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Palve V, Knezevic CE, Bejan DS, Luo Y, Li X, Novakova S, Welsh EA, Fang B, Kinose F, Haura EB, Monteiro AN, Koomen JM, Cohen MS, Lawrence HR, Rix U. The non-canonical target PARP16 contributes to polypharmacology of the PARP inhibitor talazoparib and its synergy with WEE1 inhibitors. Cell Chem Biol 2022; 29:202-214.e7. [PMID: 34329582 PMCID: PMC8782927 DOI: 10.1016/j.chembiol.2021.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 04/08/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022]
Abstract
PARP inhibitors (PARPis) display single-agent anticancer activity in small cell lung cancer (SCLC) and other neuroendocrine tumors independent of BRCA1/2 mutations. Here, we determine the differential efficacy of multiple clinical PARPis in SCLC cells. Compared with the other PARPis rucaparib, olaparib, and niraparib, talazoparib displays the highest potency across SCLC, including SLFN11-negative cells. Chemical proteomics identifies PARP16 as a unique talazoparib target in addition to PARP1. Silencing PARP16 significantly reduces cell survival, particularly in combination with PARP1 inhibition. Drug combination screening reveals talazoparib synergy with the WEE1/PLK1 inhibitor adavosertib. Global phosphoproteomics identifies disparate effects on cell-cycle and DNA damage signaling thereby illustrating underlying mechanisms of synergy, which is more pronounced for talazoparib than olaparib. Notably, silencing PARP16 further reduces cell survival in combination with olaparib and adavosertib. Together, these data suggest that PARP16 contributes to talazoparib's overall mechanism of action and constitutes an actionable target in SCLC.
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Affiliation(s)
- Vinayak Palve
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Claire E. Knezevic
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Daniel S. Bejan
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR 97239, USA
| | - Yunting Luo
- Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Xueli Li
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Silvia Novakova
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric A. Welsh
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Bin Fang
- Proteomics & Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Fumi Kinose
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Alvaro N. Monteiro
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - John M. Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Michael S. Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR 97239, USA
| | - Harshani R. Lawrence
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA,Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA.
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Phadke MS, Chen Z, Li J, Mohamed E, Davies MA, Smalley I, Duckett DR, Palve V, Czerniecki BJ, Forsyth PA, Noyes D, Adeegbe DO, Eroglu Z, Nguyen KT, Tsai KY, Rix U, Burd CE, Chen YA, Rodriguez PC, Smalley KSM. Targeted Therapy Given after Anti-PD-1 Leads to Prolonged Responses in Mouse Melanoma Models through Sustained Antitumor Immunity. Cancer Immunol Res 2021; 9:554-567. [PMID: 33653716 DOI: 10.1158/2326-6066.cir-20-0905] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/14/2021] [Accepted: 02/23/2021] [Indexed: 11/16/2022]
Abstract
Immunotherapy (IT) and targeted therapy (TT) are both effective against melanoma, but their combination is frequently toxic. Here, we investigated whether the sequence of IT (anti-PD-1)→ TT (ceritinib-trametinib or dabrafenib-trametinib) was associated with improved antitumor responses in mouse models of BRAF- and NRAS-mutant melanoma. Mice with NRAS-mutant (SW1) or BRAF-mutant (SM1) mouse melanomas were treated with either IT, TT, or the sequence of IT→TT. Tumor volumes were measured, and samples from the NRAS-mutant melanomas were collected for immune-cell analysis, single-cell RNA sequencing (scRNA-seq), and reverse phase protein analysis (RPPA). scRNA-seq demonstrated that the IT→TT sequence modulated the immune environment, leading to increased infiltration of T cells, monocytes, dendritic cells and natural killer cells, and decreased numbers of tumor-associated macrophages, myeloid-derived suppressor cells, and regulatory T cells. Durable responses to the IT→TT sequence were dependent on T-cell activity, with depletion of CD8+, but not CD4+, T cells abrogating the therapeutic response. An analysis of transcriptional heterogeneity in the melanoma compartment showed the sequence of IT→TT enriched for a population of melanoma cells with increased expression of MHC class I and melanoma antigens. RPPA analysis demonstrated that the sustained immune response induced by IT→TT suppressed tumor-intrinsic signaling pathways required for therapeutic escape. These studies establish that upfront IT improves the responses to TT in BRAF- and NRAS-mutant melanoma models.
