Transforming pluripotency: An exon-level study of malignancy-specific transcripts in human embryonal carcinoma and embryonic stem cells

Stem Cells and Development

Volumn 22, Issue 7, 2013, Pages 1136-1146

  Alagaratnam, Sharmini ^a,b   Harrison, Neil ^c   Bakken, Anne Cathrine ^a,b   Hoff, Andreas M ^a,b   Jones, Mark ^c   Sveen, Anita ^a   Moore, Harry D ^c   Andrews, Peter W ^c   Lothe, Ragnhild A ^a,b   Skotheim, Rolf I ^a,b  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b OSLO UNIVERSITY HOSPITAL   (Norway)

^c UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CARBONATE DEHYDRATASE; CHOLECYSTOKININ B RECEPTOR; DNA METHYLTRANSFERASE 3B; DOCKING PROTEIN; LIVER RECEPTOR HOMOLOG 1; NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE; PROTEIN KINASE C; TRANSGELIN; WNT PROTEIN; ZINC FINGER PROTEIN;

ALTERNATIVE RNA SPLICING; ARTICLE; CANCER STEM CELL; CELL CYCLE REGULATION; CELL SELECTION; CELL TRANSFORMATION; CHORIOCARCINOMA; CHROMOSOME 12; CHROMOSOME 15; DNA EXTRACTION; DNA METHYLATION; EMBRYO DEVELOPMENT; EMBRYONAL CARCINOMA; EMBRYONIC STEM CELL; FEEDER CELL; GENE DOSAGE; GENE EXPRESSION; HISTOLOGY; HUMAN; HUMAN CELL; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; PROMOTER REGION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION; RNA PURIFICATION; SEMINOMA; TERATOMA; TESTIS; YOLK SAC TUMOR;

ALTERNATIVE SPLICING; CARCINOMA, EMBRYONAL; CELL DIFFERENTIATION; CELL LINE; CELL LINE, TUMOR; CELL TRANSFORMATION, NEOPLASTIC; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; DNA-BINDING PROTEINS; EMBRYONAL CARCINOMA STEM CELLS; EMBRYONIC STEM CELLS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HUMANS; NUCLEAR PROTEINS; PLURIPOTENT STEM CELLS; RECEPTORS, CYTOPLASMIC AND NUCLEAR; TRANSCRIPTION FACTORS; TRANSCRIPTOME; WNT SIGNALING PATHWAY;

EID: 84875946522     PISSN: 15473287     EISSN: 15578534     Source Type: Journal    
DOI: 10.1089/scd.2012.0369     Document Type: Article

References (52)

