Quantitation of murine stroma and selective purification of the human tumor component of patient-derived xenografts for genomic analysis

PLoS ONE

Volumn 11, Issue 9, 2016, Pages

  Schneeberger, Valentina E ^a   Allaj, Viola ^a   Gardner, Eric E ^b   Poirier, J T ^a,c   Rudin, Charles M ^a,c  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

AMPLICON; ANIMAL CELL; ARTICLE; CANCER CELL LINE; CELL ISOLATION; COMPUTER MODEL; CONTROLLED STUDY; DNA DETERMINATION; FLUORESCENCE ACTIVATED CELL SORTING; GENOMICS; HISTOLOGY; HUMAN; HUMAN CELL; IMMUNOMAGNETIC SEPARATION; INTERMETHOD COMPARISON; LUNG CANCER; MULTIGENE FAMILY; MUTATIONAL ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; SEPARATION TECHNIQUE; SPECIES DIFFERENCE; STROMA; TUMOR XENOGRAFT; ANIMAL; BIOLOGY; DISEASE MODEL; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; MOUSE; NEOPLASM; PATHOLOGY; PROCEDURES; STROMA CELL; XENOGRAFT;

ANIMALS; COMPUTATIONAL BIOLOGY; DISEASE MODELS, ANIMAL; GENOMICS; HETEROGRAFTS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICE; NEOPLASMS; STROMAL CELLS;

EID: 84991275983     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0160587     Document Type: Article

References (40)

