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Klomp JE, Diehl JN, Klomp JA, Edwards AC, Yang R, Morales AJ, Taylor KE, Drizyte-Miller K, Bryant KL, Schaefer A, Johnson JL, Huntsman EM, Yaron TM, Pierobon M, Baldelli E, Prevatte AW, Barker NK, Herring LE, Petricoin EF, Graves LM, Cantley LC, Cox AD, Der CJ, Stalnecker CA. Determining the ERK-regulated phosphoproteome driving KRAS-mutant cancer. Science 2024; 384:eadk0850. [PMID: 38843329 PMCID: PMC11301400 DOI: 10.1126/science.adk0850] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 04/17/2024] [Indexed: 06/16/2024]
Abstract
To delineate the mechanisms by which the ERK1 and ERK2 mitogen-activated protein kinases support mutant KRAS-driven cancer growth, we determined the ERK-dependent phosphoproteome in KRAS-mutant pancreatic cancer. We determined that ERK1 and ERK2 share near-identical signaling and transforming outputs and that the KRAS-regulated phosphoproteome is driven nearly completely by ERK. We identified 4666 ERK-dependent phosphosites on 2123 proteins, of which 79 and 66%, respectively, were not previously associated with ERK, substantially expanding the depth and breadth of ERK-dependent phosphorylation events and revealing a considerably more complex function for ERK in cancer. We established that ERK controls a highly dynamic and complex phosphoproteome that converges on cyclin-dependent kinase regulation and RAS homolog guanosine triphosphatase function (RHO GTPase). Our findings establish the most comprehensive molecular portrait and mechanisms by which ERK drives KRAS-dependent pancreatic cancer growth.
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Affiliation(s)
- Jennifer E. Klomp
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J. Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffrey A. Klomp
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - A. Cole Edwards
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Runying Yang
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexis J. Morales
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Khalilah E. Taylor
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kristina Drizyte-Miller
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kirsten L. Bryant
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Antje Schaefer
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jared L. Johnson
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emily M. Huntsman
- Meyer Cancer Center, Weill Cornell Medicine; New York, NY 10065, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Tomer M. Yaron
- Meyer Cancer Center, Weill Cornell Medicine; New York, NY 10065, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | | | - Elisa Baldelli
- School of Systems Biology, George Mason University, Fairfax, VA 22030, USA
| | - Alex W. Prevatte
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie K. Barker
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura E. Herring
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Lee M. Graves
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lewis C. Cantley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Adrienne D. Cox
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Radiation Oncology, University of North Carolina at Chapel Hill; Chapel Hill, NC 27599, USA
| | - Channing J. Der
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Clint A. Stalnecker
- Lineberger Comprehensive Cancer Center; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Edwards AC, Stalnecker CA, Morales AJ, Taylor KE, Klomp JE, Klomp JA, Waters AM, Sudhakar N, Hallin J, Tang TT, Olson P, Post L, Christensen JG, Cox AD, Der CJ. TEAD Inhibition Overcomes YAP1/TAZ-Driven Primary and Acquired Resistance to KRASG12C Inhibitors. Cancer Res 2023; 83:4112-4129. [PMID: 37934103 PMCID: PMC10821578 DOI: 10.1158/0008-5472.can-23-2994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/01/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023]
Abstract
