Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research

BMC Medical Genomics

Volumn 8, Issue 2, 2015, Pages

  Chen, Bin ^a   Sirota, Marina ^a   Fan Minogue, Hua ^a   Hadley, Dexter ^a   Butte, Atul J ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER CELL LINE; CLINICAL FEATURE; CONTROLLED STUDY; CORRELATIONAL STUDY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE OVEREXPRESSION; LIVER CELL CARCINOMA; PRIMARY TUMOR; PRIORITY JOURNAL; RNA SEQUENCE; SAMPLING; TRANSCRIPTOMICS; TRANSLATIONAL RESEARCH; TUMOR SAMPLE; GENE EXPRESSION REGULATION; GENE ONTOLOGY; GENETICS; HUMAN; LIVER TUMOR; NONPARAMETRIC TEST; TUMOR CELL LINE;

CARCINOMA, HEPATOCELLULAR; CELL LINE, TUMOR; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE ONTOLOGY; HUMANS; LIVER NEOPLASMS; STATISTICS, NONPARAMETRIC; TRANSLATIONAL MEDICAL RESEARCH;

EID: 84962473749     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-8-S2-S5     Document Type: Article

References (35)

1. Wilding JL, Bodmer WF: Cancer cell lines for drug discovery and development. Cancer research. 2014, 74 (9): 2377-2384. 10.1158/0008-5472.CAN-13-2971.
2. Gazdar AF, Girard L, Lockwood WW, Lam WL, Minna JD: Lung cancer cell lines as tools for biomedical discovery and research. Journal of the National Cancer Institute. 2010, 102 (17): 1310-1321. 10.1093/jnci/djq279.
3. Gillet JP, Varma S, Gottesman MM: The clinical relevance of cancer cell lines. Journal of the National Cancer Institute. 2013, 105 (7): 452-458. 10.1093/jnci/djt007.
4. Gazdar AF, Gao B, Minna JD: Lung cancer cell lines: Useless artifacts or invaluable tools for medical science?. Lung cancer. 2010, 68 (3): 309-318. 10.1016/j.lungcan.2009.12.005.
5. Sandberg R, Ernberg I: Assessment of tumor characteristic gene expression in cell lines using a tissue similarity index (TSI). Proceedings of the National Academy of Sciences of the United States of America. 2005, 102 (6): 2052-2057. 10.1073/pnas.0408105102.
6. Wang H, Huang S, Shou J, Su EW, Onyia JE, Liao B, Li S: Comparative analysis and integrative classification of NCI60 cell lines and primary tumors using gene expression profiling data. BMC Genomics. 2006, 7: 166-10.1186/1471-2164-7-166.
7. Ertel A, Verghese A, Byers SW, Ochs M, Tozeren A: Pathway-specific differences between tumor cell lines and normal and tumor tissue cells. Molecular cancer. 2006, 5 (1): 55-10.1186/1476-4598-5-55.
8. Stein WD, Litman T, Fojo T, Bates SE: A Serial Analysis of Gene Expression (SAGE) database analysis of chemosensitivity: comparing solid tumors with cell lines and comparing solid tumors from different tissue origins. Cancer research. 2004, 64 (8): 2805-2816. 10.1158/0008-5472.CAN-03-3383.
9. Jahchan NS, Dudley JT, Mazur PK, Flores N, Yang D, Palmerton A, Zmoos AF, Vaka D, Tran KQ, Zhou M, et al: A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors. Cancer discovery. 2013, 3 (12): 1364-1377. 10.1158/2159-8290.CD-13-0183.
10. Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ: Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med. 2011, 3 (96): 96ra77
11. Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ: Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Science translational medicine. 2011, 3 (96): 96ra76
12. Zerbini LF, Bhasin MK, de Vasconcellos JF, Paccez JD, Gu X, Kung AL, Libermann TA: Computational repositioning and preclinical validation of pentamidine for renal cell cancer. Mol Cancer Ther. 2014, 13 (7): 1929-1941. 10.1158/1535-7163.MCT-13-0750.
13. Dudley JT, Chen R, Butte AJ: Matching cancer genomes to established cell lines for personalized oncology. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing. 2011, 243-252.
14. Cancer Genome Atlas Research N, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM: The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013, 45 (10): 1113-1120. 10.1038/ng.2764.
15. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehar J, Kryukov GV, Sonkin D, et al: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012, 483 (7391): 603-607. 10.1038/nature11003.
