|
|
Methods for Personalized Drug Effectiveness Prediction in Cancer Precision Medicine |
WANG Hongqiang1, GU Kangshen2 |
1.Precision Medicine and Biomedical Bigdata Laboratory, Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei 230031 2.Department of Tumor, The First Affiliated Hospital of Medical University of Anhui, Hefei 230031 |
|
|
Abstract How to efficiently predict individual drug effectiveness is a hot topic of cancer research. In this paper, the way to precisely estimate and predict the effectiveness of targeted-drugs of a specific patient is analyzed by reviewing and examining the basic theory and the development of targeted treatment of cancer. A paradigm of genetic testing, cancerization genetic testing mode, is proposed. Recently developed high-throughput sequencing technique is utilized and molecular pathology of individual patient based on artificial intelligence are systematically analyzed and precisely diagnosed in this mode. The conventional genetic testing paradigm only focuses on mutation detection using low-throughput sequencing technologies with one-sided and seriously biased diagnosis and the shortcoming is overcome by the cancerization testing model with over-simplicity for realizing the precision medicine. Furthermore the clinical practice of the proposed mode is discussed.
|
Received: 17 December 2016
|
|
Fund:Supported by National Natural Science Foundation of China(No.61402010,61374181), Natural Science Foundation of Anhui Province(No.1408085MF133) |
About author:: (WANG Hongqiang(Corresponding author), born in 1977, Ph.D., professor. His research interests include bioinformatics, preci-sion medicine and pattern recognition.)(GU Kangsheng, born in 1964, Ph.D., professor. His research interests include precision medicine, cancer treatment, and personalized medicine.) |
|
|
|
[1] MATSUMOTO T, SHIMIZU T, TAKAI A, et al. Exploring the Mechanisms of Gastrointestinal Cancer Development Using Deep Sequencing Analysis. Cancers, 2015, 7(2): 1037-1051. [2] BOGELSTEIN B, PAPADOPOULOS N, VELCULESCU V E, et al. Cancer Genome Landscapes. Science, 2013, 339(6127): 1546-1558. [3] SUN H J, CHEN J, NI B, et al. Recent Advances and Current Issues in Single-Cell Sequencing of Tumors. Cancer Letters, 2015, 365(1): 1-10. [4] LITCHFIELD K, SUMMERSGILL B, YOST S, et al. Whole-Exome Sequencing Reveals the Mutational Spectrum of Testicular Germ Cell Tumours. Nature Communications, 2015. DOI: 10.1038/ncomms6973. [5] MARGARET A, HAMBURG M D. Paving the Way for Personalized Medicine: FDA's Role in a New Era of Medical Product Development[M/OL]. [2016-08-25]. http://www.fda.gov/downloads/ScienceResearch/SpecialTopics/PersonalizedMedicine/UCM372421.pdf. [6] National Research Council. Toward Precision Medicine: Building a Knowledge Network for Biomedical Research and a New Taxonomy of Disease[M/OL]. [2016-08-25]. https://www.nap.edu/catalog/13284/. [7] LI G H, HUANG J F. Inferring Therapeutic Targets from Heterogeneous Data: HKDC1 Is a Novel Potential Therapeutic Target for Cancer. Bioinformatics, 2013, 30(6): 748-752. [8] DOBBELSTEIN M, MOLL U. Targeting Tumour-Supportive Cellular Machineries in Anticancer Drug Development. Nature Reviews Drug Discovery, 2014, 13(3): 179-196. [9] KRATZ J R, HE J X, VAN DEN EEDEN S K, et al. A Practical Molecular Assay to Predict Survival in Resected Non-squamous, Non-small-cell Lung Cancer: Development and International Validation Studies. The Lancet, 2012, 379(9818): 823-832. [10] TANNOCK I F, HICKMAN J A. Limits to Personalized Cancer Medicine. New England Journal of Medicine, 2016, 375(13): 1289-1294. [11] PRASAD V. Perspective: The Precision-Oncology Illusion. Nature, 2016, 537(7619).DOI: 10.1038/537s63a. [12] NORMILE D. China's Sequencing Powerhouse Comes of Age. Science, 2012, 335(6068): 516-519. [13] RUBIN M A. Make Precision Medicine Work for Cancer Care. Nature, 2015, 520(7547): 290-291. [14] 王雅杰,王 宁.