Primary/intrinsic and treatment-induced acquired resistance limit the initial response rate to and long-term efficacy of direct inhibitors of the KRASG12C mutant in cancer. To identify potential mechanisms of resistance, we applied a CRISPR/Cas9 loss-of-function screen and observed loss of multiple components of the Hippo tumor suppressor pathway, which acts to suppress YAP1/TAZ-regulated gene transcription. YAP1/TAZ activation impaired the antiproliferative and proapoptotic effects of KRASG12C inhibitor (G12Ci) treatment in KRASG12C-mutant cancer cell lines. Conversely, genetic suppression of YAP1/WWTR1 (TAZ) enhanced G12Ci sensitivity. YAP1/TAZ activity overcame KRAS dependency through two distinct TEAD transcription factor-dependent mechanisms, which phenocopy KRAS effector signaling. First, TEAD stimulated ERK-independent transcription of genes normally regulated by ERK (BIRC5, CDC20, ECT2, FOSL1, and MYC) to promote progression through the cell cycle. Second, TEAD caused activation of PI3K-AKT-mTOR signaling to overcome apoptosis. G12Ci treatment-induced acquired resistance was also caused by YAP1/TAZ-TEAD activation. Accordingly, concurrent treatment with pharmacologic inhibitors of TEAD synergistically enhanced KRASG12C inhibitor antitumor activity in vitro and prolonged tumor suppression in vivo. In summary, these observations reveal YAP1/TAZ-TEAD signaling as a crucial driver of primary and acquired resistance to KRAS inhibition and support the use of TEAD inhibitors to enhance the antitumor efficacy of KRAS-targeted therapies. SIGNIFICANCE YAP1/TAZ-TEAD activation compensates for loss of KRAS effector signaling, establishing a mechanistic basis for concurrent inhibition of TEAD to enhance the efficacy of KRASG12C-selective inhibitor treatment of KRASG12C-mutant cancers. See related commentary by Johnson and Haigis, p. 4005.
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Affiliation(s)
- A. Cole Edwards
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Clint A. Stalnecker
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Alexis Jean Morales
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Khalilah E. Taylor
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jennifer E. Klomp
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jeffrey A. Klomp
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Andrew M. Waters
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Jill Hallin
- Mirati Therapeutics, Inc., San Diego, California
| | | | - Peter Olson
- Mirati Therapeutics, Inc., San Diego, California
| | - Leonard Post
- Vivace Therapeutics, Inc., San Mateo, California
| | | | - Adrienne D. Cox
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Channing J. Der
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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3
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Pond KW, Morris JM, Alkhimenok O, Varghese RP, Cabel CR, Ellis NA, Chakrabarti J, Zavros Y, Merchant JL, Thorne CA, Paek AL. Live-cell imaging in human colonic monolayers reveals ERK waves limit the stem cell compartment to maintain epithelial homeostasis. eLife 2022; 11:e78837. [PMID: 36094159 PMCID: PMC9499537 DOI: 10.7554/elife.78837] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/11/2022] [Indexed: 11/13/2022] Open
Abstract
The establishment and maintenance of different cellular compartments in tissues is a universal requirement across all metazoans. Maintaining the correct ratio of cell types in time and space allows tissues to form patterned compartments and perform complex functions. Patterning is especially evident in the human colon, where tissue homeostasis is maintained by stem cells in crypt structures that balance proliferation and differentiation. Here, we developed a human 2D patient derived organoid screening platform to study tissue patterning and kinase pathway dynamics in single cells. Using this system, we discovered that waves of ERK signaling induced by apoptotic cells play a critical role in maintaining tissue patterning and homeostasis. If ERK is activated acutely across all cells instead of in wave-like patterns, then tissue patterning and stem cells are lost. Conversely, if ERK activity is inhibited, then stem cells become unrestricted and expand dramatically. This work demonstrates that the colonic epithelium requires coordinated ERK signaling dynamics to maintain patterning and tissue homeostasis. Our work reveals how ERK can antagonize stem cells while supporting cell replacement and the function of the gut.
