1
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Bagnyukova T, Egleston BL, Pavlov VA, Serebriiskii IG, Golemis EA, Borghaei H. Synergy of EGFR and AURKA Inhibitors in KRAS-mutated Non-small Cell Lung Cancers. CANCER RESEARCH COMMUNICATIONS 2024; 4:1227-1239. [PMID: 38639476 PMCID: PMC11078142 DOI: 10.1158/2767-9764.crc-23-0482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/29/2024] [Accepted: 04/16/2024] [Indexed: 04/20/2024]
Abstract
The most common oncogenic driver mutations for non-small cell lung cancer (NSCLC) activate EGFR or KRAS. Clinical trials exploring treatments for EGFR- or KRAS-mutated (EGFRmut or KRASmut) cancers have focused on small-molecule inhibitors targeting the driver mutations. Typically, these inhibitors perform more effectively based on combination with either chemotherapies, or other targeted therapies. For EGFRmut NSCLC, a combination of inhibitors of EGFR and Aurora-A kinase (AURKA), an oncogene commonly overexpressed in solid tumors, has shown promising activity in clinical trials. Interestingly, a number of recent studies have indicated that EGFR activity supports overall viability of tumors lacking EGFR mutations, and AURKA expression is abundant in KRASmut cell lines. In this study, we have evaluated dual inhibition of EGFR and AURKA in KRASmut NSCLC models. These data demonstrate synergy between the EGFR inhibitor erlotinib and the AURKA inhibitor alisertib in reducing cell viability and clonogenic capacity in vitro, associated with reduced activity of EGFR pathway effectors, accumulation of enhanced aneuploid cell populations, and elevated cell death. Importantly, the erlotinib-alisertib combination also synergistically reduces xenograft growth in vivo. Analysis of signaling pathways demonstrated that the combination of erlotinib and alisertib was more effective than single-agent treatments at reducing activity of EGFR and pathway effectors following either brief or extended administration of the drugs. In sum, this study indicates value of inhibiting EGFR in KRASmut NSCLC, and suggests the specific value of dual inhibition of AURKA and EGFR in these tumors. SIGNIFICANCE The introduction of specific KRAS G12C inhibitors to the clinical practice in lung cancer has opened up opportunities that did not exist before. However, G12C alterations are only a subtype of all KRAS mutations observed. Given the high expression of AURKA in KRASmut NSCLC, our study could point to a potential therapeutic option for this subgroup of patients.
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Affiliation(s)
- Tetyana Bagnyukova
- Program in Cell Signaling and Metastasis, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Brian L. Egleston
- Program in Cell Signaling and Metastasis, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Valerii A. Pavlov
- Program in Cell Signaling and Metastasis, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Ilya G. Serebriiskii
- Program in Cell Signaling and Metastasis, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Kazan Federal University, Kazan, Russian Federation
| | - Erica A. Golemis
- Program in Cell Signaling and Metastasis, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Hossein Borghaei
- Program in Cell Signaling and Metastasis, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Division of Thoracic Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
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2
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Tuo H, Li X, Du H, Li M, Xu C, Yu Z, Zhao H. FOLR1-stabilized β-catenin promotes laryngeal carcinoma progression through EGFR/AKT/GSK-3β pathway. Mol Carcinog 2024; 63:34-44. [PMID: 37702010 DOI: 10.1002/mc.23634] [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: 04/21/2023] [Revised: 08/21/2023] [Accepted: 09/06/2023] [Indexed: 09/14/2023]
Abstract
Folate receptor 1 (FOLR1) is overexpressed in numerous epithelial malignancies; however, its role in laryngeal squamous cell carcinoma (LSCC) remains unclear. In the present study, we demonstrated that FOLR1 messenger RNA and protein expression levels were higher in LSCC tissues than in the adjacent normal tissues. Additionally, FOLR1 promoted the proliferation and migration of LSCC cells, whereas small interfering RNA-mediated knockdown of β-catenin abolished these effects. Moreover, FOLR1 stabilizes β-catenin by inhibiting its ubiquitination and degradation. Furthermore, blocking the interaction between epidermal growth factor receptor (EGFR) and the EGFR/AKT/glycogen synthase (GSK)3β signaling axis both abolished FOLR1's effects on the expression and nuclear aggregation of β-catenin. In summary, our work reveals a novel mode in which FOLR1 promotes the proliferation and migration of LSCC by enhancing the stability and nuclear translocation of β-catenin through the EGFR/AKT/GSK3β axis.
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Affiliation(s)
- Huawei Tuo
- Department of Otolaryngology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Xuemei Li
- Department of Dermatology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Haixia Du
- Department of Otolaryngology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Man Li
- Department of Otolaryngology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Chenli Xu
- Department of Pathology, School of Basic Medical Science, Hubei University of Medicine, Shiyan, China
| | - Zizhong Yu
- Department of Otolaryngology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Huzi Zhao
- Department of Pathology, School of Basic Medical Science, Hubei University of Medicine, Shiyan, China
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3
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Tang S, Roberts RD, Cheng L, Li L. Osteosarcoma Multi-Omics Landscape and Subtypes. Cancers (Basel) 2023; 15:4970. [PMID: 37894336 PMCID: PMC10605601 DOI: 10.3390/cancers15204970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/12/2023] [Accepted: 09/17/2023] [Indexed: 10/29/2023] Open
Abstract
Osteosarcoma (OS) is the most common primary bone malignancy that exhibits remarkable histologic diversity and genetic heterogeneity. The complex nature of osteosarcoma has confounded precise molecular categorization, prognosis, and prediction for this disease. In this study, we performed a comprehensive multiplatform analysis on 86 osteosarcoma tumors, including somatic copy-number alteration, gene expression and methylation, and identified three molecularly distinct and clinically relevant subtypes of osteosarcoma. The subgrouping criteria was validated on another cohort of osteosarcoma tumors. Previously unappreciated osteosarcoma-type-specific changes in specific genes' copy number, expression and methylation were revealed based on the subgrouping. The subgrouping and novel gene signatures provide insights into refining osteosarcoma therapy and relationships to other types of cancer.
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Affiliation(s)
- Shan Tang
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Ryan D. Roberts
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Lijun Cheng
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Lang Li
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
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4
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Discovery of synthetic lethal interactions from large-scale pan-cancer perturbation screens. Nat Commun 2022; 13:7748. [PMID: 36517508 PMCID: PMC9751287 DOI: 10.1038/s41467-022-35378-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
The development of cancer therapies is limited by the availability of suitable drug targets. Potential candidate drug targets can be identified based on the concept of synthetic lethality (SL), which refers to pairs of genes for which an aberration in either gene alone is non-lethal, but co-occurrence of the aberrations is lethal to the cell. Here, we present SLIdR (Synthetic Lethal Identification in R), a statistical framework for identifying SL pairs from large-scale perturbation screens. SLIdR successfully predicts SL pairs even with small sample sizes while minimizing the number of false positive targets. We apply SLIdR to Project DRIVE data and find both established and potential pan-cancer and cancer type-specific SL pairs consistent with findings from literature and drug response screening data. We experimentally validate two predicted SL interactions (ARID1A-TEAD1 and AXIN1-URI1) in hepatocellular carcinoma, thus corroborating the ability of SLIdR to identify potential drug targets.
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5
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Tang S, Gökbağ B, Fan K, Shao S, Huo Y, Wu X, Cheng L, Li L. Synthetic lethal gene pairs: Experimental approaches and predictive models. Front Genet 2022; 13:961611. [PMID: 36531238 PMCID: PMC9751344 DOI: 10.3389/fgene.2022.961611] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 11/07/2022] [Indexed: 03/27/2024] Open
Abstract
Synthetic lethality (SL) refers to a genetic interaction in which the simultaneous perturbation of two genes leads to cell or organism death, whereas viability is maintained when only one of the pair is altered. The experimental exploration of these pairs and predictive modeling in computational biology contribute to our understanding of cancer biology and the development of cancer therapies. We extensively reviewed experimental technologies, public data sources, and predictive models in the study of synthetic lethal gene pairs and herein detail biological assumptions, experimental data, statistical models, and computational schemes of various predictive models, speculate regarding their influence on individual sample- and population-based synthetic lethal interactions, discuss the pros and cons of existing SL data and models, and highlight potential research directions in SL discovery.
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Affiliation(s)
- Shan Tang
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Birkan Gökbağ
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Kunjie Fan
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Shuai Shao
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Yang Huo
- Indiana University, Bloomington, IN, United States
| | - Xue Wu
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Lijun Cheng
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, United States
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6
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Proteogenomic analysis of lung adenocarcinoma reveals tumor heterogeneity, survival determinants, and therapeutically relevant pathways. Cell Rep Med 2022; 3:100819. [PMID: 36384096 PMCID: PMC9729884 DOI: 10.1016/j.xcrm.2022.100819] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/09/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022]
Abstract
We present a deep proteogenomic profiling study of 87 lung adenocarcinoma (LUAD) tumors from the United States, integrating whole-genome sequencing, transcriptome sequencing, proteomics and phosphoproteomics by mass spectrometry, and reverse-phase protein arrays. We identify three subtypes from somatic genome signature analysis, including a transition-high subtype enriched with never smokers, a transversion-high subtype enriched with current smokers, and a structurally altered subtype enriched with former smokers, TP53 alterations, and genome-wide structural alterations. We show that within-tumor correlations of RNA and protein expression associate with tumor purity and immune cell profiles. We detect and independently validate expression signatures of RNA and protein that predict patient survival. Additionally, among co-measured genes, we found that protein expression is more often associated with patient survival than RNA. Finally, integrative analysis characterizes three expression subtypes with divergent mutations, proteomic regulatory networks, and therapeutic vulnerabilities. This proteogenomic characterization provides a foundation for molecularly informed medicine in LUAD.
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7
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Tikhomirova M, Topchu I, Mazitova A, Barmin V, Ratner E, Sabirov A, Abramova Z, Deneka AY. NEDD9 Restrains dsDNA Damage Response during Non-Small Cell Lung Cancer (NSCLC) Progression. Cancers (Basel) 2022; 14:2517. [PMID: 35626121 PMCID: PMC9139181 DOI: 10.3390/cancers14102517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/05/2022] [Accepted: 05/18/2022] [Indexed: 12/10/2022] Open
Abstract
DNA damaging modalities are the backbone of treatments for non-small cell lung cancer (NSCLC). Alterations in DNA damage response (DDR) in tumor cells commonly contribute to emerging resistance to platinating agents, other targeted therapies, and radiation. The goal of this study is to identify the previously unreported role of NEDD9 scaffolding protein in controlling DDR processes and sensitivity to DNA damaging therapies. Using a siRNA-mediated approach to deplete NEDD9 in a group of human and murine KRAS/TP53-mutant NSCLC cell lines, coupled with a set of cell viability and clonogenic assays, flow cytometry analysis, and Western blotting, we evaluated the effects of NEDD9 silencing on cellular proliferation, DDR and epithelial-to-mesenchymal transition (EMT) signaling, cell cycle, and sensitivity to cisplatin and UV irradiation. Using publicly available NSCLC datasets (TCGA) and an independent cohort of primary NSCLC tumors, subsequent in silico and immunohistochemical (IHC) analyses were performed to assess relevant changes in NEDD9 RNA and protein expression across different stages of NSCLC. The results of our study demonstrate that NEDD9 depletion is associated with the increased tumorigenic capacity of NSCLC cells. These phenotypes were accompanied by significantly upregulated ATM-CHK2 signaling, shifting towards a more mesenchymal phenotype in NEDD9 depleted cells and elevated sensitivity to UV-irradiation. IHC analyses revealed an association between reduced NEDD9 protein expression and a decrease in overall (OS) and progression-free survival (PFS) of the NSCLC patients. These data, for the first time, identified NEDD9 as a negative regulator of ATM kinase activity and related DDR signaling in numerous KRAS/TP53 mutated NSCLC, with its effects on the regulation of DDR-dependent EMT signaling, sensitivity to DNA damaging modalities in tumor cells, and the survival of the patients.
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Affiliation(s)
- Mariya Tikhomirova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420000 Kazan, Russia; (M.T.); (I.T.); (A.M.); (Z.A.)
| | - Iuliia Topchu
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420000 Kazan, Russia; (M.T.); (I.T.); (A.M.); (Z.A.)
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60610, USA
| | - Aleksandra Mazitova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420000 Kazan, Russia; (M.T.); (I.T.); (A.M.); (Z.A.)
- Department of Medicine and Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Vitaly Barmin
- Moscow P.A. Gertsen Oncological Research Institute, 125284 Moscow, Russia;
| | - Ekaterina Ratner
- Republican M.Z.Sigal Clinical Oncology Hospital, 420029 Kazan, Russia; (E.R.); (A.S.)
| | - Alexey Sabirov
- Republican M.Z.Sigal Clinical Oncology Hospital, 420029 Kazan, Russia; (E.R.); (A.S.)
| | - Zinaida Abramova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420000 Kazan, Russia; (M.T.); (I.T.); (A.M.); (Z.A.)
| | - Alexander Y. Deneka
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420000 Kazan, Russia; (M.T.); (I.T.); (A.M.); (Z.A.)
