subset of BRAF-mutant cancer cells characterized by primary resistance to vemurafenib. In these cells, autocrine interleukin-6 (IL-6) secretion may contribute to the primary resistance phenotype via induction of JAK/STAT3 and MAPK signaling. In a subset of cell lines, combined IL-6/MAPK inhibition is able to overcome primary resistance to BRAF-targeted therapy. Overall, we show that the signaling plasticity exerted by primary resistant BRAF-mutant cells is achieved by their ability to mimic signaling features of oncogenic RAS, a strategy that we term "oncogene mimicry." This model may guide future strategies for overcoming primary resistance observed in these tumors.
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Affiliation(s)
- Martin L Sos
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Rebecca S Levin
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, CA 94158, USA
| | - John D Gordan
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, CA 94158, USA
| | - James T Webber
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Megan Salt
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Byron Hann
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, CA 94158, USA
| | - Frank McCormick
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sourav Bandyopadhyay
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
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Sos ML, Gordan JD, Shokat KM. Abstract PR15: Primary resistance to MAPK inhibition in BRAF-mutant cancer is determined by kinetics of feedback release. Mol Cancer Ther 2013. [DOI: 10.1158/1535-7163.pms-pr15] [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
Activating mutations in the serine/threonine kinase BRAF are among the most common genetic lesions across all cancers. Despite the clinical success of drugs that either inhibit the oncogene or its downstream effects on the MAPK pathway, only subgroups of BRAF-mutant patients enriched in different tumor lineages will respond to these therapeutics. Here, we show that MAPK-inhibition results in feedback-mediated reactivation of RAS signaling and a resulting paradoxical activation of BRAF/CRAF dimerization. We find, that the formation of paradoxical BRAF/CRAF dimers is dependent on the levels of GTP-RAS whereas transcriptional regulation of ERK signaling modulators as well as activation of receptor tyrosine kinases does not primarily contribute to this process. Using inhibitor-coupled beads, we provide evidence that MAPK inhibition leads to hyperactivation of BRAF and CRAF that results in reactivation of downstream effectors and therefore leads to primary resistance to MAPK inhibition. This feedback-dependent resistance can be suppressed by either genetic depletion of BRAF or the combination of MEK and RAF inhibitors. Overall, our data provide novel insights into the kinetics of primary resistance to MAPK inhibitors in BRAF-mutant tumors and might help to improve the efficacy of targeted therapies in these patients.
This abstract is also presented as Poster B03.
Citation Format: Martin L. Sos, John D. Gordan, Kevan M. Shokat. Primary resistance to MAPK inhibition in BRAF-mutant cancer is determined by kinetics of feedback release. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr PR15.
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Affiliation(s)
- Martin L. Sos
- Howard Hughes Medical Institute University of California, San Francisco, CA
| | - John D. Gordan
- Howard Hughes Medical Institute University of California, San Francisco, CA
| | - Kevan M. Shokat
- Howard Hughes Medical Institute University of California, San Francisco, CA
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Dondeti VR, Wubbenhorst B, Lal P, Gordan JD, D'Andrea K, Attiyeh EF, Simon MC, Nathanson KL. Integrative genomic analyses of sporadic clear cell renal cell carcinoma define disease subtypes and potential new therapeutic targets. Cancer Res 2011; 72:112-21. [PMID: 22094876 DOI: 10.1158/0008-5472.can-11-1698] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Sporadic clear cell renal cell carcinoma (ccRCC), the most common type of adult kidney cancer, is often associated with genomic copy number aberrations on chromosomes 3p and 5q. Aberrations on chromosome 3p are associated with inactivation of the tumor suppressor gene von-Hippel Lindau (VHL), which activates the hypoxia-inducible factors HIF1α and HIF2α. In contrast, ccRCC genes on chromosome 5q remain to be defined. In this study, we conducted an integrated analysis of high-density copy number and gene expression data for 54 sporadic ccRCC tumors that identified the secreted glycoprotein STC2 (stanniocalcin 2) and the proteoglycan VCAN (versican) as potential 5q oncogenes in ccRCCs. In functional assays, STC2 and VCAN each promoted tumorigenesis by inhibiting cell death. Using the same approach, we also investigated the two VHL-deficient subtypes of ccRCC, which express both HIF1α and HIF2α (H1H2) or only HIF2α (H2). This analysis revealed a distinct pattern of genomic aberrations in each group, with the H1H2 group displaying, on average, a more aberrant genome than the H2 group. Together our findings provide a significant advance in understanding ccRCCs by offering a molecular definition of two subtypes with distinct characteristics as well as two potential chromosome 5q oncogenes, the overexpression of which is sufficient to promote tumorigenesis by limiting cell death.
