PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes

Breast Cancer Research

Volumn 10, Issue 3, 2008, Pages

  Git, Anna ^a   Spiteri, Inmaculada ^a   Blenkiron, Cherie ^a   Dunning, Mark J ^a   Pole, Jessica C M ^a   Chin, Suet Feung ^a   Wang, Yanzhong ^a,b   Smith, James ^c   Livesey, Frederick J ^c   Caldas, Carlos ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; OLIGONUCLEOTIDE; RNA; TRANSFER RNA;

ARTICLE; BREAST TUMOR; CHEMISTRY; CULTURE TECHNIQUE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; HUMAN; METABOLISM; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; PATHOLOGY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TUMOR CELL LINE;

BREAST NEOPLASMS; CELL CULTURE TECHNIQUES; CELL LINE, TUMOR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MICRORNAS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; RNA, NEOPLASM; RNA, TRANSFER; TRANSCRIPTION, GENETIC;

EID: 55749102724     PISSN: 14655411     EISSN: 1465542X     Source Type: Journal    
DOI: 10.1186/bcr2109     Document Type: Article

References (79)

1. Burdall SE, Hanby AM, Lansdown MR, Speirs V. Breast cancer cell lines: friend or foe?. Breast Cancer Res 2003, 5:89-95. 154155, 12631387.
2. Gudjonsson T, Adriance MC, Sternlicht MD, Petersen OW, Bissell MJ. Myoepithelial cells: their origin and function in breast morphogenesis and neoplasia. J Mammary Gland Biol Neoplasia 2005, 10:261-272.
3. Bissell MJ, Radisky DC, Rizki A, Weaver VM, Petersen OW. The organizing principle: microenvironmental influences in the normal and malignant breast. Differentiation 2002, 70:537-546.
4. Bissell MJ. The differentiated state of normal and malignant cells or how to define a 'normal' cell in culture. Int Rev Cytol 1981, 70:27-100.
5. Whitehead RH, Bertoncello I, Webber LM, Pedersen JS. A new human breast carcinoma cell line (PMC42) with stem cell characteristics. I. Morphologic characterization. J Natl Cancer Inst 1983, 70:649-661.
6. Whitehead RH, Monaghan P, Webber LM, Bertoncello I, Vitali AA. A new human breast carcinoma cell line (PMC42) with stem cell characteristics. II. Characterization of cells growing as organoids. J Natl Cancer Inst 1983, 71:1193-1203.
7. Whitehead RH, Quirk SJ, Vitali AA, Funder JW, Sutherland RL, Murphy LC. A new human breast carcinoma cell line (PMC42) with stem cell characteristics. III. Hormone receptor status and responsiveness. J Natl Cancer Inst 1984, 73:643-648.
8. Ackland ML, Newgreen DF, Fridman M, Waltham MC, Arvanitis A, Minichiello J, Price JT, Thompson EW. Epidermal growth factor-induced epithelio-mesenchymal transition in human breast carcinoma cells. Lab Invest 2003, 83:435-448.
9. Ackland ML, Michalczyk A, Whitehead RH. PMC42, a novel model for the differentiated human breast. Exp Cell Res 2001, 263:14-22.
10. Zhang H, Wang ZZ. Mechanisms that mediate stem cell self-renewal and differentiation. J Cell Biochem 2008, 103:709-718.
11. Hobert O. Architecture of a microRNA-controlled gene regulatory network that diversifies neuronal cell fates. Cold Spring Harb Symp Quant Biol 2006, 71:181-188.
12. Callis TE, Chen JF, Wang DZ. MicroRNAs in skeletal and cardiac muscle development. DNA Cell Biol 2007, 26:219-225.
13. Fatica A, Rosa A, Fazi F, Ballarino M, Morlando M, De Angelis FG, Caffarelli E, Nervi C, Bozzoni I. MicroRNAs and hematopoietic differentiation. Cold Spring Harb Symp Quant Biol 2006, 71:205-210.