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Affiliation(s)
- Manali S Phadke
- The Department of Tumor Biology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Zhihua Chen
- The Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jiannong Li
- The Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Eslam Mohamed
- The Department of Immunology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Michael A Davies
- The Department of Melanoma Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Inna Smalley
- The Department of Tumor Biology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Derek R Duckett
- The Department of Drug Discovery, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Vinayak Palve
- The Department of Drug Discovery, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Brian J Czerniecki
- The Department of Immunology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Peter A Forsyth
- The Department of Neurooncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - David Noyes
- The Department of Malignant Hematology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Dennis O Adeegbe
- The Department of Immunology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Zeynep Eroglu
- The Department of Cutaneous Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kimberly T Nguyen
- The Department of Tumor Biology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kenneth Y Tsai
- The Department of Tumor Biology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
- The Department of Cutaneous Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Uwe Rix
- The Department of Drug Discovery, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Christin E Burd
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, Ohio
| | - Yian A Chen
- The Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Paulo C Rodriguez
- The Department of Immunology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Keiran S M Smalley
- The Department of Tumor Biology, The Moffitt Cancer Center and Research Institute, Tampa, Florida.
- The Department of Cutaneous Oncology, The Moffitt Cancer Center and Research Institute, Tampa, Florida
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Palve V, Liao Y, Remsing Rix LL, Rix U. Turning liabilities into opportunities: Off-target based drug repurposing in cancer. Semin Cancer Biol 2020; 68:209-229. [PMID: 32044472 DOI: 10.1016/j.semcancer.2020.02.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/29/2020] [Accepted: 02/03/2020] [Indexed: 12/12/2022]
Abstract
Targeted drugs and precision medicine have transformed the landscape of cancer therapy and significantly improved patient outcomes in many cases. However, as therapies are becoming more and more tailored to smaller patient populations and acquired resistance is limiting the duration of clinical responses, there is an ever increasing demand for new drugs, which is not easily met considering steadily rising drug attrition rates and development costs. Considering these challenges drug repurposing is an attractive complementary approach to traditional drug discovery that can satisfy some of these needs. This is facilitated by the fact that most targeted drugs, despite their implicit connotation, are not singularly specific, but rather display a wide spectrum of target selectivity. Importantly, some of the unintended drug "off-targets" are known anticancer targets in their own right. Others are becoming recognized as such in the process of elucidating off-target mechanisms that in fact are responsible for a drug's anticancer activity, thereby revealing potentially new cancer vulnerabilities. Harnessing such beneficial off-target effects can therefore lead to novel and promising precision medicine approaches. Here, we will discuss experimental and computational methods that are employed to specifically develop single target and network-based off-target repurposing strategies, for instance with drug combinations or polypharmacology drugs. By illustrating concrete examples that have led to clinical translation we will furthermore examine the various scientific and non-scientific factors that cumulatively determine the success of these efforts and thus can inform the future development of new and potentially lifesaving off-target based drug repurposing strategies for cancers that constitute important unmet medical needs.
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Affiliation(s)
- Vinayak Palve
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Yi Liao
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Lily L Remsing Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, USA.