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Affiliation(s)
- Kelvin W Pond
- Department of Cellular and Molecular Medicine, University of ArizonaTucsonUnited States
- Department of Molecular and Cellular Biology, The University of ArizonaTucsonUnited States
- University of Arizona Cancer CenterTucsonUnited States
| | - Julia M Morris
- Department of Cellular and Molecular Medicine, University of ArizonaTucsonUnited States
| | - Olga Alkhimenok
- Department of Molecular and Cellular Biology, The University of ArizonaTucsonUnited States
| | - Reeba P Varghese
- Department of Cellular and Molecular Medicine, University of ArizonaTucsonUnited States
- Cancer Biology Graduate Interdisciplinary Program, University of ArizonaTucsonUnited States
| | - Carly R Cabel
- Department of Cellular and Molecular Medicine, University of ArizonaTucsonUnited States
- Cancer Biology Graduate Interdisciplinary Program, University of ArizonaTucsonUnited States
| | - Nathan A Ellis
- Department of Cellular and Molecular Medicine, University of ArizonaTucsonUnited States
- University of Arizona Cancer CenterTucsonUnited States
| | - Jayati Chakrabarti
- Department of Cellular and Molecular Medicine, University of ArizonaTucsonUnited States
| | - Yana Zavros
- Department of Cellular and Molecular Medicine, University of ArizonaTucsonUnited States
- University of Arizona Cancer CenterTucsonUnited States
| | | | - Curtis A Thorne
- Department of Cellular and Molecular Medicine, University of ArizonaTucsonUnited States
- University of Arizona Cancer CenterTucsonUnited States
| | - Andrew L Paek
- Department of Molecular and Cellular Biology, The University of ArizonaTucsonUnited States
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Ritu K, Kumar P, Singh A, Nupur K, Spalgias S, Mrigpuri P, Rajkumar. Untangling the KRAS mutated lung cancer subsets and its therapeutic implications. MOLECULAR BIOMEDICINE 2021; 2:40. [PMID: 34918209 PMCID: PMC8677854 DOI: 10.1186/s43556-021-00061-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
The Kirsten rat sarcoma virus transforming protein (KRAS) mutations (predominate in codons 12, 13, and 61) and genomically drive nearly one-third of lung carcinomas. These mutations have complex functions in tumorigenesis, and influence the tumor response to chemotherapy and tyrosine kinase inhibitors resulting in a poorer patient prognosis. Recent attempts using targeted therapies against KRAS alone have met with little success. The existence of specific subsets of lung cancer based on KRAS mutations and coexisting mutations are suggested. Their interactions need further elaboration before newer promising targeted therapies for KRAS mutant lung cancers can be used as earlier lines of therapy. We summarize the existing knowledge of KRAS mutations and their coexisting mutations that is relevant to lung cancer treatment, in this review. We elaborate on the prognostic impact of clinical and pathologic characteristics of lung cancer patients associated with KRAS mutations. We briefly review the currently available techniques for KRAS mutation detection on biopsy and cytology samples. Finally, we discuss the new therapeutic strategies for targeting KRAS-mutant non-small cell lung cancer (NSCLC). These may herald a new era in the treatment of KRASG12Cmutated NSCLC as well as be helpful to develop demographic subsets to predict targeted therapies and prognosis of lung cancer patients.
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Kim HJ, Lee HN, Jeong MS, Jang SB. Oncogenic KRAS: Signaling and Drug Resistance. Cancers (Basel) 2021; 13:cancers13225599. [PMID: 34830757 PMCID: PMC8616169 DOI: 10.3390/cancers13225599] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/11/2022] Open
Abstract
RAS proteins play a role in many physiological signals transduction processes, including cell growth, division, and survival. The Ras protein has amino acids 188-189 and functions as GTPase. These proteins are switch molecules that cycle between inactive GDP-bound and active GTP-bound by guanine nucleotide exchange factors (GEFs). KRAS is one of the Ras superfamily isoforms (N-RAS, H-RAS, and K-RAS) that frequently mutate in cancer. The mutation of KRAS is essentially performing the transformation in humans. Since most RAS proteins belong to GTPase, mutated and GTP-bound active RAS is found in many cancers. Despite KRAS being an important molecule in mostly human cancer, including pancreatic and breast, numerous efforts in years past have persisted in cancer therapy targeting KRAS mutant. This review summarizes the biological characteristics of these proteins and the recent progress in the exploration of KRAS-targeted anticancer, leading to new insight.