14. Caldas C, Brenton JD. Sizing up miRNAs as cancer genes. Nat Med 2005, 11:712-714.
15. Hutvagner G, . (ed) MicroRNAs and cancer (entire issue). Oncogene 2006, 25:6154-6227. (ed).
16. Stamps AC, Davies SC, Burman J, O'Hare MJ. Analysis of proviral integration in human mammary epithelial cell lines immortalized by retroviral infection with a temperature-sensitive SV40 T-antigen construct. Int J Cancer 1994, 57:865-874.
17. Lasfargues EY, Ozzello L. Cultivation of human breast carcinomas. J Natl Cancer Inst 1958, 21:1131-1147.
18. Gazdar AF, Kurvari V, Virmani A, Gollahon L, Sakaguchi M, Westerfield M, Kodagoda D, Stasny V, Cunningham HT, Wistuba II, Tomlinson G, Tonk V, Ashfaq R, Leitch AM, Minna JD, Shay JW. Characterization of paired tumor and non-tumor cell lines established from patients with breast cancer. Int J Cancer 1998, 78:766-774.
19. Soule HD, Vazguez J, Long A, Albert S, Brennan M. A human cell line from a pleural effusion derived from a breast carcinoma. J Natl Cancer Inst 1973, 51:1409-1416.
20. Satya-Prakash KL, Pathak S, Hsu TC, Olive M, Cailleau R. Cytogenetic analysis on eight human breast tumor cell lines: high frequencies of 1q, 11q and HeLa-like marker chromosomes. Cancer Genet Cytogenet 1981, 3:61-73.
21. Hambly RJ, Double JA, Thompson MJ, Bibby MC. Establishment and characterisation of new cell lines from human breast tumours initially established as tumour xenografts in NMRI nude mice. Breast Cancer Res Treat 1997, 43:247-258.
22. Cell Line Identity Typing. , http://www.sanger.ac.uk/genetics/CGP/Genotyping/synlinestable.shtml
23. Davidson JM, Gorringe KL, Chin SF, Orsetti B, Besret C, Courtay-Cahen C, Roberts I, Theillet C, Caldas C, Edwards PA. Molecular cytogenetic analysis of breast cancer cell lines. Br J Cancer 2000, 83:1309-1317.
24. SKY Karyotypes and FISH analysis of Epithelial Cancer Cell Lines. , http://www.path.cam.ac.uk/~pawefish/
25. Briand P, Petersen OW, Van Deurs B. A new diploid nontumorigenic human breast epithelial cell line isolated and propagated in chemically defined medium. In Vitro Cell Dev Biol 1987, 23:181-188.
26. Soule HD, Maloney TM, Wolman SR, Peterson WD, Brenz R, McGrath CM, Russo J, Pauley RJ, Jones RF, Brooks SC. Isolation and characterization of a spontaneously immortalized human breast epithelial cell line, MCF-10. Cancer Res 1990, 50:6075-6086.
27. University of Texas MD Anderson Cancer Center breast cancer cell line database. , http://www.mdanderson.org/departments/cancerbiology/dIndex.cfm?pn=31062032-B0EB-11D4-80FB00508B603A14
28. The Department of Biochemistry & Molecular Biology, Georgetown University Nuclear Receptor Resource. , http://nrr.georgetown.edu/NRR/nrrhome.htm
29. Lawrence Berkeley National Laboratory cancer cell collection. , http://icbp.lbl.gov/breastcancer/celllines.php
30. Charafe-Jauffret E, Ginestier C, Monville F, Finetti P, Adélaïde J, Cervera N, Fekairi S, Xerri L, Jacquemier J, Birnbaum D, Bertucci F. Gene expression profiling of breast cell lines identifies potential new basal markers. Oncogene 2006, 25:2273-2284.
31. Dunning MJ, Smith ML, Ritchie ME, Tavare S. beadarray: R classes and methods for Illumina bead-based data. Bioinformatics 2007, 23:2183-2184.
32. Lönnstedt I, Rimini R, Nilsson P. Empirical bayes microarray ANOVA and grouping cell lines by equal expression levels. Stat Appl Genet Mol Biol 2005, 4:Article7.
