1
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Xu H, Zhang Z, Zhang Z, Peng J, Gao Y, Li K, Chen J, Du J, Yan S, Zhang D, Zhou X, Shi X, Liu Y. Effects of insulin-like peptide 7 in Bemisia tabaci MED on tomato chlorosis virus transmission. PEST MANAGEMENT SCIENCE 2023; 79:1508-1517. [PMID: 36533303 DOI: 10.1002/ps.7329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 12/11/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Tomato chlorosis virus (ToCV) is a semi-persistent plant virus that is primarily transmitted by the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae). It causes a serious disease that lowers tomato yield. Insulin-like peptide (ILP), an insulin homolog, regulates trehalose metabolism in a variety of insects. In a previous study, we discovered that trehalose metabolism is required for whiteflies to transmit ToCV effectively. Furthermore, transcriptome sequencing revealed that the BtILP7 gene was highly expressed in B. tabaci infected with ToCV. Therefore, the whitefly ILP7 gene may facilitate the transmission of ToCV and be an attractive target for the control of whiteflies and subsequently ToCV. RESULTS The ToCV content in B. tabaci MED was found to be correlated with BtILP7 gene expression. Subsequent RNA interference (RNAi) of the BtILP7 gene had a significant impact on B. tabaci MED's trehalose metabolism and reproductive capacity, as well as ability to transmit ToCV. CONCLUSIONS These results indicate that the BtILP7 gene was closely related to ToCV transmission by regulating trehalose metabolism and reproduction behavior, thus providing a secure and environmentally friendly management strategy for the control of whiteflies and ToCV-caused disease. © 2022 Society of Chemical Industry.
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Affiliation(s)
- HuiNan Xu
- Longping Branch, School of Biology, Hunan University, Changsha, China
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - ZhanHong Zhang
- Institute of Vegetable, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Zhuo Zhang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Jing Peng
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yang Gao
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - KaiLong Li
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Jianbin Chen
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Jiao Du
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Shuo Yan
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - DeYong Zhang
- Longping Branch, School of Biology, Hunan University, Changsha, China
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - XuGuo Zhou
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
| | - XiaoBin Shi
- Longping Branch, School of Biology, Hunan University, Changsha, China
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yong Liu
- Longping Branch, School of Biology, Hunan University, Changsha, China
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
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2
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Plasmid-driven RNA interference in fish cell lines. In Vitro Cell Dev Biol Anim 2022; 58:189-193. [PMID: 35275331 DOI: 10.1007/s11626-022-00645-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 11/05/2022]
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3
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Nikiforov PO, Hejja B, Chahwan R, Soeller C, Gielen F, Chimerel C. Functional Phenotype Flow Cytometry: On Chip Sorting of Individual Cells According to Responses to Stimuli. Adv Biol (Weinh) 2021; 5:e2100220. [PMID: 34160140 DOI: 10.1002/adbi.202100220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/21/2021] [Indexed: 11/11/2022]
Abstract
The ability to effectively separate and isolate biological cells into specific and well-defined subpopulations is crucial for the advancement of our understanding of cellular heterogeneity and its relevance to living systems. Here is described the development of the functional phenotype flow cytometer (FPFC), a new device designed to separate cells on the basis of their in situ real-time phenotypic responses to stimuli. The FPFC performs a cascade of cell processing steps on a microfluidic platform: introduces biological cells one at a time into a solution of a biological reagent that acts as a stimulus, incubates the cells with the stimulus solution in a flow, and sorts the cells into subpopulations according to their phenotypic responses to the provided stimulus. The presented implementation of the FPFC uses intracellular fluorescence as a readout, incubates cells for 75 s, and operates at a throughput of up to 4 cells min-1 -resulting in the profiling and sorting of hundreds of cells within a few hours. The design and operation of the FPFC are validated by sorting cells from the human Burkitt's lymphoma cancerous cell line Ramos on the basis of their response to activation of the B cell antigen receptor (BCR) by a targeted monoclonal antibody.
