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Identification of known and novel germ cell cancer specific (embryonic) miRs in serum by high throughput profiling

ABSTRACT: Very recently, a number of independent studies showed that serum levels of embryonic micro-RNA (miR) clusters 371-3 and 302abc/367 are predictive for the presence of testicular type II germ cell tumors. These miRs could be used to sensitively detect SE and EC components which are indeed known to express these miRs [1-7]. This study investigates ca 750 miRs in a high throughput approach to validate these previously identified markers and identify novel potential miR markers for testicular type II germ cell tumors. 1. Belge, G., et al., Serum levels of microRNAs miR-371-3: a novel class of serum biomarkers for testicular germ cell tumors? Eur Urol, 2012. 61(5): p. 1068-9. 2. Dieckmann, K.P., et al., MicroRNAs miR-371-3 in serum as diagnostic tools in the management of testicular germ cell tumours. Br J Cancer, 2012. 107(10): p. 1754-60. 3. Gillis, A.J., et al., Targeted serum miRNA (TSmiR) test for diagnosis and follow-up of (testicular) germ cell cancer patients: a proof of principle. Mol Oncol, 2013. 7(6): p. 1083-92. 4. Gillis, A.J., et al., High-throughput microRNAome analysis in human germ cell tumours. J Pathol, 2007. 213(3): p. 319-28. 5. Murray, M.J. and N. Coleman, Testicular cancer: a new generation of biomarkers for malignant germ cell tumours. Nat Rev Urol, 2012. 9(6): p. 298-300. 6. Murray, M.J., et al., Identification of microRNAs From the miR-371~373 and miR-302 clusters as potential serum biomarkers of malignant germ cell tumors. Am J Clin Pathol, 2011. 135(1): p. 119-25. 7. Voorhoeve, P.M., et al., A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors. Cell, 2006. 124(6): p. 1169-81.

ORGANISM(S): Homo sapiens

PROVIDER: GSE59520 | GEO | 2014/10/02

SECONDARY ACCESSION(S): PRJNA255505

REPOSITORIES: GEO

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Project description:Malignant germ-cell-tumours (GCTs) are characterised by microRNA (miRNA/miR-) dysregulation, with universal over-expression of miR-371~373 and miR-302/367 clusters regardless of patient age, tumour site, or subtype (seminoma/yolk-sac-tumour/embryonal carcinoma). These miRNAs are released into the bloodstream, presumed within extracellular-vesicles (EVs) and represent promising biomarkers. Here, we comprehensively examined the role of EVs, and their miRNA cargo, on (fibroblast/endothelial/macrophage) cells representative of the testicular GCT (TGCT) tumour microenvironment (TME). Small RNA next-generation-sequencing was performed on 34 samples, comprising representative malignant GCT cell lines/EVs and controls (testis fibroblast [Hs1.Tes] cell-line/EVs and testis/ovary samples). TME cells received TGCT co-culture, TGCT-derived EVs, and a miRNA overexpression system (miR-371a-OE) to assess functional relevance. TGCT cells secreted EVs into culture media. MiR-371~373 and miR-302/367 cluster miRNAs were overexpressed in all TGCT cells/subtypes compared with control cells and were highly abundant in TGCT-derived EVs, with miR-371a-3p/miR-371a-5p the most abundant. TGCT co-culture resulted in increased levels of miRNAs from the miR-371~373 and miR-302/367 clusters in TME (fibroblast) cells. Next, fluorescent labelling demonstrated TGCT-derived EVs were internalised by all TME (fibroblast/endothelial/macrophage) cells. TME (fibroblast/endothelial) cell treatment with EVs derived from different TGCT subtypes resulted in increased miR-371~373 and miR-302/367 miRNA levels, and other generic (eg, miR-205-5p/miR-148-3p) and subtype-specific (seminoma, eg, miR-203a-3p; yolk-sac-tumour, eg, miR-375-3p) miRNAs. MiR-371a-OE in TME cells resulted in increased collagen contraction (fibroblasts) and angiogenesis (endothelial cells), via direct mRNA downregulation and alteration of relevant pathways. TGCT cells communicate with nontumour stromal TME cells through release of EVs enriched in oncogenic miRNAs, potentially contributing to tumour progression.