肿瘤分子靶向药物分类及作用机制.中国实用外科杂志, 2010, 30(7): 526-528. (WANG Y J, WANG N. Types of Tumor Molecular Targeted Therapies and Mechanisms of Artificial. Chinese Journal of Practical Surgery, 2010, 30(7): 526-528.) [15] EDER J, SEDRANI R, WIESMANN C. The Discovery of First-in-Class Drugs: Origins and Evolution. Nature Reviews Drug Discovery, 2014, 13(8): 577-587. [16] ROTH A D, TEJPAR S, DELORENZI M, et al. Prognostic Role of KRAS and BRAF in Stage II and III Resected Colon Cancer: Results of the Translational Study on the PETACC-3, EORTC 40993, SAKK 60-00 Trial. Journal of Clinical Oncology, 2010, 28(3): 466-474. [17] PRAHALLAD A, SUN C, HUANG S D, et al. Unresponsiveness of Colon Cancer to BRAF(V600E) Inhibition through Feedback Activation of EGFR. Nature, 2012, 483(7388): 100-103. [18] CHAPMAN P B, HAUSCHILD A, ROBERT C, et al. Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation. New England Journal of Medicine, 2011, 364(26): 2507-2516. [19] POULIKAKOS P I, PERSAUD Y, JANAKIRAMAN M, et al. RAF Inhibitor Resistance Is Mediated by Dimerization of Aberrantly Spliced BRAF(V600E). Nature, 2011, 480(7377): 387-390. [20] NAZARIAN R, SHI H B, WANG Q, et al. Melanomas Acquire Resistance to B-RAF(V600E) Inhibition by RTK or N-RAS Upregulation. Nature, 2010, 468(7326): 973-977. [21] DOUILLARD J Y, KIM E, HIRSH V. Gefitinib(IRESSA) versus Docetaxel in Patients with Locally Advanced or Metastatic Non-small-Cell Lung Cancer Pre-treated with Platinum-Based Chemotherapy: A Randomized, Open-Label Phase III Study (INTEREST). Journal of Thoracic Oncology, 2007, 2(8): S305-S306. [22] JIANG Y C, QIU Y, MINN A , et al. Assessing Intratumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing. Proceeding of the National Academy of Sciences of the United States of America, 2016, 113(37): E5528-E5537. [23] DULBECCO R. A Turning Point in Cancer Research: Sequencing the Human Genome. Science, 1986, 231(4742): 1055-1056. [24] WANG H Q, ZHENG C H, ZHAO X M. jNMFMA: A Joint Non-negative Matrix Factorization Meta-analysis of Transcriptomics Data. Bioinformatics, 2015, 31(4): 572-580. [25] ZENG T, SUN S Y, WANG Y, et al. Network Biomarkers Reveal Dysfunctional Gene Regulations during Disease Progression. FEBS Journal, 2013, 280(22): 5682-5695. [26] WANG H Q, TSAI C J. CorSig: A General Framework for Estimating Statistical Significance of Correlation and Its Application to Gene Co-expression Analysis. PLoS ONE, 2013, 8(10): e77429. [27] WANG H Q, WONG H S, ZHU H L, et al. A Neural Network-Based Biomarker Association Information Extraction Approach for Cancer Classification. Journal of Biomedical Informatics, 2009, 42(4): 654-666. [28] BROOKSBANK C, BERGMAN M T, APWEILER R, et al. The European Bioinformatics Institute's Data Resources 2014. Nucleic Acids Research, 2014. 42(D1): D18-D25. [29] ZHU F, SHI Z, QIU C, et al. Therapeutic Target Database Update 2012: A Resource for Facilitating Target-Oriented Drug Discovery. Nucleic Acids Research, 2012, 40(D1): D1128-D1136. [30] CREIXELL P, SCHOOF E M, SIMPSON C D, et al. Kinome-Wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling. Cell, 2016, 163(1): 202-217. [31] NEAPOLITAN R, HORVATH C, JIANG X. Pan-cancer Analysis of TCGA Data Reveals Notable Signaling Pathways. BMC Cancer, 2015, 15(1). DOI: 10.1186/s12885-015-1484-6. [32] MA X K ,GAO L, KARAMANLIDIS G, et al. Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks. PLoS Computational Biology, 2015. 11(6): e1004332. [33] AKSOY B A, DEMIR E, BABUR , et al. Prediction of Individualized Therapeutic Vulnerabilities in Cancer from Genomic Profiles. Bioinformatics, 2014, 30(14): 2051-2059. [34] LOSCALZO J. Systems Biology and Personalized Medicine. Proceedings of the American Thoracic Society, 2011, 8(2): 196-198. [35] HOOD L, HEATH J R, PHELPS M E, et al. Systems Biology and New Technologies Enable Predictive and Preventative Medicine. Science, 2004, 306(5696): 640-643. [36] LU C, KING R D. An Investigation into the Population Abundance Distribution of mRNAs, Proteins, and Metabolites in Biological Systems. Bioinformatics, 2009, 25(16): 2020-2027. [37] ZADRAN S, REMACLE F, LEVINE R D. miRNA and mRNA Cancer Signatures Determined by Analysis of Expression Levels in Large Cohorts of Patients. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(47): 19160-19165. [38] SCHADT E E. Molecular Networks as Sensors and Drivers of Common Human Diseases. Nature, 2009, 461(7261): 218-223. [39] BARABSI A, GULBAHCE N, LOSCALZO J. Network Medicine: A Network-Based Approach to Human Disease. Nature Reviews Genetics, 2011, 12: 56-68. [40] AUFFRAY C, CHEN Z, HOOD L. Systems Medicine: The Future of Medical Genomics and Healthcare. Genome Medicine, 2009, 1(1). DOI: 10.1186/gm2. [41] BIBAULT J E, FUMAGALLI I, FERT C, et al. Personalized Radiation Therapy and Biomarker-Driven Treatment Strategies: A Systematic Review. Cancer and Metastasis Reviews, 2013, 32(3): 479-492. [42] 钱其军,吴孟超.肿瘤精准细胞免疫治疗:梦想照进现实.中国 肿瘤生物治疗杂志, 2015, 22(2): 151-158. (QIAN Q J, WU M C. Cancer Precision Cell Immunotherapy: Dream into Reality. Chinese Journal of Cancer Biotherapy, 2015, 22(2): 151-158.) [43] RADOVICH M, KIEL P J, NANCE S M, et al. Clinical Benefit of a Precision Medicine Based Approach for Guiding Treatment of Refractory Cancers. Oncotarget, 2016, 7(35): 56491-56500. [44] CHEN Y A, TRIPATHI L P, DESSAILLY B H, et al. Integrated Pathway Clusters with Coherent Biological Themes for Target Prioritisation. PLoS ONE, 2014, 9(6): e99030. [45] MA H, ZHAO H. Drug Target Inference through Pathway Analysis of Genomics Data. Advanced Drug Delivery Reviews, 2013, 65(7): 966-972. [46] MCCORMICK F. Signalling Networks That Cause Cancer. Trends in Cell Biology, 1999, 9(12): 53-56. [47] BARBIE D A, TAMOYO P, BOEHM J S, et al. Systematic RNA Interference Reveals that Oncogenic KRAS-Driven Cancers Require TBK1. Nature, 2009, 462(7269): 108-112. [48] DOWNWARD J. Signatures Guide Drug Choice. Nature, 2006, 439: 274-275. [49] SOLIT D B, GARRAWAY L A, PRATILAS C A, et al. BRAF Mutation Predicts Sensitivity to MEK Inhibition. Nature, 2006, 439(7074): 358-362. [50] KALF R R J, MIHAESCU R, KUNDU S, et al. Variations in Predicted Risks in Personal Genome Testing for Common Complex Diseases. Genetics in Medicine, 2014, 16(1): 85-91. [51] STERCKX S, COCKBAIN J, HOWARD H, et al. "Trust Is Not Something You Can Reclaim Easily": Patenting in the Field of Direct-to-Consumer Genetic Testing. Genetics in Medicine, 2013, 15(5): 382-387. [52] MICHOR F, BEAL K. Improving Cancer Treatment via Mathematical Modeling: Surmounting the Challenges Is Worth the Effort. Cell, 2015, 163(5): 1059-1063. |
|
|
|