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Affiliation(s)
- Petar O Nikiforov
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Beata Hejja
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Richard Chahwan
- Institute of Experimental Immunology, University of Zurich, Zurich, 8057, Switzerland
| | - Christian Soeller
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Fabrice Gielen
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Catalin Chimerel
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
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4
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Tzeng YDT, Liu PF, Li JY, Liu LF, Kuo SY, Hsieh CW, Lee CH, Wu CH, Hsiao M, Chang HT, Shu CW. Kinome-Wide siRNA Screening Identifies Src-Enhanced Resistance of Chemotherapeutic Drugs in Triple-Negative Breast Cancer Cells. Front Pharmacol 2018; 9:1285. [PMID: 30473665 PMCID: PMC6238227 DOI: 10.3389/fphar.2018.01285] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/22/2018] [Indexed: 12/24/2022] Open
Abstract
Background: Chemotherapy is the main treatment for triple-negative breast cancer (TNBC), which lack molecular markers for diagnosis and therapy. Cancer cells activate chemoresistant pathways and lead to therapeutic failure for patients with TNBC. Several kinases have been identified as chemoresistant genes. However, the involvement of kinases in the chemoresistance in TNBC cells is not fully understood. Methods: We employed a kinome siRNA library to screen whether targeting any kinases could increase the chemosensitivity of TNBC cell lines. The effects of kinase on cell viability in various breast cancer cells were validated with ATP level and colony formation. Protein expression and phosphorylation were determined by immunoblotting. The Cancer Genome Atlas (TCGA) dataset was collected to analyze the correlation of Src expression with prognosis of TNBC patients. Results: Primary screening and validation for the initial hits showed that Src kinase was a potential doxorubicin-resistant kinase in the TNBC cell lines MDA-MB-231 and Hs578T. Both siRNA against Src and the Src inhibitor dasatinib enhanced the cytotoxic effects of doxorubicin in TNBC cells. Moreover, phosphorylation of AKT and signal transducer and activator of transcription 3 (STAT3), downstream effectors of Src, were accordingly decreased in Src-silenced or -inhibited TNBC cells. Additionally, TCGA data analysis indicated that Src expression levels in tumor tissues were higher than those in tumor-adjacent normal tissues in patients with TNBC. High co-expression level of Src and STAT3 was also significantly correlated with poor prognosis in patients. Conclusion: Our results showed that Src-STAT3 axis might be involved in chemoresistance of TNBC cells.
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Affiliation(s)
- Yen-Dun Tony Tzeng
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Pei-Feng Liu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Nursing, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan
| | - Ju-Yueh Li
- Department of Obstetrics and Gynecology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Li-Feng Liu
- School of Medicine for International Students, I-Shou University, Kaohsiung, Taiwan.,Institute of Biological Science & Technology, I-Shou University, Kaohsiung, Taiwan
| | - Soong-Yu Kuo
- Department of Biotechnology, Fooyin University, Kaohsiung, Taiwan
| | - Chiao-Wei Hsieh
- Institute of Biological Science & Technology, I-Shou University, Kaohsiung, Taiwan
| | - Cheng-Hsin Lee
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chih-Hsuan Wu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hong-Tai Chang
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chih-Wen Shu
- School of Medicine for International Students, I-Shou University, Kaohsiung, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
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5
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Jung J, Kang Y, Paik H, Kwon M, Yu H, Lee D. Deconvoluting essential gene signatures for cancer growth from genomic expression in compound-treated cells. Bioinformatics 2018; 35:1167-1173. [DOI: 10.1093/bioinformatics/bty774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 08/10/2018] [Accepted: 08/31/2018] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jinmyung Jung
- Bio-Synergy Research Center, 291 Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea
- Department of Data Science, College of Information Technology, The University of Suwon, Bongdam-eup, Hwaseong, Republic of Korea
| | - Yeeok Kang
- Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hyojung Paik
- Korea Institute of Science and Technology Information, Center for Applied Scientific Computing, Division of Supercomputing, Daejeon, Republic of Korea
| | - Mijin Kwon
- Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hasun Yu
- Bio-Synergy Research Center, 291 Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Doheon Lee
- Bio-Synergy Research Center, 291 Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea
- Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea
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6
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Allan KJ, Mahoney DJ, Baird SD, Lefebvre CA, Stojdl DF. Genome-wide RNAi Screening to Identify Host Factors That Modulate Oncolytic Virus Therapy. J Vis Exp 2018. [PMID: 29683442 DOI: 10.3791/56913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
High-throughput genome-wide RNAi (RNA interference) screening technology has been widely used for discovering host factors that impact virus replication. Here we present the application of this technology to uncovering host targets that specifically modulate the replication of Maraba virus, an oncolytic rhabdovirus, and vaccinia virus with the goal of enhancing therapy. While the protocol has been tested for use with oncolytic Maraba virus and oncolytic vaccinia virus, this approach is applicable to other oncolytic viruses and can also be utilized for identifying host targets that modulate virus replication in mammalian cells in general. This protocol describes the development and validation of an assay for high-throughput RNAi screening in mammalian cells, the key considerations and preparation steps important for conducting a primary high-throughput RNAi screen, and a step-by-step guide for conducting a primary high-throughput RNAi screen; in addition, it broadly outlines the methods for conducting secondary screen validation and tertiary validation studies. The benefit of high-throughput RNAi screening is that it allows one to catalogue, in an extensive and unbiased fashion, host factors that modulate any aspect of virus replication for which one can develop an in vitro assay such as infectivity, burst size, and cytotoxicity. It has the power to uncover biotherapeutic targets unforeseen based on current knowledge.