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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8
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Komatsu M, Nakamura K, Takeda T, Chiwaki F, Banno K, Aoki D, Takeshita F, Sasaki H. Aurora kinase blockade drives de novo addiction of cervical squamous cell carcinoma to druggable EGFR signalling. Oncogene 2022; 41:2326-2339. [DOI: 10.1038/s41388-022-02256-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/08/2022] [Accepted: 02/17/2022] [Indexed: 12/24/2022]
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9
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Ex vivo organotypic cultures for synergistic therapy prioritization identify patient-specific responses to combined MEK and Src inhibition in colorectal cancer. NATURE CANCER 2022; 3:219-231. [PMID: 35145327 DOI: 10.1038/s43018-021-00325-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 12/10/2021] [Indexed: 12/22/2022]
Abstract
Translating preclinical studies to effective treatment protocols and identifying specific therapeutic responses in individuals with cancer is challenging. This may arise due to the complex genetic makeup of tumor cells and the impact of their multifaceted tumor microenvironment on drug response. To find new clinically relevant drug combinations for colorectal cancer (CRC), we prioritized the top five synergistic combinations from a large in vitro screen for ex vivo testing on 29 freshly resected human CRC tumors and found that only the combination of mitogen-activated protein kinase kinase (MEK) and proto-oncogene tyrosine-protein kinase Src (Src) inhibition was effective when tested ex vivo. Pretreatment phosphorylated Src (pSrc) was identified as a predictive biomarker for MEK and Src inhibition only in the absence of KRASG12 mutations. Overall, we demonstrate the potential of using ex vivo platforms to identify drug combinations and discover MEK and Src dual inhibition as an effective drug combination in a predefined subset of individuals with CRC.
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10
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Jain AP, Radhakrishnan A, Pinto S, Patel K, Kumar M, Nanjappa V, Raja R, Keshava Prasad TS, Mathur PP, Sidransky D, Chatterjee A, Gowda H. How to Achieve Therapeutic Response in Erlotinib-Resistant Head and Neck Squamous Cell Carcinoma? New Insights from Stable Isotope Labeling with Amino Acids in Cell Culture-Based Quantitative Tyrosine Phosphoproteomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:605-616. [PMID: 34432535 DOI: 10.1089/omi.2021.0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Resistance to cancer chemotherapy is a major global health burden. Epidermal growth factor receptor (EGFR) is a proven therapeutic target for multiple cancers of epithelial origin. Despite its overexpression in >90% of head and neck squamous cell carcinoma (HNSCC) patients, tyrosine kinase inhibitors such as erlotinib have shown a modest response in clinical trials. Cellular heterogeneity is thought to play an important role in HNSCC therapeutic resistance. Genomic alterations alone cannot explain all resistance mechanisms at play in a heterogeneous system. It is thus important to understand the biochemical mechanisms associated with drug resistance to determine potential strategies to achieve clinical response. We investigated tyrosine kinase signaling networks in erlotinib-resistant cells using quantitative tyrosine phosphoproteomics approach. We observed altered phosphorylation of proteins involved in cell adhesion and motility in erlotinib-resistant cells. Bioinformatics analysis revealed enrichment of pathways related to regulation of the actin cytoskeleton, extracellular matrix (ECM)-receptor interaction, and endothelial migration. Of importance, enrichment of the focal adhesion kinase (PTK2) signaling pathway downstream of EGFR was also observed in erlotinib-resistant cells. To the best of our knowledge, we present the first report of tyrosine phosphoproteome profiling in erlotinib-resistant HNSCC, with an eye to inform new ways to achieve clinical response. Our findings suggest that common signaling networks are at play in driving resistance to EGFR-targeted therapies in HNSCC and other cancers. Most notably, our data suggest that the PTK2 pathway genes may potentially play a significant role in determining clinical response to erlotinib in HNSCC tumors.
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Affiliation(s)
- Ankit P Jain
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, India
| | | | - Sneha Pinto
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Krishna Patel
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Manish Kumar
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | | | - Remya Raja
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Premendu P Mathur
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, India.,Department of Biochemistry & Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery; Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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11
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Cui X, Han L, Liu Y, Li Y, Sun W, Song B, Zhou W, Zhang Y, Wang H. siGCD: a web server to explore survival interaction of genes, cells and drugs in human cancers. Brief Bioinform 2021; 22:6210070. [PMID: 33822887 DOI: 10.1093/bib/bbab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/19/2021] [Accepted: 02/12/2021] [Indexed: 11/13/2022] Open
Abstract
It is pivotal and remains challenge for cancer precision treatment to identify the survival outcome interactions between genes, cells and drugs. Here, we present siGCD, a web-based tool for analysis and visualization of the survival interaction of Genes, Cells and Drugs in human cancers. siGCD utilizes the cancer heterogeneity to simulate the manipulated gene expression, cell infiltration and drug treatment, which overcomes the data and experimental limitations. To illustrate the performance of siGCD, we identified the survival interaction partners of EGFR (gene level), T cells (cell level) and sorafenib (drug level), and our prediction was consistent with previous reports. Moreover, we validate the synergistic effect of regorafenib and glyburide, and found that glyburide could significantly improve the regorafenib response. These results demonstrate that siGCD could benefit cancer precision medicine in a wide range of advantageous application scenarios including gene regulatory network construction, immune cell regulatory gene identification, drug (especially multiple target drugs) response biomarker screening and combination therapeutic design.
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Affiliation(s)
- XiuLiang Cui
- National Center for Liver Cancer, the Second Military Medical University, Shanghai 200438, China
| | - Lu Han
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing China
| | - Yang Liu
- Institute for Hepatology, The Second Affiliated Hospital, South University of Science and Technology, 29 Bulan Road, Longgang District, Shenzhen 518112, China
| | - Ying Li
- Department of Pharmacy, Eastern Hepatobiliary Surgery Hospital, the Second Military Medical University, Shanghai 200438, China
| | - Wen Sun
- National Center for Liver Cancer, the Second Military Medical University, Shanghai 200438, China
| | - Bin Song
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200438, China
| | - Wenxia Zhou
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing China
| | - Yongxiang Zhang
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing China
| | - Hongyang Wang
- National Center for Liver Cancer, the Second Military Medical University, Shanghai 200438, China.,International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University, 200438, Shanghai, China
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12
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Abbas N, Swamy PMG, Dhiwar P, Patel S, Giles D. Development of Fused and Substituted Pyrimidine Derivatives as Potent Anticancer Agents (A Review). Pharm Chem J 2021. [DOI: 10.1007/s11094-021-02346-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Cooperative Blockade of CK2 and ATM Kinases Drives Apoptosis in VHL-Deficient Renal Carcinoma Cells through ROS Overproduction. Cancers (Basel) 2021; 13:cancers13030576. [PMID: 33540838 PMCID: PMC7867364 DOI: 10.3390/cancers13030576] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Renal cell carcinoma (RCC) is the eighth leading malignancy in the world, accounting for 4% of all cancers with poor outcome when metastatic. Protein kinases are highly druggable proteins, which are often aberrantly activated in cancers. The aim of our study was to identify candidate targets for metastatic clear cell renal cell carcinoma therapy, using chemo-genomic-based high-throughput screening. We found that the combined inhibition of the CK2 and ATM kinases in renal tumor cells and patient-derived tumor samples induces synthetic lethality. Mechanistic investigations unveil that this drug combination triggers apoptosis through HIF-2α-(Hypoxic inducible factor HIF-2α) dependent reactive oxygen species (ROS) overproduction, giving a new option for patient care in metastatic RCC. Abstract Kinase-targeted agents demonstrate antitumor activity in advanced metastatic clear cell renal cell carcinoma (ccRCC), which remains largely incurable. Integration of genomic approaches through small-molecules and genetically based high-throughput screening holds the promise of improved discovery of candidate targets for cancer therapy. The 786-O cell line represents a model for most ccRCC that have a loss of functional pVHL (von Hippel-Lindau). A multiplexed assay was used to study the cellular fitness of a panel of engineered ccRCC isogenic 786-O VHL− cell lines in response to a collection of targeted cancer therapeutics including kinase inhibitors, allowing the interrogation of over 2880 drug–gene pairs. Among diverse patterns of drug sensitivities, investigation of the mechanistic effect of one selected drug combination on tumor spheroids and ex vivo renal tumor slice cultures showed that VHL-defective ccRCC cells were more vulnerable to the combined inhibition of the CK2 and ATM kinases than wild-type VHL cells. Importantly, we found that HIF-2α acts as a key mediator that potentiates the response to combined CK2/ATM inhibition by triggering ROS-dependent apoptosis. Importantly, our findings reveal a selective killing of VHL-deficient renal carcinoma cells and provide a rationale for a mechanism-based use of combined CK2/ATM inhibitors for improved patient care in metastatic VHL-ccRCC.
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14
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Broyde J, Simpson DR, Murray D, Paull EO, Chu BW, Tagore S, Jones SJ, Griffin AT, Giorgi FM, Lachmann A, Jackson P, Sweet-Cordero EA, Honig B, Califano A. Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses. Nat Biotechnol 2021; 39:215-224. [PMID: 32929263 PMCID: PMC7878435 DOI: 10.1038/s41587-020-0652-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/23/2020] [Indexed: 02/08/2023]
Abstract
Tumor-specific elucidation of physical and functional oncoprotein interactions could improve tumorigenic mechanism characterization and therapeutic response prediction. Current interaction models and pathways, however, lack context specificity and are not oncoprotein specific. We introduce SigMaps as context-specific networks, comprising modulators, effectors and cognate binding-partners of a specific oncoprotein. SigMaps are reconstructed de novo by integrating diverse evidence sources-including protein structure, gene expression and mutational profiles-via the OncoSig machine learning framework. We first generated a KRAS-specific SigMap for lung adenocarcinoma, which recapitulated published KRAS biology, identified novel synthetic lethal proteins that were experimentally validated in three-dimensional spheroid models and established uncharacterized crosstalk with RAB/RHO. To show that OncoSig is generalizable, we first inferred SigMaps for the ten most mutated human oncoproteins and then for the full repertoire of 715 proteins in the COSMIC Cancer Gene Census. Taken together, these SigMaps show that the cell's regulatory and signaling architecture is highly tissue specific.
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Affiliation(s)
- Joshua Broyde
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - David R Simpson
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, UCSF Benioff Children's Hospital, San Francisco, CA, USA
| | - Diana Murray
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Evan O Paull
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Brennan W Chu
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Somnath Tagore
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sunny J Jones
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aaron T Griffin
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Federico M Giorgi
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Alexander Lachmann
- Mount Sinai Center for Bioinformatics; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peter Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University, Palo Alto, CA, USA
- Department of Pathology, Stanford University, Palo Alto, CA, USA
| | - E Alejandro Sweet-Cordero
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, UCSF Benioff Children's Hospital, San Francisco, CA, USA.
| | - Barry Honig
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
- Department of Medicine, Columbia University, New York, NY, USA.
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA.
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
- Department of Medicine, Columbia University, New York, NY, USA.
- JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Motor Neuron Center and Columbia Initiative in Stem Cells, Columbia University, New York, NY, USA.
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15
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Caston RA, Shah F, Starcher CL, Wireman R, Babb O, Grimard M, McGeown J, Armstrong L, Tong Y, Pili R, Rupert J, Zimmers TA, Elmi AN, Pollok KE, Motea EA, Kelley MR, Fishel ML. Combined inhibition of Ref-1 and STAT3 leads to synergistic tumour inhibition in multiple cancers using 3D and in vivo tumour co-culture models. J Cell Mol Med 2021; 25:784-800. [PMID: 33274592 PMCID: PMC7812272 DOI: 10.1111/jcmm.16132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/19/2020] [Accepted: 11/09/2020] [Indexed: 12/26/2022] Open
Abstract
With a plethora of molecularly targeted agents under investigation in cancer, a clear need exists to understand which pathways can be targeted simultaneously with multiple agents to elicit a maximal killing effect on the tumour. Combination therapy provides the most promise in difficult to treat cancers such as pancreatic. Ref-1 is a multifunctional protein with a role in redox signalling that activates transcription factors such as NF-κB, AP-1, HIF-1α and STAT3. Formerly, we have demonstrated that dual targeting of Ref-1 (redox factor-1) and STAT3 is synergistic and decreases cell viability in pancreatic cancer cells. Data presented here extensively expands upon this work and provides further insights into the relationship of STAT3 and Ref-1 in multiple cancer types. Using targeted small molecule inhibitors, Ref-1 redox signalling was blocked along with STAT3 activation, and tumour growth evaluated in the presence and absence of the relevant tumour microenvironment. Our study utilized qPCR, cytotoxicity and in vivo analysis of tumour and cancer-associated fibroblasts (CAF) response to determine the synergy of Ref-1 and STAT3 inhibitors. Overall, pancreatic tumours grown in the presence of CAFs were sensitized to the combination of STAT3 and Ref-1 inhibition in vivo. In vitro bladder and pancreatic cancer demonstrated the most synergistic responses. By disabling both of these important pathways, this combination therapy has the capacity to hinder crosstalk between the tumour and its microenvironment, leading to improved tumour response.