16. Domcke S, Sinha R, Levine DA, Sander C, Schultz N: Evaluating cell lines as tumour models by comparison of genomic profiles. Nature communications. 2013, 4: 2126
17. Rahib L, Smith BD, Aizenberg R, Rosenzweig AB, Fleshman JM, Matrisian LM: Projecting cancer incidence and deaths to 2030: the unexpected burden of thyroid, liver, and pancreas cancers in the United States. Cancer research. 2014, 74 (11): 2913-2921. 10.1158/0008-5472.CAN-14-0155.
18. Villanueva A, Llovet JM: Targeted therapies for hepatocellular carcinoma. Gastroenterology. 2011, 140 (5): 1410-1426. 10.1053/j.gastro.2011.03.006.
19. Bagi CM, Andresen CJ: Models of hepatocellular carcinoma and biomarker strategy. Cancers. 2010, 2 (3): 1441-1452. 10.3390/cancers2031441.
20. Lee JH, Ku JL, Park YJ, Lee KU, Kim WH, Park JG: Establishment and characterization of four human hepatocellular carcinoma cell lines containing hepatitis B virus DNA. World journal of gastroenterology: WJG. 1999, 5 (4): 289-295.
21. Expression Project for Oncology. [ http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2109 ]
22. Marin JJ, Martinez-Becerra P, Rosales R, Monte MJ: Chemotherapy in the treatment of primary liver tumours. Cancer Therapy. 2008, 6 (2)
23. Huang da W, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009, 4 (1): 44-57.
24. Chao Y, Chan WK, Birkhofer MJ, Hu OY, Wang SS, Huang YS, Liu M, Whang-Peng J, Chi KH, Lui WY, et al: Phase II and pharmacokinetic study of paclitaxel therapy for unresectable hepatocellular carcinoma patients. Br J Cancer. 1998, 78 (1): 34-39. 10.1038/bjc.1998.438.
25. Wilkening S, Stahl F, Bader A: Comparison of primary human hepatocytes and hepatoma cell line Hepg2 with regard to their biotransformation properties. Drug Metab Dispos. 2003, 31 (8): 1035-1042. 10.1124/dmd.31.8.1035.
26. Westerink WM, Schoonen WG: Cytochrome P450 enzyme levels in HepG2 cells and cryopreserved primary human hepatocytes and their induction in HepG2 cells. Toxicology in vitro: an international journal published in association with BIBRA. 2007, 21 (8): 1581-1591. 10.1016/j.tiv.2007.05.014.
27. Brandon EF, Raap CD, Meijerman I, Beijnen JH, Schellens JH: An update on in vitro test methods in human hepatic drug biotransformation research: pros and cons. Toxicology and applied pharmacology. 2003, 189 (3): 233-246. 10.1016/S0041-008X(03)00128-5.
28. Guo L, Dial S, Shi L, Branham W, Liu J, Fang JL, Green B, Deng H, Kaput J, Ning B: Similarities and differences in the expression of drug-metabolizing enzymes between human hepatic cell lines and primary human hepatocytes. Drug Metab Dispos. 2011, 39 (3): 528-538. 10.1124/dmd.110.035873.
29. Xin H, Wang K, Hu G, Xie F, Ouyang K, Tang X, Wang M, Wen D, Zhu Y, Qin X: Establishment and characterization of 7 novel hepatocellular carcinoma cell lines from patient-derived tumor xenografts. PloS one. 2014, 9 (1): e85308-10.1371/journal.pone.0085308.
30. Igney FH, Krammer PH: Immune escape of tumors: apoptosis resistance and tumor counterattack. Journal of leukocyte biology. 2002, 71 (6): 907-920.
31. Mills JB, Rose KA, Sadagopan N, Sahi J, de Morais SM: Induction of drug metabolism enzymes and MDR1 using a novel human hepatocyte cell line. J Pharmacol Exp Ther. 2004, 309 (1): 303-309. 10.1124/jpet.103.061713.
32. Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J, et al: Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature. 2012, 483 (7391): 570-575. 10.1038/nature11005.
33. Chen R, Li L, Butte AJ: AILUN: reannotating gene expression data automatically. Nat Methods. 2007, 4 (11): 879-10.1038/nmeth1107-879.
34. Guo Y, Sheng Q, Li J, Ye F, Samuels DC, Shyr Y: Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data. PloS one. 2013, 8 (8): e71462-10.1371/journal.pone.0071462.
35. Anders S, Huber W: Differential expression analysis for sequence count data. Genome biology. 2010, 11 (10): R106-10.1186/gb-2010-11-10-r106.