1. Khaled WT, Liu P. Cancer mouse models: past, present and future. Seminars in cell & developmental biology. 2014; 27:54-60. doi: 10.1016/j.semcdb.2014.04.003 PMID: 24718321.
2. Das Thakur M, Pryer NK, Singh M. Mouse tumour models to guide drug development and identify resistance mechanisms. J Pathol. 2014; 232(2):103-11. doi: 10.1002/path.4285 PMID: 24122209.
3. Gillet JP, Varma S, Gottesman MM. The clinical relevance of cancer cell lines. J Natl Cancer Inst. 2013; 105(7):452-8. doi: 10.1093/jnci/djt007 PMID: 23434901; PubMed Central PMCID: PMC3691946.
4. Dangles-Marie V, Pocard M, Richon S, Weiswald LB, Assayag F, Saulnier P, et al. Establishment of human colon cancer cell lines from fresh tumors versus xenografts: comparison of success rate and cell line features. Cancer Res. 2007; 67(1):398-407. doi: 10.1158/0008-5472.CAN-06-0594 PMID: 17210723.
5. Daniel VC, Marchionni L, Hierman JS, Rhodes JT, Devereux WL, Rudin CM, et al. A primaryxenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro. Cancer Res. 2009; 69(8):3364-73. doi: 10.1158/0008-5472.CAN-08-4210 PMID: 19351829; PubMed Central PMCID: PMC2821899.
6. Lefrancois D, Olschwang S, Delattre O, Muleris M, Dutrillaux AM, Thomas G, et al. Preservation of chromosome and DNA characteristics of human colorectal adenocarcinomas after passage in nude mice. Int J Cancer. 1989; 44(5):871-8. PMID: 2573580.
7. Rosfjord E, Lucas J, Li G, Gerber HP. Advances in patient-derived tumor xenografts: from target identification to predicting clinical response rates in oncology. Biochem Pharmacol. 2014; 91(2):135-43. doi: 10.1016/j.bcp.2014.06.008 PMID: 24950467.
8. Rubio-Viqueira B, Jimeno A, Cusatis G, Zhang X, Iacobuzio-Donahue C, Karikari C, et al. An in vivo platform for translational drug development in pancreatic cancer. Clin Cancer Res. 2006; 12(15):4652-61. doi: 10.1158/1078-0432.CCR-06-0113 PMID: 16899615.
9. Siolas D, Hannon GJ. Patient-derived tumor xenografts: transforming clinical samples into mouse models. Cancer Res. 2013; 73(17):5315-9. doi: 10.1158/0008-5472.CAN-13-1069 PMID: 23733750; PubMed Central PMCID: PMC3766500.
10. Burg-Kurland CL, Purnell DM, Combs JW, Valerio MG, Harris CC, Trump BF. Immunocytochemical evaluation of primaryhuman esophageal carcinomas and their xenografts for keratin, beta-chorionic gonadotropin, placental lactogen, alpha-fetoprotein, carcinoembryonic antigen, and nonspecific crossreacting antigen. Cancer Res. 1986; 46(11):5730-7. PMID: 2428482.
11. Gray DR, Huss WJ, Yau JM, Durham LE, Werdin ES, Funkhouser WK Jr., et al. Short-termhuman prostate primaryxenografts: an in vivo model of human prostate cancer vasculature and angiogenesis. Cancer Res. 2004; 64(5):1712-21. PMID: 14996731.
12. Huang P, Westmoreland SV, Jain RK, Fukumura D. Spontaneous nonthymic tumors in SCID mice. Comparative medicine. 2011; 61(3):227-34. PMID: 21819692; PubMed Central PMCID: PMC3123755.
13. Malaney P, Nicosia SV, Dave V. One mouse, one patient paradigm: New avatars of personalized cancer therapy. Cancer Lett. 2014; 344(1):1-12. doi: 10.1016/j.canlet.2013.10.010 PMID: 24157811; PubMed Central PMCID: PMC4092874.
14. Whittle JR, Lewis MT, Lindeman GJ, Visvader JE. Patient-derived xenograft models of breast cancer and their predictive power. Breast Cancer Res. 2015; 17:17. doi: 10.1186/s13058-015-0523-1 PMID: 25849559; PubMed Central PMCID: PMC4323263.
15. Hidalgo M, Amant F, Biankin AV, Budinska E, Byrne AT, Caldas C, et al. Patient-derived xenograft models: an emerging platform for translational cancer research. Cancer Discov. 2014; 4(9):998-1013. doi: 10.1158/2159-8290.CD-14-0001 PMID: 25185190; PubMed Central PMCID: PMC4167608.
16. Karagiannis GS, Poutahidis T, Erdman SE, Kirsch R, Riddell RH, Diamandis EP. Cancer-associated fibroblasts drive the progression of metastasis through both paracrine and mechanical pressure on cancer tissue. Mol Cancer Res. 2012; 10(11):1403-18. doi: 10.1158/1541-7786.MCR-12-0307 PMID: 23024188; PubMed Central PMCID: PMC4399759.
17. Curry JM, Sprandio J, Cognetti D, Luginbuhl A, Bar-ad V, Pribitkin E, et al. Tumor microenvironment in head and neck squamous cell carcinoma. Semin Oncol. 2014; 41(2):217-34. doi: 10.1053/j. seminoncol.2014.03.003 PMID: 24787294.
18. Quail DF, Joyce JA. Microenvironmental regulation of tumor progression and metastasis. Nat Med. 2013; 19(11):1423-37. doi: 10.1038/nm.3394 PMID: 24202395; PubMed Central PMCID: PMC3954707.
19. Whatcott CJ, Diep CH, Jiang P, Watanabe A, LoBello J, Sima C, et al. Desmoplasia in PrimaryTumors and Metastatic Lesions of Pancreatic Cancer. Clin Cancer Res. 2015; 21(15):3561-8. doi: 10.1158/ 1078-0432.CCR-14-1051 PMID: 25695692; PubMed Central PMCID: PMC4526394.
20. Mita MM, Sargsyan L, Mita AC, Spear M. Vascular-disrupting agents in oncology. Expert opinion on investigational drugs. 2013; 22(3):317-28. doi: 10.1517/13543784.2013.759557 PMID: 23316880.