1. Gupta PB, CL Chaffer and RA Weinberg. (2009). Cancer stem cells: mirage or reality? Nat Med 15:1010-1012.
2. Cairns J. (1975). Mutation selection and the natural history of cancer. Nature 255:197-200.
3. Mullighan CG, S Goorha, I Radtke, CB Miller, E Coustan- Smith, JD Dalton, K Girtman, S Mathew, J Ma, et al. (2007). Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446:758-764.
4. Ieta K, F Tanaka, N Haraguchi, Y Kita, H Sakashita, K Mimori, T Matsumoto, H Inoue, H Kuwano and M Mori. (2008). Biological and genetic characteristics of tumorinitiating cells in colon cancer. Ann Surg Oncol 15:638-648.
5. Majeti R, MW Becker, Q Tian, TL Lee, X Yan, R Liu, JH Chiang, L Hood, MF Clarke and IL Weissman. (2009). Dysregulated gene expression networks in human acute myelogenous leukemia stem cells. Proc Natl Acad Sci U S A 106:3396-3401.
6. Andrews PW, MM Matin, AR Bahrami, I Damjanov, P Gokhale and JS Draper. (2005). Embryonic stem (ES) cells and embryonal carcinoma (EC) cells: opposite sides of the same coin. Biochem Soc Trans 33:1526-1530.
7. Josephson R, CJ Ording, Y Liu, S Shin, U Lakshmipathy, A Toumadje, B Love, JD Chesnut, PW Andrews, MS Rao and JM Auerbach. (2007). Qualification of embryonal carcinoma 2102Ep as a reference for human embryonic stem cell research. Stem Cells 25:437-446.
8. Sperger JM, X Chen, JS Draper, JE Antosiewicz, CH Chon, SB Jones, JD Brooks, PW Andrews, PO Brown and JA Thomson. (2003). Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors. Proc Natl Acad Sci U S A 100:13350-13355.
9. Dormeyer W, D van Hoof, SR Braam, AJR Heck, CL Mummery and J Krijgsveld. (2008). Plasma membrane proteomics of human embryonic stem cells and human embryonal carcinoma cells. J Proteome Res 7:2936-2951.
10. Looijenga LH, AJ Gillis, H Stoop, R Hersmus and JW Oosterhuis. (2007). Relevance of microRNAs in normal and malignant development, including human testicular germ cell tumours. Int J Androl 30:304-314.
11. Baker DE, NJ Harrison, E Maltby, K Smith, HD Moore, PJ Shaw, PR Heath, H Holden and PW Andrews. (2007). Adaptation to culture of human embryonic stem cells and oncogenesis in vivo. Nat Biotechnol 25:207-215.
12. Fazeli A, CG Liew, MM Matin, S Elliott, LF Jeanmeure, PC Wright, H Moore and PW Andrews. (2011). Altered patterns of differentiation in karyotypically abnormal human embryonic stem cells. Int J Dev Biol 55:175-180.
13. Kraggerud SM, RI Skotheim, J Szymanska, M Eknæs, SD Fossa, AE Stenwig, P Peltomäki and RA Lothe. (2002). Genome profiles of familial/bilateral and sporadic testicular germ cell tumors. Genes Chromosomes Cancer 34: 168-174.
14. Skotheim RI and RA Lothe. (2003). The testicular germ cell tumour genome. APMIS 111:136-151.
15. Hentze H, R Graichen and A Colman. (2007). Cell therapy and the safety of embryonic stem cell-derived grafts. Trends Biotechnol 25:24-32.
16. Andrews PW, I Damjanov, D Simon, GS Banting, C Carlin, NC Dracopoli and J Føgh. (1984). Pluripotent embryonal carcinoma clones derived from the human teratocarcinoma cell line Tera-2. Differentiation in vivo and in vitro. Lab Invest 50:147-162.
17. Skotheim RI, GE Lind, O Monni, JM Nesland, VM Abeler, SD Fossa, N Duale, G Brunborg, O Kallioniemi, PW Andrews and RA Lothe. (2005). Differentiation of human embryonal carcinomas in vitro and in vivo reveals expression profiles relevant to normal development. Cancer Res 65:5588-5598.
18. Tusher VG, R Tibshirani and G Chu. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98:5116-5121.
19. Huang DW, BT Sherman and RA Lempicki. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44-57.
20. Duncan D, N Prodduturi and B Zhang. (2010). WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit. BMC Bioinformatics 11:10.
21. Korkola JE, J Houldsworth, RS Chadalavada, AB Olshen, D Dobrzynski, VE Reuter, GJ Bosl and RS Chaganti. (2006). Down-regulation of stem cell genes, including those in a 200- kb gene cluster at 12p13.31, is associated with in vivo differentiation of human male germ cell tumors. Cancer Res 66:820-827.
22. Charafe-Jauffret E, C Ginestier, F Iovino, J Wicinski, N Cervera, P Finetti, MH Hur, ME Diebel, F Monville, et al. (2009). Breast cancer cell lines contain functional cancer stem cells with metastatic capacity and a distinct molecular signature. Cancer Res 69:1302-1313.
23. Seo DC, JM Sung, HJ Cho, H Yi, KH Seo, IS Choi, DK Kim, JS Kim, A El-Ayam and HC Shin. (2007). Gene expression profiling of cancer stem cell in human lung adenocarcinoma A549 cells. Mol Cancer 6:75.
24. Birnie R, SD Bryce, C Roome, V Dussupt, A Droop, SH Lang, PA Berry, CF Hyde, JL Lewis, et al. (2008). Gene expression profiling of human prostate cancer stem cells reveals a proinflammatory phenotype and the importance of extracellular matrix interactions. Genome Biol 9:R83.
25. Chaerkady R, CL Kerr, K Kandasamy, A Marimuthu, JD Gearhart and A Pandey. (2010). Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics 10:1359-1373.
