1
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Lokhandwala J, Matlack JK, Smalley TB, Miner RE, Tran TH, Binning JM. Structural basis for FN3K-mediated protein deglycation. Structure 2024:S0969-2126(24)00281-8. [PMID: 39173621 DOI: 10.1016/j.str.2024.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/05/2024] [Accepted: 07/28/2024] [Indexed: 08/24/2024]
Abstract
Protein glycation is a universal, non-enzymatic modification that occurs when a sugar covalently attaches to a primary amine. These spontaneous modifications may have deleterious or regulatory effects on protein function, and their removal is mediated by the conserved metabolic kinase fructosamine-3-kinase (FN3K). Despite its crucial role in protein repair, we currently have a poor understanding of how FN3K engages or phosphorylates its substrates. By integrating structural biology and biochemistry, we elucidated the catalytic mechanism for FN3K-mediated protein deglycation. Our work identifies key amino acids required for binding and phosphorylating glycated substrates and reveals the molecular basis of an evolutionarily conserved protein repair pathway. Additional structural-functional studies revealed unique structural features of human FN3K as well as differences in the dimerization behavior and regulation of FN3K family members. Our findings improve our understanding of the structure of FN3K and its catalytic mechanism, which opens new avenues for therapeutically targeting FN3K.
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Affiliation(s)
- Jameela Lokhandwala
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jenet K Matlack
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Tracess B Smalley
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Robert E Miner
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Cancer Chemical Biology PhD Program, University of South Florida, Tampa, FL 33612, USA
| | - Timothy H Tran
- Chemical Biology Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jennifer M Binning
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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2
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Vala DP, Dunne Miller A, Atmasidha A, Parmar MP, Patel CD, Upadhyay DB, Bhalodiya SS, González-Bakker A, Khan AN, Nogales J, Padrón JM, Banerjee S, Patel HM. Click-chemistry mediated synthesis of OTBN-1,2,3-Triazole derivatives exhibiting STK33 inhibition with diverse anti-cancer activities. Bioorg Chem 2024; 149:107485. [PMID: 38824700 DOI: 10.1016/j.bioorg.2024.107485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 05/20/2024] [Indexed: 06/04/2024]
Abstract
There is a continuous and pressing need to establish new brain-penetrant bioactive compounds with anti-cancer properties. To this end, a new series of 4'-((4-substituted-4,5-dihydro-1H-1,2,3-triazol-1-yl)methyl)-[1,1'-biphenyl]-2-carbonitrile (OTBN-1,2,3-triazole) derivatives were synthesized by click chemistry. The series of bioactive compounds were designed and synthesized from diverse alkynes and N3-OTBN, using copper (II) acetate monohydrate in aqueous dimethylformamide at room temperature. Besides being highly cost-effective and significantly reducing synthesis, the reaction yielded 91-98 % of the target products without the need of any additional steps or chromatographic techniques. Two analogues exhibit promising anti-cancer biological activities. Analogue 4l shows highly specific cytostatic activity against lung cancer cells, while analogue 4k exhibits pan-cancer anti-growth activity. A kinase screen suggests compound 4k has single-digit micromolar activity against kinase STK33. High STK33 RNA expression correlates strongly with poorer patient outcomes in both adult and pediatric glioma. Compound 4k potently inhibits cell proliferation, invasion, and 3D neurosphere formation in primary patient-derived glioma cell lines. The observed anti-cancer activity is enhanced in combination with specific clinically relevant small molecule inhibitors. Herein we establish a novel biochemical kinase inhibitory function for click-chemistry-derived OTBN-1,2,3-triazole analogues and further report their anti-cancer activity in vitro for the first time.
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Affiliation(s)
- Disha P Vala
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar-388 120, Gujarat, India.
| | - Amy Dunne Miller
- Department of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK.
| | - Aditi Atmasidha
- Department of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK.
| | - Mehul P Parmar
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar-388 120, Gujarat, India
| | - Chirag D Patel
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar-388 120, Gujarat, India
| | - Dipti B Upadhyay
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar-388 120, Gujarat, India
| | - Savan S Bhalodiya
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar-388 120, Gujarat, India
| | - Aday González-Bakker
- BioLab, Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, 38206 La Laguna, Spain.
| | - Adam N Khan
- BioLab, Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, 38206 La Laguna, Spain.
| | - Joaquina Nogales
- Department of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK.
| | - José M Padrón
- BioLab, Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, 38206 La Laguna, Spain.
| | - Sourav Banerjee
- Department of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK.
| | - Hitendra M Patel
- Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar-388 120, Gujarat, India.
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3
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Ku AF, Sharma KL, Ta HM, Sutton CM, Bohren KM, Wang Y, Chamakuri S, Chen R, Hakenjos JM, Jimmidi R, Kent K, Li F, Li JY, Ma L, Madasu C, Palaniappan M, Palmer SS, Qin X, Robers MB, Sankaran B, Tan Z, Vasquez YM, Wang J, Wilkinson J, Yu Z, Ye Q, Young DW, Teng M, Kim C, Matzuk MM. Reversible male contraception by targeted inhibition of serine/threonine kinase 33. Science 2024; 384:885-890. [PMID: 38781365 DOI: 10.1126/science.adl2688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/03/2024] [Indexed: 05/25/2024]
Abstract
Men or mice with homozygous serine/threonine kinase 33 (STK33) mutations are sterile owing to defective sperm morphology and motility. To chemically evaluate STK33 for male contraception with STK33-specific inhibitors, we screened our multibillion-compound collection of DNA-encoded chemical libraries, uncovered potent STK33-specific inhibitors, determined the STK33 kinase domain structure bound with a truncated hit CDD-2211, and generated an optimized hit CDD-2807 that demonstrates nanomolar cellular potency (half-maximal inhibitory concentration = 9.2 nanomolar) and favorable metabolic stability. In mice, CDD-2807 exhibited no toxicity, efficiently crossed the blood-testis barrier, did not accumulate in brain, and induced a reversible contraceptive effect that phenocopied genetic STK33 perturbations without altering testis size. Thus, STK33 is a chemically validated, nonhormonal contraceptive target, and CDD-2807 is an effective tool compound.
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Affiliation(s)
- Angela F Ku
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kiran L Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hai Minh Ta
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Courtney M Sutton
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kurt M Bohren
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yong Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruihong Chen
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - John M Hakenjos
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ravikumar Jimmidi
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Katarzyna Kent
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jian-Yuan Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lang Ma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chandrashekhar Madasu
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen S Palmer
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Zhi Tan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yasmin M Vasquez
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jian Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Zhifeng Yu
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qiuji Ye
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Damian W Young
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Choel Kim
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Martin M Matzuk
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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4
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Schwartz PB, Walcheck MT, Nukaya M, Pavelec DM, Matkowskyj KA, Ronnekleiv-Kelly SM. Chronic jetlag accelerates pancreatic neoplasia in conditional Kras-mutant mice. Chronobiol Int 2023; 40:417-437. [PMID: 36912021 PMCID: PMC10337099 DOI: 10.1080/07420528.2023.2186122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/14/2023] [Accepted: 02/25/2023] [Indexed: 03/14/2023]
Abstract
Misalignment of the circadian clock compared to environmental cues causes circadian desynchrony, which is pervasive in humans. Clock misalignment can lead to various pathologies including obesity and diabetes, both of which are associated with pancreatic ductal adenocarcinoma - a devastating cancer with an 80% five-year mortality rate. Although circadian desynchrony is associated with an increased risk of several solid-organ cancers, the correlation between clock misalignment and pancreas cancer is unclear. Using a chronic jetlag model, we investigated the impact of clock misalignment on pancreas cancer initiation in mice harboring a pancreas-specific activated Kras mutation. We found that chronic jetlag accelerated the development of pancreatic cancer precursor lesions, with a concomitant increase in precursor lesion grade. Cell-autonomous knock-out of the clock in pancreatic epithelial cells of Kras-mutant mice demonstrated no acceleration of precursor lesion formation, indicating non-cell-autonomous clock dysfunction was responsible for the expedited tumor development. Therefore, we applied single-cell RNA sequencing over time and identified fibroblasts as the cell population manifesting the greatest clock-dependent changes, with enrichment of specific cancer-associated fibroblast pathways due to circadian misalignment.
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Affiliation(s)
- Patrick B Schwartz
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Morgan T Walcheck
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Manabu Nukaya
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | | | - Kristina A Matkowskyj
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
- William S Middleton Memorial Veterans Hospital, Madison, Wisconsin
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Sean M Ronnekleiv-Kelly
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
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5
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Poloznikov A, Nikulin S, Bolotina L, Kachmazov A, Raigorodskaya M, Kudryavtseva A, Bakhtogarimov I, Rodin S, Gaisina I, Topchiy M, Asachenko A, Novosad V, Tonevitsky A, Alekseev B. 9-ING-41, a Small Molecule Inhibitor of GSK-3β, Potentiates the Effects of Chemotherapy on Colorectal Cancer Cells. Front Pharmacol 2021; 12:777114. [PMID: 34955846 PMCID: PMC8696016 DOI: 10.3389/fphar.2021.777114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common and lethal types of cancer. Although researchers have made significant efforts to study the mechanisms underlying CRC drug resistance, our knowledge of this disease is still limited, and novel therapies are in high demand. It is urgent to find new targeted therapy considering limited chemotherapy options. KRAS mutations are the most frequent molecular alterations in CRC. However, there are no approved K-Ras targeted therapies for these tumors yet. GSK-3β is demonstrated to be a critically important kinase for the survival and proliferation of K-Ras–dependent pancreatic cancer cells. In this study, we tested combinations of standard-of-care therapy and 9-ING-41, a small molecule inhibitor of GSK-3β, in CRC cell lines and patient-derived tumor organoid models of CRC. We demonstrate that 9-ING-41 inhibits the growth of CRC cells via a distinct from chemotherapy mechanism of action. Although molecular biomarkers of 9-ING-41 efficacy are yet to be identified, the addition of 9-ING-41 to the standard-of-care drugs 5-FU and oxaliplatin could significantly enhance growth inhibition in certain CRC cells. The results of the transcriptomic analysis support our findings of cell cycle arrest and DNA repair deficiency in 9-ING-41–treated CRC cells. Notably, we find substantial similarity in the changes of the transcriptomic profile after inhibition of GSK-3β and suppression of STK33, another critically important kinase for K-Ras–dependent cells, which could be an interesting point for future research. Overall, the results of this study provide a rationale for the further investigation of GSK-3 inhibitors in combination with standard-of-care treatment of CRC.