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Kate S, Paleja N, Patil R, Bhalerao S, Dhande S, Palve V, Targe M, Nagarkar R, Fernandes L. Breast cancer specific graded prognostic assessment (BC-GPA) score and outcome of HER 2 positive breast cancer patients with brain metastases: A single centre retrospective analysis. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz100.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Palve V, Bagwan J, Krishnan NM, Pareek M, Chandola U, Suresh A, Siddappa G, James BL, Kekatpure V, Kuriakose MA, Panda B. Detection of High-Risk Human Papillomavirus in Oral Cavity Squamous Cell Carcinoma Using Multiple Analytes and Their Role in Patient Survival. J Glob Oncol 2019; 4:1-33. [PMID: 30398949 PMCID: PMC7010445 DOI: 10.1200/jgo.18.00058] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Accurate detection of human papillomavirus (HPV) in oral cavity squamous cell carcinoma (OSCC) is essential to understanding the role of HPV in disease prognosis and management of patients. We used different analytes and methods to understand the true prevalence of HPV in a cohort of patients with OSCC with different molecular backgrounds, and we correlated HPV data with patient survival. METHODS We integrated data from multiple analytes (HPV DNA, HPV RNA, and p16), assays (immunohistochemistry, polymerase chain reaction [PCR], quantitative PCR [qPCR], and digital PCR), and molecular changes (somatic mutations and DNA methylation) from 153 patients with OSCC to correlate p16 expression, HPV DNA, and HPV RNA with HPV incidence and patient survival. RESULTS High prevalence (33% to 58%) of HPV16/18 DNA did not correlate with the presence of transcriptionally active viral genomes (15%) in tumors. Eighteen percent of the tumors were p16 positive and only 6% were both HPV DNA and HPV RNA positive. Most tumors with relatively high copy number HPV DNA and/or HPV RNA, but not with HPV DNA alone (irrespective of copy number), were wild-type for TP53 and CASP8 genes. In our study, p16 protein, HPV DNA, and HPV RNA, either alone or in combination, did not correlate with patient survival. Nine HPV-associated genes stratified the virus-positive from the virus-negative tumor group with high confidence ( P < .008) when HPV DNA copy number and/or HPV RNA were considered to define HPV positivity, and not HPV DNA alone, irrespective of copy number ( P < .2). CONCLUSION In OSCC, the presence of both HPV RNA and p16 is rare. HPV DNA alone is not an accurate measure of HPV positivity and therefore may not be informative. HPV DNA, HPV RNA, and p16 do not correlate with patients' outcome.
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Affiliation(s)
- Vinayak Palve
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Jamir Bagwan
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Neeraja M Krishnan
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Manisha Pareek
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Udita Chandola
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Amritha Suresh
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Gangotri Siddappa
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Bonney L James
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Vikram Kekatpure
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Moni Abraham Kuriakose
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
| | - Binay Panda
- Vinayak Palve, Jamir Bagwan, Neeraja M. Krishnan, Manisha Pareek, Udita Chandola, and Binay Panda, Ganit Labs, Institute of Bioinformatics and Applied Biotechnology; Amritha Suresh, Gangotri Siddappa, Bonney L. James, and Moni Abraham Kuriakose, Mazumdar Shaw Centre for Translational Cancer Research; and Vikram Kekatpure and Moni Abraham Kuriakose, Mazumdar Shaw Medical Centre, Bangalore; Neeraja M. Krishnan and Binay Panda, Ganit Labs Foundation, Delhi, India
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Krishnan NM, Katoh H, Palve V, Pareek M, Sato R, Ishikawa S, Panda B. Functional genomics screen with pooled shRNA library and gene expression profiling with extracts of Azadirachta indica identify potential pathways for therapeutic targets in head and neck squamous cell carcinoma. PeerJ 2019; 7:e6464. [PMID: 30842898 PMCID: PMC6398373 DOI: 10.7717/peerj.6464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/16/2019] [Indexed: 01/20/2023] Open
Abstract
Tumor suppression by the extracts of Azadirachta indica (neem) works via anti-proliferation, cell cycle arrest, and apoptosis, demonstrated previously using cancer cell lines and live animal models. However, very little is known about the molecular targets and pathways that neem extracts and their associated compounds act through. Here, we address this using a genome-wide functional pooled shRNA screen on head and neck squamous cell carcinoma cell lines treated with crude neem leaf extracts, known for their anti-tumorigenic activity. We analyzed differences in global clonal sizes of the shRNA-infected cells cultured under no treatment and treatment with neem leaf extract conditions, assayed using next-generation sequencing. We found 225 genes affected the cancer cell growth in the shRNA-infected cells treated with neem extract. Pathway enrichment analyses of whole-genome gene expression data from cells temporally treated with neem extract revealed important roles played by the TGF-β pathway and HSF-1-related gene network. Our results indicate that neem extract affects various important molecular signaling pathways in head and neck cancer cells, some of which may be therapeutic targets for this devastating tumor.