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Affiliation(s)
- Rachel A. Caston
- Department of Pediatrics and Herman B Wells Center for Pediatric ResearchIndiana University School of MedicineIndianapolisINUSA
| | - Fenil Shah
- Department of Pediatrics and Herman B Wells Center for Pediatric ResearchIndiana University School of MedicineIndianapolisINUSA
| | - Colton L. Starcher
- Department of Biochemistry and Molecular BiologyIndiana University School of MedicineIndianapolisINUSA
| | - Randall Wireman
- Department of Pediatrics and Herman B Wells Center for Pediatric ResearchIndiana University School of MedicineIndianapolisINUSA
| | - Olivia Babb
- Department of Pediatrics and Herman B Wells Center for Pediatric ResearchIndiana University School of MedicineIndianapolisINUSA
| | - Michelle Grimard
- Department of Pediatrics and Herman B Wells Center for Pediatric ResearchIndiana University School of MedicineIndianapolisINUSA
| | - Jack McGeown
- Department of Pediatrics and Herman B Wells Center for Pediatric ResearchIndiana University School of MedicineIndianapolisINUSA
| | - Lee Armstrong
- Department of Pediatrics and Herman B Wells Center for Pediatric ResearchIndiana University School of MedicineIndianapolisINUSA
| | - Yan Tong
- Department of BiostatisticsIndiana University School of MedicineIndianapolisINUSA
| | - Roberto Pili
- Department of Pharmacology and ToxicologyIndiana University School of MedicineIndianapolisINUSA
- Department of UrologyIndiana University School of MedicineIndianapolisINUSA
- Department of Hematology and OncologyIndiana University School of MedicineIndianapolisINUSA
- Indiana University Simon Comprehensive Cancer CenterIndiana University School of MedicineIndianapolisINUSA
| | - Joseph Rupert
- Department of Biochemistry and Molecular BiologyIndiana University School of MedicineIndianapolisINUSA
- Indiana University Simon Comprehensive Cancer CenterIndiana University School of MedicineIndianapolisINUSA
- Department of SurgeryIndiana University School of MedicineIndianapolisINUSA
| | - Teresa A. Zimmers
- Department of Biochemistry and Molecular BiologyIndiana University School of MedicineIndianapolisINUSA
- Indiana University Simon Comprehensive Cancer CenterIndiana University School of MedicineIndianapolisINUSA
- Department of SurgeryIndiana University School of MedicineIndianapolisINUSA
- Richard L. Roudebush Veterans Administration Medical CenterIndianapolisINUSA
| | - Adily N. Elmi
- Department of Pediatrics and Herman B Wells Center for Pediatric ResearchIndiana University School of MedicineIndianapolisINUSA
| | - Karen E. Pollok
- Department of Pediatrics and Herman B Wells Center for Pediatric ResearchIndiana University School of MedicineIndianapolisINUSA
- Department of Pharmacology and ToxicologyIndiana University School of MedicineIndianapolisINUSA
- Indiana University Simon Comprehensive Cancer CenterIndiana University School of MedicineIndianapolisINUSA
| | - Edward A. Motea
- Department of Biochemistry and Molecular BiologyIndiana University School of MedicineIndianapolisINUSA
- Indiana University Simon Comprehensive Cancer CenterIndiana University School of MedicineIndianapolisINUSA
| | - Mark R. Kelley
- Department of Pediatrics and Herman B Wells Center for Pediatric ResearchIndiana University School of MedicineIndianapolisINUSA
- Department of Biochemistry and Molecular BiologyIndiana University School of MedicineIndianapolisINUSA
- Department of Pharmacology and ToxicologyIndiana University School of MedicineIndianapolisINUSA
- Indiana University Simon Comprehensive Cancer CenterIndiana University School of MedicineIndianapolisINUSA
| | - Melissa L. Fishel
- Department of Pediatrics and Herman B Wells Center for Pediatric ResearchIndiana University School of MedicineIndianapolisINUSA
- Department of Pharmacology and ToxicologyIndiana University School of MedicineIndianapolisINUSA
- Indiana University Simon Comprehensive Cancer CenterIndiana University School of MedicineIndianapolisINUSA
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16
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Lin CC, Huang YK, Cho CF, Lin YS, Lo CC, Kuo TT, Tseng GC, Cheng WC, Chang WC, Hsiao TH, Lai LC, Shih JY, Liu YH, Chao KC, Hsu JL, Lee PC, Sun X, Hung MC, Sher YP. Targeting positive feedback between BASP1 and EGFR as a therapeutic strategy for lung cancer progression. Theranostics 2020; 10:10925-10939. [PMID: 33042262 PMCID: PMC7532684 DOI: 10.7150/thno.49425] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023] Open
Abstract
Rationale: Brain metastasis in patients with lung cancer is life-threatening. However, the molecular mechanism for this catastrophic disease remains elusive, and few druggable targets are available. Therefore, this study aimed to identify and characterize proteins that could be used as therapeutic targets. Methods: Proteomic analyses were conducted to identify differentially expressed membrane proteins between brain metastatic lung cancer cells and primary lung cancer cells. A neuronal growth-associated protein, brain acid soluble protein 1 (BASP1), was chosen for further investigation. The clinical relevance of BASP1 in lung adenocarcinoma was first assessed. Tyrosine kinase activity assays and in vitro and in vivo functional assays were conducted to explore the oncogenic mechanisms of BASP1. Results: The protein levels of BASP1 were positively associated with tumor progression and poor prognosis in patients with lung adenocarcinoma. Membrane-bound BASP1 increased EGFR signaling and stabilized EGFR proteins by facilitating their escape from the ubiquitin-proteasome pathway. Reciprocally, activation of EGFR recruited more BASP1 to the plasma membrane, generating a positive feedback loop between BASP1 and EGFR. Moreover, the synergistic therapeutic effects of EGFR tyrosine kinase inhibitor and arsenic trioxide led to a reduction in the level of BASP1 protein observed in lung cancer cells with acquired resistance to EGFR inhibitors. Conclusions: The reciprocal interaction between BASP1 and EGFR facilitates EGFR signaling in brain metastatic lung cancer. Targeting the newly identified BASP1-EGFR interaction could open new venues for lung cancer treatment.
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17
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Wei R, Wang Z, Zhang Y, Wang B, Shen N, E L, Li X, Shang L, Shang Y, Yan W, Zhang X, Ma W, Wang C. Bioinformatic analysis revealing mitotic spindle assembly regulated NDC80 and MAD2L1 as prognostic biomarkers in non-small cell lung cancer development. BMC Med Genomics 2020; 13:112. [PMID: 32795325 PMCID: PMC7437940 DOI: 10.1186/s12920-020-00762-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 08/04/2020] [Indexed: 01/08/2023] Open
Abstract
Background Lung cancer has been the leading cause of tumor related death, and 80% ~ 85% of it is non-small cell lung cancer (NSCLC). Even with the rising molecular targeted therapies, for example EGFR, ROS1 and ALK, the treatment is still challenging. The study is to identify credible responsible genes during the development of NSCLC using bioinformatic analysis, developing new prognostic biomarkers and potential gene targets to the disease. Methods Firstly, three genes expression profiles GSE44077, GSE18842 and GSE33532 were picked from Gene Expression Omnibus (GEO) to analyze the genes with different expression level (GDEs) between NSCLC and normal lung samples, and the cellular location, molecular function and the biology pathways the GDEs enriched in were analyzed. Then, gene function modules of GDEs were explored based on the protein-protein interaction network (PPI), and the top module which contains most genes was identified, followed by containing genes annotation and survival analysis. Moreover, multivariate cox regression analysis was performed in addition to the Kaplan meier survival to narrow down the key genes scale. Further, the clinical pathological features of the picked key genes were explored using TCGA data. Results Three GEO profiles shared a total of 664 GDEs, including 232 up-regulated and 432 down-regulated genes. Based on the GDEs PPI network, the top function module containing a total of 69 genes was identified, and 31 of 69 genes were mitotic cell cycle regulation related. And survival analysis of the 31 genes revealed that 17/31 genes statistical significantly related to NSCLC overall survival, including 4 spindle assembly checkpoints, namely NDC80, BUB1B, MAD2L1 and AURKA. Further, multivariate cox regression analysis identified NDC80 and MAD2L1 as independent prognostic indicators in lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) respectively. Interestingly, pearson correlation analysis indicated strong connection between the four genes NDC80, BUB1B, MAD2L1 and AURKA, and their clinical pathological features were addressed. Conclusions Using bioinformatic analysis of GEO combined with TCGA data, we revealed two independent prognostic indicators in LUAD and LUSC respectively and analyzed their clinical features. However, more detailed experiments and clinical trials are needed to verify their drug targets role in clinical medical use.
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Affiliation(s)
- Rong Wei
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Ziyue Wang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Yaping Zhang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Bin Wang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Ningning Shen
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Li E
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Xin Li
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Lifang Shang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Yangwei Shang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Wenpeng Yan
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Xiaoqin Zhang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China
| | - Wenxia Ma
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China.
| | - Chen Wang
- Department of Pathology, The Second Hospital of ShanXi Medical University, No.382 WuYi Road, Tai Yuan City, 030000, ShanXi Province, China.
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18
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RNA interference screening methods to identify proliferation determinants and mechanisms of resistance to immune attack. Methods Enzymol 2020; 636:299-322. [PMID: 32178823 DOI: 10.1016/bs.mie.2019.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
We have used RNA interference (RNAi) screening technology to reveal unknown components of biological signaling pathways including survival mechanisms of estrogen-independent breast cancer cell growth and cancer cell resistance to immune attack. In this chapter, a detailed protocol describing the use of RNAi screening to identify factors important for the proliferation of estrogen-independent MCF7 breast cancer cells will be described. Resistance to therapies that target the estrogen pathway remains a challenge in the treatment of estrogen receptor-positive breast cancer. To address this challenge, small interfering-RNA (siRNA)-based libraries targeting an estrogen receptor (ER)- and aromatase-centered network, including 631 genes relevant to estrogen signaling, was designed and constructed for RNAi screening. This protocol will include the following parts: (1) selection of RNAi transfection reagent for specific cells; (2) optimization of RNAi screening conditions using Z'-factor; (3) procedure of ER-network gene siRNA library screening using automated machines under optimized experimental conditions; and (4) method of analysis for RNAi screening data to identify specific determinants important for cell proliferation. 46 genes were found to be selectively required for the survival of estrogen-independent MCF7-derived cells.
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19
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Labots M, Pham TV, Honeywell RJ, Knol JC, Beekhof R, de Goeij-de Haas R, Dekker H, Neerincx M, Piersma SR, van der Mijn JC, van der Peet DL, Meijerink MR, Peters GJ, van Grieken NC, Jiménez CR, Verheul HM. Kinase Inhibitor Treatment of Patients with Advanced Cancer Results in High Tumor Drug Concentrations and in Specific Alterations of the Tumor Phosphoproteome. Cancers (Basel) 2020; 12:cancers12020330. [PMID: 32024067 PMCID: PMC7072422 DOI: 10.3390/cancers12020330] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/20/2020] [Accepted: 01/29/2020] [Indexed: 12/22/2022] Open
Abstract
Identification of predictive biomarkers for targeted therapies requires information on drug exposure at the target site as well as its effect on the signaling context of a tumor. To obtain more insight in the clinical mechanism of action of protein kinase inhibitors (PKIs), we studied tumor drug concentrations of protein kinase inhibitors (PKIs) and their effect on the tyrosine-(pTyr)-phosphoproteome in patients with advanced cancer. Tumor biopsies were obtained from 31 patients with advanced cancer before and after 2 weeks of treatment with sorafenib (SOR), erlotinib (ERL), dasatinib (DAS), vemurafenib (VEM), sunitinib (SUN) or everolimus (EVE). Tumor concentrations were determined by LC-MS/MS. pTyr-phosphoproteomics was performed by pTyr-immunoprecipitation followed by LC-MS/MS. Median tumor concentrations were 2–10 µM for SOR, ERL, DAS, SUN, EVE and >1 mM for VEM. These were 2–178 × higher than median plasma concentrations. Unsupervised hierarchical clustering of pTyr-phosphopeptide intensities revealed patient-specific clustering of pre- and on-treatment profiles. Drug-specific alterations of peptide phosphorylation was demonstrated by marginal overlap of robustly up- and downregulated phosphopeptides. These findings demonstrate that tumor drug concentrations are higher than anticipated and result in drug specific alterations of the phosphoproteome. Further development of phosphoproteomics-based personalized medicine is warranted.