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Affiliation(s)
- Andrey Poloznikov
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia.,P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
| | - Sergey Nikulin
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia.,P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia.,School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Larisa Bolotina
- P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
| | - Andrei Kachmazov
- P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
| | | | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ildar Bakhtogarimov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Rodin
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Irina Gaisina
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, IL, United States
| | - Maxim Topchiy
- A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Asachenko
- A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russia
| | - Victor Novosad
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia.,Scientific Research Centre Bioclinicum, Moscow, Russia.,Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Boris Alekseev
- P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
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6
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Targeting STK33: from inhibition to degradation. Future Med Chem 2021; 14:127-129. [PMID: 34605274 DOI: 10.4155/fmc-2021-0224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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7
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Meng M, Zhong K, Jiang T, Liu Z, Kwan HY, Su T. The current understanding on the impact of KRAS on colorectal cancer. Biomed Pharmacother 2021; 140:111717. [PMID: 34044280 DOI: 10.1016/j.biopha.2021.111717] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023] Open
Abstract
KRAS (kirsten rat sarcoma viral oncogene) is a member of the RAS family. KRAS mutations are one of most dominant mutations in colorectal cancer (CRC). The impact of KRAS mutations on the prognosis and survival of CRC patients drives many research studies to explore potential therapeutics or target therapy for the KRAS mutant CRC. This review summarizes the current understanding of the pathological consequences of the KRAS mutations in the development of CRC; and the impact of the mutations on the response and the sensitivity to the current front-line chemotherapy. The current therapeutic strategies for treating KRAS mutant CRC, the difficulties and challenges will also be discussed.
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Affiliation(s)
- Mingjing Meng
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Keying Zhong
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Ting Jiang
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhongqiu Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
| | - Hiu Yee Kwan
- Centre for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
| | - Tao Su
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
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8
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Gorfe AA, Cho KJ. Approaches to inhibiting oncogenic K-Ras. Small GTPases 2021; 12:96-105. [PMID: 31438765 PMCID: PMC7849769 DOI: 10.1080/21541248.2019.1655883] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/29/2019] [Accepted: 08/06/2019] [Indexed: 02/06/2023] Open
Abstract
Activating somatic K-Ras mutations are associated with >15% all human tumors and up to 90% of specific tumor types such as pancreatic cancer. Successfully inhibiting abnormal K-Ras signaling would therefore be a game changer in cancer therapy. However, K-Ras has long been considered an undruggable target for various reasons. This view is now changing by the discovery of allosteric inhibitors that directly target K-Ras and inhibit its functions, and by the identification of new mechanisms to dislodge it from the plasma membrane and thereby abrogate its cellular activities. In this review, we will discuss recent progresses and challenges to inhibiting aberrant K-Ras functions by these two approaches. We will also provide a broad overview of other approaches such as inhibition of K-Ras effectors, and offer a brief perspective on the way forward.
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Affiliation(s)
- Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Programs of Biochemistry & Cell and Therapeutics & Pharmacology, MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
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9
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Development of synthetic lethality in cancer: molecular and cellular classification. Signal Transduct Target Ther 2020; 5:241. [PMID: 33077733 PMCID: PMC7573576 DOI: 10.1038/s41392-020-00358-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 12/27/2022] Open
Abstract
Recently, genetically targeted cancer therapies have been a topic of great interest. Synthetic lethality provides a new approach for the treatment of mutated genes that were previously considered unable to be targeted in traditional genotype-targeted treatments. The increasing researches and applications in the clinical setting made synthetic lethality a promising anticancer treatment option. However, the current understandings on different conditions of synthetic lethality have not been systematically assessed and the application of synthetic lethality in clinical practice still faces many challenges. Here, we propose a novel and systematic classification of synthetic lethality divided into gene level, pathway level, organelle level, and conditional synthetic lethality, according to the degree of specificity into its biological mechanism. Multiple preclinical findings of synthetic lethality in recent years will be reviewed and classified under these different categories. Moreover, synthetic lethality targeted drugs in clinical practice will be briefly discussed. Finally, we will explore the essential implications of this classification as well as its prospects in eliminating existing challenges and the future directions of synthetic lethality.
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10
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Kattan WE, Hancock JF. RAS Function in cancer cells: translating membrane biology and biochemistry into new therapeutics. Biochem J 2020; 477:2893-2919. [PMID: 32797215 PMCID: PMC7891675 DOI: 10.1042/bcj20190839] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023]
Abstract
The three human RAS proteins are mutated and constitutively activated in ∼20% of cancers leading to cell growth and proliferation. For the past three decades, many attempts have been made to inhibit these proteins with little success. Recently; however, multiple methods have emerged to inhibit KRAS, the most prevalently mutated isoform. These methods and the underlying biology will be discussed in this review with a special focus on KRAS-plasma membrane interactions.
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Affiliation(s)
- Walaa E. Kattan
- Department of Integrative Biology and Pharmacology, McGovern Medical School University of Texas Health Science Center at Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, TX 77030, USA
| | - John F. Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School University of Texas Health Science Center at Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, TX 77030, USA
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11
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Haley B, Roudnicky F. Functional Genomics for Cancer Drug Target Discovery. Cancer Cell 2020; 38:31-43. [PMID: 32442401 DOI: 10.1016/j.ccell.2020.04.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 02/06/2020] [Accepted: 04/08/2020] [Indexed: 12/15/2022]
Abstract
Functional genomics describes a field of biology that uses a range of approaches for assessing gene function with high-throughput molecular, genetic, and cellular technologies. The near limitless potential for applying these concepts to study the activities of all genetic loci has completely upended how today's cancer biologists tackle drug target discovery. We provide an overview of contemporary functional genomics platforms, highlighting areas of distinction and complementarity across technologies, so as to aid in the development or interpretation of cancer-focused screening efforts.
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Affiliation(s)
- Benjamin Haley
- Molecular Biology Department, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Filip Roudnicky
- Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel 4070, Switzerland.
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12
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Lin A, Sheltzer JM. Discovering and validating cancer genetic dependencies: approaches and pitfalls. Nat Rev Genet 2020; 21:671-682. [DOI: 10.1038/s41576-020-0247-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2020] [Indexed: 12/21/2022]
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13
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Uras IZ, Moll HP, Casanova E. Targeting KRAS Mutant Non-Small-Cell Lung Cancer: Past, Present and Future. Int J Mol Sci 2020; 21:E4325. [PMID: 32560574 PMCID: PMC7352653 DOI: 10.3390/ijms21124325] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is the most frequent cancer with an aggressive clinical course and high mortality rates. Most cases are diagnosed at advanced stages when treatment options are limited and the efficacy of chemotherapy is poor. The disease has a complex and heterogeneous background with non-small-cell lung cancer (NSCLC) accounting for 85% of patients and lung adenocarcinoma being the most common histological subtype. Almost 30% of adenocarcinomas of the lung are driven by an activating Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation. The ability to inhibit the oncogenic KRAS has been the holy grail of cancer research and the search for inhibitors is immensely ongoing as KRAS-mutated tumors are among the most aggressive and refractory to treatment. Therapeutic strategies tailored for KRAS+ NSCLC rely on the blockage of KRAS functional output, cellular dependencies, metabolic features, KRAS membrane associations, direct targeting of KRAS and immunotherapy. In this review, we provide an update on the most recent advances in anti-KRAS therapy for lung tumors with mechanistic insights into biological diversity and potential clinical implications.
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Affiliation(s)
- Iris Z. Uras
- Department of Pharmacology, Center of Physiology and Pharmacology & Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria
| | - Herwig P. Moll
- Department of Physiology, Center of Physiology and Pharmacology & Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria; (H.P.M.); (E.C.)
| | - Emilio Casanova
- Department of Physiology, Center of Physiology and Pharmacology & Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria; (H.P.M.); (E.C.)