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Affiliation(s)
- Vijay R Dondeti
- Department of Medicine, Abramson Family Cancer Research Institute, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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45
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Dondeti VR, Wubbenhorst B, Lal P, Gordan JD, D'Andrea K, Attiyeh EF, Simon MC, Nathanson KL. Abstract 346: Integrative genomic analysis of sporadic clear cell renal cell carcinoma. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Sporadic clear cell Renal Cell Carcinoma (ccRCC) is the most common type of adult kidney cancer. Using high-density copy-number profiling and gene expression profiles, we performed an integrated genomic analysis of 54 sporadic tumor samples. We took a two pronged approach, focusing on 1) all samples and 2) comparing ccRCCs that express both HIF1α and HIF2α (H1H2) and those that express only HIF2α (H2), sub-types of ccRCC that we previously described. For all samples at a frequency over 10%, we identified regions of amplification on 1q, 5q, 7q, 8q, 12p, and 20q, and regions of deletion on 1p, 3p, 6q, 8p, 9p, and 14q, as previously described. We used our integrative analysis to identify target genes that had consistent copy-number and gene expression changes (e.g. amplified and upregulated or deleted and downregulated) within regions on chromosomes 5 and 7. Combining our data with an independent dataset (Beroukhim et al., 2009) and including a literature based analysis, we were able to narrow down to three target genes, which we subsequently validated using a renal cancer cell line. We then compared genomic changes in H1H2 and H2 ccRCCs. Prior data suggested that H2 ccRCCs have increased expression of genes involved in double strand break repair, thus potentially greater genomic stability. Using high-density copy-number data, we have confirmed that H2 tumors have significantly fewer genomic aberrations compared to H1H2 tumors (for amplifications p=0.032 and for deletions p=0.003). In addition, using GISTIC, we found that deletion of chromosome 6 is significantly more common in H1H2 tumors (p<0.001), whereas deletion of chromosome 9 is significantly more common in H2 tumors (p<0.001). Of note, deletion of chromosome 9 previously has been associated with poor prognosis. Thus, correlations between the copy-number data and gene expression profiles indicate that the H1H2 and H2 classes of ccRCC tumors may each have a distinct set of drivers of tumorigenesis; target gene validation for these groups is underway. These experiments provide novel insights into the biology of clear cell Renal Cell Carcinoma (ccRCC).
Beroukhim et al. Patterns of Gene Expression and Copy-Number Alternations in von-Hippel Lindau Disease-Associated and Sporadic Clear Cell Carcinoma of the Kidney. Can Res 2009; 69: (11):4674-81.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 346. doi:10.1158/1538-7445.AM2011-346
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Affiliation(s)
- Vijay R. Dondeti
- 1University of Pennsylvania School of Medicine, Philadelphia, PA
| | | | - Priti Lal
- 1University of Pennsylvania School of Medicine, Philadelphia, PA
| | | | - Kurt D'Andrea
- 1University of Pennsylvania School of Medicine, Philadelphia, PA
| | | | - M Celeste Simon
- 1University of Pennsylvania School of Medicine, Philadelphia, PA
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46
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Affiliation(s)
- John D. Gordan
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA
| | | | - R. Kate Kelley
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA
| | - Andrew H. Ko
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA
| | | | - Alan P. Venook
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA
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47
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Wright TM, Brannon AR, Gordan JD, Mikels AJ, Mitchell C, Chen S, Espinosa I, van de Rijn M, Pruthi R, Wallen E, Edwards L, Nusse R, Rathmell WK. Ror2, a developmentally regulated kinase, promotes tumor growth potential in renal cell carcinoma. Oncogene 2009; 28:2513-23. [PMID: 19448672 PMCID: PMC2771692 DOI: 10.1038/onc.2009.116] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Inappropriate kinase expression and subsequent promiscuous activity defines the transformation of many solid tumors including renal cell carcinoma (RCC). Thus, the expression of novel tumor-associated kinases has the potential to dramatically shape tumor cell behavior. Further, identifying tumor-associated kinases can lend insight into patterns of tumor growth and characteristics. Here, we report the identification of the RTK-like orphan receptor 2 (Ror2), a new tumor-associated kinase in RCC cell lines and primary tumors. Ror2 is an orphan receptor tyrosine kinase with physiological expression normally seen in the embryonic kidney. However, in RCC, Ror2 expression correlated with expression of genes involved at the extracellular matrix, including Twist and matrix metalloprotease-2 (MMP2). Expression of MMP2 in RCC cells was suppressed by Ror2 knockdown, placing Ror2 as a mediator of MMP2 regulation in RCC and a potential regulator of extracellular matrix remodeling. The suppression of Ror2 not only inhibited cell migration, but also inhibited anchorage-independent growth in soft agar and growth in an orthotopic xenograft model. These findings suggest a novel pathway of tumor-promoting activity by Ror2 within a subset of renal carcinomas, with significant implications for unraveling the tumorigenesis of RCC.
