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

Abstract

Adult male germ cell tumors (GCTs) comprise distinct groups: seminomas and nonseminomas, which include pluripotent embryonal carcinomas as well as other histologic subtypes exhibiting various stages of differentiation. Almost all GCTs show 12p gain, but the target genes have not been clearly defined. To identify 12p target genes, we examined Affymetrix (Santa Clara, CA) U133A+B microarray (f83% coverage of 12p genes) expression profiles of 17 seminomas, 84 nonseminoma GCTs, and 5 normal testis samples. Seventy-three genes on 12p were significantly overexpressed, including GLUT3 and REA (overexpressed in all GCTs) and CCND2 and FLJ22028 (overexpressed in all GCTs, except choriocarcinomas). We characterized a 200-kb gene cluster at 12p13.31 that exhibited coordinated overexpression in embryonal carcinomas and seminomas, which included the known stem cell genes NANOG, STELLA, and GDF3 and two previously uncharacterized genes. A search for other coordinately regulated genomic clusters of stem cell genes did not reveal any genomic regions similar to that at 12p13.31. Comparison of embryonal carcinoma with seminomas revealed relative overexpression of several stem cell-associated genes in embryonal carcinoma, including several core ''stemness'' genes (EBAF, TDGF1, and SOX2) and several downstream targets of WNT, NODAL, and FGF signaling (FGF4, NODAL, and ZFP42). Our results indicate that 12p gain is a functionally relevant change leading to activation of proliferation and reestablishment/maintenance of stem cell function through activation of key stem cell genes. Furthermore, the differential expression of core stem cell genes may explain the differences in pluripotency between embryonal carcinomas and seminomas. (Cancer Res 2006; 66(2): 820-7)

In vivo differentiation and genomic evolution in adult male germ cell tumors

“…A total of 32 specimens were primary testicular tumors, 8 were from patients with mediastinal primaries or metastases, and the remaining 34 were from metastatic sites other than the mediastinum. All of these samples were previously profiled for expression using Affymetrix U133A1B microarrays [GEO Accession Number GSE3218; see (Korkola et al, 2006) for further information].…”

“…All of the tumors that were used for this study were previously profiled using Affymetrix U133A1B microarrays for expression analysis (Korkola, et al 2005(Korkola, et al , 2006, facilitating the identification of potential target genes that mapped to altered regions. We focused on regions that had at least two contiguous BAC clones that were altered in at least 40% of cases, and looked for genes that were significantly differentially expressed with at least a twofold change relative to tumors without the alteration or fourfold relative to normal testes.…”

“…There were eight regions that showed gains in at least 40% of cases (Table 2). Since 12p has previously been studied for differential expression (Korkola et al, 2006), we did not analyze this region. Of the remaining seven regions, only 7p had genes (UPP1, ANLN, 242206_at, and 227247_at) that showed greater than twofold expression differences between samples with gains compared to those without.…”

“…Additionally, a number of tumors show subregional, high-level amplification of 12p (Bourdon et al, 2002;Looijenga and Oosterhuis, 2002;Zafarana et al, 2003). Extensive studies of 12p have identified a number of candidate target genes, including CCND2 and a cluster of stem cell genes at 12p13.31 (Houldsworth et al, 1997;Clark et al, 2004;Korkola et al, 2006). In addition to 12p, other chromosomal regions have also been identified that are frequently altered in GCTs (von Eyben, 2004), including gains on regions of 2p, 4q, 6p, 7, 8, 17q, 19p, and 21, and losses on chromosomes 4, 10q, 12q, 11, 13, and 18, (Korn et al, 1996;Murty et al, 1999;Kraggerud et al, 2002;Draper et al, 2004;von Eyben, 2004).…”

Transformation, genomic instability and senescence mediated by platelet/megakaryocyte glycoprotein Ibα

“…Consistent with our previous report (Rogulski et al, 2005b), a notable correlation between c-Myc and GpIba expression was seen (Figure 6b). Finally, a search of the Oncomine database (http://www.oncomine.org; Rhodes et al, 2004) indicated that GpIba transcripts were overexpressed in germ cell tumors vs normal testicular tissue (P ¼ 0.001; Korkola et al, 2006), in imatinibresistant chronic myelogenous leukemia vs untreated chronic-phase disease (P ¼ 7 Â 10 À7 ; Radich et al, 2006;Figure 6c), and in c-src-transformed primary human mammary epithelial cells (Bild et al, 2006).…”