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Affiliation(s)
- Kristina J Allan
- Children's Hospital of Eastern Ontario (CHEO) Research Institute; Department of Biology, Microbiology and Immunology, University of Ottawa
| | - Douglas J Mahoney
- Children's Hospital of Eastern Ontario (CHEO) Research Institute; Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary
| | - Stephen D Baird
- Children's Hospital of Eastern Ontario (CHEO) Research Institute
| | | | - David F Stojdl
- Children's Hospital of Eastern Ontario (CHEO) Research Institute; Department of Biology, Microbiology and Immunology, University of Ottawa; Department of Pediatrics, University of Ottawa;
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7
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Harrington J, Carter L, Basu B, Cook N. Drug development and clinical trial design in pancreatico-biliary malignancies. Curr Probl Cancer 2018; 42:73-94. [PMID: 29402439 DOI: 10.1016/j.currproblcancer.2018.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/27/2017] [Accepted: 01/04/2018] [Indexed: 02/08/2023]
Abstract
Pancreatico-biliary (P-B) tumors arise from the pancreas, bile duct, and ampulla of Vater. Despite their close anatomical location, they have different etiology and biology. However, they uniformly share a poor prognosis, with no major improvements observed in overall survival over decades, even in the face of progress in diagnostic imaging and surgical techniques, and advances in systemic and loco-regional radiation therapies. To date, cytotoxic treatment has been associated with modest benefits in the advanced disease setting, and survival for patients with stage IV disease has not exceeded a year. Therefore, there is a pressing need to identify better treatments which may impact more significantly. Frequently, encouraging signals of potential efficacy for novel agents in early phase clinical trials have been followed by disappointing failures in larger phase III trials, raising the valid question of how drug development can be optimized for patients with pancreatic adenocarcinoma and biliary tract malignancies. In this article we summarize the current therapeutic options for these patients and their limitations. The biological context of these cancers is reviewed, highlighting features that may make them resistant to standard chemotherapeutics and could be potential therapeutic targets. We discuss the role of early phase clinical trials, defined as phase I and non-randomised phase II trials, within the clinical context and current therapeutic landscape of P-B tumors and postulate how translational studies and trial design may enable better realization of emerging targets together with a proposed model for future patient management. A detailed summary of current phase I clinical trials in P-B tumors is provided.
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Affiliation(s)
- Jennifer Harrington
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK
| | - Louise Carter
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Bristi Basu
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK; Department of Oncology, University of Cambridge, Cambridge, UK
| | - Natalie Cook
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, University of Manchester, Manchester, UK.
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8
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Novel Early Phase Clinical Trial Design in Oncology. Pharmaceut Med 2017. [DOI: 10.1007/s40290-017-0205-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Kasoju N, Wang H, Zhang B, George J, Gao S, Triffitt JT, Cui Z, Ye H. Transcriptomics of human multipotent mesenchymal stromal cells: Retrospective analysis and future prospects. Biotechnol Adv 2017; 35:407-418. [DOI: 10.1016/j.biotechadv.2017.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 04/19/2017] [Accepted: 04/20/2017] [Indexed: 12/28/2022]
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10
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Fu J, Fernandez D, Ferrer M, Titus SA, Buehler E, Lal-Nag MA. RNAi High-Throughput Screening of Single- and Multi-Cell-Type Tumor Spheroids: A Comprehensive Analysis in Two and Three Dimensions. SLAS DISCOVERY 2017; 22:525-536. [PMID: 28277887 DOI: 10.1177/2472555217696796] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The widespread use of two-dimensional (2D) monolayer cultures for high-throughput screening (HTS) to identify targets in drug discovery has led to attrition in the number of drug targets being validated. Solid tumors are complex, aberrantly growing microenvironments that harness structural components from stroma, nutrients fed through vasculature, and immunosuppressive factors. Increasing evidence of stromally-derived signaling broadens the complexity of our understanding of the tumor microenvironment while stressing the importance of developing better models that reflect these interactions. Three-dimensional (3D) models may be more sensitive to certain gene-silencing events than 2D models because of their components of hypoxia, nutrient gradients, and increased dependence on cell-cell interactions and therefore are more representative of in vivo interactions. Colorectal cancer (CRC) and breast cancer (BC) models composed of epithelial cells only, deemed single-cell-type tumor spheroids (SCTS) and multi-cell-type tumor spheroids (MCTS), containing fibroblasts were developed for RNAi HTS in 384-well microplates with flat-bottom wells for 2D screening and round-bottom, ultra-low-attachment wells for 3D screening. We describe the development of a high-throughput assay platform that can assess physiologically relevant phenotypic differences between screening 2D versus 3D SCTS, 3D SCTS, and MCTS in the context of different cancer subtypes. This assay platform represents a paradigm shift in how we approach drug discovery that can reduce the attrition rate of drugs that enter the clinic.