- Ludwig Boltzmann Institute for Cancer Research (LBI-CR), 1090 Vienna, Austria
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14
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Ku AA, Hu HM, Zhao X, Shah KN, Kongara S, Wu D, McCormick F, Balmain A, Bandyopadhyay S. Integration of multiple biological contexts reveals principles of synthetic lethality that affect reproducibility. Nat Commun 2020; 11:2375. [PMID: 32398776 PMCID: PMC7217969 DOI: 10.1038/s41467-020-16078-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/08/2020] [Indexed: 12/30/2022] Open
Abstract
Synthetic lethal screens have the potential to identify new vulnerabilities incurred by specific cancer mutations but have been hindered by lack of agreement between studies. In the case of KRAS, we identify that published synthetic lethal screen hits significantly overlap at the pathway rather than gene level. Analysis of pathways encoded as protein networks could identify synthetic lethal candidates that are more reproducible than those previously reported. Lack of overlap likely stems from biological rather than technical limitations as most synthetic lethal phenotypes are strongly modulated by changes in cellular conditions or genetic context, the latter determined using a pairwise genetic interaction map that identifies numerous interactions that suppress synthetic lethal effects. Accounting for pathway, cellular and genetic context nominates a DNA repair dependency in KRAS-mutant cells, mediated by a network containing BRCA1. We provide evidence for why most reported synthetic lethals are not reproducible which is addressable using a multi-faceted testing framework.
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Affiliation(s)
- Angel A Ku
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Hsien-Ming Hu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Xin Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Khyati N Shah
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Sameera Kongara
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Di Wu
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Sourav Bandyopadhyay
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94158, USA.
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15
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Wienen-Schmidt B, Schmidt D, Gerber HD, Heine A, Gohlke H, Klebe G. Surprising Non-Additivity of Methyl Groups in Drug-Kinase Interaction. ACS Chem Biol 2019; 14:2585-2594. [PMID: 31638770 DOI: 10.1021/acschembio.9b00476] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Drug optimization is guided by biophysical methods with increasing popularity. In the context of lead structure modifications, the introduction of methyl groups is a simple but potentially powerful approach. Hence, it is crucial to systematically investigate the influence of ligand methylation on biophysical characteristics such as thermodynamics. Here, we investigate the influence of ligand methylation in different positions and combinations on the drug-kinase interaction. Binding modes and complex structures were analyzed using protein crystallography. Thermodynamic signatures were measured via isothermal titration calorimetry (ITC). An extensive computational analysis supported the understanding of the underlying mechanisms. We found that not only position but also stereochemistry of the methyl group has an influence on binding potency as well as the thermodynamic signature of ligand binding to the protein. Strikingly, the combination of single methyl groups does not lead to additive effects. In our case, the merger of two methyl groups in one ligand leads to an entirely new alternative ligand binding mode in the protein ligand complex. Moreover, the combination of the two methyl groups also resulted in a nonadditive thermodynamic profile of ligand binding. Molecular dynamics (MD) simulations revealed distinguished characteristic motions of the ligands in solution explaining the pronounced thermodynamic changes. The unexpected drastic change in protein ligand interaction highlights the importance of crystallographic control even for minor modifications such as the introduction of a methyl group. For an in-depth understanding of ligand binding behavior, MD simulations have shown to be a powerful tool.
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Affiliation(s)
- Barbara Wienen-Schmidt
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Denis Schmidt
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Hans-Dieter Gerber
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute for Complex Systems - Structural Biochemistry (ICS 6), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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16
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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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17
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Colic M, Hart T. Chemogenetic interactions in human cancer cells. Comput Struct Biotechnol J 2019; 17:1318-1325. [PMID: 31921397 PMCID: PMC6945272 DOI: 10.1016/j.csbj.2019.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 12/26/2022] Open
Abstract
Chemogenetic profiling enables the identification of genes that enhance or suppress the phenotypic effect of chemical compounds. Using this approach in cancer therapies could improve our ability to predict the response of specific tumor genotypes to chemotherapeutic agents, thus accelerating the development of personalized drug therapy. In the not so distant past, this strategy was only applied in model organisms because there was no feasible technology to thoroughly exploit desired genetic mutations and their impact on drug efficacy in human cells. Today, with the advent of CRISPR gene-editing technology and its application to pooled library screens in mammalian cells, chemogenetic screens are performed directly in human cell lines with high sensitivity and specificity. Chemogenetic profiling provides insights into drug mechanism-of-action, genetic vulnerabilities, and resistance mechanisms, all of which will help to accurately deliver the right drug to the right target in the right patient while minimizing side effects.
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Affiliation(s)
- Medina Colic
- Department of Bioinformatics and Computational Biology and Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Traver Hart
- Department of Bioinformatics and Computational Biology and Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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18
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Abstract
RAS genes are the most commonly mutated oncogenes in cancer, but effective therapeutic strategies to target RAS-mutant cancers have proved elusive. A key aspect of this challenge is the fact that direct inhibition of RAS proteins has proved difficult, leading researchers to test numerous alternative strategies aimed at exploiting RAS-related vulnerabilities or targeting RAS effectors. In the past few years, we have witnessed renewed efforts to target RAS directly, with several promising strategies being tested in clinical trials at different stages of completion. Important advances have also been made in approaches designed to indirectly target RAS by improving inhibition of RAS effectors, exploiting synthetic lethal interactions or metabolic dependencies, using therapeutic combination strategies or harnessing the immune system. In this Review, we describe historical and ongoing efforts to target RAS-mutant cancers and outline the current therapeutic landscape in the collective quest to overcome the effects of this crucial oncogene.
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19
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Mues M, Karra L, Romero-Moya D, Wandler A, Hangauer MJ, Ksionda O, Thus Y, Lindenbergh M, Shannon K, McManus MT, Roose JP. High-Complexity shRNA Libraries and PI3 Kinase Inhibition in Cancer: High-Fidelity Synthetic Lethality Predictions. Cell Rep 2019; 27:631-647.e5. [PMID: 30970263 PMCID: PMC6690758 DOI: 10.1016/j.celrep.2019.03.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/11/2018] [Accepted: 03/13/2019] [Indexed: 12/24/2022] Open
Abstract
Deregulated signal transduction is a cancer hallmark, and its complexity and interconnectivity imply that combination therapy should be considered, but large data volumes that cover the complexity are required in user-friendly ways. Here, we present a searchable database resource of synthetic lethality with a PI3 kinase signal transduction inhibitor by performing a saturation screen with an ultra-complex shRNA library containing 30 independent shRNAs per gene target. We focus on Ras-PI3 kinase signaling with T cell leukemia as a screening platform for multiple clinical and experimental reasons. Our resource predicts multiple combination-based therapies with high fidelity, ten of which we confirmed with small molecule inhibitors. Included are biochemical assays, as well as the IPI145 (duvelisib) inhibitor. We uncover the mechanism of synergy between the PI3 kinase inhibitor GDC0941 (pictilisib) and the tubulin inhibitor vincristine and demonstrate broad synergy in 28 cell lines of 5 cancer types and efficacy in preclinical leukemia mouse trials.
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Affiliation(s)
- Marsilius Mues
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laila Karra
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Damia Romero-Moya
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anica Wandler
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew J Hangauer
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Olga Ksionda
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yvonne Thus
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Marthe Lindenbergh
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kevin Shannon
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael T McManus
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA.
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20
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Schmitt A, Feldmann G, Zander T, Reinhardt HC. Targeting Defects in the Cellular DNA Damage Response for the Treatment of Pancreatic Ductal Adenocarcinoma. Oncol Res Treat 2018; 41:619-625. [DOI: 10.1159/000493401] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 08/31/2018] [Indexed: 12/12/2022]
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21
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Lindsay CR, Jamal-Hanjani M, Forster M, Blackhall F. KRAS: Reasons for optimism in lung cancer. Eur J Cancer 2018; 99:20-27. [PMID: 29894909 DOI: 10.1016/j.ejca.2018.05.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/21/2018] [Accepted: 05/13/2018] [Indexed: 01/07/2023]
Abstract
Despite being the most frequent gain-of-function genetic alteration in human cancer, KRAS mutation has to date offered only limited potential as a prognostic and predictive biomarker. Results from the phase III SELECT-1 trial in non-small cell lung cancer (NSCLC) recently added to a number of historical and more contemporary disappointments in targeting KRAS mutant disease, including farnesyl transferase inhibition and synthetic lethality partners such as STK33. This narrative review uses the context of these previous failures to demonstrate how the knowledge gained from these experiences can be used as a platform for exciting advances in NSCLC on the horizon. It now seems clear that mutational subtype (most commonly G12C) of individual mutations is of greater relevance than the categorical evaluation of KRAS mutation presence or otherwise. A number of direct small molecules targeted to these subtypes are in development and have shown promising biological activity, with some in the late stages of preclinical validation.
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Affiliation(s)
- C R Lindsay
- Division of Molecular and Clinical Cancer Sciences, University of Manchester, Manchester, UK; Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK; Cancer Research UK Lung Cancer Centre of Excellence, London and Manchester, UK.
| | - M Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, London and Manchester, UK; Department of Oncology, University College of London Hospital and UCL Cancer Institute, London, UK
| | - M Forster
- Cancer Research UK Lung Cancer Centre of Excellence, London and Manchester, UK; Department of Oncology, University College of London Hospital and UCL Cancer Institute, London, UK
| | - F Blackhall
- Division of Molecular and Clinical Cancer Sciences, University of Manchester, Manchester, UK; Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK; Cancer Research UK Lung Cancer Centre of Excellence, London and Manchester, UK
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22
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Aguirre AJ, Hahn WC. Synthetic Lethal Vulnerabilities in KRAS-Mutant Cancers. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a031518. [PMID: 29101114 DOI: 10.1101/cshperspect.a031518] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
KRAS is the most commonly mutated oncogene in human cancer. Most KRAS-mutant cancers depend on sustained expression and signaling of KRAS, thus making it a high-priority therapeutic target. Unfortunately, development of direct small molecule inhibitors of KRAS function has been challenging. An alternative therapeutic strategy for KRAS-mutant malignancies involves targeting codependent vulnerabilities or synthetic lethal partners that are preferentially essential in the setting of oncogenic KRAS. KRAS activates numerous effector pathways that mediate proliferation and survival signals. Moreover, cancer cells must cope with substantial oncogenic stress conferred by mutant KRAS. These oncogenic signaling pathways and compensatory coping mechanisms of KRAS-mutant cancer cells form the basis for synthetic lethal interactions. Here, we review the compendium of previously identified codependencies in KRAS-mutant cancers, including the results of numerous functional genetic screens aimed at identifying KRAS synthetic lethal targets. Importantly, many of these vulnerabilities may represent tractable therapeutic opportunities.