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Affiliation(s)
- Hyeon Jin Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Korea; (H.J.K.); (H.N.L.)
| | - Han Na Lee
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Korea; (H.J.K.); (H.N.L.)
| | - Mi Suk Jeong
- Institute for Plastic Information and Energy Materials and Sustainable Utilization of Photovoltaic Energy Research Center, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Korea
- Correspondence: (M.S.J.); (S.B.J.); Tel.: +82-51-510-2523 (S.B.J.); Fax: +82-51-581-2544 (S.B.J.)
| | - Se Bok Jang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Korea; (H.J.K.); (H.N.L.)
- Correspondence: (M.S.J.); (S.B.J.); Tel.: +82-51-510-2523 (S.B.J.); Fax: +82-51-581-2544 (S.B.J.)
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Drugging the undruggable proteins in cancer: A systems biology approach. Curr Opin Chem Biol 2021; 66:102079. [PMID: 34426091 DOI: 10.1016/j.cbpa.2021.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 12/30/2022]
Abstract
In recent years, the research community has, with comprehensive systems biology approaches and related technologies, gained insight into the vast complexity of numerous cancers. These approaches allow an in-depth exploration that cannot be achieved solely using conventional low-throughput methods, which do not closely mimic the natural cellular environment. In this review, we discuss recent integrative multiple omics approaches for understanding and modulating previously identified 'undruggable' targets such as members of the RAS family, MYC, TP53, and various E3 ligases and deubiquitinases. We describe how these technologies have revolutionized drug discovery by overcoming an array of biological and technological challenges and how, in the future, they will be pivotal in assessing cancer states in individual patients, allowing for the prediction and application of personalized disease treatments.
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Wu HZ, Xiao JQ, Xiao SS, Cheng Y. KRAS: A Promising Therapeutic Target for Cancer Treatment. Curr Top Med Chem 2019; 19:2081-2097. [PMID: 31486755 DOI: 10.2174/1568026619666190905164144] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 02/06/2023]
Abstract
Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) is the most commonly mutated oncogene in human cancer. The developments of many cancers depend on sustained expression and signaling of KRAS, which makes KRAS a high-priority therapeutic target. Scientists have not successfully developed drugs that target KRAS, although efforts have been made last three decades. In this review, we highlight the emerging experimental strategies of impairing KRAS membrane localization and the direct targeting of KRAS. We also conclude the combinatorial therapies and RNA interference technology for the treatment of KRAS mutant cancers. Moreover, the virtual screening approach to discover novel KRAS inhibitors and synthetic lethality interactors of KRAS are discussed in detail.
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Affiliation(s)
- Hai-Zhou Wu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
| | - Jia-Qi Xiao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
| | - Song-Shu Xiao
- Department of Gynecology and Obstetrics, The Third Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yan Cheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410008, China
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The Use of Genetically Engineered Mouse Models for Studying the Function of Mutated Driver Genes in Pancreatic Cancer. J Clin Med 2019; 8:jcm8091369. [PMID: 31480737 PMCID: PMC6780401 DOI: 10.3390/jcm8091369] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer is often treatment-resistant, with the emerging standard of care, gemcitabine, affording only a few months of incrementally-deteriorating survival. Reflecting on the history of failed clinical trials, genetically engineered mouse models (GEMMs) in oncology research provides the inspiration to discover new treatments for pancreatic cancer that come from better knowledge of pathogenesis mechanisms, not only of the derangements in and consequently acquired capabilities of the cancer cells, but also in the aberrant microenvironment that becomes established to support, sustain, and enhance neoplastic progression. On the other hand, the existing mutational profile of pancreatic cancer guides our understanding of the disease, but leaves many important questions of pancreatic cancer biology unanswered. Over the past decade, a series of transgenic and gene knockout mouse modes have been produced that develop pancreatic cancers with features reflective of metastatic pancreatic ductal adenocarcinoma (PDAC) in humans. Animal models of PDAC are likely to be essential to understanding the genetics and biology of the disease and may provide the foundation for advances in early diagnosis and treatment.