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Affiliation(s)
- Mariette Labots
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Thang V. Pham
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Richard J. Honeywell
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Jaco C. Knol
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Robin Beekhof
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Richard de Goeij-de Haas
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Henk Dekker
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Maarten Neerincx
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Sander R. Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Johannes C. van der Mijn
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Donald L. van der Peet
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands;
| | - Martijn R. Meijerink
- Department of Radiology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands;
| | - Godefridus J. Peters
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
| | - Nicole C.T. van Grieken
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands;
| | - Connie R. Jiménez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands; (M.L.); (T.V.P.); (R.J.H.); (J.C.K.); (R.B.); (R.d.G.-d.H.); (H.D.); (M.N.); (S.R.P.); (J.C.v.d.M.); (G.J.P.)
- Correspondence: or (C.R.J.); (H.M.W.V.)
| | - Henk M.W. Verheul
- Department of Medical Oncology, RadboudUMC, Radboud University, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands
- Correspondence: or (C.R.J.); (H.M.W.V.)
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20
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Du J, Yan L, Torres R, Gong X, Bian H, Marugán C, Boehnke K, Baquero C, Hui YH, Chapman SC, Yang Y, Zeng Y, Bogner SM, Foreman RT, Capen A, Donoho GP, Van Horn RD, Barnard DS, Dempsey JA, Beckmann RP, Marshall MS, Chio LC, Qian Y, Webster YW, Aggarwal A, Chu S, Bhattachar S, Stancato LF, Dowless MS, Iversen PW, Manro JR, Walgren JL, Halstead BW, Dieter MZ, Martinez R, Bhagwat SV, Kreklau EL, Lallena MJ, Ye XS, Patel BKR, Reinhard C, Plowman GD, Barda DA, Henry JR, Buchanan SG, Campbell RM. Aurora A-Selective Inhibitor LY3295668 Leads to Dominant Mitotic Arrest, Apoptosis in Cancer Cells, and Shows Potent Preclinical Antitumor Efficacy. Mol Cancer Ther 2019; 18:2207-2219. [PMID: 31530649 DOI: 10.1158/1535-7163.mct-18-0529] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 04/29/2019] [Accepted: 09/06/2019] [Indexed: 11/16/2022]
Abstract
Although Aurora A, B, and C kinases share high sequence similarity, especially within the kinase domain, they function distinctly in cell-cycle progression. Aurora A depletion primarily leads to mitotic spindle formation defects and consequently prometaphase arrest, whereas Aurora B/C inactivation primarily induces polyploidy from cytokinesis failure. Aurora B/C inactivation phenotypes are also epistatic to those of Aurora A, such that the concomitant inactivation of Aurora A and B, or all Aurora isoforms by nonisoform-selective Aurora inhibitors, demonstrates the Aurora B/C-dominant cytokinesis failure and polyploidy phenotypes. Several Aurora inhibitors are in clinical trials for T/B-cell lymphoma, multiple myeloma, leukemia, lung, and breast cancers. Here, we describe an Aurora A-selective inhibitor, LY3295668, which potently inhibits Aurora autophosphorylation and its kinase activity in vitro and in vivo, persistently arrests cancer cells in mitosis, and induces more profound apoptosis than Aurora B or Aurora A/B dual inhibitors without Aurora B inhibition-associated cytokinesis failure and aneuploidy. LY3295668 inhibits the growth of a broad panel of cancer cell lines, including small-cell lung and breast cancer cells. It demonstrates significant efficacy in small-cell lung cancer xenograft and patient-derived tumor preclinical models as a single agent and in combination with standard-of-care agents. LY3295668, as a highly Aurora A-selective inhibitor, may represent a preferred approach to the current pan-Aurora inhibitors as a cancer therapeutic agent.
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Affiliation(s)
- Jian Du
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana.
| | - Lei Yan
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | | | - Xueqian Gong
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Huimin Bian
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | | | | | | | - Yu-Hua Hui
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | | | - Yanzhu Yang
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Yi Zeng
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Sarah M Bogner
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Robert T Foreman
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Andrew Capen
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Gregory P Donoho
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Robert D Van Horn
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Darlene S Barnard
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Jack A Dempsey
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Richard P Beckmann
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Mark S Marshall
- Ped-Hematology/Oncology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Li-Chun Chio
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Yuewei Qian
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Yue W Webster
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Amit Aggarwal
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Shaoyou Chu
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Shobha Bhattachar
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Louis F Stancato
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Michele S Dowless
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Phillip W Iversen
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Jason R Manro
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Jennie L Walgren
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Bartley W Halstead
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Matthew Z Dieter
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Ricardo Martinez
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Shripad V Bhagwat
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Emiko L Kreklau
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | | | - Xiang S Ye
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Bharvin K R Patel
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Christoph Reinhard
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Gregory D Plowman
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - David A Barda
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - James R Henry
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Sean G Buchanan
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Robert M Campbell
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
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21
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Lee JW, Parameswaran J, Sandoval-Schaefer T, Eoh KJ, Yang DH, Zhu F, Mehra R, Sharma R, Gaffney SG, Perry EB, Townsend JP, Serebriiskii IG, Golemis EA, Issaeva N, Yarbrough WG, Koo JS, Burtness B. Combined Aurora Kinase A (AURKA) and WEE1 Inhibition Demonstrates Synergistic Antitumor Effect in Squamous Cell Carcinoma of the Head and Neck. Clin Cancer Res 2019; 25:3430-3442. [PMID: 30755439 DOI: 10.1158/1078-0432.ccr-18-0440] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 01/17/2019] [Accepted: 02/07/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Human papillomavirus (HPV)-negative head and neck squamous cell carcinomas (HNSCC) commonly bear disruptive mutations in TP53, resulting in treatment resistance. In these patients, direct targeting of p53 has not been successful, but synthetic lethal approaches have promise. Although Aurora A kinase (AURKA) is overexpressed and an oncogenic driver, its inhibition has only modest clinical effects in HPV-negative HNSCC. We explored a novel combination of AURKA and WEE1 inhibition to overcome intrinsic resistance to AURKA inhibition.Experimental Design: AURKA protein expression was determined by fluorescence-based automated quantitative analysis of patient specimens and correlated with survival. We evaluated treatment with the AURKA inhibitor alisertib (MLN8237) and the WEE1 inhibitor adavosertib (AZD1775), alone or in combination, using in vitro and in vivo HNSCC models. RESULTS Elevated nuclear AURKA correlated with worse survival among patients with p16(-) HNSCC. Alisertib caused spindle defects, G2-M arrest and inhibitory CDK1 phosphorylation, and cytostasis in TP53 mutant HNSCC FaDu and UNC7 cells. Addition of adavosertib to alisertib instead triggered mitotic entry and mitotic catastrophe. Moreover, in FaDu and Detroit 562 xenografts, this combination demonstrated synergistic effects on tumor growth and extended overall survival compared with either vehicle or single-agent treatment. CONCLUSIONS Combinatorial treatment with adavosertib and alisertib leads to synergistic antitumor effects in in vitro and in vivo HNSCC models. These findings suggest a novel rational combination, providing a promising therapeutic avenue for TP53-mutated cancers.
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Affiliation(s)
- Jong Woo Lee
- Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Janaki Parameswaran
- Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Teresa Sandoval-Schaefer
- Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Kyung Jin Eoh
- Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Dong-Hua Yang
- Biosample Repository, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Fang Zhu
- Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Ranee Mehra
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Roshan Sharma
- Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Stephen G Gaffney
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut
| | - Elizabeth B Perry
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut
| | - Ilya G Serebriiskii
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Erica A Golemis
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Natalia Issaeva
- Section of Otolaryngology, Department of Surgery, Yale University School of Medicine, New Haven, Connecticut
| | - Wendell G Yarbrough
- Section of Otolaryngology, Department of Surgery, Yale University School of Medicine, New Haven, Connecticut
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Ja Seok Koo
- Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Barbara Burtness
- Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut.
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22
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Data mining for mutation-specific targets in acute myeloid leukemia. Leukemia 2019; 33:826-843. [PMID: 30728456 DOI: 10.1038/s41375-019-0387-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/06/2018] [Accepted: 10/24/2018] [Indexed: 01/08/2023]
Abstract
Three mutation-specific targeted therapies have recently been approved by the FDA for the treatment of acute myeloid leukemia (AML): midostaurin for FLT3 mutations, enasidenib for relapsed or refractory cases with IDH2 mutations, and ivosidenib for cases with an IDH1 mutation. Together, these agents offer a mutation-directed treatment approach for up to 45% of de novo adult AML cases, a welcome deluge after a prolonged drought. At the same time, a number of computational tools have recently been developed that promise to further accelerate progress in mutation-specific therapy for AML and other cancers. Technical advances together with comprehensively annotated AML tissue banks have resulted in the availability of large and complex data sets for exploration by the end-user, including (i) microarray gene expression, (ii) exome sequencing, (iii) deep sequencing data of sub-clone heterogeneity, (iv) RNA sequencing of gene expression (bulk and single cell), (v) DNA methylation and chromatin, (vi) and germline quantitative trait loci. Yet few clinicians or experimental hematologists have the time or the training to access or analyze these repositories. This review summarizes the data sets and bioinformatic tools currently available to further the discovery of mutation-specific targets with an emphasis on web-based applications that are open, accessible, user-friendly, and do not require coding experience to navigate. We show examples of how available data can be mined to identify potential targets using synthetic lethality, drug repurposing, epigenetic sub-grouping, and proteomic networks while also highlighting strengths and limitations and the need for superior models for validation.
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23
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YES1 amplification is a mechanism of acquired resistance to EGFR inhibitors identified by transposon mutagenesis and clinical genomics. Proc Natl Acad Sci U S A 2018; 115:E6030-E6038. [PMID: 29875142 PMCID: PMC6042104 DOI: 10.1073/pnas.1717782115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In ∼30% of patients with EGFR-mutant lung adenocarcinomas whose disease progresses on EGFR inhibitors, the basis for acquired resistance remains unclear. We have integrated transposon mutagenesis screening in an EGFR-mutant cell line and clinical genomic sequencing in cases of acquired resistance to identify mechanisms of resistance to EGFR inhibitors. The most prominent candidate genes identified by insertions in or near the genes during the screen were MET, a gene whose amplification is known to mediate resistance to EGFR inhibitors, and the gene encoding the Src family kinase YES1. Cell clones with transposon insertions that activated expression of YES1 exhibited resistance to all three generations of EGFR inhibitors and sensitivity to pharmacologic and siRNA-mediated inhibition of YES1 Analysis of clinical genomic sequencing data from cases of acquired resistance to EGFR inhibitors revealed amplification of YES1 in five cases, four of which lacked any other known mechanisms of resistance. Preinhibitor samples, available for two of the five patients, lacked YES1 amplification. None of 136 postinhibitor samples had detectable amplification of other Src family kinases (SRC and FYN). YES1 amplification was also found in 2 of 17 samples from ALK fusion-positive lung cancer patients who had progressed on ALK TKIs. Taken together, our findings identify acquired amplification of YES1 as a recurrent and targetable mechanism of resistance to EGFR inhibition in EGFR-mutant lung cancers and demonstrate the utility of transposon mutagenesis in discovering clinically relevant mechanisms of drug resistance.
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24
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Targeted delivery of chemotherapy using HSP90 inhibitor drug conjugates is highly active against pancreatic cancer models. Oncotarget 2018; 8:4399-4409. [PMID: 27779106 PMCID: PMC5354841 DOI: 10.18632/oncotarget.12642] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/19/2016] [Indexed: 12/27/2022] Open
Abstract
The lack of effective treatment modalities is a major problem in pancreatic cancer (PCa), a devastating malignancy that is nearly universally driven by the “undruggable” KRAS and TP53 cancer genes. Poor tumor tissue penetration is the major source of resistance in pancreatic cancer where chemotherapy is the mainstay of treatment. In this study we exploited the selective tumor-targeting properties of the heat shock 90 protein inhibitors as the vehicle for drug delivery to pancreatic tumor tissues. STA-12-8666 is a novel esterase-cleavable conjugate of an HSP90i and a topoisomerase I inhibitor, SN-38. STA-12-8666 selectively binds activated HSP90 and releases its cytotoxic payload resulting in drug accumulation in pancreatic cancer cells in vivo. We investigated the preclinical activity of STA-12-8666 in patient derived xenograft and genetic models of pancreatic cancer. Treatment with STA-12-8666 of the KPC mice (knock-in alleles of LSL-KrasG12D, Tp53fl/fl and Pdx1-Cre transgene) at the advanced stages of pancreatic tumors doubled their survival (49 days vs. 74 days, p=0.008). STA-12-8666 also demonstrated dramatically superior activity in comparison to equimolar doses of irinotecan against 5 patient-derived pancreatic adenocarcinoma xenografts with prolonged remissions in some tumors. Analysis of activity of STA-12-8666 against tumor tissues and matched cell lines demonstrated prolonged accumulation and release of cytotoxic payload in the tumor leading to DNA damage response and cell cycle arrest. Our results provide a proof-of-principle validation that HSP90i-based drug conjugates can overcome the notorious treatment resistance by utilizing the inherently high affinity of pancreatic cancer cells to HSP90 antagonists.