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Affiliation(s)
- Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
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23
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Kota S, Hou S, Guerrant W, Madoux F, Troutman S, Fernandez-Vega V, Alekseeva N, Madala N, Scampavia L, Kissil J, Spicer TP. A novel three-dimensional high-throughput screening approach identifies inducers of a mutant KRAS selective lethal phenotype. Oncogene 2018; 37:4372-4384. [PMID: 29743592 PMCID: PMC6138545 DOI: 10.1038/s41388-018-0257-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/04/2018] [Accepted: 03/16/2018] [Indexed: 01/01/2023]
Abstract
The RAS proteins are the most frequently mutated oncogenes in cancer, with highest frequency found in pancreatic, lung, and colon tumors. Moreover, the activity of RAS is required for the proliferation and/or survival of these tumor cells and thus represents a high-value target for therapeutic development. Direct targeting of RAS has proven challenging for multiple reasons stemming from the biology of the protein, the complexity of downstream effector pathways and upstream regulatory networks. Thus, significant efforts have been directed at identifying downstream targets on which RAS is dependent. These efforts have proven challenging, in part due to confounding factors such as reliance on two-dimensional adherent monolayer cell cultures that inadequately recapitulate the physiologic context to which cells are exposed in vivo. To overcome these issues, we implemented a High Throughput Screening (HTS) approach using a spheroid-based 3-dimensional culture format, thought to more closely reflect conditions experienced by cells in vivo. Using isogenic cell pairs, differing in the status of KRAS, we identified Proscillaridin A as a selective inhibitor of cells harboring the oncogenic KRasG12V allele. Significantly, the identification of Proscillaridin A was facilitated by the 3D screening platform and would not have been discovered employing standard 2D culturing methods.
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Affiliation(s)
- Smitha Kota
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA
| | - Shurong Hou
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA
| | - William Guerrant
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA
| | - Franck Madoux
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA.,Amgen Inc., Thousand Oaks, CA, USA
| | - Scott Troutman
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA
| | | | - Nina Alekseeva
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA
| | - Neeharika Madala
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA
| | - Louis Scampavia
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA
| | - Joseph Kissil
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA.
| | - Timothy P Spicer
- Department of Molecular Medicine, The Scripps Research Institute, Florida, USA.
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24
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Kong F, Sun T, Kong X, Xie D, Li Z, Xie K. Krüppel-like Factor 4 Suppresses Serine/Threonine Kinase 33 Activation and Metastasis of Gastric Cancer through Reversing Epithelial-Mesenchymal Transition. Clin Cancer Res 2018; 24:2440-2451. [PMID: 29367428 DOI: 10.1158/1078-0432.ccr-17-3346] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/21/2017] [Accepted: 01/17/2018] [Indexed: 12/11/2022]
Abstract
Background: Cancers with aberrant expression of Serine/threonine kinase 33 (STK33) has been reported to be particularly aggressive. However, its expression, clinical significance, and biological functions in gastric cancer remain largely unknown. In the present study, we determined the expression and function of STK33 in gastric cancer and delineated the clinical significance of the Krüppel-like factor 4 (KLF4)/STK33 signaling pathway.Methods: STK33 expression and its association with multiple clinicopathologic characteristics were analyzed immunohistochemically in human gastric cancer specimens. STK33 knockdown and overexpression were used to dissect the underlying mechanism of its functions in gastric cancer cells. Regulation and underlying mechanisms of STK33 expression by KLF4 in gastric cancer cells were studied using cell and molecular biological methods.Results: Drastically higher expression of STK33 was observed in gastric cancer and gastric intraepithelial neoplasia tissues compared with adjacent normal gastric tissues. Increased STK33 expression correlated directly with tumor size, lymph node, and distant metastasis; and patients with low STK33 expression gastric cancer were predicted to have a favorable prognosis. Enforced expression of STK33 promoted gastric cancer cell proliferation, migration, and invasion in vitro and in vivo, whereas reduced STK33 did the opposite. Moreover, STK33 promoted epithelial-mesenchymal transition (EMT) in vitro Mechanistically, KLF4 transcriptionally inhibited STK33 expression in gastric cancer cells. KLF4-mediated inhibition of gastric cancer cell invasion was reversed by upregulation of STK33 expression.Conclusions: STK33 has pro-tumor function and is a critical downstream mediator of KLF4 in gastric cancer. STK33 may serve as a potential prognostic marker and therapeutic target for gastric cancer. Clin Cancer Res; 24(10); 2440-51. ©2018 AACR.
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Affiliation(s)
- Fanyang Kong
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Tao Sun
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China.,Department of Gastroenterology, PLA Air Force General Hospital, Beijing, People's Republic of China
| | - Xiangyu Kong
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Dacheng Xie
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhaoshen Li
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China.
| | - Keping Xie
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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25
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Kong F, Kong X, Du Y, Chen Y, Deng X, Zhu J, Du J, Li L, Jia Z, Xie D, Li Z, Xie K. STK33 Promotes Growth and Progression of Pancreatic Cancer as a Critical Downstream Mediator of HIF1α. Cancer Res 2017; 77:6851-6862. [PMID: 29038348 DOI: 10.1158/0008-5472.can-17-0067] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 07/06/2017] [Accepted: 10/05/2017] [Indexed: 11/16/2022]
Abstract
The serine/threonine kinase STK33 has been implicated in cancer cell proliferation. Here, we provide evidence of a critical role for STK33 in the pathogenesis and metastatic progression of pancreatic ductal adenocarcinoma (PDAC). STK33 expression in PDAC was regulated by the hypoxia-inducible transcription factor HIF1α. In human PDAC specimens, STK33 was overexpressed and associated with poor prognosis. Enforced STK33 expression promoted PDAC proliferation, migration, invasion, and tumor growth, whereas STK33 depletion exerted opposing effects. Mechanistic investigations showed that HIF1α regulated STK33 via direct binding to a hypoxia response element in its promoter. In showing that dysregulated HIF1α/STK33 signaling promotes PDAC growth and progression, our results suggest STK33 as a candidate therapeutic target to improve PDAC treatment. Cancer Res; 77(24); 6851-62. ©2017 AACR.
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Affiliation(s)
- Fanyang Kong
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Gastroenterology, Changhai Hospital, Shanghai, P.R. China
| | - Xiangyu Kong
- Department of Gastroenterology, Changhai Hospital, Shanghai, P.R. China
| | - Yiqi Du
- Department of Gastroenterology, Changhai Hospital, Shanghai, P.R. China
| | - Ying Chen
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Pathology, Changhai Hospital, Shanghai, P.R. China
| | - Xuan Deng
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, P.R. China
| | - Jianwei Zhu
- Department of Gastroenterology, Changhai Hospital, Shanghai, P.R. China
| | - Jiawei Du
- Department of Oncology and Tumor Institute, Shanghai East Hospital, Shanghai Tongji University, Shanghai, P.R. China
| | - Lei Li
- Department of Gastroenterology, Changhai Hospital, Shanghai, P.R. China
| | - Zhiliang Jia
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dacheng Xie
- Department of Oncology and Tumor Institute, Shanghai East Hospital, Shanghai Tongji University, Shanghai, P.R. China
| | - Zhaoshen Li
- Department of Gastroenterology, Changhai Hospital, Shanghai, P.R. China.
| | - Keping Xie
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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26
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Drewry DH, Wells CI, Andrews DM, Angell R, Al-Ali H, Axtman AD, Capuzzi SJ, Elkins JM, Ettmayer P, Frederiksen M, Gileadi O, Gray N, Hooper A, Knapp S, Laufer S, Luecking U, Michaelides M, Müller S, Muratov E, Denny RA, Saikatendu KS, Treiber DK, Zuercher WJ, Willson TM. Progress towards a public chemogenomic set for protein kinases and a call for contributions. PLoS One 2017; 12:e0181585. [PMID: 28767711 PMCID: PMC5540273 DOI: 10.1371/journal.pone.0181585] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/03/2017] [Indexed: 01/01/2023] Open
Abstract
Protein kinases are highly tractable targets for drug discovery. However, the biological function and therapeutic potential of the majority of the 500+ human protein kinases remains unknown. We have developed physical and virtual collections of small molecule inhibitors, which we call chemogenomic sets, that are designed to inhibit the catalytic function of almost half the human protein kinases. In this manuscript we share our progress towards generation of a comprehensive kinase chemogenomic set (KCGS), release kinome profiling data of a large inhibitor set (Published Kinase Inhibitor Set 2 (PKIS2)), and outline a process through which the community can openly collaborate to create a KCGS that probes the full complement of human protein kinases.