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Affiliation(s)
- Neeraja M Krishnan
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.,Ganit Labs Foundation, New Delhi, India
| | - Hiroto Katoh
- Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,JST, PRESTO, Saitama, Japan
| | - Vinayak Palve
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Manisha Pareek
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Reiko Sato
- Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shumpei Ishikawa
- Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Binay Panda
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.,Ganit Labs Foundation, New Delhi, India
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Ctortecka C, Palve V, Kuenzi BM, Fang B, Sumi NJ, Izumi V, Novakova S, Kinose F, Remsing Rix LL, Haura EB, Koomen JM, Rix U. Functional Proteomics and Deep Network Interrogation Reveal a Complex Mechanism of Action of Midostaurin in Lung Cancer Cells. Mol Cell Proteomics 2018; 17:2434-2447. [PMID: 30217950 PMCID: PMC6283294 DOI: 10.1074/mcp.ra118.000713] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 08/16/2018] [Indexed: 12/21/2022] Open
Abstract
Lung cancer is associated with high prevalence and mortality, and despite significant successes with targeted drugs in genomically defined subsets of lung cancer and immunotherapy, the majority of patients currently does not benefit from these therapies. Through a targeted drug screen, we found the recently approved multi-kinase inhibitor midostaurin to have potent activity in several lung cancer cells independent of its intended target, PKC, or a specific genomic marker. To determine the underlying mechanism of action we applied a layered functional proteomics approach and a new data integration method. Using chemical proteomics, we identified multiple midostaurin kinase targets in these cells. Network-based integration of these targets with quantitative tyrosine and global phosphoproteomics data using protein-protein interactions from the STRING database suggested multiple targets are relevant for the mode of action of midostaurin. Subsequent functional validation using RNA interference and selective small molecule probes showed that simultaneous inhibition of TBK1, PDPK1 and AURKA was required to elicit midostaurin's cellular effects. Immunoblot analysis of downstream signaling nodes showed that combined inhibition of these targets altered PI3K/AKT and cell cycle signaling pathways that in part converged on PLK1. Furthermore, rational combination of midostaurin with the potent PLK1 inhibitor BI2536 elicited strong synergy. Our results demonstrate that combination of complementary functional proteomics approaches and subsequent network-based data integration can reveal novel insight into the complex mode of action of multi-kinase inhibitors, actionable targets for drug discovery and cancer vulnerabilities. Finally, we illustrate how this knowledge can be used for the rational design of synergistic drug combinations with high potential for clinical translation.
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Affiliation(s)
- Claudia Ctortecka
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Vinayak Palve
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Brent M Kuenzi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612; Cancer Biology PhD Program, University of South Florida, Tampa, Florida 33620
| | - Bin Fang
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Natalia J Sumi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612; Cancer Biology PhD Program, University of South Florida, Tampa, Florida 33620
| | - Victoria Izumi
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Silvia Novakova
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Fumi Kinose
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Lily L Remsing Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - John Matthew Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612.
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8
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Palve V, Pareek M, Krishnan NM, Siddappa G, Suresh A, Kuriakose MA, Panda B. A minimal set of internal control genes for gene expression studies in head and neck squamous cell carcinoma. PeerJ 2018; 6:e5207. [PMID: 30128175 PMCID: PMC6097490 DOI: 10.7717/peerj.5207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/20/2018] [Indexed: 12/25/2022] Open
Abstract
Selection of the right reference gene(s) is crucial in the analysis and interpretation of gene expression data. The aim of the present study was to discover and validate a minimal set of internal control genes in head and neck tumor studies. We analyzed data from multiple sources (in house whole-genome gene expression microarrays, previously published quantitative real-time PCR (qPCR) data and RNA-seq data from TCGA) to come up with a list of 18 genes (discovery set) that had the lowest variance, a high level of expression across tumors, and their matched normal samples. The genes in the discovery set were ranked using four different algorithms (BestKeeper, geNorm, NormFinder, and comparative delta Ct) and a web-based comparative tool, RefFinder, for their stability and variance in expression across tissues. Finally, we validated their expression using qPCR in an additional set of tumor:matched normal samples that resulted in five genes (RPL30, RPL27, PSMC5, MTCH1, and OAZ1), out of which RPL30 and RPL27 were most stable and were abundantly expressed across the tissues. Our data suggest that RPL30 or RPL27 in combination with either PSMC5 or MTCH1 or OAZ1 can be used as a minimal set of control genes in head and neck tumor gene expression studies.