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Calabrese DR, Zlotkowski K, Alden S, Hewitt WM, Connelly CM, Wilson RM, Gaikwad S, Chen L, Guha R, Thomas CJ, Mock BA, Schneekloth JS. Characterization of clinically used oral antiseptics as quadruplex-binding ligands. Nucleic Acids Res 2019; 46:2722-2732. [PMID: 29481610 PMCID: PMC5888870 DOI: 10.1093/nar/gky084] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/20/2018] [Indexed: 12/25/2022] Open
Abstract
Approaches to characterize the nucleic acid-binding properties of drugs and druglike small molecules are crucial to understanding the behavior of these compounds in cellular systems. Here, we use a Small Molecule Microarray (SMM) profiling approach to identify the preferential interaction between chlorhexidine, a widely used oral antiseptic, and the G-quadruplex (G4) structure in the KRAS oncogene promoter. The interaction of chlorhexidine and related drugs to the KRAS G4 is evaluated using multiple biophysical methods, including thermal melt, fluorescence titration and surface plasmon resonance (SPR) assays. Chlorhexidine has a specific low micromolar binding interaction with the G4, while related drugs have weaker and/or less specific interactions. Through NMR experiments and docking studies, we propose a plausible binding mode driven by both aromatic stacking and groove binding interactions. Additionally, cancer cell lines harbouring oncogenic mutations in the KRAS gene exhibit increased sensitivity to chlorhexidine. Treatment of breast cancer cells with chlorhexidine decreases KRAS protein levels, while a KRAS gene transiently expressed by a promoter lacking a G4 is not affected. This work confirms that known ligands bind broadly to G4 structures, while other drugs and druglike compounds can have more selective interactions that may be biologically relevant.
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Affiliation(s)
- David R Calabrese
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Katherine Zlotkowski
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Stephanie Alden
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - William M Hewitt
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Colleen M Connelly
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Robert M Wilson
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Snehal Gaikwad
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892-4258, USA
| | - Lu Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Rajarshi Guha
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Beverly A Mock
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892-4258, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
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10
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Recent Studies on Ponatinib in Cancers Other Than Chronic Myeloid Leukemia. Cancers (Basel) 2018; 10:cancers10110430. [PMID: 30423915 PMCID: PMC6267038 DOI: 10.3390/cancers10110430] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/24/2018] [Accepted: 11/07/2018] [Indexed: 02/08/2023] Open
Abstract
Ponatinib is a third line drug for the treatment of chronic myeloid leukemia patients, especially those that develop the gatekeeper mutation T315I, which is resistant to the first and the second line drugs imatinib, nilotinib, dasatinib and bosutinib. The compound was first identified as a pan Bcr-Abl and Src kinase inhibitor. Further studies have indicated that it is a multitargeted inhibitor that is active on FGFRs, RET, AKT, ERK1/2, KIT, MEKK2 and other kinases. For this reason, the compound has been evaluated on several cancers in which these kinases play important roles, including thyroid, breast, ovary and lung cancer, neuroblastoma, rhabdoid tumours and in myeloproliferative disorders. Ponatinib is also being tested in clinical trials to evaluate its activity in FLT3-ITD acute myelogenous leukemia, head and neck cancers, certain type of lung cancer, gastrointestinal stromal tumours and other malignancies. In this review we report the most recent preclinical and clinical studies on ponatinib in cancers other than CML, with the aim of giving a complete overview of this interesting compound.