Project description:Germ cell tumors (GCT) originate from germ cells at different developmental stages (GCT type I – V) They are thought to inherit their methylation profile from (early embryonic) germ cells which undergo a characteristic epigenetic “reset” during maturation. This study aims to provide insight into the developmental timing and underlying biology of the various subtypes of GCTs and their (embryonic) cells of origin by identifying specific and global methylation differences between GCT subtypes. In total, 91 type I-IV GCTs and four cell lines were profiled using the Illumina HumanMethylation450 BeadChip (450K) platform. The data were pre-processed using a validated pipeline and analyzed using an in-house generated extension of the annotation manifest. Marked methylation differences were identified between GCT subtypes both on the global and local level (i.e. differentially methylated regions, imprinting control regions, promoters, etc). GCT subtypes indeed show major similarities to specific stages of (early) developing embryonic germ cells with regard to their methylation profile. The extended annotation manifest for the Illumina 450K platform and methylation datasets are readily available on GEO (GEO accession: GSE58538, GPL18809), providing an integrated hypothesis generating data source for future research. 91 germ cell tumors of various histologies were investigated for their methylation profile. Methylation detection was performed using Illumina’s HumanMethylation450 BeadChip. 14 type I teratomas (TE) were included of which 6 were located sacral (3 male: I.TE.s.m; 3 female: I.TE.s.f), 4 were located in the testis (I.TE.t) and 3 were located in the ovary (I.TE.o). 30 pure embryonal carcinomas (EC) were included as well as 21 mixed non seminomas (mNS). 12 seminomas of the testis (SE) were included as well as 4 dysgerminomas (their couterpart in the ovary). Finally, 4 spermatocytic seminomas (SS) and three dermoid cysts were analyzed. For a detailed overview the histological classification of germ cell tumors please see the publication linked to this data or associated literature [1-3]. Four cell lines were included, al modelling type II GCTs. Cell lines derived from EC include NT2[4-8], NCCIT [5, 9] and 2102EP[4-8]. TCam-2 closely resembles SE [10-12]. 1. Oosterhuis, J.W. and L.H. Looijenga, Testicular germ-cell tumours in a broader perspective. Nat Rev Cancer, 2005. 5(3): p. 210-22. 2. Looijenga, L.H., Human testicular (non)seminomatous germ cell tumours: the clinical implications of recent pathobiological insights. J Pathol, 2009. 218(2): p. 146-62. 3. Woodward, P.J., et al., Testicular germ cell tumors, in World Health Organization Classification of Tumours Pathology and Genetics of the Urinary System and Male Genital Organs., J.N. Eble, et al., Editors. 2004, IARC Press: Lyon. p. 17-278. 4. Andrews, P.W., et al., A comparative study of eight cell lines derived from human testicular teratocarcinoma. Int J Cancer, 1980. 26(3): p. 269-80. 5. Andrews, P.W., et al., Comparative analysis of cell surface antigens expressed by cell lines derived from human germ cell tumours. Int J Cancer, 1996. 66(6): p. 806-16. 6. Wang, N., et al., Nonrandom abnormalities in chromosome 1 in human testicular cancers. Cancer Res, 1980. 40(3): p. 796-802. 7. Fogh, J. and G. Trempe, New Human Tumor Cell Lines, in Human Tumor Cells in Vitro, J. Fogh, Editor. 1975, Springer US. p. 115-159. 8. Fogh, J., Cultivation, characterization, and identification of human tumor cells with emphasis on kidney, testis, and bladder tumors. Natl Cancer Inst Monogr, 1978(49): p. 5-9. 9. Teshima, S., et al., Four new human germ cell tumor cell lines. Lab Invest, 1988. 59(3): p. 328-36. 10. Eckert, D., et al., TCam-2 but not JKT-1 cells resemble seminoma in cell culture. Cell Tissue Res, 2008. 331(2): p. 529-38. 11. de Jong, J., et al., Further characterization of the first seminoma cell line TCam-2. Genes Chromosomes Cancer, 2008. 47(3): p. 185-96. 12. Mizuno, Y., et al., [Establishment and characterization of a new human testicular germ cell tumor cell line (TCam-2)]. Nihon Hinyokika Gakkai Zasshi, 1993. 84(7): p. 1211-8.

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Identification of known and novel germ cell cancer specific (embryonic) miRs in serum by high throughput profiling

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