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Affiliation(s)
- Vinayak Palve
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Manisha Pareek
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Neeraja M Krishnan
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Gangotri Siddappa
- Head and Neck Oncology, Mazumdar Shaw Centre for Translational Research, Bangalore, India
| | - Amritha Suresh
- Head and Neck Oncology, Mazumdar Shaw Centre for Translational Research, Bangalore, India
| | - Moni A Kuriakose
- Head and Neck Oncology, Mazumdar Shaw Centre for Translational Research, Bangalore, India
| | - Binay Panda
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
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Krishnan NM, Dhas K, Nair J, Palve V, Bagwan J, Siddappa G, Suresh A, Kekatpure VD, Kuriakose MA, Panda B. A Minimal DNA Methylation Signature in Oral Tongue Squamous Cell Carcinoma Links Altered Methylation with Tumor Attributes. Mol Cancer Res 2016; 14:805-19. [DOI: 10.1158/1541-7786.mcr-15-0395] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 04/24/2016] [Indexed: 11/16/2022]
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Krishnan N, Gupta S, Palve V, Varghese L, Pattnaik S, Jain P, Khyriem C, Hariharan A, Dhas K, Nair J, Pareek M, Prasad V, Siddappa G, Suresh A, Kekatpure V, Kuriakose M, Panda B. Integrated analysis of oral tongue squamous cell carcinoma identifies key variants and pathways linked to risk habits, HPV, clinical parameters and tumor recurrence. F1000Res 2015; 4:1215. [PMID: 26834999 PMCID: PMC4706066 DOI: 10.12688/f1000research.7302.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/04/2015] [Indexed: 12/25/2022] Open
Abstract
Oral tongue squamous cell carcinomas (OTSCC) are a homogeneous group of tumors characterized by aggressive behavior, early spread to lymph nodes and a higher rate of regional failure. Additionally, the incidence of OTSCC among younger population (<50yrs) is on the rise; many of whom lack the typical associated risk factors of alcohol and/or tobacco exposure. We present data on single nucleotide variations (SNVs), indels, regions with loss of heterozygosity (LOH), and copy number variations (CNVs) from fifty-paired oral tongue primary tumors and link the significant somatic variants with clinical parameters, epidemiological factors including human papilloma virus (HPV) infection and tumor recurrence. Apart from the frequent somatic variants harbored in TP53, CASP8, RASA1, NOTCH and CDKN2A genes, significant amplifications and/or deletions were detected in chromosomes 6-9, and 11 in the tumors. Variants in CASP8 and CDKN2A were mutually exclusive. CDKN2A, PIK3CA, RASA1 and DMD variants were exclusively linked to smoking, chewing, HPV infection and tumor stage. We also performed a whole-genome gene expression study that identified matrix metalloproteases to be highly expressed in tumors and linked pathways involving arachidonic acid and NF-k-B to habits and distant metastasis, respectively. Functional knockdown studies in cell lines demonstrated the role of CASP8 in a HPV-negative OTSCC cell line. Finally, we identified a 38-gene minimal signature that predicts tumor recurrence using an ensemble machine-learning method. Taken together, this study links molecular signatures to various clinical and epidemiological factors in a homogeneous tumor population with a relatively high HPV prevalence.