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11
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Moustakim M, Felce SL, Zaarour N, Farnie G, McCann FE, Brennan PE. Target Identification Using Chemical Probes. Methods Enzymol 2018; 610:27-58. [PMID: 30390803 DOI: 10.1016/bs.mie.2018.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemical probes are small molecules with potency and selectivity for a single or small number of protein targets. A good chemical probe engages its target intracellularly and is accompanied by a chemically similar, but inactive molecule to be used as a negative control in cellular phenotypic screening. The utility of these chemical probes is ultimately governed by how well they are developed and characterized. Chemical probes either as single entities, or in chemical probes sets are being increasingly used to interrogate the biological relevance of a target in a disease model. This chapter lays out the core properties of chemical probes, summarizes the seminal and emerging techniques used to demonstrate robust intracellular target engagement. Translation of target engagement assays to disease-relevant phenotypic assays using primary patient-derived cells and tissues is also reviewed. Two examples of epigenetic chemical probe discovery and utility are presented whereby target engagement pointed to novel disease associations elucidated from poorly understood protein targets. Finally, a number of examples are discussed whereby chemical probe sets, or "chemogenomic libraries" are used to illuminate new target-disease links which may represent future directions for chemical probe utility.
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Affiliation(s)
- Moses Moustakim
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Suet Ling Felce
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Nancy Zaarour
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom; Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Gillian Farnie
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom.
| | - Fiona E McCann
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom; Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom.
| | - Paul E Brennan
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, United Kingdom.
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12
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Sissung TM, Ley AM, Strope JD, McCrea EM, Beedie S, Peer CJ, Shukla S, van Velkinburgh J, Reece K, Troutman S, Campbell T, Fernandez E, Huang P, Smith J, Thakkar N, Venzon DJ, Brenner S, Lee W, Merino M, Luo J, Jager W, Price DK, Chau CH, Figg WD. Differential Expression of OATP1B3 Mediates Unconjugated Testosterone Influx. Mol Cancer Res 2017; 15:1096-1105. [PMID: 28389619 PMCID: PMC5540879 DOI: 10.1158/1541-7786.mcr-16-0477] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/06/2017] [Accepted: 04/04/2017] [Indexed: 12/21/2022]
Abstract
Castration-resistant prostate cancer (CRPC) has greater intratumoral testosterone concentrations than similar tumors from eugonadal men; simple diffusion does not account for this observation. This study was undertaken to ascertain the androgen uptake kinetics, functional, and clinical relevance of de novo expression of the steroid hormone transporter OATP1B3 (SLCO1B3). Experiments testing the cellular uptake of androgens suggest that testosterone is an excellent substrate of OATP1B3 (Km = 23.2 μmol/L; Vmax = 321.6 pmol/mg/minute), and cells expressing a doxycycline-inducible SLCO1B3 construct had greater uptake of a clinically relevant concentration of 3H-testosterone (50 nmol/L; 1.6-fold, P = 0.0027). When compared with Slco1b2 (-/-) mice, Slco1b2 (-/-)/hSLCO1B3 knockins had greater hepatic uptake (15% greater AUC, P = 0.0040) and lower plasma exposure to 3H-testosterone (17% lower AUC, P = 0.0030). Of 82 transporters genes, SLCO1B3 is the second-most differentially expressed transporter in CRPC cell lines (116-fold vs. androgen-sensitive cells), with a differentially spliced cancer-type ct-SLCO1B3 making up the majority of SLCO1B3 expression. Overexpression of SLCO1B3 in androgen-responsive cells results in 1.5- to 2-fold greater testosterone uptake, whereas siRNA knockdown of SLCO1B3 in CRPC cells did not change intracellular testosterone concentration. Primary human prostate tumors express SLCO1B3 to a greater extent than ct-SLCO1B3 (26% of total SLCO1B3 expression vs. 0.08%), suggesting that androgen uptake in these tumor cells also is greater. Non-liver tumors do not differentially express SLCO1B3.Implications: This study suggests that de novo OATP1B3 expression in prostate cancer drives greater androgen uptake and is consistent with previous observations that greater OATP1B3 activity results in the development of androgen deprivation therapy resistance and shorter overall survival. Mol Cancer Res; 15(8); 1096-105. ©2017 AACR.