33. BABELOMICS. New Release v3.0. , http://babelomics.bioinfo.cipf.es
34. Al-Shahrour F, Diaz-Uriarte R, Dopazo J. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 2004, 20:578-580.
35. Vaquerizas JM, Conde L, Yankilevich P, Cabezon A, Minguez P, Diaz-Uriarte R, Al-Shahrour F, Herrero J, Dopazo J. GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res 2005, (33 Web Server):W616-620. 1160260, 15980548.
36. Vaquerizas JM, Dopazo J, Diaz-Uriarte R. DNMAD: web-based diagnosis and normalization for microarray data. Bioinformatics 2004, 20:3656-3658.
37. Herrero J, Diaz-Uriarte R, Dopazo J. Gene expression data preprocessing. Bioinformatics 2003, 19:655-656.
38. CIMminer. , http://discover.nci.nih.gov/cimminer
39. Weinstein JN, Myers TG, O'Connor PM, Friend SH, Fornace AJ, Kohn KW, Fojo T, Bates SE, Rubinstein LV, Anderson NL, Buolamwini JK, van Osdol WW, Monks AP, Scudiero DA, Sausville EA, Zaharevitz DW, Bunow B, Viswanadhan VN, Johnson GS, Wittes RE, Paull KD. An information-intensive approach to the molecular pharmacology of cancer. Science 1997, 275:343-349.
40. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR. MicroRNA expression profiles classify human cancers. Nature 2005, 435:834-838.
41. Shi R, Chiang VL. Facile means for quantifying microRNA expression by real-time PCR. Biotechniques 2005, 39:519-525.
42. Pole JC, Courtay-Cahen C, Garcia MJ, Blood KA, Cooke SL, Alsop AE, Tse DM, Caldas C, Edwards PA. High-resolution analysis of chromosome rearrangements on 8p in breast, colon and pancreatic cancer reveals a complex pattern of loss, gain and translocation. Oncogene 2006, 25:5693-5706.
43. Garcia MJ, Pole JC, Chin SF, Teschendorff A, Naderi A, Ozdag H, Vias M, Kranjac T, Subkhankulova T, Paish C, Ellis I, Brenton JD, Edwards PA, Caldas C. A 1 Mb minimal amplicon at 8p11-12 in breast cancer identifies new candidate oncogenes. Oncogene 2005, 24:5235-5245.
44. Fiegler H, Carr P, Douglas EJ, Burford DC, Hunt S, Scott CE, Smith J, Vetrie D, Gorman P, Tomlinson IP, Carter NP. DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones. Genes Chromosomes Cancer 2003, 36:361-374.
45. Huang HE, Chin SF, Ginestier C, Bardou VJ, Adélaïde J, Iyer NG, Garcia MJ, Pole JC, Callagy GM, Hewitt SM, Gullick WJ, Jacquemier J, Caldas C, Chaffanet M, Birnbaum D, Edwards PA. A recurrent chromosome breakpoint in breast cancer at the NRG1/neuregulin 1/heregulin gene. Cancer Res 2004, 64:6840-6844.
46. Ijssel P, Tijssen M, Chin SF, Eijk P, Carvalho B, Hopmans E, Holstege H, Bangarusamy DK, Jonkers J, Meijer GA, Caldas C, Ylstra B. Human and mouse oligonucleotide-based array CGH. Nucleic Acids Res 2005, 33:e192. 1316119, 16361265.
47. Chin SF, Teschendorff AE, Marioni JC, Wang Y, Barbosa-Morais NL, Thorne NP, Costa JL, Pinder SE, Wiel MA, Green AR, Ellis IO, Porter PL, Tavaré S, Brenton JD, Ylstra B, Caldas C. High-resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol 2007, 8:R215. 2246289, 17925008.
48. Smyth GK, Michaud J, Scott HS. Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 2005, 21:2067-2075.
49. Herschkowitz JI, Simin K, Weigman VJ, Mikaelian I, Usary J, Hu Z, Rasmussen KE, Jones LP, Assefnia S, Chandrasekharan S, Backlund MG, Yin Y, Khramtsov AI, Bastein R, Quackenbush J, Glazer RI, Brown PH, Green JE, Kopelovich L, Furth PA, Palazzo JP, Olopade OI, Bernard PS, Churchill GA, Van Dyke T, Perou CM. Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol 2007, 8:R76. 1929138, 17493263.