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Affiliation(s)
- Jiaqi Fu
- 1 Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Daniel Fernandez
- 1 Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Marc Ferrer
- 1 Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Steven A Titus
- 1 Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Eugen Buehler
- 1 Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Madhu A Lal-Nag
- 1 Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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11
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Abstract
Recent advances in genomic sequencing and omics-based capabilities are uncovering tremendous therapeutic opportunities and rapidly transforming the field of cancer medicine. Molecularly targeted agents aim to exploit key tumor-specific vulnerabilities such as oncogenic or non-oncogenic addiction and synthetic lethality. Additionally, immunotherapies targeting the host immune system are proving to be another promising and complementary approach. Owing to substantial tumor genomic and immunologic complexities, combination strategies are likely to be required to adequately disrupt intricate molecular interactions and provide meaningful long-term benefit to patients. To optimize the therapeutic success and application of combination therapies, systematic scientific discovery will need to be coupled with novel and efficient clinical trial approaches. Indeed, a paradigm shift is required to drive precision medicine forward, from the traditional "drug-centric" model of clinical development in pursuit of small incremental benefits in large heterogeneous groups of patients, to a "strategy-centric" model to provide customized transformative treatments in molecularly stratified subsets of patients or even in individual patients. Crucially, to combat the numerous challenges facing combination drug development-including our growing but incomplete understanding of tumor biology, technical and informatics limitations, and escalating financial costs-aligned goals and multidisciplinary collaboration are imperative to collectively harness knowledge and fuel continual innovation.
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Affiliation(s)
- Daphne Day
- Drug Development Program, Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, M5G 2M9, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,OICR Research Fellow, Ontario Institute for Cancer Research, Toronto, Ontario, M5G 0A3, Canada
| | - Lillian L Siu
- Drug Development Program, Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, M5G 2M9, Canada. .,Department of Medicine, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.
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12
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Mao L, Liu C, Wang Z, Niu X, Xue L, Zhou Z, Cai Z, Yu M, Li Y, Wu D, Li L. A genome-wide loss-of-function screening method for minimizing false-negatives caused by functional redundancy. Cell Res 2016; 26:1067-70. [PMID: 27561817 PMCID: PMC5034115 DOI: 10.1038/cr.2016.97] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Li Mao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai 200031, China
| | - Chenglin Liu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Zhen Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaofeng Niu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai 200031, China
| | - Liang Xue
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai 200031, China
| | - Zhilei Zhou
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai 200031, China
| | - Zhenying Cai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai 200031, China
| | - Meng Yu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai 200031, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 200031, China
| | - Yixue Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Dianqing Wu
- Vascular Biology and Therapeutic Program and Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Lin Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai 200031, China
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13
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Venkatesham A, Kachare D, Schepers G, Rozenski J, Froeyen M, Van Aerschot A. Hybridisation potential of 1',3'-Di-O-methylaltropyranoside nucleic acids. Molecules 2015; 20:4020-41. [PMID: 25741897 PMCID: PMC6272658 DOI: 10.3390/molecules20034020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 02/16/2015] [Accepted: 02/24/2015] [Indexed: 01/16/2023] Open
Abstract
In further study of our series of six-membered ring-containing nucleic acids, different 1',3'-di-O-methyl altropyranoside nucleoside analogs (DMANA) were synthesized comprising all four base moieties, adenine, cytosine, uracil and guanine. Following assembly into oligonucleotides (ONs), their affinity for natural oligonucleotides was evaluated by thermal denaturation of the respective duplexes. Data were compared with results obtained previously for both anhydrohexitol (HNAs) and 3'-O-methylated altrohexitol modified ONs (MANAs). We hereby demonstrate that ONs modified with DMANA monomers, unlike some of our previously described analogues with constrained 6-membered hexitol rings, did not improve thermodynamic stability of dsRNA complexes, most probably in view of an energetic penalty when forced in the required 1C4 pairing conformation. Overall, a single incorporation was more or less tolerated or even positive for the adenine congener, but incorporation of a second modification afforded a slight destabilization (except for A), while a fully modified sequence displayed a thermal stability of -0.3 °C per modification. The selectivity of pairing remained very high, and the new modification upon incorporation into a DNA strand, strongly destabilized the corresponding DNA duplexes. Unfortunately, this new modification does not bring any advantage to be further evaluated for antisense or siRNA applications.
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Affiliation(s)
- Akkaladevi Venkatesham
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Dhuldeo Kachare
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Guy Schepers
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Mathy Froeyen
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
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