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Affiliation(s)
- Tristan M Sissung
- Clinical Pharmacology Program, Office of the Clinical Director, NCI, Bethesda, Maryland
| | - Ariel M Ley
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, NCI, Bethesda, Maryland
| | - Jonathan D Strope
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, NCI, Bethesda, Maryland
| | - Edel M McCrea
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, NCI, Bethesda, Maryland
| | - Shaunna Beedie
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, NCI, Bethesda, Maryland
| | - Cody J Peer
- Clinical Pharmacology Program, Office of the Clinical Director, NCI, Bethesda, Maryland
| | | | | | - Kelie Reece
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, NCI, Bethesda, Maryland
| | - Sarah Troutman
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, NCI, Bethesda, Maryland
| | - Tessa Campbell
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, NCI, Bethesda, Maryland
| | - Elena Fernandez
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, NCI, Bethesda, Maryland
| | - Phoebe Huang
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, NCI, Bethesda, Maryland
| | - Jordan Smith
- Laboratory of Cancer Biology and Genetics, NCI, Bethesda, Maryland
| | - Nilay Thakkar
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky
| | - David J Venzon
- Biostatistics and Data Management Section, NCI, Bethesda, Maryland
| | - Stefan Brenner
- Department of Clinical Pharmacy and Diagnostics, University of Vienna, Vienna, Austria
| | - Wooin Lee
- College of Pharmacy, Seoul National University, Seoul, Korea
| | - Maria Merino
- Translational Surgical Pathology Section, NCI, Bethesda, Maryland
| | - Ji Luo
- Laboratory of Cancer Biology and Genetics, NCI, Bethesda, Maryland
| | - Walter Jager
- Department of Clinical Pharmacy and Diagnostics, University of Vienna, Vienna, Austria
| | - Douglas K Price
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, NCI, Bethesda, Maryland
| | - Cindy H Chau
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, NCI, Bethesda, Maryland
| | - William D Figg
- Clinical Pharmacology Program, Office of the Clinical Director, NCI, Bethesda, Maryland.
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, NCI, Bethesda, Maryland
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Abstract
The allure of phenotypic screening, combined with the industry preference for target-based approaches, has prompted the development of innovative chemical biology technologies that facilitate the identification of new therapeutic targets for accelerated drug discovery. A chemogenomic library is a collection of selective small-molecule pharmacological agents, and a hit from such a set in a phenotypic screen suggests that the annotated target or targets of that pharmacological agent may be involved in perturbing the observable phenotype. In this Review, we describe opportunities for chemogenomic screening to considerably expedite the conversion of phenotypic screening projects into target-based drug discovery approaches. Other applications are explored, including drug repositioning, predictive toxicology and the discovery of novel pharmacological modalities.
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Smith JL, Lee LC, Read A, Li Q, Yu B, Lee CS, Luo J. One-step immortalization of primary human airway epithelial cells capable of oncogenic transformation. Cell Biosci 2016; 6:57. [PMID: 27891214 PMCID: PMC5106784 DOI: 10.1186/s13578-016-0122-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/03/2016] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The ability to transform normal human cells into cancer cells with the introduction of defined genetic alterations is a valuable method for understanding the mechanisms of oncogenesis. Easy establishment of immortalized but non-transformed human cells from various tissues would facilitate these genetic analyses. RESULTS We report here a simple, one-step immortalization method that involves retroviral vector mediated co-expression of the human telomerase protein and a shRNA targeting the CDKN2A gene locus. We demonstrate that this method could successfully immortalize human small airway epithelial cells while maintaining their chromosomal stability. We further showed that these cells retain p53 activity and can be transformed by the KRAS oncogene. CONCLUSIONS Our method simplifies the immortalization process and is broadly applicable for establishing immortalized epithelial cell lines from primary human tissues for cancer research.