50. Jongeneel CV, Iseli C, Stevenson BJ, Riggins GJ, Lal A, Mackay A, Harris RA, O'Hare MJ, Neville AM, Simpson AJ, Strausberg RL. Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. Proc Natl Acad Sci USA 2003, 100:4702-4705. 153619, 12671075.
51. Adriance MC, Inman JL, Petersen OW, Bissell MJ. Myoepithelial cells: good fences make good neighbors. Breast Cancer Res 2005, 7:190-197. 1242144, 16168137.
52. Bissell MJ, Labarge MA. Context, tissue plasticity, and cancer: are tumor stem cells also regulated by the microenvironment?. Cancer Cell 2005, 7:17-23.
53. Perou CM, Sørlie T, Eisen MB, Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lønning PE, Børresen-Dale AL, Brown PO, Botstein D. Molecular portraits of human breast tumours. Nature 2000, 406:747-752.
54. Hu Z, Fan C, Oh DS, Marron JS, He X, Qaqish BF, Livasy C, Carey LA, Reynolds E, Dressler L, Nobel A, Parker J, Ewend MG, Sawyer LR, Wu J, Liu Y, Nanda R, Tretiakova M, Ruiz Orrico A, Dreher D, Palazzo JP, Perreard L, Nelson E, Mone M, Hansen H, Mullins M, Quackenbush JF, Ellis MJ, Olopade OI, Bernard PS, Perou CM. The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 2006, 7:96. 1468408, 16643655.
55. Saito Y, Liang G, Egger G, Friedman JM, Chuang JC, Coetzee GA, Jones PA. Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells. Cancer Cell 2006, 9:435-443.
56. Mattie MD, Benz CC, Bowers J, Sensinger K, Wong L, Scott GK, Fedele V, Ginzinger D, Getts R, Haqq C. Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Mol Cancer 2006, 5:24. 1563474, 16784538.
57. Bandrés E, Cubedo E, Agirre X, Malumbres R, Zárate R, Ramirez N, Abajo A, Navarro A, Moreno I, Monzó M, García-Foncillas J. Identification by real-time PCR of 13 mature microRNAs differentially expressed in colorectal cancer and non-tumoral tissues. Mol Cancer 2006, 5:29. 1550420, 16854228.
58. Murakami Y, Yasuda T, Saigo K, Urashima T, Toyoda H, Okanoue T, Shimotohno K. Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues. Oncogene 2006, 25:2537-2545.
59. Iorio MV, Visone R, Di Leva G, Donati V, Petrocca F, Casalini P, Taccioli C, Volinia S, Liu CG, Alder H, Calin GA, Ménard S, Croce CM. MicroRNA signatures in human ovarian cancer. Cancer Res 2007, 67:8699-8707.
60. Akao Y, Nakagawa Y, Naoe T. MicroRNAs 143 and 145 are possible common onco-microRNAs in human cancers. Oncol Rep 2006, 16:845-850.
61. Iorio MV, Ferracin M, Liu CG, Veronese A, Spizzo R, Sabbioni S, Magri E, Pedriali M, Fabbri M, Campiglio M, Ménard S, Palazzo JP, Rosenberg A, Musiani P, Volinia S, Nenci I, Calin GA, Querzoli P, Negrini M, Croce CM. MicroRNA gene expression deregulation in human breast cancer. Cancer Res 2005, 65:7065-7070.
62. Yanaihara N, Caplen N, Bowman E, Seike M, Kumamoto K, Yi M, Stephens RM, Okamoto A, Yokota J, Tanaka T, Calin GA, Liu CG, Croce CM, Harris CC. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 2006, 9:189-198.