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25
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Manem VSK, Salgado R, Aftimos P, Sotiriou C, Haibe-Kains B. Network science in clinical trials: A patient-centered approach. Semin Cancer Biol 2017; 52:135-150. [PMID: 29278737 DOI: 10.1016/j.semcancer.2017.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 02/08/2023]
Abstract
There has been a paradigm shift in translational oncology with the advent of novel molecular diagnostic tools in the clinic. However, several challenges are associated with the integration of these sophisticated tools into clinical oncology and daily practice. High-throughput profiling at the DNA, RNA and protein levels (omics) generate a massive amount of data. The analysis and interpretation of these is non-trivial but will allow a more thorough understanding of cancer. Linear modelling of the data as it is often used today is likely to limit our understanding of cancer as a complex disease, and at times under-performs to capture a phenotype of interest. Network science and systems biology-based approaches, using machine learning and network science principles, that integrate multiple data sources, can uncover complex changes in a biological system. This approach will integrate a large number of potential biomarkers in preclinical studies to better inform therapeutic decisions and ultimately make substantial progress towards precision medicine. It will however require development of a new generation of clinical trials. Beyond discussing the challenges of high-throughput technologies, this review will develop a framework on how to implement a network science approach in new clinical trial designs in order to advance cancer care.
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Affiliation(s)
- Venkata S K Manem
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Roberto Salgado
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Brussels, Belgium; Department of Pathology, GZA Hospitals Antwerp, Belgium
| | - Philippe Aftimos
- Medical Oncology Clinic, Institut Jules Bordet - Université Libre de Bruxelles, Brussels, Belgium
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Brussels, Belgium; Medical Oncology Clinic, Institut Jules Bordet - Université Libre de Bruxelles, Brussels, Belgium
| | - Benjamin Haibe-Kains
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Ontario Institute of Cancer Research, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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26
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Zhang YW, Nasto RE, Jablonski SA, Serebriiskii IG, Surana R, Murray J, Johnson M, Riggins RB, Clarke R, Golemis EA, Weiner LM. RNA Interference Screening to Identify Proliferation Determinants in Breast Cancer Cells. Bio Protoc 2017; 7:e2435. [PMID: 29250574 DOI: 10.21769/bioprotoc.2435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
RNAi screening technology has revealed unknown determinants of various biological signaling pathways in biomedical studies. This protocol provided detailed information about how to use RNAi screening to identify proliferation determinants in breast tumor cells. siRNA-based libraries targeting against Estrogen receptor (ER)-network, including 631 genes relevant to estrogen signaling, was constructed for screening in breast cancer cells. Briefly, reverse transfection of siRNA induced transient gene knockdown in MCF7 cells. First, the transfection reagent for MCF7 cells was selected. Next, the Z'-score assay was used to monitor if screening conditions yielded efficiently. Then, the ER-network siRNA library screening was preceded by automatic machines under optimized experimental conditions.
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Affiliation(s)
- Yong-Wei Zhang
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Rochelle E Nasto
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.,Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA.,School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Sandra A Jablonski
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Ilya G Serebriiskii
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA.,Kazan Federal University, Kazan, Russia
| | - Rishi Surana
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Joseph Murray
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Michael Johnson
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Rebecca B Riggins
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Robert Clarke
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Erica A Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Louis M Weiner
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
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27
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Kurup S, McAllister B, Liskova P, Mistry T, Fanizza A, Stanford D, Slawska J, Keller U, Hoellein A. Design, synthesis and biological activity of N 4-phenylsubstituted-7H-pyrrolo[2,3-d]pyrimidin-4-amines as dual inhibitors of aurora kinase A and epidermal growth factor receptor kinase. J Enzyme Inhib Med Chem 2017; 33:74-84. [PMID: 29115879 PMCID: PMC6009956 DOI: 10.1080/14756366.2017.1376666] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Simultaneous inhibition of multiple kinases has been suggested to provide synergistic effects on inhibition of tumour growth and resistance. This study describes the design, synthesis and evaluation of 18 compounds incorporating a pyrrolo[2,3-d]pyrimidine scaffold for dual inhibition of epidermal growth factor receptor kinase (EGFR) and aurora kinase A (AURKA). Compounds 1-18 of this study demonstrate nanomolar inhibition of EGFR and micromolar inhibition of AURKA. Compounds 1-18 allow for a structure-activity relationships (SAR) analysis of the 4-anilino moiety for dual EGFR and AURKA inhibition. Compound 6, a 4-methoxyphenylpyrrolo[2,3-d]pyrimidin-4-amine, demonstrates single-digit micromolar inhibition of both AURKA and EGFR and provides evidence of a single molecule with dual activity against EGFR and AURKA. Compound 2, the most potent inhibitor of EGFR and AURKA from this series, has been further evaluated in four different squamous cell head and neck cancer cell lines for downstream effects resulting from AURKA and EGFR inhibition.
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Affiliation(s)
- Sonali Kurup
- a College of Pharmacy , Roosevelt University , Schaumburg , IL , USA
| | | | - Pavlina Liskova
- a College of Pharmacy , Roosevelt University , Schaumburg , IL , USA
| | - Trusha Mistry
- a College of Pharmacy , Roosevelt University , Schaumburg , IL , USA
| | - Anthony Fanizza
- b Department of Chemistry , Harper College , Palatine , IL , USA
| | - Dan Stanford
- b Department of Chemistry , Harper College , Palatine , IL , USA
| | - Jolanta Slawska
- c III. Medical Department , Technische Universität München , Munich , Germany
| | - Ulrich Keller
- c III. Medical Department , Technische Universität München , Munich , Germany.,d German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Alexander Hoellein
- c III. Medical Department , Technische Universität München , Munich , Germany
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28
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Abstract
The design of modern oncology clinical trials seeks to match patients' cancer molecular biomarkers with medications that specifically target those biomarkers, a general paradigm shift in cancer care coined clinical cancer biology. This approach exploits the synthetic lethality between a specific genetic alteration in the cancer cell and a drug: rapid termination of exaggerated kinase activity exemplifies this phenomenon. Synthetic lethality-based investigations are driven by rapidly evolving technologies for cancer molecular profiling. As these technologies evolve, future clinical trials will test drugs' activity based on the molecular mechanisms rather than by the tumor's appearance under a microscope.
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Affiliation(s)
- Igor Astsaturov
- Department of Hematology and Oncology, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
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29
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Gaponova AV, Deneka AY, Beck TN, Liu H, Andrianov G, Nikonova AS, Nicolas E, Einarson MB, Golemis EA, Serebriiskii IG. Identification of evolutionarily conserved DNA damage response genes that alter sensitivity to cisplatin. Oncotarget 2017; 8:19156-19171. [PMID: 27863405 PMCID: PMC5386675 DOI: 10.18632/oncotarget.13353] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/27/2016] [Indexed: 01/08/2023] Open
Abstract
Ovarian, head and neck, and other cancers are commonly treated with cisplatin and other DNA damaging cytotoxic agents. Altered DNA damage response (DDR) contributes to resistance of these tumors to chemotherapies, some targeted therapies, and radiation. DDR involves multiple protein complexes and signaling pathways, some of which are evolutionarily ancient and involve protein orthologs conserved from yeast to humans. To identify new regulators of cisplatin-resistance in human tumors, we integrated high throughput and curated datasets describing yeast genes that regulate sensitivity to cisplatin and/or ionizing radiation. Next, we clustered highly validated genes based on chemogenomic profiling, and then mapped orthologs of these genes in expanded genomic networks for multiple metazoans, including humans. This approach identified an enriched candidate set of genes involved in the regulation of resistance to radiation and/or cisplatin in humans. Direct functional assessment of selected candidate genes using RNA interference confirmed their activity in influencing cisplatin resistance, degree of γH2AX focus formation and ATR phosphorylation, in ovarian and head and neck cancer cell lines, suggesting impaired DDR signaling as the driving mechanism. This work enlarges the set of genes that may contribute to chemotherapy resistance and provides a new contextual resource for interpreting next generation sequencing (NGS) genomic profiling of tumors.
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Affiliation(s)
- Anna V Gaponova
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.,Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan 420008, Russian Federation
| | - Alexander Y Deneka
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.,Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan 420008, Russian Federation
| | - Tim N Beck
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.,Department of Biochemistry & Molecular Biology, Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Hanqing Liu
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.,Department of Pharmaceutics, Jiangsu University, School of Pharmacy, Jingkou District Zhenjiang, Jiangsu 212013, China
| | - Gregory Andrianov
- Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan 420008, Russian Federation
| | - Anna S Nikonova
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Emmanuelle Nicolas
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Margret B Einarson
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Erica A Golemis
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Ilya G Serebriiskii
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.,Department of Biochemistry and Biotechnology, Kazan Federal University, Kazan 420008, Russian Federation
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30
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Overview of Current Treatment Options and Investigational Targeted Therapies for Locally Advanced Squamous Cell Carcinoma of the Head and Neck. Am J Clin Oncol 2017; 39:396-406. [PMID: 26967327 DOI: 10.1097/coc.0000000000000283] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Patients with squamous cell carcinoma of the head and neck (SCCHN) typically present with locally advanced (LA) stage III or IV disease and are treated with combined-modality therapy with chemotherapy, radiotherapy, and surgery (if resectable). These aggressive, upfront treatment measures are often associated with substantial morbidity, and about half the patients develop locoregional or distant recurrences. Thus, new therapeutic strategies are needed that offer similar efficacy benefits with less toxicity. Current research is focused on selectively targeting signaling pathways involved in the proliferation and malignant transformation of SCCHN cells and the tumor microenvironment. For example, the ErbB receptor pathway has been implicated in the development and progression of SCCHN, and several agents targeting this pathway and downstream effectors are in various phases of clinical investigation. Cetuximab, a monoclonal antibody against epidermal growth factor receptor (EGFR), is the only currently approved targeted therapy for the treatment of LA SCCHN. Additional agents targeting EGFR and other ErbB family members, including monoclonal antibodies (eg, panitumumab, nimotuzumab) and small-molecule tyrosine kinase inhibitors (eg, erlotinib, afatinib, lapatinib) are being studied in LA SCCHN with varying results. Other treatment strategies for LA SCCHN include targeting downstream effectors of signaling and resistance mechanisms to EGFR inhibitors (eg, mammalian target of rapamycin, Src family, and Aurora kinase family). Data from ongoing and future clinical trials will continue to refine current treatment paradigms for LA SCCHN and provide new therapeutic options and potential predictive biomarkers to improve patient efficacy and safety and abrogate resistance.
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31
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Holbeck SL, Camalier R, Crowell JA, Govindharajulu JP, Hollingshead M, Anderson LW, Polley E, Rubinstein L, Srivastava A, Wilsker D, Collins JM, Doroshow JH. The National Cancer Institute ALMANAC: A Comprehensive Screening Resource for the Detection of Anticancer Drug Pairs with Enhanced Therapeutic Activity. Cancer Res 2017; 77:3564-3576. [PMID: 28446463 PMCID: PMC5499996 DOI: 10.1158/0008-5472.can-17-0489] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/13/2017] [Accepted: 04/24/2017] [Indexed: 12/22/2022]
Abstract
To date, over 100 small-molecule oncology drugs have been approved by the FDA. Because of the inherent heterogeneity of tumors, these small molecules are often administered in combination to prevent emergence of resistant cell subpopulations. Therefore, new combination strategies to overcome drug resistance in patients with advanced cancer are needed. In this study, we performed a systematic evaluation of the therapeutic activity of over 5,000 pairs of FDA-approved cancer drugs against a panel of 60 well-characterized human tumor cell lines (NCI-60) to uncover combinations with greater than additive growth-inhibitory activity. Screening results were compiled into a database, termed the NCI-ALMANAC (A Large Matrix of Anti-Neoplastic Agent Combinations), publicly available at https://dtp.cancer.gov/ncialmanac Subsequent in vivo experiments in mouse xenograft models of human cancer confirmed combinations with greater than single-agent efficacy. Concomitant detection of mechanistic biomarkers for these combinations in vivo supported the initiation of two phase I clinical trials at the NCI to evaluate clofarabine with bortezomib and nilotinib with paclitaxel in patients with advanced cancer. Consequently, the hypothesis-generating NCI-ALMANAC web-based resource has demonstrated value in identifying promising combinations of approved drugs with potent anticancer activity for further mechanistic study and translation to clinical trials. Cancer Res; 77(13); 3564-76. ©2017 AACR.