21. Von Hoff DD, Ramanathan RK, Borad MJ, Laheru DA, Smith LS, Wood TE, et al. Gemcitabine plus nab-paclitaxel is an active regimen in patients with advanced pancreatic cancer: a phase I/II trial. J Clin Oncol. 2011; 29(34):4548-54. doi: 10.1200/JCO.2011.36.5742 PMID: 21969517; PubMed Central PMCID: PMC3565012.
22. Tichet M, Prod'Homme V, Fenouille N, Ambrosetti D, Mallavialle A, Cerezo M, et al. Tumour-derived SPARC drives vascular permeability and extravasation through endothelial VCAM1 signalling to promote metastasis. Nature communications. 2015; 6:6993. doi: 10.1038/ncomms7993 PMID: 25925867.
23. Tso KY, Lee SD, Lo KW, Yip KY. Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts? BMC Genomics. 2014; 15:1172. doi: 10.1186/1471-2164-15-1172 PMID: 25539684; PubMed Central PMCID: PMCPMC4326289.
24. Rossello FJ, Tothill RW, Britt K, Marini KD, Falzon J, Thomas DM, et al. Next-generation sequence analysis of cancer xenograft models. PloS one. 2013; 8(9):e74432. doi: 10.1371/journal.pone.0074432 PMID: 24086345; PubMed Central PMCID: PMCPMC3784448.
25. Conway T, Wazny J, Bromage A, Tymms M, Sooraj D, Williams ED, et al. Xenome-a tool for classifying reads from xenograft samples. Bioinformatics. 2012; 28(12):i172-8. doi: 10.1093/bioinformatics/ bts236 PMID: 22689758; PubMed Central PMCID: PMCPMC3371868.
26. Lin MT, Tseng LH, Kamiyama H, Kamiyama M, Lim P, Hidalgo M, et al. Quantifying the relative amount of mouse and human DNA in cancer xenografts using species-specific variation in gene length. Bio-Techniques. 2010; 48(3):211-8. Epub 2010/04/03. doi: 10.2144/000113363 PMID: 20359302; PubMed Central PMCID: PMC3065779.
27. Cheng DT, Mitchell TN, Zehir A, Shah RH, Benayed R, Syed A, et al. Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology. The Journal of molecular diagnostics: JMD. 2015; 17(3):251-64. doi: 10.1016/j.jmoldx.2014.12.006 PMID: 25801821.
28. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. doi: 10.1093/bioinformatics/btp324 PMID: 19451168; PubMed Central PMCID: PMCPMC2705234.
29. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. doi: 10.1093/bioinformatics/btp352 PMID: 19505943; PubMed Central PMCID: PMCPMC2723002.
30. Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, et al. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nature methods. 2015; 12(7):623-30. doi: 10.1038/nmeth.3407 PMID: 25984700; PubMed Central PMCID: PMCPMC4856034.
31. Yalcin B, Wong K, Bhomra A, Goodson M, Keane TM, Adams DJ, et al. The fine-scale architecture of structural variants in 17 mouse genomes. Genome Biol. 2012; 13(3):R18. doi: 10.1186/gb-2012-13-3-r18 PMID: 22439878; PubMed Central PMCID: PMCPMC3439969.
32. Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013; 31 (3):213-9. doi: 10.1038/nbt.2514 PMID: 23396013; PubMed Central PMCID: PMC3833702.
33. Liu J, Kibiki G, Maro V, Maro A, Kumburu H, Swai N, et al. Multiplex reverse transcription PCR Luminex assay for detection and quantitation of viral agents of gastroenteritis. Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology. 2011; 50(4):308-13. doi: 10.1016/j. jcv.2010.12.009 PMID: 21256076; PubMed Central PMCID: PMC3059344.
34. Travis WD, Brambilla E, Nicholson AG, Yatabe Y, Austin JH, Beasley MB, et al. The 2015 World Health Organization Classification of Lung Tumors: Impact of Genetic, Clinical and Radiologic Advances Since the 2004 Classification. J Thorac Oncol. 2015; 10(9):1243-60. doi: 10.1097/JTO. 0000000000000630 PMID: 26291008.
35. Henderson VC, Kimmelman J, Fergusson D, Grimshaw JM, Hackam DG. Threats to validity in the design and conduct of preclinical efficacy studies: a systematic review of guidelines for in vivo animal experiments. PLoS medicine. 2013; 10(7):e1001489. doi: 10.1371/journal.pmed.1001489 PMID: 23935460; PubMed Central PMCID: PMC3720257.
36. Kris MG, Johnson BE, Berry LD, Kwiatkowski DJ, Iafrate AJ, Wistuba II, et al. Using multiplexed assays of oncogenic drivers in lung cancers to select targeted drugs. Jama. 2014; 311(19):1998-2006. Epub 2014/05/23. doi: 10.1001/jama.2014.3741 PMID: 24846037; PubMed Central PMCID: PMC4163053.
37. Gorges TM, Tinhofer I, Drosch M, Rose L, Zollner TM, Krahn T, et al. Circulating tumour cells escape from EpCAM-based detection due to epithelial-to-mesenchymal transition. BMC cancer. 2012; 12:178. doi: 10.1186/1471-2407-12-178 PMID: 22591372; PubMed Central PMCID: PMC3502112.
38. Raimondi C, Gradilone A, Gazzaniga P. Controversies in circulating tumor cell count during therapy. Expert Rev Mol Diagn. 2013; 13(5):499-507. doi: 10.1586/erm.13.33 PMID: 23782256.
39. van der Gun BT, Melchers LJ, Ruiters MH, de Leij LF, McLaughlin PM, Rots MG. EpCAM in carcinogenesis: the good, the bad or the ugly. Carcinogenesis. 2010; 31(11):1913-21. doi: 10.1093/carcin/bgq187 PMID: 20837599.
40. Engels B, Rowley DA, Schreiber H. Targeting stroma to treat cancers. Semin Cancer Biol. 2012; 22 (1):41-9. doi: 10.1016/j.semcancer.2011.12.008 PMID: 22212863; PubMed Central PMCID: PMC3321387.