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Affiliation(s)
- T M Wright
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA
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48
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Gordan JD, Lal P, Dondeti VR, Letrero R, Parekh KN, Oquendo CE, Greenberg RA, Flaherty KT, Rathmell WK, Keith B, Simon MC, Nathanson KL. HIF-alpha effects on c-Myc distinguish two subtypes of sporadic VHL-deficient clear cell renal carcinoma. Cancer Cell 2008; 14:435-46. [PMID: 19061835 PMCID: PMC2621440 DOI: 10.1016/j.ccr.2008.10.016] [Citation(s) in RCA: 392] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2008] [Revised: 09/30/2008] [Accepted: 10/24/2008] [Indexed: 01/16/2023]
Abstract
von Hippel-Lindau (VHL) tumor suppressor loss results in hypoxia-inducible factor alpha (HIF-alpha) stabilization and occurs in 70% of sporadic clear cell renal carcinomas (ccRCCs). To determine whether opposing influences of HIF-1alpha and HIF-2alpha on c-Myc activity regulate human ccRCC progression, we analyzed VHL genotype and HIF-alpha expression in 160 primary tumors, which segregated into three groups with distinct molecular characteristics. Interestingly, ccRCCs with intact VHL, as well as pVHL-deficient HIF-1alpha/HIF-2alpha-expressing ccRCCs, exhibited enhanced Akt/mTOR and ERK/MAPK signaling. In contrast, pVHL-deficient ccRCCs expressing only HIF-2alpha displayed elevated c-Myc activity, resulting in enhanced proliferation and resistance to replication stress. These reproducible distinctions in ccRCC behavior delineate HIF-alpha effects on c-Myc in vivo and suggest molecular criteria for selecting targeted therapies.
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Affiliation(s)
- John D. Gordan
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Priti Lal
- Department of Pathology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Vijay R. Dondeti
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Richard Letrero
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Krishna N. Parekh
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - C. Elisa Oquendo
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Roger A. Greenberg
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Keith T. Flaherty
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - W. Kimryn Rathmell
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian Keith
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - M. Celeste Simon
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Corresponding author: M. Celeste Simon, Ph.D., 451 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104, Phone: (215) 746-5532, Fax: (215) 746-5511,
| | - Katherine L. Nathanson
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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Young RM, Wang SJ, Gordan JD, Ji X, Liebhaber SA, Simon MC. Hypoxia-mediated selective mRNA translation by an internal ribosome entry site-independent mechanism. J Biol Chem 2008; 283:16309-19. [PMID: 18430730 DOI: 10.1074/jbc.m710079200] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Although it is advantageous for hypoxic cells to inhibit protein synthesis and conserve energy, it is also important to translate mRNAs critical for adaptive responses to hypoxic stress. Because internal ribosome entry sites (IRES) have been postulated to mediate this preferential synthesis, we analyzed the 5 '-untranslated regions from a panel of stress-regulated mRNAs for m(7)GTP cap-independent translation and identified putative IRES elements in encephalomyocarditis virus, vascular endothelial growth factor, hypoxia-inducible factors (HIFs) 1alpha and 2alpha, glucose transporter-like protein 1, p57(Kip2), La, BiP, and triose phosphate isomerase transcripts. However, when capped and polyadenylated dicistronic RNAs were synthesized in vitro and transfected into cells, cellular IRES-mediated translation accounted for less than 1% that of the level of cap-dependent translation. Moreover, hypoxic stress failed to activate cap-independent synthesis, indicating that it is unlikely that this is the primary mechanism for the maintenance of the translation of these mRNAs under low O(2). Furthermore, although HIF-1alpha is frequently cited as an example of an mRNA that is preferentially translated, we demonstrate that under different levels and durations of hypoxic stress, changes in newly synthesized HIF-1alpha and beta-actin protein levels mirror alterations in corresponding mRNA abundance. In addition, our data suggest that cyclin-dependent kinase inhibitor p57(Kip2) and vascular endothelial growth factor mRNAs are selectively translated by an IRES-independent mechanism under hypoxic stress.
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Affiliation(s)
- Regina M Young
- Abramson Family Cancer Research Institute, Departments of Genetics and Medicine, University of Pennsylvania School of Medicine, and Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia Pennsylvania 19104, USA
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Abstract
O(2) deprivation (hypoxia) and cellular proliferation engage opposite cellular pathways, yet often coexist during tumor growth. The ability of cells to grow during hypoxia results in part from crosstalk between hypoxia-inducible factors (HIFs) and the proto-oncogene c-Myc. Acting alone, HIF and c-Myc partially regulate complex adaptations undertaken by tumor cells growing in low O(2). However, acting in concert these transcription factors reprogram metabolism, protein synthesis, and cell cycle progression, to "fine tune" adaptive responses to hypoxic environments.
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Affiliation(s)
- John D. Gordan
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, 421 Curie Blvd., Philadelphia, PA 19104, USA
| | - Craig B. Thompson
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, 421 Curie Blvd., Philadelphia, PA 19104, USA
| | - M. Celeste Simon
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, 421 Curie Blvd., Philadelphia, PA 19104, USA
- Howard Hughes Medical Institute, 421 Curie Blvd., Philadelphia, PA 19104, USA
- Corresponding author: M. Celeste Simon, Ph.D., 451 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104, Phone: (215) 746-5532, Fax: (215) 746-5511,
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