63. Blenkiron C, Goldstein LD, Thorne NP, Spiteri I, Chin SF, Dunning MJ, Barbosa-Morais NL, Teschendorff AE, Green AR, Ellis IO, Tavaré S, Caldas C, Miska EA. MicroRNA expression profiling of human breast cancer identifies new markers of tumour subtype. Genome Biol 2007, 8:R214. 2246288, 17922911.
64. Romaniuk E, McLaughlin LW, Neilson T, Romaniuk PJ. The effect of acceptor oligoribonucleotide sequence on the T4 RNA ligase reaction. Eur J Biochem 1982, 125:639-643.
65. Peltier HJ, Latham GJ. Normalization of microRNA expression levels in quantitative RT-PCR assays: identification of suitable reference RNA targets in normal and cancerous human solid tissues. RNA 2008, 14:844-852.
66. Bloomston M, Frankel WL, Petrocca F, Volinia S, Alder H, Hagan JP, Liu CG, Bhatt D, Taccioli C, Croce CM. MicroRNA expression patterns to differentiate pancreatic adenocarcinoma from normal pancreas and chronic pancreatitis. JAMA 2007, 297:1901-1908.
67. Michael MZ, SM OC, van Holst Pellekaan NG, Young GP, James RJ. Reduced accumulation of specific microRNAs in colorectal neoplasia. Mol Cancer Res 2003, 1:882-891.
68. Gaur A, Jewell DA, Liang Y, Ridzon D, Moore JH, Chen C, Ambros VR, Israel MA. Characterization of microRNA expression levels and their biological correlates in human cancer cell lines. Cancer Res 2007, 67:2456-2468.
69. Shingara J, Keiger K, Shelton J, Laosinchai-Wolf W, Powers P, Conrad R, Brown D, Labourier E. An optimized isolation and labeling platform for accurate microRNA expression profiling. RNA 2005, 11:1461-1470. 1370829, 16043497.
70. Cao H, Garcia F, McNiven MA. Differential distribution of dynamin isoforms in mammalian cells. Mol Biol Cell 1998, 9:2595-2609. 25532, 9725914.
71. Haslam SZ, Woodward TL. Host microenvironment in breast cancer development: epithelial-cell-stromal-cell interactions and steroid hormone action in normal and cancerous mammary gland. Breast Cancer Res 2003, 5:208-215. 165024, 12817994.
72. Streuli CH, Schmidhauser C, Bailey N, Yurchenco P, Skubitz AP, Roskelley C, Bissell MJ. Laminin mediates tissue-specific gene expression in mammary epithelia. J Cell Biol 1995, 129:591-603. 2120432, 7730398.
73. Grigoriadis A, Mackay A, Reis-Filho JS, Steele D, Iseli C, Stevenson BJ, Jongeneel CV, Valgeirsson H, Fenwick K, Iravani M, Leao M, Simpson AJ, Strausberg RL, Jat PS, Ashworth A, Neville AM, O'Hare MJ. Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data. Breast Cancer Res 2006, 8:R56. 1779497, 17014703.
74. Liang Y, Ridzon D, Wong L, Chen C. Characterization of microRNA expression profiles in normal human tissues. BMC Genomics 2007, 8:166. 1904203, 17565689.
75. Cheng AM, Byrom MW, Shelton J, Ford LP. Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis. Nucleic Acids Res 2005, 33:1290-1297. 552951, 15741182.
76. Flynt AS, Li N, Thatcher EJ, Solnica-Krezel L, Patton JG. Zebrafish miR-214 modulates Hedgehog signaling to specify muscle cell fate. Nat Genet 2007, 39:259-263.
77. Hornstein E, Shomron N. Canalization of development by microRNAs. Nat Genet 2006, 38(Suppl):S20-24.
78. Thomson JM, Newman M, Parker JS, Morin-Kensicki EM, Wright T, Hammond SM. Extensive post-transcriptional regulation of microRNAs and its implications for cancer. Genes Dev 2006, 20:2202-2207. 1553203, 16882971.
79. Petersen OW, Gudjonsson T, Villadsen R, Bissell MJ, Ronnov-Jessen L. Epithelial progenitor cell lines as models of normal breast morphogenesis and neoplasia. Cell Prolif 2003, 36(Suppl 1):33-44.