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Affiliation(s)
- David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Carrow I. Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David M. Andrews
- AstraZeneca, Darwin Building, Cambridge Science Park, Cambridge, United Kingdom
| | - Richard Angell
- Drug Discovery Group, Translational Research Office, University College London School of Pharmacy, 29–39 Brunswick Square, London, United Kingdom
| | - Hassan Al-Ali
- Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Alison D. Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Stephen J. Capuzzi
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jonathan M. Elkins
- Structural Genomics Consortium, Universidade Estadual de Campinas—UNICAMP, Campinas, Sao Paulo, Brazil
| | | | - Mathias Frederiksen
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Opher Gileadi
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Nathanael Gray
- Harvard Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana−Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Alice Hooper
- Drug Discovery Group, Translational Research Office, University College London School of Pharmacy, 29–39 Brunswick Square, London, United Kingdom
| | - Stefan Knapp
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, and Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 15, Frankfurt am Main, Germany
| | - Stefan Laufer
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, Tübingen, Germany
| | - Ulrich Luecking
- Bayer Pharma AG, Drug Discovery, Müllerstrasse 178, Berlin, Germany
| | - Michael Michaelides
- Oncology Chemistry, AbbVie, 1 North Waukegan Road, North Chicago, Illinois, United States of America
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, and Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 15, Frankfurt am Main, Germany
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - R. Aldrin Denny
- Worldwide Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts, United States of America
| | - Kumar S. Saikatendu
- Global Research Externalization, Takeda California, Inc., 10410 Science Center Drive, San Diego, California, United States of America
| | | | - William J. Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Jaiswal A, Peddinti G, Akimov Y, Wennerberg K, Kuznetsov S, Tang J, Aittokallio T. Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells. Genome Med 2017; 9:51. [PMID: 28569207 PMCID: PMC5452371 DOI: 10.1186/s13073-017-0440-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/15/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Genome-wide loss-of-function profiling is widely used for systematic identification of genetic dependencies in cancer cells; however, the poor reproducibility of RNA interference (RNAi) screens has been a major concern due to frequent off-target effects. Currently, a detailed understanding of the key factors contributing to the sub-optimal consistency is still a lacking, especially on how to improve the reliability of future RNAi screens by controlling for factors that determine their off-target propensity. METHODS We performed a systematic, quantitative analysis of the consistency between two genome-wide shRNA screens conducted on a compendium of cancer cell lines, and also compared several gene summarization methods for inferring gene essentiality from shRNA level data. We then devised novel concepts of seed essentiality and shRNA family, based on seed region sequences of shRNAs, to study in-depth the contribution of seed-mediated off-target effects to the consistency of the two screens. We further investigated two seed-sequence properties, seed pairing stability, and target abundance in terms of their capability to minimize the off-target effects in post-screening data analysis. Finally, we applied this novel methodology to identify genetic interactions and synthetic lethal partners of cancer drivers, and confirmed differential essentiality phenotypes by detailed CRISPR/Cas9 experiments. RESULTS Using the novel concepts of seed essentiality and shRNA family, we demonstrate how genome-wide loss-of-function profiling of a common set of cancer cell lines can be actually made fairly reproducible when considering seed-mediated off-target effects. Importantly, by excluding shRNAs having higher propensity for off-target effects, based on their seed-sequence properties, one can remove noise from the genome-wide shRNA datasets. As a translational application case, we demonstrate enhanced reproducibility of genetic interaction partners of common cancer drivers, as well as identify novel synthetic lethal partners of a major oncogenic driver, PIK3CA, supported by a complementary CRISPR/Cas9 experiment. CONCLUSIONS We provide practical guidelines for improved design and analysis of genome-wide loss-of-function profiling and demonstrate how this novel strategy can be applied towards improved mapping of genetic dependencies of cancer cells to aid development of targeted anticancer treatments.
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Affiliation(s)
- Alok Jaiswal
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Gopal Peddinti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Yevhen Akimov
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Sergey Kuznetsov
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
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28
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Beijersbergen RL, Wessels LF, Bernards R. Synthetic Lethality in Cancer Therapeutics. ANNUAL REVIEW OF CANCER BIOLOGY 2017. [DOI: 10.1146/annurev-cancerbio-042016-073434] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Treatment with targeted drugs has primarily focused on the genes and pathways that are mutated in cancer, which severely limits the repertoire of drug targets. Synthetic lethality exploits the notion that the presence of a mutation in a cancer gene is often associated with a new vulnerability that can be targeted therapeutically, thus greatly expanding the arsenal of potential drug targets. Here we discuss both the experimental and the computational biology tools that can be used to identify synthetic lethal interactions. We also discuss strategies for using synthetic lethality to discover new drug targets and in the rational design of more potent drug combinations. We review the progress made and future opportunities offered by synthetic lethal approaches to treating cancer more effectively.
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Affiliation(s)
- Roderick L. Beijersbergen
- Division of Molecular Carcinogenesis and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Lodewyk F.A. Wessels
- Division of Molecular Carcinogenesis and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - René Bernards
- Division of Molecular Carcinogenesis and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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29
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Leung AWY, de Silva T, Bally MB, Lockwood WW. Synthetic lethality in lung cancer and translation to clinical therapies. Mol Cancer 2016; 15:61. [PMID: 27686855 PMCID: PMC5041331 DOI: 10.1186/s12943-016-0546-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/21/2016] [Indexed: 01/06/2023] Open
Abstract
Lung cancer is a heterogeneous disease consisting of multiple histological subtypes each driven by unique genetic alterations. Despite the development of targeted therapies that inhibit the oncogenic mutations driving a subset of lung cancer cases, there is a paucity of effective treatments for the majority of lung cancer patients and new strategies are urgently needed. In recent years, the concept of synthetic lethality has been established as an effective approach for discovering novel cancer-specific targets as well as a method to improve the efficacy of existing drugs which provide partial but insufficient benefits for patients. In this review, we discuss the concept of synthetic lethality, the various types of synthetic lethal interactions in the context of oncology and the approaches used to identify these interactions, including recent advances that have transformed the ability to discover novel synthetic lethal combinations on a global scale. Lastly, we describe the specific synthetic lethal interactions identified in lung cancer to date and explore the pharmacological challenges and considerations in translating these discoveries to the clinic.
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Affiliation(s)
- Ada W. Y. Leung
- Experimental Therapeutics, BC Cancer Research Centre, 675 West 10th Ave, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Rm. G227-2211 Wesbrook Mall, Vancouver, BC V6T 2B5 Canada
| | - Tanya de Silva
- Department of Pathology and Laboratory Medicine, University of British Columbia, Rm. G227-2211 Wesbrook Mall, Vancouver, BC V6T 2B5 Canada
- Integrative Oncology, BC Cancer Research Centre, 675 West 10th Ave, Vancouver, BC V5Z 1L3 Canada
| | - Marcel B. Bally
- Experimental Therapeutics, BC Cancer Research Centre, 675 West 10th Ave, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Rm. G227-2211 Wesbrook Mall, Vancouver, BC V6T 2B5 Canada
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3 Canada
- Centre for Drug Research and Development, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3 Canada
| | - William W. Lockwood
- Department of Pathology and Laboratory Medicine, University of British Columbia, Rm. G227-2211 Wesbrook Mall, Vancouver, BC V6T 2B5 Canada
- Integrative Oncology, BC Cancer Research Centre, 675 West 10th Ave, Vancouver, BC V5Z 1L3 Canada
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30
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Jackson RA, Chen ES. Synthetic lethal approaches for assessing combinatorial efficacy of chemotherapeutic drugs. Pharmacol Ther 2016; 162:69-85. [DOI: 10.1016/j.pharmthera.2016.01.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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31
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Zeitouni D, Pylayeva-Gupta Y, Der CJ, Bryant KL. KRAS Mutant Pancreatic Cancer: No Lone Path to an Effective Treatment. Cancers (Basel) 2016; 8:cancers8040045. [PMID: 27096871 PMCID: PMC4846854 DOI: 10.3390/cancers8040045] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/08/2016] [Accepted: 04/11/2016] [Indexed: 02/06/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is among the deadliest cancers with a dismal 7% 5-year survival rate and is projected to become the second leading cause of cancer-related deaths by 2020. KRAS is mutated in 95% of PDACs and is a well-validated driver of PDAC growth and maintenance. However, despite comprehensive efforts, an effective anti-RAS drug has yet to reach the clinic. Different paths to inhibiting RAS signaling are currently under investigation in the hope of finding a successful treatment. Recently, direct RAS binding molecules have been discovered, challenging the perception that RAS is an “undruggable” protein. Other strategies currently being pursued take an indirect approach, targeting proteins that facilitate RAS membrane association or downstream effector signaling. Unbiased genetic screens have identified synthetic lethal interactors of mutant RAS. Most recently, metabolic targets in pathways related to glycolytic signaling, glutamine utilization, autophagy, and macropinocytosis are also being explored. Harnessing the patient’s immune system to fight their cancer is an additional exciting route that is being considered. The “best” path to inhibiting KRAS has yet to be determined, with each having promise as well as potential pitfalls. We will summarize the state-of-the-art for each direction, focusing on efforts directed toward the development of therapeutics for pancreatic cancer patients with mutated KRAS.