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Affiliation(s)
- Neeraja Krishnan
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Saurabh Gupta
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Vinayak Palve
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Linu Varghese
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Swetansu Pattnaik
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Prach Jain
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Costerwell Khyriem
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Arun Hariharan
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Kunal Dhas
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Jayalakshmi Nair
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Manisha Pareek
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Venkatesh Prasad
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India
| | - Gangotri Siddappa
- Integrated Head and Neck Oncology Program, Mazumdar Shaw Centre for Translational Research, Bangalore, 560 099, India
| | - Amritha Suresh
- Integrated Head and Neck Oncology Program, Mazumdar Shaw Centre for Translational Research, Bangalore, 560 099, India
| | - Vikram Kekatpure
- Head and Neck Oncology, Mazumdar Shaw Medical Centre, Bangalore, 560 099, India
| | - Moni Kuriakose
- Integrated Head and Neck Oncology Program, Mazumdar Shaw Centre for Translational Research, Bangalore, 560 099, India; Head and Neck Oncology, Mazumdar Shaw Medical Centre, Bangalore, 560 099, India
| | - Binay Panda
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560 100, India; Strand Life Sciences, Bangalore, 560 024, India
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Palve V, Mallick S, Ghaisas G, Kannan S, Teni T. Overexpression of Mcl-1L splice variant is associated with poor prognosis and chemoresistance in oral cancers. PLoS One 2014; 9:e111927. [PMID: 25409302 PMCID: PMC4237324 DOI: 10.1371/journal.pone.0111927] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 10/09/2014] [Indexed: 12/28/2022] Open
Abstract
Background Altered expression of Mcl-1, an anti-apoptotic member of the Bcl-2 family, has been linked to the progression and outcome of a variety of malignancies. We have previously reported the overexpression of Mcl-1 protein in human oral cancers. The present study aimed to evaluate the clinicopathological significance of the expression of three known Mcl-1 isoforms in oral tumors and the effect of targeting Mcl-1L isoform on chemosensitivity of oral cancer cells. Methods The expression of Mcl-1 isoforms- Mcl-1L, Mcl-1S & Mcl-1ES was analyzed in 130 paired oral tumors and 9 oral cell lines using quantitative real-time PCR & protein by western blotting. The Mcl-1 mRNA levels were correlated with clinicopathological parameters and outcome of oral cancer patients. The effect of Mcl-1L shRNA or Obatoclax (a small molecule Mcl-1 inhibitor), in combination with Cisplatin on chemosensitivity of oral cancer cells was also assessed. Results Anti-apoptotic Mcl-1L was predominantly expressed, over low or undetectable pro-apoptotic Mcl-1S and Mcl-1ES isoforms. The Mcl-1L transcripts were significantly overexpressed in all cancer cell lines and in 64% oral tumors versus adjacent normals (P<0.02). In oral cancer patients, high Mcl-1L expression was significantly associated with node positivity (P = 0.021), advanced tumor size (P = 0.013) and poor overall survival (P = 0.002). Multivariate analysis indicated Mcl-1L to be an independent prognostic factor for oral cancers (P = 0.037). Mcl-1L shRNA knockdown or its inhibition by Obatoclax in combination with Cisplatin synergistically reduced viability and growth of oral cancer cells than either treatment alone. Conclusion Our studies suggest that overexpression of Mcl-1L is associated with poor prognosis and chemoresistance in oral cancers. Mcl-1L is an independent prognostic factor and a potential therapeutic target in oral cancers.
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Affiliation(s)
- Vinayak Palve
- Teni Lab, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai-410210, India
| | - Sanchita Mallick
- Teni Lab, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai-410210, India
| | - Gauri Ghaisas
- Teni Lab, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai-410210, India
| | - Sadhana Kannan
- Epidemiology and Clinical Trial Unit (ECTU), Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai-410210, India
| | - Tanuja Teni
- Teni Lab, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai-410210, India
- * E-mail:
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Mallick S, Patil R, Gyanchandani R, Pawar S, Palve V, Kannan S, Pathak KA, Choudhary M, Teni TR. Human oral cancers have altered expression of Bcl-2 family members and increased expression of the anti-apoptotic splice variant ofMcl-1. J Pathol 2009; 217:398-407. [DOI: 10.1002/path.2459] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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