26. Liu Y, S Shin, X Zeng, M Zhan, R Gonzalez, FJ Mueller, CM Schwartz, H Xue, H Li, et al. (2006). Genome wide profiling of human embryonic stem cells (hESCs), their derivatives and embryonal carcinoma cells to develop base profiles of U.S. Federal government approved hESC lines. BMC Dev Biol 6:20-35.
27. Enver T, S Soneji, C Joshi, J Brown, F Iborra, T Orntoft, T Thykjaer, E Maltby, K Smith, et al. (2005). Cellular differentiation hierarchies in normal and culture-adapted human embryonic stem cells. Hum Mol Genet 14:3129-3140.
28. Hayashi K, SMC Lopes, F Tang and MA Surani. (2008). Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states. Cell Stem Cell 3:391-401.
29. Saitou M, SC Barton and MA Surani. (2002). A molecular programme for the specification of germ cell fate in mice. Nature 418:293-300.
30. Bowles J, RP Teasdale, K James and P Koopman. (2003). Dppa3 is a marker of pluripotency and has a human homologue that is expressed in germ cell tumours. Cytogenet Genome Res 101:261-265.
31. Kapur K, Y Xing, Z Ouyang and W Wong. (2007). Exon arrays provide accurate assessments of gene expression. Genome Biol 8:R82.
32. Yeo M, HJ Park, DK Kim, YB Kim, JY Cheong, KJ Lee and SW Cho. (2010). Loss of SM22 is a characteristic signature of colon carcinogenesis and its restoration suppresses colon tumorigenicity in vivo and in vitro. Cancer 116:2581-2589.
33. Metzger E, A Imhof, D Patel, P Kahl, K Hoffmeyer, N Friedrichs, JM Muller, H Greschik, J Kirfel, et al. (2010). Phosphorylation of histone H3T6 by PKCbI controls demethylation at histone H3K4. Nature 464:792-796.
34. Chao C, X Han, K Ives, J Park, AA Kolokoltsov, RA Davey, MP Moyer and MR Hellmich. (2010). CCK2 receptor expression transforms non-tumorigenic human NCM356 colonic epithelial cells into tumor forming cells. Int J Cancer 126:864-875.
35. Bourdon V, F Naef, PH Rao, V Reuter, SC Mok, GJ Bosl, S Koul, VVVS Murty, RS Kucherlapati and RSK Chaganti. (2002). Genomic and expression analysis of the 12p11-p12 amplicon using EST arrays identifies two novel amplified and overexpressed genes. Cancer Res 62:6218-6223.
36. Nakamura Y, T Suzuki, Y Arai and H Sasano. (2009). 17betahydroxysteroid dehydrogenase type 11 (Pan1b) expression in human prostate cancer. Neoplasma 56:317-320.
37. Zaravinos A, GI Lambrou, I Boulalas, D Delakas and DA Spandidos. (2011). Identification of common differentially expressed genes in urinary bladder cancer. PLoS One 6:e18135.
38. Heng JCD, B Feng, J Han, J Jiang, P Kraus, JH Ng, YL Orlov, M Huss, L Yang, et al. (2010). The nuclear receptor Nr5a2 can replace Oct4 in the reprogramming of murine somatic cells to pluripotent cells. Cell Stem Cell 6:167-174.
39. Nusse R. (2008). Wnt signaling and stem cell control. Cell Res 18:523-527.
40. Logan CY and R Nusse. (2004). The Wnt signaling pathway in development and disease. Annu Rev Cell Dev Biol 20:781-810.
41. Jiang X, Y Yu, HW Yang, NYR Agar, L Frado and MD Johnson. (2010). The imprinted gene PEG3 inhibits Wnt signaling and regulates glioma growth. J Biol Chem 285:8472-8480.
42. Chand AL, KA Herridge, EW Thompson and CD Clyne. (2010). The orphan nuclear receptor LRH-1 promotes breast cancer motility and invasion. Endocr Relat Cancer 17: 965-975.
43. Schoonjans K, L Dubuquoy, J Mebis, E Fayard, O Wendling, C Haby, K Geboes and J Auwerx. (2005). Liver receptor homolog 1 contributes to intestinal tumor formation through effects on cell cycle and inflammation. Proc Natl Acad Sci U S A 102:2058-2062.
44. Wagner RT, X Xu, F Yi, BJ Merrill and AJ Cooney. (2010). Canonical Wnt/b-Catenin regulation of Liver Receptor Homolog-1 mediates pluripotency gene expression. Stem Cells 28:1794-1804.
45. Gaspar JA, MX Doss, J Winkler, V Wagh, J Hescheler, R Kolde, J Vilo, H Schulz and A Sachinidis. (2012). Gene expression signatures defining fundamental biological processes in pluripotent, early, and late differentiated embryonic stem cells. Stem Cells Dev 21:2471-2484.
46. Guo G and A Smith. (2010). A genome-wide screen in EpiSCs identifies Nr5a nuclear receptors as potent inducers of ground state pluripotency. Development 137:3185-3192.
47. The International Stem Cell Initiative. (2011). Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat Biotechnol 29:1132-1144.
48. Tang F, C Barbacioru, Y Wang, E Nordman, C Lee, N Xu, X Wang, J Bodeau, BB Tuch, et al. (2009). mRNA-Seq wholetranscriptome analysis of a single cell. Nat Methods 6: 377-382.
49. Kanai Y. (2008). Alterations of DNA methylation and clinicopathological diversity of human cancers. Pathol Int 58:544-558.
50. Soejima K, W Fang and BJ Rollins. (2003). DNA methyltransferase 3b contributes to oncogenic transformation induced by SV40T antigen and activated Ras. Oncogene 22:4723-4733.
51. Saito Y, Y Kanai, M Sakamoto, H Saito, H Ishii and S Hirohashi. (2002). Overexpression of a splice variant of DNA methyltransferase 3b, DNMT3b4, associated with DNA hypomethylation on pericentromeric satellite regions during human hepatocarcinogenesis. Proc Natl Acad Sci U S A 99:10060-10065.
52. Zwaka TP and JA Thomson. (2005). A germ cell origin of embryonic stem cells? Development 132:227-233.