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Affiliation(s)
- Daniel Zeitouni
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Yuliya Pylayeva-Gupta
- Lineberger Comprehensive Cancer Center, 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.
| | - Kirsten L Bryant
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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32
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Jensen KJ, Moyer CB, Janes KA. Network Architecture Predisposes an Enzyme to Either Pharmacologic or Genetic Targeting. Cell Syst 2016; 2:112-121. [PMID: 26942229 DOI: 10.1016/j.cels.2016.01.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Chemical inhibition and genetic knockdown of enzymes are not equivalent in cells, but network-level mechanisms that cause discrepancies between knockdown and inhibitor perturbations are not understood. Here we report that enzymes regulated by negative feedback are robust to knockdown but susceptible to inhibition. Using the Raf-MEK-ERK kinase cascade as a model system, we find that ERK activation is resistant to genetic knockdown of MEK but susceptible to a comparable degree of chemical MEK inhibition. We demonstrate that negative feedback from ERK to Raf causes this knockdown-versus-inhibitor discrepancy in vivo. Exhaustive mathematical modeling of three-tiered enzyme cascades suggests that this result is general: negative autoregulation or feedback favors inhibitor potency, whereas positive autoregulation or feedback favors knockdown potency. Our findings provide a rationale for selecting pharmacologic versus genetic perturbations in vivo and point out the dangers of using knockdown approaches in search of drug targets.
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Affiliation(s)
- Karin J Jensen
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Sanofi Oncology, Cambridge, MA 02139, USA
| | - Christian B Moyer
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
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Porrello A, Piergentili RB. Contextualizing the Genes Altered in Bladder Neoplasms in Pediatric andTeen Patients Allows Identifying Two Main Classes of Biological ProcessesInvolved and New Potential Therapeutic Targets. Curr Genomics 2016; 17:33-61. [PMID: 27013923 PMCID: PMC4780474 DOI: 10.2174/1389202916666151014222603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/29/2015] [Accepted: 07/08/2015] [Indexed: 12/19/2022] Open
Abstract
Research on bladder neoplasms in pediatric and teen patients (BNPTP) has described 21 genes, which are variously involved in this disease and are mostly responsible for deregulated cell proliferation. However, due to the limited number of publications on this subject, it is still unclear what type of relationships there are among these genes and which are the chances that, while having different molecular functions, they i) act as downstream effector genes of well-known pro- or anti- proliferative stimuli and/or interplay with biochemical pathways having oncological relevance or ii) are specific and, possibly, early biomarkers of these pathologies. A Gene Ontology (GO)-based analysis showed that these 21 genes are involved in biological processes, which can be split into two main classes: cell regulation-based and differentiation/development-based. In order to understand the involvement/overlapping with main cancer-related pathways, we performed a meta-analysis dependent on the 189 oncogenic signatures of the Molecular Signatures Database (OSMSD) curated by the Broad Institute. We generated a binary matrix with 53 gene signatures having at least one hit; this analysis i) suggests that some genes of the original list show inconsistencies and might need to be experimentally re- assessed or evaluated as biomarkers (in particular, ACTA2) and ii) allows hypothesizing that important (proto)oncogenes (E2F3, ERBB2/HER2, CCND1, WNT1, and YAP1) and (putative) tumor suppressors (BRCA1, RBBP8/CTIP, and RB1-RBL2/p130) may participate in the onset of this disease or worsen the observed phenotype, thus expanding the list of possible molecular targets for the treatment of BNPTP.
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Affiliation(s)
- A. Porrello
- Comprehensive Cancer Center (LCCC), University of North Carolina (UNC)-Chapel Hill, Chapel Hill, 27599 NC, USA
| | - R. b Piergentili
- Institute of Molecular Biology and Pathology at CNR (CNR-IBPM); Department of Biology and Biotechnologies, Sapienza – Università di Roma, Italy
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34
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Yang T, Song B, Zhang J, Yang GS, Zhang H, Yu WF, Wu MC, Lu JH, Shen F. STK33 promotes hepatocellular carcinoma through binding to c-Myc. Gut 2016; 65:124-33. [PMID: 25398772 PMCID: PMC4717356 DOI: 10.1136/gutjnl-2014-307545] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 10/29/2014] [Indexed: 01/28/2023]
Abstract
OBJECTIVE STK33 has been reported to play an important role in cancer cell proliferation. We investigated the role of STK33 in hepatocellular carcinoma (HCC) and its underlying mechanisms. DESIGN 251 patients with HCC were analysed for association between STK33 expression and clinical stage and survival rate. Tamoxifen (TAM)-inducible, hepatocyte-specific STK33 transgenic and knockout mice models were used to study the role of STK33 in liver tumorigenesis. HCC cell lines were used to study the role of STK33 in cell proliferation in vitro and in vivo. RESULTS STK33 expression was found to be frequently upregulated in patients with HCC. Significant associations were found between increased expression of STK33 and advanced HCC staging and shorter disease-free survival of patients. Overexpression of STK33 increased HCC cell proliferation both in vitro and in vivo, whereas suppression of STK33 inhibited this effect. Using a TAM-inducible, hepatocyte-specific STK33 transgenic mouse model, we found that overexpression of STK33 resulted in increased hepatocyte proliferation, leading to tumour cell burst. Using a TAM-inducible, hepatocyte-specific STK33 knockout mouse model, we found that, when subjected to the diethylnitrosamine (DEN) liver cancer bioassay, STK33KO(flox/flox, Alb-ERT2-Cre) mice exhibited a markedly lower incidence of tumour formation compared with control mice. The underlying mechanism may be that STK33 binds directly to c-Myc and increases its transcriptional activity. In particular, the C-terminus of STK33 blocks STK33/c-Myc association, downregulates HCC cell proliferation, and reduces DEN-induced liver tumour cell number and tumour size. CONCLUSIONS STK33 plays an essential role in hepatocellular proliferation and liver tumorigenesis. The C-terminus of STK33 could be a potential therapeutic target in the treatment of patients with STK33-overexpressed HCC.
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Affiliation(s)
- Tian Yang
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Bin Song
- The 3rd Department of General Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jin Zhang
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Guang-Shun Yang
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Han Zhang
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Wei-Feng Yu
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Meng-Chao Wu
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Jun-Hua Lu
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Feng Shen
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
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35
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Wang QJ, Yu Z, Griffith K, Hanada KI, Restifo NP, Yang JC. Identification of T-cell Receptors Targeting KRAS-Mutated Human Tumors. Cancer Immunol Res 2015; 4:204-14. [PMID: 26701267 DOI: 10.1158/2326-6066.cir-15-0188] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/11/2015] [Indexed: 12/13/2022]
Abstract
KRAS is one of the most frequently mutated proto-oncogenes in human cancers. The dominant oncogenic mutations of KRAS are single amino acid substitutions at codon 12, in particular G12D and G12V present in 60% to 70% of pancreatic cancers and 20% to 30% of colorectal cancers. The consistency, frequency, and tumor specificity of these "neoantigens" make them attractive therapeutic targets. Recent data associate T cells that target mutated antigens with clinical immunotherapy responses in patients with metastatic melanoma, lung cancer, or cholangiocarcinoma. Using HLA-peptide prediction algorithms, we noted that HLA-A*11:01 could potentially present mutated KRAS variants. By immunizing HLA-A*11:01 transgenic mice, we generated murine T cells and subsequently isolated T-cell receptors (TCR) highly reactive to the mutated KRAS variants G12V and G12D. Peripheral blood lymphocytes (PBL) transduced with these TCRs could recognize multiple HLA-A*11:01(+) tumor lines bearing the appropriate KRAS mutations. In a xenograft model of large established tumor, adoptive transfer of these transduced PBLs reactive with an HLA-A*11:01, G12D-mutated pancreatic cell line could significantly reduce its growth in NSG mice (P = 0.002). The success of adoptive transfer of TCR-engineered T cells against melanoma and other cancers supports clinical trials with these T cells that recognize mutated KRAS in patients with a variety of common cancer types.
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Affiliation(s)
- Qiong J Wang
- Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland.
| | - Zhiya Yu
- Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Kayla Griffith
- Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Ken-ichi Hanada
- Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Nicholas P Restifo
- Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - James C Yang
- Surgery Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland.
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36
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Zhan T, Boutros M. Towards a compendium of essential genes - From model organisms to synthetic lethality in cancer cells. Crit Rev Biochem Mol Biol 2015; 51:74-85. [PMID: 26627871 PMCID: PMC4819810 DOI: 10.3109/10409238.2015.1117053] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Essential genes are defined by their requirement to sustain life in cells or whole organisms. The systematic identification of essential gene sets not only allows insights into the fundamental building blocks of life, but may also provide novel therapeutic targets in oncology. The discovery of essential genes has been tightly linked to the development and deployment of various screening technologies. Here, we describe how gene essentiality was addressed in different eukaryotic model organisms, covering a range of organisms from yeast to mouse. We describe how increasing knowledge of evolutionarily divergent genomes facilitate identification of gene essentiality across species. Finally, the impact of gene essentiality and synthetic lethality on cancer research and the clinical translation of screening results are highlighted.