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Affiliation(s)
- Susan L Holbeck
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, Maryland
| | - Richard Camalier
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, Maryland
| | - James A Crowell
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, Maryland
| | - Jeevan Prasaad Govindharajulu
- Clinical Pharmacodynamics Program, Applied/Developmental Research Directorate, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Melinda Hollingshead
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, Maryland
| | - Lawrence W Anderson
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, Maryland
| | - Eric Polley
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, Maryland
| | - Larry Rubinstein
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, Maryland
| | - Apurva Srivastava
- Clinical Pharmacodynamics Program, Applied/Developmental Research Directorate, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Deborah Wilsker
- Clinical Pharmacodynamics Program, Applied/Developmental Research Directorate, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Jerry M Collins
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, Maryland
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, Maryland.
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
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Vyse S, Howitt A, Huang PH. Exploiting Synthetic Lethality and Network Biology to Overcome EGFR Inhibitor Resistance in Lung Cancer. J Mol Biol 2017; 429:1767-1786. [PMID: 28478283 PMCID: PMC6175049 DOI: 10.1016/j.jmb.2017.04.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/25/2017] [Accepted: 04/27/2017] [Indexed: 12/16/2022]
Abstract
Despite the recent approval of third-generation therapies, overcoming resistance to epidermal growth factor receptor (EGFR) inhibitors remains a major challenge in non-small cell lung cancer. Conceptually, synthetic lethality holds the promise of identifying non-intuitive targets for tackling both acquired and intrinsic resistance in this setting. However, translating these laboratory findings into effective clinical strategies continues to be elusive. Here, we provide an overview of the synthetic lethal approaches that have been employed to study EGFR inhibitor resistance and review the oncogene and non-oncogene signalling mechanisms that have thus far been unveiled by synthetic lethality screens. We highlight the potential challenges associated with progressing these discoveries into the clinic including context dependency, signalling plasticity, and tumour heterogeneity, and we offer a perspective on emerging network biology and computational solutions to exploit these phenomena for cancer therapy and biomarker discovery. We conclude by presenting a number of tangible steps to bolster our understanding of fundamental synthetic lethality mechanisms and advance these findings beyond the confines of the laboratory.
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Affiliation(s)
- Simon Vyse
- Division of Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Annie Howitt
- Division of Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Paul H Huang
- Division of Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK.
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33
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Systematic discovery of mutation-specific synthetic lethals by mining pan-cancer human primary tumor data. Nat Commun 2017; 8:15580. [PMID: 28561042 PMCID: PMC5460027 DOI: 10.1038/ncomms15580] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/10/2017] [Indexed: 01/03/2023] Open
Abstract
Two genes are synthetically lethal (SL) when defects in both are lethal to a cell but a single defect is non-lethal. SL partners of cancer mutations are of great interest as pharmacological targets; however, identifying them by cell line-based methods is challenging. Here we develop MiSL (Mining Synthetic Lethals), an algorithm that mines pan-cancer human primary tumour data to identify mutation-specific SL partners for specific cancers. We apply MiSL to 12 different cancers and predict 145,891 SL partners for 3,120 mutations, including known mutation-specific SL partners. Comparisons with functional screens show that MiSL predictions are enriched for SLs in multiple cancers. We extensively validate a SL interaction identified by MiSL between the IDH1 mutation and ACACA in leukaemia using gene targeting and patient-derived xenografts. Furthermore, we apply MiSL to pinpoint genetic biomarkers for drug sensitivity. These results demonstrate that MiSL can accelerate precision oncology by identifying mutation-specific targets and biomarkers. There are no robust methods for systematically identifying mutation-specific synthetic lethal (SL) partners in cancer. Here, the authors develop a computational algorithm that uses pan-cancer data to detect mutation-andcancer-specific SL partners and they validate a novel SL interaction between mutant IDH and loss of ACACA in leukaemia.
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34
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Beglyarova N, Banina E, Zhou Y, Mukhamadeeva R, Andrianov G, Bobrov E, Lysenko E, Skobeleva N, Gabitova L, Restifo D, Pressman M, Serebriiskii IG, Hoffman JP, Paz K, Behrens D, Khazak V, Jablonski SA, Golemis EA, Weiner LM, Astsaturov I. Screening of Conditionally Reprogrammed Patient-Derived Carcinoma Cells Identifies ERCC3-MYC Interactions as a Target in Pancreatic Cancer. Clin Cancer Res 2016; 22:6153-6163. [PMID: 27384421 PMCID: PMC5161635 DOI: 10.1158/1078-0432.ccr-16-0149] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 05/17/2016] [Accepted: 06/06/2016] [Indexed: 12/18/2022]
Abstract
PURPOSE Even when diagnosed prior to metastasis, pancreatic ductal adenocarcinoma (PDAC) is a devastating malignancy with almost 90% lethality, emphasizing the need for new therapies optimally targeting the tumors of individual patients. EXPERIMENTAL DESIGN We first developed a panel of new physiologic models for study of PDAC, expanding surgical PDAC tumor samples in culture using short-term culture and conditional reprogramming with the Rho kinase inhibitor Y-27632, and creating matched patient-derived xenografts (PDX). These were evaluated for sensitivity to a large panel of clinical agents, and promising leads further evaluated mechanistically. RESULTS Only a small minority of tested agents was cytotoxic in minimally passaged PDAC cultures in vitro Drugs interfering with protein turnover and transcription were among most cytotoxic. Among transcriptional repressors, triptolide, a covalent inhibitor of ERCC3, was most consistently effective in vitro and in vivo causing prolonged complete regression in multiple PDX models resistant to standard PDAC therapies. Importantly, triptolide showed superior activity in MYC-amplified PDX models and elicited rapid and profound depletion of the oncoprotein MYC, a transcriptional regulator. Expression of ERCC3 and MYC was interdependent in PDACs, and acquired resistance to triptolide depended on elevated ERCC3 and MYC expression. The Cancer Genome Atlas analysis indicates ERCC3 expression predicts poor prognosis, particularly in CDKN2A-null, highly proliferative tumors. CONCLUSIONS This provides initial preclinical evidence for an essential role of MYC-ERCC3 interactions in PDAC, and suggests a new mechanistic approach for disruption of critical survival signaling in MYC-dependent cancers. Clin Cancer Res; 22(24); 6153-63. ©2016 AACR.
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Affiliation(s)
- Natalya Beglyarova
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Eugenia Banina
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Yan Zhou
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | - Grigorii Andrianov
- Department of Biochemistry, Kazan Federal University, Kazan, Russian Federation
| | - Egor Bobrov
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Elena Lysenko
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Natalya Skobeleva
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Linara Gabitova
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Diana Restifo
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Max Pressman
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Ilya G Serebriiskii
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - John P Hoffman
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Keren Paz
- Champions Oncology, Baltimore, Maryland
| | - Diana Behrens
- EPO Experimental Pharmacology and Oncology GmbH, Berlin, Germany
| | | | - Sandra A Jablonski
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Erica A Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Louis M Weiner
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Igor Astsaturov
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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35
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Chang JG, Chen CC, Wu YY, Che TF, Huang YS, Yeh KT, Shieh GS, Yang PC. Uncovering synthetic lethal interactions for therapeutic targets and predictive markers in lung adenocarcinoma. Oncotarget 2016; 7:73664-73680. [PMID: 27655641 PMCID: PMC5342006 DOI: 10.18632/oncotarget.12046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/24/2016] [Indexed: 12/28/2022] Open
Abstract
Two genes are called synthetic lethal (SL) if their simultaneous mutation leads to cell death, but mutation of either individual does not. Targeting SL partners of mutated cancer genes can selectively kill cancer cells, but leave normal cells intact. We present an integrated approach to uncover SL gene pairs as novel therapeutic targets of lung adenocarcinoma (LADC). Of 24 predicted SL pairs, PARP1-TP53 was validated by RNAi knockdown to have synergistic toxicity in H1975 and invasive CL1-5 LADC cells; additionally FEN1-RAD54B, BRCA1-TP53, BRCA2-TP53 and RB1-TP53 were consistent with the literature. While metastasis remains a bottleneck in cancer treatment and inhibitors of PARP1 have been developed, this result may have therapeutic potential for LADC, in which TP53 is commonly mutated. We also demonstrated that silencing PARP1 enhanced the cell death induced by the platinum-based chemotherapy drug carboplatin in lung cancer cells (CL1-5 and H1975). IHC of RAD54B↑, BRCA1↓-RAD54B↑, FEN1(N)↑-RAD54B↑ and PARP1↑-RAD54B↑ were shown to be prognostic markers for 131 Asian LADC patients, and all markers except BRCA1↓-RAD54B↑ were further confirmed by three independent gene expression data sets (a total of 426 patients) including The Cancer Genome Atlas (TCGA) cohort of LADC. Importantly, we identified POLB-TP53 and POLB as predictive markers for the TCGA cohort (230 subjects), independent of age and stage. Thus, POLB and POLB-TP53 may be used to stratify future non-Asian LADC patients for therapeutic strategies.
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Affiliation(s)
- Jan-Gowth Chang
- Department of Laboratory Medicine and Epigenome Research Center, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Chia-Cheng Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Yi-Ying Wu
- Graduate Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ting-Fang Che
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Syuan Huang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Kun-Tu Yeh
- Department of Pathology, Changhua Christian Hospital, Changhua, Taiwan
- Department of Pathology, School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Grace S. Shieh
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Pan-Chyr Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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36
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Zhang G, Scarborough H, Kim J, Rozhok AI, Chen YA, Zhang X, Song L, Bai Y, Fang B, Liu RZ, Koomen J, Tan AC, Degregori J, Haura EB. Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors. Sci Signal 2016; 9:rs12. [PMID: 27811184 DOI: 10.1126/scisignal.aaf5011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Patients with lung cancers harboring anaplastic lymphoma kinase (ALK) gene fusions benefit from treatment with ALK inhibitors, but acquired resistance inevitably arises. A better understanding of proximal ALK signaling mechanisms may identify sensitizers to ALK inhibitors that disrupt the balance between prosurvival and proapoptotic effector signals. Using affinity purification coupled with mass spectrometry in an ALK fusion lung cancer cell line (H3122), we generated an ALK signaling network and investigated signaling activity using tyrosine phosphoproteomics. We identified a network of 464 proteins composed of subnetworks with differential response to ALK inhibitors. A small hairpin RNA screen targeting 407 proteins in this network revealed 64 and 9 proteins that when knocked down sensitized cells to crizotinib and alectinib, respectively. Among these, knocking down fibroblast growth factor receptor substrate 2 (FRS2) or coiled-coil and C2 domain-containing protein 1A (CC2D1A), both scaffolding proteins, sensitized multiple ALK fusion cell lines to the ALK inhibitors crizotinib and alectinib. Collectively, our data set provides a resource that enhances our understanding of signaling and drug resistance networks consequent to ALK fusions and identifies potential targets to improve the efficacy of ALK inhibitors in patients.
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Affiliation(s)
- Guolin Zhang
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Hannah Scarborough
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jihye Kim
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Andrii I Rozhok
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Yian Ann Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Xiaohui Zhang
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Lanxi Song
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Yun Bai
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Bin Fang
- Proteomics Core Facility, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Richard Z Liu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - John Koomen
- Department of Molecular Oncology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Aik Choon Tan
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - James Degregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
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37
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Beck TN, Georgopoulos R, Shagisultanova EI, Sarcu D, Handorf EA, Dubyk C, Lango MN, Ridge JA, Astsaturov I, Serebriiskii IG, Burtness BA, Mehra R, Golemis EA. EGFR and RB1 as Dual Biomarkers in HPV-Negative Head and Neck Cancer. Mol Cancer Ther 2016; 15:2486-2497. [PMID: 27507850 DOI: 10.1158/1535-7163.mct-16-0243] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/28/2016] [Indexed: 11/16/2022]
Abstract
Clinical decision making for human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) is predominantly guided by disease stage and anatomic location, with few validated biomarkers. The epidermal growth factor receptor (EGFR) is an important therapeutic target, but its value in guiding therapeutic decision making remains ambiguous. We integrated analysis of clinically annotated tissue microarrays with analysis of data available through the TCGA, to investigate the idea that expression signatures involving EGFR, proteins regulating EGFR function, and core cell-cycle modulators might serve as prognostic or drug response-predictive biomarkers. This work suggests that consideration of the expression of NSDHL and proteins that regulate EGFR recycling in combination with EGFR provides a useful prognostic biomarker set. In addition, inactivation of the tumor suppressor retinoblastoma 1 (RB1), reflected by CCND1/CDK6-inactivating phosphorylation of RB1 at T356, inversely correlated with expression of EGFR in patient HNSCC samples. Moreover, stratification of cases with high EGFR by expression levels of CCND1, CDK6, or the CCND1/CDK6-regulatory protein p16 (CDKN2A) identified groups with significant survival differences. To further explore the relationship between EGFR and RB1-associated cell-cycle activity, we evaluated simultaneous inhibition of RB1 phosphorylation with the CDK4/6 inhibitor palbociclib and of EGFR activity with lapatinib or afatinib. These drug combinations had synergistic inhibitory effects on the proliferation of HNSCC cells and strikingly limited ERK1/2 phosphorylation in contrast to either agent used alone. In summary, combinations of CDK and EGFR inhibitors may be particularly useful in EGFR and pT356RB1-expressing or CCND1/CDK6-overexpressing HPV-negative HNSCC. Mol Cancer Ther; 15(10); 2486-97. ©2016 AACR.