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Affiliation(s)
- Jordan L. Smith
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH., Bethesda, MD USA
- University of Massachusetts Medical School and the Graduate School of Biomedical Sciences, Worcester, MA USA
| | - Liam C. Lee
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH., Bethesda, MD USA
- Graduate Program, Cambridge University, Cambridge, UK
| | - Abigail Read
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH., Bethesda, MD USA
| | - Qiuning Li
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH., Bethesda, MD USA
- ShanghaiTech University, Shanghai, China
| | - Bing Yu
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH., Bethesda, MD USA
- Janssen R&D Shanghai Discovery Center, Shanghai, China
| | - Chih-Shia Lee
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH., Bethesda, MD USA
| | - Ji Luo
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH., Bethesda, MD USA
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Fraietta I, Gasparri F. The development of high-content screening (HCS) technology and its importance to drug discovery. Expert Opin Drug Discov 2016; 11:501-14. [PMID: 26971542 DOI: 10.1517/17460441.2016.1165203] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
INTRODUCTION High-content screening (HCS) was introduced about twenty years ago as a promising analytical approach to facilitate some critical aspects of drug discovery. Its application has spread progressively within the pharmaceutical industry and academia to the point that it today represents a fundamental tool in supporting drug discovery and development. AREAS COVERED Here, the authors review some of significant progress in the HCS field in terms of biological models and assay readouts. They highlight the importance of high-content screening in drug discovery, as testified by its numerous applications in a variety of therapeutic areas: oncology, infective diseases, cardiovascular and neurodegenerative diseases. They also dissect the role of HCS technology in different phases of the drug discovery pipeline: target identification, primary compound screening, secondary assays, mechanism of action studies and in vitro toxicology. EXPERT OPINION Recent advances in cellular assay technologies, such as the introduction of three-dimensional (3D) cultures, induced pluripotent stem cells (iPSCs) and genome editing technologies (e.g., CRISPR/Cas9), have tremendously expanded the potential of high-content assays to contribute to the drug discovery process. Increasingly predictive cellular models and readouts, together with the development of more sophisticated and affordable HCS readers, will further consolidate the role of HCS technology in drug discovery.
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Affiliation(s)
- Ivan Fraietta
- a Department of Biology , Nerviano Medical Sciences S.r.l ., Nerviano , Milano , Italy
| | - Fabio Gasparri
- a Department of Biology , Nerviano Medical Sciences S.r.l ., Nerviano , Milano , Italy
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16
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Cromm PM, Spiegel J, Grossmann TN, Waldmann H. Direkte Modulation von Aktivität und Funktion kleiner GTPasen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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17
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Cromm PM, Spiegel J, Grossmann TN, Waldmann H. Direct Modulation of Small GTPase Activity and Function. Angew Chem Int Ed Engl 2015; 54:13516-37. [DOI: 10.1002/anie.201504357] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 12/19/2022]
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Baell JB. Screening-based translation of public research encounters painful problems. ACS Med Chem Lett 2015; 6:229-34. [PMID: 25941544 DOI: 10.1021/acsmedchemlett.5b00032] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Indexed: 12/22/2022] Open
Abstract
Whether identified through high throughput screening or in silico screening, and whether target-based or phenotypic, sets of hits will contain chemical con artists. Such pan-assay interference compounds (PAINS) and other subversive compounds continue to pollute the scientific literature. There are several angles of attack to aid identification of such nonprogressable molecules. One of these rules above all, and this is a demonstration of genuine structure-activity relationships. Recognition of this, which will require a greater effort in medicinal chemistry, will be of general benefit.
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Affiliation(s)
- Jonathan B. Baell
- Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
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Wylie PG, Onley DJ, Hammerstein AF, Bowen WP. Advances in Laser Scanning Imaging Cytometry for High-Content Screening. Assay Drug Dev Technol 2015; 13:66-78. [DOI: 10.1089/adt.2014.607] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Paul G. Wylie
- TTP Labtech Limited, Melbourn, Hertfordshire, United Kingdom
| | - David J. Onley
- TTP Labtech Limited, Melbourn, Hertfordshire, United Kingdom
| | | | - Wayne P. Bowen
- TTP Labtech Limited, Melbourn, Hertfordshire, United Kingdom
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