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Affiliation(s)
- Tianzuo Zhan
- a Department of Cell and Molecular Biology , Division of Signaling and Functional Genomics, Medical Faculty Mannheim, German Cancer Research Center (DKFZ), Heidelberg University , Heidelberg , Germany and.,b Department of Medicine II , Medical Faculty Mannheim, University Hospital Mannheim, Heidelberg University , Mannheim , Germany
| | - Michael Boutros
- a Department of Cell and Molecular Biology , Division of Signaling and Functional Genomics, Medical Faculty Mannheim, German Cancer Research Center (DKFZ), Heidelberg University , Heidelberg , Germany and
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37
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Hennek J, Alves J, Yao E, Goueli SA, Zegzouti H. Bioluminescent kinase strips: A novel approach to targeted and flexible kinase inhibitor profiling. Anal Biochem 2015; 495:9-20. [PMID: 26628096 DOI: 10.1016/j.ab.2015.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/11/2015] [Accepted: 11/16/2015] [Indexed: 11/19/2022]
Abstract
In addition to target efficacy, drug safety is a major requirement during the drug discovery process and is influenced by target specificity. Therefore, it is imperative that every new drug candidate be profiled against various liability panels that include protein kinases. Here, an effective methodology to streamline kinase inhibitor profiling is described. An accessible standardized profiling system for 112 protein kinases covering all branches of the kinome was developed. This approach consists of creating different sets of kinases and their corresponding substrates in multi-tube strips. The kinase stocks are pre-standardized for optimal kinase activity and used for inhibitor profiling using a bioluminescent ADP detection assay. We show that these strips can routinely generate inhibitor selectivity profiles for small or broad kinase family panels. Lipid kinases were also assembled in strip format and profiled together with protein kinases. We identified two specific PI3K inhibitors that have off-target effects on CK2 that were not reported before and would have been missed if compounds were not profiled against lipid and protein kinases simultaneously. To validate the accuracy of the data generated by this method, we confirmed that the inhibition potencies observed are consistent with published values produced by more complex technologies such as radioactivity assays.
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Affiliation(s)
- J Hennek
- R&D Department, Promega Corporation, Madison, WI 53711, USA
| | - J Alves
- R&D Department, Promega Corporation, Madison, WI 53711, USA
| | - E Yao
- SignalChem Pharmaceuticals, Richmond, British Columbia V6V 2J2, Canada
| | - S A Goueli
- R&D Department, Promega Corporation, Madison, WI 53711, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - H Zegzouti
- R&D Department, Promega Corporation, Madison, WI 53711, USA.
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Modeling K-Ras-driven lung adenocarcinoma in mice: preclinical validation of therapeutic targets. J Mol Med (Berl) 2015; 94:121-35. [DOI: 10.1007/s00109-015-1360-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 10/22/2015] [Indexed: 01/10/2023]
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Lautwein T, Lerch S, Schäfer D, Schmidt ER. The serine/threonine kinase 33 is present and expressed in palaeognath birds but has become a unitary pseudogene in neognaths about 100 million years ago. BMC Genomics 2015. [PMID: 26199010 PMCID: PMC4509753 DOI: 10.1186/s12864-015-1769-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Serine/threonine kinase 33 (STK33) has been shown to be conserved across all major vertebrate classes including reptiles, mammals, amphibians and fish, suggesting its importance within vertebrates. It has been shown to phosphorylate vimentin and might play a role in spermatogenesis and organ ontogenesis. In this study we analyzed the genomic locus and expression of stk33 in the class Aves, using a combination of large scale next generation sequencing data analysis and traditional PCR. Results Within the subclass Palaeognathae we analyzed the white-throated tinamou (Tinamus guttatus), the African ostrich (Struthio camelus) and the emu (Dromaius novaehollandiae). For the African ostrich we were able to generate a 62,778 bp long genomic contig and an mRNA sequence that encodes a protein showing highly significant similarity to STK33 proteins from other vertebrates. The emu has been shown to encode and transcribe a functional STK33 as well. For the white-throated tinamou we were able to identify 13 exons by sequence comparison encoding a protein similar to STK33 as well. In contrast, in all 28 neognath birds analyzed, we could not find evidence for the existence of a functional copy of stk33 or its expression. In the genomes of these 28 bird species, we found only remnants of the stk33 locus carrying several large genomic deletions, leading to the loss of multiple exons. The remaining exons have acquired various indels and premature stop codons. Conclusions We were able to elucidate and describe the genomic structure and the transcription of a functional stk33 gene within the subclass Palaeognathae, but we could only find degenerate remnants of stk33 in all neognath birds analyzed. This led us to the conclusion that stk33 became a unitary pseudogene in the evolutionary history of the class Aves at the paleognath-neognath branch point during the late cretaceous period about 100 million years ago. We hypothesize that the pseudogenization of stk33 might have become fixed in neognaths due to either genetic redundancy or a non-orthologous gene displacement and present potential candidate genes for such an incident. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1769-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tobias Lautwein
- Institute for Molecular Genetics, Johannes Gutenberg University Mainz, Johann-Joachim-Becherweg 32, 55128, Mainz, Germany.
| | - Steffen Lerch
- Institute for Molecular Genetics, Johannes Gutenberg University Mainz, Johann-Joachim-Becherweg 32, 55128, Mainz, Germany. .,Departement of Neurology, University Medical Center, Johannes Gutenberg-University Mainz, Langenbeckstr.1, 55131, Mainz, Germany.
| | - Daniel Schäfer
- Institute for Molecular Genetics, Johannes Gutenberg University Mainz, Johann-Joachim-Becherweg 32, 55128, Mainz, Germany. .,Departement of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany.
| | - Erwin R Schmidt
- Institute for Molecular Genetics, Johannes Gutenberg University Mainz, Johann-Joachim-Becherweg 32, 55128, Mainz, Germany.
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Identification of novel therapeutic targets in acute leukemias with NRAS mutations using a pharmacologic approach. Blood 2015; 125:3133-43. [PMID: 25833960 DOI: 10.1182/blood-2014-12-615906] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/25/2015] [Indexed: 12/14/2022] Open
Abstract
Oncogenic forms of NRAS are frequently associated with hematologic malignancies and other cancers, making them important therapeutic targets. Inhibition of individual downstream effector molecules (eg, RAF kinase) have been complicated by the rapid development of resistance or activation of bypass pathways. For the purpose of identifying novel targets in NRAS-transformed cells, we performed a chemical screen using mutant NRAS transformed Ba/F3 cells to identify compounds with selective cytotoxicity. One of the compounds identified, GNF-7, potently and selectively inhibited NRAS-dependent cells in preclinical models of acute myelogenous leukemia and acute lymphoblastic leukemia. Mechanistic analysis revealed that its effects were mediated in part through combined inhibition of ACK1/AKT and of mitogen-activated protein kinase kinase kinase kinase 2 (germinal center kinase). Similar to genetic synthetic lethal approaches, these results suggest that small molecule screens can be used to identity novel therapeutic targets in cells addicted to RAS oncogenes.
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Wang P, Cheng H, Wu J, Yan A, Zhang L. STK33 plays an important positive role in the development of human large cell lung cancers with variable metastatic potential. Acta Biochim Biophys Sin (Shanghai) 2015; 47:214-23. [PMID: 25662617 DOI: 10.1093/abbs/gmu136] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Serine/threonine kinase 33 (STK33) is a novel protein that has attracted considerable interest in recent years. Previous research has revealed that STK33 expression plays a special role in cancer cell proliferation. However, the mechanisms of STK33 induction of cancer cells remain largely unknown. In this study, it is demonstrated that STK33 expression varies in NL9980 and L9981 cells which are homogeneous cell lines with similar genetic backgrounds. STK33 can promote cell migration and invasion and suppress p53 gene expression in the NL9980 and L9981 cells. In addition, this protein also promotes epithelial-mesenchymal transition (EMT). Moreover, STK33 knockdown decreases tumor-related gene expression and inhibits cell migration, invasion, and EMT, suggesting that STK33 may be a mediator of signaling pathways that are involved in cancer. In conclusion, our results suggest that STK33 may be an important prognostic marker and a therapeutic target for the metastatic progression of human lung cancer.
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Affiliation(s)
- Ping Wang
- Department of Thoracic Surgery, First People's Hospital of Yunnan Province, Kunming 650031, China
| | - Hongzhong Cheng
- Department of Thoracic Surgery, First People's Hospital of Yunnan Province, Kunming 650031, China
| | - Jianqiang Wu
- Department of Thoracic Surgery, First People's Hospital of Yunnan Province, Kunming 650031, China
| | - Anrun Yan
- Department of Thoracic Surgery, First People's Hospital of Yunnan Province, Kunming 650031, China
| | - Libin Zhang
- Department of Thoracic Surgery, First People's Hospital of Yunnan Province, Kunming 650031, China
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Stock JK, Jones NP, Hammonds T, Roffey J, Dillon C. Addressing the Right Targets in Oncology. ACTA ACUST UNITED AC 2015; 20:305-17. [DOI: 10.1177/1087057114564349] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translating existing and emerging knowledge of cancer biology into effective novel therapies remains a great challenge in drug discovery. A firm understanding of the target biology, confidence in the supporting preclinical research, and access to diverse chemical matter is required to lower attrition rates and prosecute targets effectively. Understanding past successes and failures will aid in refining this process to deliver further therapeutic benefit to patients. In this review, we suggest that early oncology drug discovery should focus on selection and prosecution of cancer targets with strong disease biology rather than on more chemically “druggable” targets with only modest disease-linkage. This approach offers higher potential benefit but also increases the need for innovative and alternative approaches. These include using different methods to validate novel targets and identify chemical matter, as well as raising the standards and our interpretation of the scientific literature. The combination of skills required for this emphasizes the need for broader early collaborations between academia and industry.