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Affiliation(s)
- Tim N Beck
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania. Molecular and Cell Biology & Genetics Program, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Rachel Georgopoulos
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania. Department of Otolaryngology Head and Neck Surgery, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Elena I Shagisultanova
- Breast Cancer Program, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - David Sarcu
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania. Department of Otolaryngology Head and Neck Surgery, Temple University School of Medicine, Philadelphia, Pennsylvania
| | | | - Cara Dubyk
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Miriam N Lango
- Surgical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - John A Ridge
- Surgical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Igor Astsaturov
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania. Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Ilya G Serebriiskii
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania. Kazan Federal University, Kazan, Russia
| | | | - Ranee Mehra
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania. Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Erica A Golemis
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania. Molecular and Cell Biology & Genetics Program, Drexel University College of Medicine, Philadelphia, Pennsylvania.
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38
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Yan M, Wang C, He B, Yang M, Tong M, Long Z, Liu B, Peng F, Xu L, Zhang Y, Liang D, Lei H, Subrata S, Kelley KW, Lam EWF, Jin B, Liu Q. Aurora-A Kinase: A Potent Oncogene and Target for Cancer Therapy. Med Res Rev 2016; 36:1036-1079. [PMID: 27406026 DOI: 10.1002/med.21399] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 05/18/2016] [Accepted: 06/08/2016] [Indexed: 02/06/2023]
Abstract
The Aurora kinase family is comprised of three serine/threonine kinases, Aurora-A, Aurora-B, and Aurora-C. Among these, Aurora-A and Aurora-B play central roles in mitosis, whereas Aurora-C executes unique roles in meiosis. Overexpression or gene amplification of Aurora kinases has been reported in a broad range of human malignancies, pointing to their role as potent oncogenes in tumorigenesis. Aurora kinases therefore represent promising targets for anticancer therapeutics. A number of Aurora kinase inhibitors (AKIs) have been generated; some of which are currently undergoing clinical evaluation. Recent studies have unveiled novel unexpected functions of Aurora kinases during cancer development and the mechanisms underlying the anticancer actions of AKIs. In this review, we discuss the most recent advances in Aurora-A kinase research and targeted cancer therapy, focusing on the oncogenic roles and signaling pathways of Aurora-A kinases in promoting tumorigenesis, the recent preclinical and clinical AKI data, and potential alternative routes for Aurora-A kinase inhibition.
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Affiliation(s)
- Min Yan
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China.,Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chunli Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Bin He
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Mengying Yang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Mengying Tong
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Zijie Long
- Institute of Hematology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bing Liu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Fei Peng
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Lingzhi Xu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Yan Zhang
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Dapeng Liang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Haixin Lei
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Sen Subrata
- Department of Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keith W Kelley
- Laboratory of Immunophysiology, Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Pathology, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Eric W-F Lam
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Bilian Jin
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China.
| | - Quentin Liu
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China. .,Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China. .,Institute of Hematology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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39
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Beck TN, Korobeynikov VA, Kudinov AE, Georgopoulos R, Solanki NR, Andrews-Hoke M, Kistner TM, Pépin D, Donahoe PK, Nicolas E, Einarson MB, Zhou Y, Boumber Y, Proia DA, Serebriiskii IG, Golemis EA. Anti-Müllerian Hormone Signaling Regulates Epithelial Plasticity and Chemoresistance in Lung Cancer. Cell Rep 2016; 16:657-71. [PMID: 27396341 DOI: 10.1016/j.celrep.2016.06.043] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 05/19/2016] [Accepted: 06/08/2016] [Indexed: 12/19/2022] Open
Abstract
Anti-Müllerian hormone (AMH) and its type II receptor AMHR2, both previously thought to primarily function in gonadal tissue, were unexpectedly identified as potent regulators of transforming growth factor (TGF-β)/bone morphogenetic protein (BMP) signaling and epithelial-mesenchymal transition (EMT) in lung cancer. AMH is a TGF-β/BMP superfamily member, and AMHR2 heterodimerizes with type I receptors (ALK2, ALK3) also used by the type II receptor for BMP (BMPR2). AMH signaling regulates expression of BMPR2, ALK2, and ALK3, supports protein kinase B-nuclear factor κB (AKT-NF-κB) and SMAD survival signaling, and influences BMP-dependent signaling in non-small cell lung cancer (NSCLC). AMH and AMHR2 are selectively expressed in epithelial versus mesenchymal cells, and loss of AMH/AMHR2 induces EMT. Independent induction of EMT reduces expression of AMH and AMHR2. Importantly, EMT associated with depletion of AMH or AMHR2 results in chemoresistance but sensitizes cells to the heat shock protein 90 (HSP90) inhibitor ganetespib. Recognition of this AMH/AMHR2 axis helps to further elucidate TGF-β/BMP resistance-associated signaling and suggests new strategies for therapeutic targeting of EMT.
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Affiliation(s)
- Tim N Beck
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Vladislav A Korobeynikov
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Medical Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexander E Kudinov
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | | | - Nehal R Solanki
- Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Program in Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | | | | | - David Pépin
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital and Department of Surgery, Harvard Medical School, Boston, MA 02114, USA
| | - Patricia K Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital and Department of Surgery, Harvard Medical School, Boston, MA 02114, USA
| | - Emmanuelle Nicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Margret B Einarson
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Yan Zhou
- Department of Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA 19140, USA
| | - Yanis Boumber
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | | | - Ilya G Serebriiskii
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Kazan Federal University, 420000 Kazan, Russian Federation
| | - Erica A Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, PA 19129, USA.
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40
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Wang YL, Overstreet AM, Chen MS, Wang J, Zhao HJ, Ho PC, Smith M, Wang SC. Combined inhibition of EGFR and c-ABL suppresses the growth of triple-negative breast cancer growth through inhibition of HOTAIR. Oncotarget 2016; 6:11150-61. [PMID: 25883211 PMCID: PMC4484446 DOI: 10.18632/oncotarget.3441] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 02/26/2015] [Indexed: 01/19/2023] Open
Abstract
Triple-negative breast cancer (TNBC) does not express conventional therapeutic targets and is the only type of malignant breast cancer for which no designated FDA-approved targeted therapy is available. Although overexpression of epidermal growth factor receptor (EGFR) is frequently found in TNBC, the therapeutic effect of EGFR inhibitors in TNBC has been underwhelming. Here we show that co-treatment with clinically validated inhibitors of c-ABL (imatinib) and EGFR (lapatinib) results in synergistic growth inhibition in TNBC cells. The dual treatment leads to synergistic repression of the long non-coding RNA (lncRNA) HOTAIR (HOX Antisense Intergenic RNA). HOTAIR has been known to induce tumor growth and metastasis in breast cancer. Depleting HOTAIR alone phenocopies the dual treatment in growth suppression. We show that expression of HOTAIR is regulated by β-catenin through a LEF1/TCF4-binding site. The dual treatment blocks nuclear expression of β-catenin and prevents its recruitment to the HOTAIR promoter. Consistently, forced expression of β-catenin rescued HOTAIR expression and cell viability in the presence of both drugs. Upregulation of HOTAIR is associated with TNBC in cell lines and a cohort of primary tumors. This study elucidates a previously unidentified mechanism in TNBC linking signaling with lncRNA regulation which may be exploited for therapeutic gain.
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Affiliation(s)
- Yuan-Liang Wang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Anne-Marie Overstreet
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Min-Shan Chen
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jiang Wang
- Department of Pathology & Lab Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Hua-Jun Zhao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,School of Pharmacy, Zhejiang Chinese Medical University, Zhejiang, China
| | - Po-Chun Ho
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Molly Smith
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Cancer and Cell Biology Graduate Program, University of Cincinnati, Cincinnati, OH, USA
| | - Shao-Chun Wang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Cancer and Cell Biology Graduate Program, University of Cincinnati, Cincinnati, OH, USA
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41
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Pancari P, Mehra R. Systemic therapy for squamous cell carcinoma of the head and neck. Surg Oncol Clin N Am 2016; 24:437-54. [PMID: 25979393 DOI: 10.1016/j.soc.2015.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The use of systemic therapy as part of curative treatment and palliation is an evolving paradigm for squamous cell cancer of the head and neck (SCCHN), which historically has been treated with local modalities. At present, the treatment armamentarium includes traditional cytotoxic therapy, targeted biological agents, and emerging immunotherapeutics. This article discusses the use of all of these systemic approaches for the curative and palliative treatment of SCCHN.
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Affiliation(s)
- Philip Pancari
- Department of Medical Oncology, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Ranee Mehra
- Department of Medical Oncology, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
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Pathak HB, Zhou Y, Sethi G, Hirst J, Schilder RJ, Golemis EA, Godwin AK. A Synthetic Lethality Screen Using a Focused siRNA Library to Identify Sensitizers to Dasatinib Therapy for the Treatment of Epithelial Ovarian Cancer. PLoS One 2015; 10:e0144126. [PMID: 26637171 PMCID: PMC4670180 DOI: 10.1371/journal.pone.0144126] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/15/2015] [Indexed: 02/07/2023] Open
Abstract
Molecular targeted therapies have been the focus of recent clinical trials for the treatment of patients with recurrent epithelial ovarian cancer (EOC). The majority have not fared well as monotherapies for improving survival of these patients. Poor bioavailability, lack of predictive biomarkers, and the presence of multiple survival pathways can all diminish the success of a targeted agent. Dasatinib is a tyrosine kinase inhibitor of the Src-family kinases (SFK) and in preclinical studies shown to have substantial activity in EOC. However, when evaluated in a phase 2 clinical trial for patients with recurrent or persistent EOC, it was found to have minimal activity. We hypothesized that synthetic lethality screens performed using a cogently designed siRNA library would identify second-site molecular targets that could synergize with SFK inhibition and improve dasatinib efficacy. Using a systematic approach, we performed primary siRNA screening using a library focused on 638 genes corresponding to a network centered on EGFR, HER2, and the SFK-scaffolding proteins BCAR1, NEDD9, and EFS to screen EOC cells in combination with dasatinib. We followed up with validation studies including deconvolution screening, quantitative PCR to confirm effective gene silencing, correlation of gene expression with dasatinib sensitivity, and assessment of the clinical relevance of hits using TCGA ovarian cancer data. A refined list of five candidates (CSNK2A1, DAG1, GRB2, PRKCE, and VAV1) was identified as showing the greatest potential for improving sensitivity to dasatinib in EOC. Of these, CSNK2A1, which codes for the catalytic alpha subunit of protein kinase CK2, was selected for additional evaluation. Synergistic activity of the clinically relevant inhibitor of CK2, CX-4945, with dasatinib in reducing cell proliferation and increasing apoptosis was observed across multiple EOC cell lines. This overall approach to improving drug efficacy can be applied to other targeted agents that have similarly shown poor clinical activity.
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Affiliation(s)
- Harsh B. Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- University of Kansas Cancer Center, Kansas City, Kansas, United States of America
- * E-mail:
| | - Yan Zhou
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Geetika Sethi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jeff Hirst
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Russell J. Schilder
- Department of Gynecologic Medical Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Erica A. Golemis
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- University of Kansas Cancer Center, Kansas City, Kansas, United States of America
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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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Nikonova AS, Deneka AY, Eckman L, Kopp MC, Hensley HH, Egleston BL, Golemis EA. Opposing Effects of Inhibitors of Aurora-A and EGFR in Autosomal-Dominant Polycystic Kidney Disease. Front Oncol 2015; 5:228. [PMID: 26528438 PMCID: PMC4607875 DOI: 10.3389/fonc.2015.00228] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/01/2015] [Indexed: 01/24/2023] Open
Abstract
Aurora-A kinase (AURKA) overexpression in numerous tumors induces aneuploidy, in part because of cytokinetic defects. Alisertib and other small-molecule inhibitors targeting AURKA are effective in some patients as monotherapies or combination therapies. Epidermal growth factor receptor (EGFR) pro-proliferative signaling activity is commonly elevated in cancer, and the EGFR inhibitor erlotinib is commonly used as a standard of care agent for cancer. An erlotinib/alisertib combination therapy is currently under assessment in clinical trials, following pre-clinical studies that indicated synergy of these drugs in cancer. We were interested in further exploring the activity of this drug combination. Beyond well-established functions for AURKA in mitotic progression, additional non-mitotic AURKA functions include control of ciliary stability and calcium signaling. Interestingly, alisertib exacerbates the disease phenotype in mouse models for autosomal-dominant polycystic kidney disease (ADPKD), a common inherited syndrome induced by aberrant signaling from PKD1 and PKD2, cilia-localized proteins that have calcium channel activity. EGFR is also more active in ADPKD, making erlotinib also of potential interest in this disease setting. In this study, we have explored the interaction of alisertib and erlotinib in an ADPKD model. These experiments indicated erlotinib-restrained cystogenesis, opposing alisertib action. Erlotinib also interacted with alisertib to regulate proliferative signaling proteins, albeit in a complicated manner. Results suggest a nuanced role of AURKA signaling in different pathogenic conditions and inform the clinical use of AURKA inhibitors in cancer patients with comorbidities.