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Affiliation(s)
- Julie K. Stock
- Cancer Research Technology Discovery Laboratories, London, UK
| | - Neil P. Jones
- Cancer Research Technology Discovery Laboratories, London, UK
| | - Tim Hammonds
- Cancer Research Technology Discovery Laboratories, London, UK
| | - Jon Roffey
- Cancer Research Technology Discovery Laboratories, London, UK
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Huang L, Chen C, Zhang G, Ju Y, Zhang J, Wang H, Li J. STK33 overexpression in hypopharyngeal squamous cell carcinoma: possible role in tumorigenesis. BMC Cancer 2015; 15:13. [PMID: 25603720 PMCID: PMC4305229 DOI: 10.1186/s12885-015-1009-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 01/06/2015] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The role of serine/threonine kinase 33 (STK33) gene in tumorigenesis is still controversial. This study was aimed to investigate whether STK33 had the effect on hypopharyngeal squamous cell carcinoma (HSCC) and relevant genes, as well as the potential relation to ERK1/2 pathway. METHODS Immunohistochemistry was performed to investigate STK33 expression in human HSCC specimens. MTT, immunofluorescence, clone formation and matrigel invasion assays were employed to detect the effects of STK33 knockdown (STK33-RNAi) and/or PD98059 on major oncogenic properties of a HSCC cell line (Fadu), while, real-time PCR and western blot were used to examine the expressions of relevant genes. RESULTS STK33 was over-expressed in HSCC specimens, which was significantly associated with certain clinicopathological parameters. STK33-RNAi in Fadu cells resulted in inhibition of proliferation, induction of apoptosis, reduction of clone formation, and decline in the migration and invasion. These effects were potentiated by administration of PD98059. Mechanistic studies revealed that STK33-RNAi led to an increase in Caspse-3, Nm-23-H1 and E-Cadherin expressions and a reduction in Bcl-2, Ki-67 and Vimentin expressions. Moreover, PD98059 significantly reduced both ERK1/2 and STK33 expressions in Fadu cells. CONCLUSIONS STK33 is a potential oncogene and a promising diagnostic marker for HSCC. STK33 may promote tumorigenesis and progression of HSCC, and serve as a valuable molecular target for treatment of HSCC.
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Affiliation(s)
- Lingyan Huang
- Department of Otolaryngology-Head and Neck Surgery, Provincial Hospital Affiliated to Shandong University, Jingwu Street 324, Jinan, 250021, P.R. China. .,Department of Pathology, General Hospital of Ningxia Medical University, Yinchuan, 750004, P.R. China. .,Department of Pathology, Medical College, Shandong University, Jinan, 250021, P.R. China.
| | - Chen Chen
- Department of Otolaryngology-Head and Neck Surgery, Provincial Hospital Affiliated to Shandong University, Jingwu Street 324, Jinan, 250021, P.R. China. .,Department of Pathology, Medical College, Shandong University, Jinan, 250021, P.R. China.
| | - Guodong Zhang
- Department of Otolaryngology-Head and Neck Surgery, Provincial Hospital Affiliated to Shandong University, Jingwu Street 324, Jinan, 250021, P.R. China.
| | - Yuanrong Ju
- Intensive Care Unit, Provincial Hospital Affiliated to Shandong University, Jinan, 250021, P.R. China.
| | - Jianzhong Zhang
- Department of Pathology, General Hospital of Ningxia Medical University, Yinchuan, 750004, P.R. China.
| | - Haibo Wang
- Department of Otolaryngology-Head and Neck Surgery, Provincial Hospital Affiliated to Shandong University, Jingwu Street 324, Jinan, 250021, P.R. China.
| | - Jianfeng Li
- Department of Otolaryngology-Head and Neck Surgery, Provincial Hospital Affiliated to Shandong University, Jingwu Street 324, Jinan, 250021, P.R. China. .,Department of Pathology, Medical College, Shandong University, Jinan, 250021, P.R. China.
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Lee SL, Dempsey-Hibbert NC, Vimalachandran D, Wardle TD, Sutton P, Williams JHH. Targeting Heat Shock Proteins in Colorectal Cancer. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-3-319-17211-8_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Affiliation(s)
- Donal P McLornan
- From King's College Hospital NHS Foundation Trust, London (D.P.M., G.J.M.); and Moffitt Cancer Center, Tampa, FL (A.L.)
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Paul JM, Templeton SD, Baharani A, Freywald A, Vizeacoumar FJ. Building high-resolution synthetic lethal networks: a 'Google map' of the cancer cell. Trends Mol Med 2014; 20:704-15. [PMID: 25446836 DOI: 10.1016/j.molmed.2014.09.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/05/2014] [Accepted: 09/17/2014] [Indexed: 02/08/2023]
Abstract
The most commonly used therapies for cancer involve delivering high doses of radiation or toxic chemicals to the patient that also cause substantial damage to normal tissue. To overcome this, researchers have recently resorted to a basic biological concept called 'synthetic lethality' (SL) that takes advantage of interactions between gene pairs. The identification of SL interactions is of considerable therapeutic interest because if a particular gene is SL with a tumor-causing mutation, then the targeting that gene carries therapeutic advantages. Mapping these interactions in the context of human cancer cells could hold the key to effective, targeted cancer treatments. In this review, we cover the recent advances that aim to identify these SL interactions using unbiased genetic screens.
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Affiliation(s)
- James M Paul
- Department of Biochemistry, University of Saskatchewan, Saskatoon, S7N 5E5 Canada; Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8 Canada
| | - Shaina D Templeton
- Department of Biochemistry, University of Saskatchewan, Saskatoon, S7N 5E5 Canada
| | - Akanksha Baharani
- Department of Biochemistry, University of Saskatchewan, Saskatoon, S7N 5E5 Canada
| | - Andrew Freywald
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8 Canada
| | - Franco J Vizeacoumar
- Department of Biochemistry, University of Saskatchewan, Saskatoon, S7N 5E5 Canada; Saskatchewan Cancer Agency, Saskatoon, SK S7N 4H4, Canada.
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Abstract
Despite more than three decades of intensive effort, no effective pharmacological inhibitors of the RAS oncoproteins have reached the clinic, prompting the widely held perception that RAS proteins are 'undruggable'. However, recent data from the laboratory and the clinic have renewed our hope for the development of RAS-inhibitory molecules. In this Review, we summarize the progress and the promise of five key approaches. Firstly, we focus on the prospects of using direct inhibitors of RAS. Secondly, we address the issue of whether blocking RAS membrane association is a viable approach. Thirdly, we assess the status of targeting RAS downstream effector signalling, which is arguably the most favourable current approach. Fourthly, we address whether the search for synthetic lethal interactors of mutant RAS still holds promise. Finally, RAS-mediated changes in cell metabolism have recently been described and we discuss whether these changes could be exploited for new therapeutic directions. We conclude with perspectives on how additional complexities, which are not yet fully understood, may affect each of these approaches.
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Abstract
The great majority of targeted anticancer drugs inhibit mutated oncogenes that display increased activity. Yet many tumors do not contain such actionable aberrations, such as those harboring loss-of-function mutations. The notion of targeting synthetic lethal vulnerabilities in cancer cells has provided an alternative approach to exploiting more of the genetic and epigenetic changes acquired during tumorigenesis. Here, we review synthetic lethality as a therapeutic concept that exploits the inherent differences between normal cells and cancer cells. Furthermore, we provide an overview of the screening approaches that can be used to identify synthetic lethal interactions in human cells and present several recently identified interactions that may be pharmacologically exploited. Finally, we indicate some of the challenges of translating synthetic lethal interactions into the clinic and how these may be overcome.
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Affiliation(s)
- Ferran Fece de la Cruz
- CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences, A1090 Vienna, Austria;
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49
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Canaani D. Application of the concept synthetic lethality toward anticancer therapy: A promise fulfilled? Cancer Lett 2014; 352:59-65. [DOI: 10.1016/j.canlet.2013.08.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/02/2013] [Accepted: 08/12/2013] [Indexed: 11/24/2022]
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Hart T, Brown KR, Sircoulomb F, Rottapel R, Moffat J. Measuring error rates in genomic perturbation screens: gold standards for human functional genomics. Mol Syst Biol 2014; 10:733. [PMID: 24987113 PMCID: PMC4299491 DOI: 10.15252/msb.20145216] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Technological advancement has opened the door to systematic genetics in mammalian cells.
Genome-scale loss-of-function screens can assay fitness defects induced by partial gene knockdown,
using RNA interference, or complete gene knockout, using new CRISPR techniques. These screens can
reveal the basic blueprint required for cellular proliferation. Moreover, comparing healthy to
cancerous tissue can uncover genes that are essential only in the tumor; these genes are targets for
the development of specific anticancer therapies. Unfortunately, progress in this field has been
hampered by off-target effects of perturbation reagents and poorly quantified error rates in
large-scale screens. To improve the quality of information derived from these screens, and to
provide a framework for understanding the capabilities and limitations of CRISPR technology, we
derive gold-standard reference sets of essential and nonessential genes, and provide a Bayesian
classifier of gene essentiality that outperforms current methods on both RNAi and CRISPR screens.
Our results indicate that CRISPR technology is more sensitive than RNAi and that both techniques
have nontrivial false discovery rates that can be mitigated by rigorous analytical methods.
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Affiliation(s)
- Traver Hart
- Donnelly Centre and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
| | - Kevin R Brown
- Donnelly Centre and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
| | - Fabrice Sircoulomb
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, ON, Canada
| | - Robert Rottapel
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, ON, Canada Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada Division of Rheumatology, Department of Medicine, St. Michael's Hospital, Toronto, ON, Canada
| | - Jason Moffat
- Donnelly Centre and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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