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Affiliation(s)
- Anna S Nikonova
- Program in Molecular Therapeutics, Fox Chase Cancer Center , Philadelphia, PA , USA
| | - Alexander Y Deneka
- Program in Molecular Therapeutics, Fox Chase Cancer Center , Philadelphia, PA , USA ; Cancer Biology, Drexel University College of Medicine , Philadelphia, PA , USA
| | - Louisa Eckman
- Program in Molecular Therapeutics, Fox Chase Cancer Center , Philadelphia, PA , USA
| | - Meghan C Kopp
- Cancer Biology, Drexel University College of Medicine , Philadelphia, PA , USA
| | - Harvey H Hensley
- Program in Molecular Therapeutics, Fox Chase Cancer Center , Philadelphia, PA , USA
| | - Brian L Egleston
- Program in Molecular Therapeutics, Fox Chase Cancer Center , Philadelphia, PA , USA
| | - Erica A Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center , Philadelphia, PA , USA
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Gabitova L, Restifo D, Gorin A, Manocha K, Handorf E, Yang DH, Cai KQ, Klein-Szanto AJ, Cunningham D, Kratz LE, Herman GE, Golemis EA, Astsaturov I. Endogenous Sterol Metabolites Regulate Growth of EGFR/KRAS-Dependent Tumors via LXR. Cell Rep 2015; 12:1927-38. [PMID: 26344763 DOI: 10.1016/j.celrep.2015.08.023] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 07/10/2015] [Accepted: 08/07/2015] [Indexed: 02/04/2023] Open
Abstract
Meiosis-activating sterols (MAS) are substrates of SC4MOL and NSDHL in the cholesterol pathway and are important for normal organismal development. Oncogenic transformation by epidermal growth factor receptor (EGFR) or RAS increases the demand for cholesterol, suggesting a possibility for metabolic interference. To test this idea in vivo, we ablated Nsdhl in adult keratinocytes expressing KRAS(G12D). Strikingly, Nsdhl inactivation antagonized the growth of skin tumors while having little effect on normal skin. Loss of Nsdhl induced the expression of ATP-binding cassette (ABC) transporters ABCA1 and ABCG1, reduced the expression of low-density lipoprotein receptor (LDLR), decreased intracellular cholesterol, and was dependent on the liver X receptor (LXR) α. Importantly, EGFR signaling opposed LXRα effects on cholesterol homeostasis, whereas an EGFR inhibitor synergized with LXRα agonists in killing cancer cells. Inhibition of SC4MOL or NSDHL, or activation of LXRα by sterol metabolites, can be an effective strategy against carcinomas with activated EGFR-KRAS signaling.
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Affiliation(s)
- Linara Gabitova
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan 420000, Russia
| | - Diana Restifo
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Andrey Gorin
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan 420000, Russia
| | - Kunal Manocha
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Elizabeth Handorf
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Dong-Hua Yang
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Kathy Q Cai
- Histopathology Facility, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Andres J Klein-Szanto
- Histopathology Facility, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - David Cunningham
- The Research Institute at Nationwide Children's Hospital and Department of Pediatrics, The Ohio State University, Columbus, OH 43205, USA
| | - Lisa E Kratz
- Kennedy Krieger Institute, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Gail E Herman
- The Research Institute at Nationwide Children's Hospital and Department of Pediatrics, The Ohio State University, Columbus, OH 43205, USA
| | - Erica A Golemis
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Igor Astsaturov
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan 420000, Russia.
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Niu H, Manfredi M, Ecsedy JA. Scientific Rationale Supporting the Clinical Development Strategy for the Investigational Aurora A Kinase Inhibitor Alisertib in Cancer. Front Oncol 2015; 5:189. [PMID: 26380220 PMCID: PMC4547019 DOI: 10.3389/fonc.2015.00189] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/07/2015] [Indexed: 01/08/2023] Open
Abstract
Alisertib (MLN8237) is a selective small molecule inhibitor of Aurora A kinase that is being developed in multiple cancer indications as a single agent and in combination with other therapies. A significant amount of research has elucidated a role for Aurora A in orchestrating numerous activities of cells transiting through mitosis and has begun to shed light on potential non-mitotic roles for Aurora A as well. These biological insights laid the foundation for multiple clinical trials evaluating the antitumor activity of alisertib in both solid cancers and heme-lymphatic malignancies. Several key facets of Aurora A biology as well as empirical data collected in experimental systems and early clinical trials have directed the development of alisertib toward certain cancer types, including neuroblastoma, small cell lung cancer, neuroendocrine prostate cancer, atypical teratoid/rhabdoid tumors, and breast cancer among others. In addition, these scientific insights provided the rationale for combining alisertib with other therapies, including microtubule perturbing agents, such as taxanes, EGFR inhibitors, hormonal therapies, platinums, and HDAC inhibitors among others. Here, we link the key aspects of the current clinical development of alisertib to the originating scientific rationale and provide an overview of the alisertib clinical experience to date.
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Affiliation(s)
- Huifeng Niu
- Department of Translational Medicine, Takeda Pharmaceuticals International Co, Cambridge, MA, USA
| | - Mark Manfredi
- Department of Oncology Biology, Takeda Pharmaceuticals International Co, Cambridge, MA, USA
| | - Jeffrey A. Ecsedy
- Department of Translational Medicine, Takeda Pharmaceuticals International Co, Cambridge, MA, USA
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Gavriilidis P, Giakoustidis A, Giakoustidis D. Aurora Kinases and Potential Medical Applications of Aurora Kinase Inhibitors: A Review. J Clin Med Res 2015; 7:742-51. [PMID: 26345296 PMCID: PMC4554212 DOI: 10.14740/jocmr2295w] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2015] [Indexed: 12/17/2022] Open
Abstract
Aurora kinases (AKs) represent a novel group of serine/threonine kinases. They were originally described in 1995 by David Glover in the course of studies of mutant alleles characterized with unusual spindle pole configuration in Drosophila melanogaster. Thus far, three AKs A, B, and C have been discovered in human healthy and neoplastic cells. Each one locates in different subcellular locations and they are all nuclear proteins. AKs are playing an essential role in mitotic events such as monitoring of the mitotic checkpoint, creation of bipolar mitotic spindle and alignment of centrosomes on it, also regulating centrosome separation, bio-orientation of chromosomes and cytokinesis. Any inactivation of them can have catastrophic consequences on mitotic events of spindle formation, alignment of centrosomes and cytokinesis, resulting in apoptosis. Overexpression of AKs has been detected in diverse solid and hematological cancers and has been linked with a dismal prognosis. After discovery and identification of the first aurora kinase inhibitor (AKI) ZM447439 as a potential drug for targeted therapy in cancer treatment, approximately 30 AKIs have been introduced in cancer treatment.
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Affiliation(s)
- Paschalis Gavriilidis
- Department of Surgical Oncology, Theageneio Anticancer Hospital, Thessaloniki, Greece
| | - Alexandros Giakoustidis
- Department of Transplantation Surgery, Hippokrateion University Hospital, Thessaloniki, Greece
| | - Dimitrios Giakoustidis
- Department of Transplantation Surgery, Hippokrateion University Hospital, Thessaloniki, Greece
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Acquisition of estrogen independence induces TOB1-related mechanisms supporting breast cancer cell proliferation. Oncogene 2015; 35:1643-56. [PMID: 26165839 DOI: 10.1038/onc.2015.226] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 04/19/2015] [Accepted: 05/04/2015] [Indexed: 12/19/2022]
Abstract
Resistance to therapies targeting the estrogen pathway remains a challenge in the treatment of estrogen receptor-positive breast cancer. To address this challenge, a systems biology approach was used. A library of small interfering RNAs targeting an estrogen receptor (ER)- and aromatase-centered network identified 46 genes that are dispensable in estrogen-dependent MCF7 cells, but are selectively required for the survival of estrogen-independent MCF7-derived cells and multiple additional estrogen-independent breast cancer cell lines. Integration of this information identified a tumor suppressor gene TOB1 as a critical determinant of estrogen-independent ER-positive breast cell survival. Depletion of TOB1 selectively promoted G1 phase arrest and sensitivity to AKT and mammalian target of rapmycin (mTOR) inhibitors in estrogen-independent cells but not in estrogen-dependent cells. Phosphoproteomic profiles from reverse-phase protein array analysis supported by mRNA profiling identified a significant signaling network reprogramming by TOB1 that differed in estrogen-sensitive and estrogen-resistant cell lines. These data support a novel function for TOB1 in mediating survival of estrogen-independent breast cancers. These studies also provide evidence for combining TOB1 inhibition and AKT/mTOR inhibition as a therapeutic strategy, with potential translational significance for the management of patients with ER-positive breast cancers.
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The response of head and neck squamous cell carcinoma to cetuximab treatment depends on Aurora kinase A polymorphism. Oncotarget 2015; 5:5428-38. [PMID: 24980817 PMCID: PMC4170642 DOI: 10.18632/oncotarget.2117] [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] [Indexed: 02/05/2023] Open
Abstract
Objectives The aim of this study was to evaluate the efficiency of cetuximab-based anti-EGFR treatment and Aurora kinase A / B knockdown as a function of Aurora kinase polymorphism in HNSCC cell lines. Materials and methods First, protein expression of Aurora kinase A / B and EGFR and Aurora kinase A polymorphism were studied in tumour samples. The survival and proliferation of Aurora kinase A homo- (Cal27) and heterozygous (HN) HNSCC cell lines was evaluated using a colony formation assay and a flow cytometric assay. Also, aneuploidy was determined. EGFR signalling pathway were visualised by western blotting. Results Immunohistochemistry revealed the overexpression of Aurora kinase A / B in HNSCC. The knockdown of each kinase caused a significant decrease in clonogenic survival, independent of Aurora kinase A polymorphism. In contrast, cetuximab treatment impaired clonogenic survival only in the Aurora kinase A-homozygous cell line (Cal27). Conclusion This study provides in vitro evidence for the predictive value of Aurora kinase A polymorphism in the efficiency of cetuximab treatment. Resistance to cetuximab treatment can be overcome by simultaneous Aurora kinase A/B knockdown.
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Ramirez UD, Nikonova AS, Liu H, Pecherskaya A, Lawrence SH, Serebriiskii IG, Zhou Y, Robinson MK, Einarson MB, Golemis EA, Jaffe EK. Compounds identified by virtual docking to a tetrameric EGFR extracellular domain can modulate Grb2 internalization. BMC Cancer 2015; 15:436. [PMID: 26016476 PMCID: PMC4451962 DOI: 10.1186/s12885-015-1415-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 05/05/2015] [Indexed: 01/27/2023] Open
Abstract
Background Overexpression or mutation of the epidermal growth factor receptor (EGFR) potently enhances the growth of many solid tumors. Tumor cells frequently display resistance to mechanistically-distinct EGFR-directed therapeutic agents, making it valuable to develop therapeutics that work by additional mechanisms. Current EGFR-targeting therapeutics include antibodies targeting the extracellular domains, and small molecules inhibiting the intracellular kinase domain. Recent studies have identified a novel prone extracellular tetrameric EGFR configuration, which we identify as a potential target for drug discovery. Methods Our focus is on the prone EGFR tetramer, which contains a novel protein-protein interface involving extracellular domain III. This EGFR tetramer is computationally targeted for stabilization by small molecule ligand binding. This study performed virtual screening of a Life Chemicals, Inc. small molecule library of 345,232 drug-like compounds against a molecular dynamics simulation of protein-protein interfaces distinct to the novel tetramer. One hundred nine chemically diverse candidate molecules were selected and evaluated using a cell-based high-content imaging screen that directly assessed induced internalization of the EGFR effector protein Grb2. Positive hits were further evaluated for influence on phosphorylation of EGFR and its effector ERK1/2. Results Fourteen hit compounds affected internalization of Grb2, an adaptor responsive to EGFR activation. Most hits had limited effect on cell viability, and minimally influenced EGFR and ERK1/2 phosphorylation. Docked hit compound poses generally include Arg270 or neighboring residues, which are also involved in binding the effective therapeutic cetuximab, guiding further chemical optimization. Conclusions These data suggest that the EGFR tetrameric configuration offers a novel cancer drug target. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1415-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ursula D Ramirez
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Anna S Nikonova
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Hanqing Liu
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Anna Pecherskaya
- Translational Facility, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Sarah H Lawrence
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Ilya G Serebriiskii
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA. .,Kazan Federal University, Kazan, Russia.
| | - Yan Zhou
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Matthew K Robinson
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Margret B Einarson
- Translational Facility, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Erica A Golemis
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
| | - Eileen K Jaffe
- Molecular Therapeutics Program, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA, 19111, USA.
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