Detection of Novel Amplicons in Prostate Cancer by Comprehensive Genomic Profiling of Prostate Cancer Cell Lines Using Oligonucleotide-Based ArrayCGH

Abstract

BackgroundThe purpose of this study was to prove the feasibility of a longmer oligonucleotide microarray platform to profile gene copy number alterations in prostate cancer cell lines and to quickly indicate novel candidate genes, which may play a role in carcinogenesis.Methods/Results and FindingsGenome-wide screening for regions of genetic gains and losses on nine prostate cancer cell lines (PC3, DU145, LNCaP, CWR22, and derived sublines) was carried out using comparative genomic hybridization on a 35,000 feature oligonucleotide microarray (arrayCGH). Compared to conventional chromosomal CGH, more deletions and small regions of gains, particularly in pericentromeric regions and regions next to the telomeres, were detected. As validation of the high-resolution of arrayCGH we further analyzed a small amplicon of 1.7 MB at 9p13.3, which was found in CWR22 and CWR22-Rv1. Increased copy number was confirmed by fluorescence in situ hybridization using the BAC clone RP11-165H19 from the amplified region comprising the two genes interleukin 11 receptor alpha (IL11-RA) and dynactin 3 (DCTN3). Using quantitative real time PCR (qPCR) we could demonstrate that IL11-RA is the gene with the highest copy number gain in the cell lines compared to DCTN3 suggesting IL11-RA to be the amplification target. Screening of 20 primary prostate carcinomas by qPCR revealed an IL11-RA copy number gain in 75% of the tumors analyzed. Gain of DCTN3 was only found in two cases together with a gain of IL11-RA.Conclusions/SignificanceArrayCGH using longmer oligonucleotide microarrays is feasible for high-resolution analysis of chomosomal imbalances. Characterization of a small gained region at 9p13.3 in prostate cancer cell lines and primary prostate cancer samples by fluorescence in situ hybridization and quantitative PCR has revealed interleukin 11 receptor alpha gene as a candidate target of amplification with an amplification frequency of 75% in prostate carcinomas. Frequent amplification of IL11-RA in prostate cancer is a potential mechanism of IL11-RA overexpression in this tumor type.

Identification ofIL11RAandMELKamplification in gastric cancer by comprehensive genomic profiling of gastric cancer cell lines

“…On the other hand, the gain of the 16p21-p23 region in ACP03 and the gains of the 6p11-p12, 12p11.1 and 18p11.2-p11.3 regions in AGP01 were only detected by cCGH. This may be due to technical reasons, as cCGH is more sensitive than aCGH for detecting large chromosome regions, as previously discussed by Kamradt et al[24]. …”

“…Because this region harbors several tumor-related genes, several studies in the literature have correlated gene copy number alterations of 9p13 with cancer[24,34]. Sarhadi et al[34] observed that the gain of chromosome 9p13 encompasses many genes, such as KIAA1161 , C9orf24 , C9orf25 , DNAI1 , ENHO , CNTFR , LOC415056 , C9orf23 , DCTN3 , ARID3C , SIGMAR1 , GALT , IL11RA , CCL27 , CCL19 , CCL21 and FAM205A , in different types of cancer.…”

“…Kamradt et al[24] analyzed a small amplicon at 9p13.3 in prostate cancer cell lines and validated IL11RA copy number gain in 75% (15/20) of prostate tumors. In addition, it has been demonstrated that IL11RA is overexpressed in GC, colon cancer, breast cancer, prostate cancer and osteosarcoma[35-41].…”

Array comparative genomic hybridization analysis of olfactory neuroblastoma

“…30,31 These authors suggested the involvement of three genes, including UBE2R2 (GeneID: 54926), DCTN3 (GeneID: 11258), and IL-11RA (GeneID: 3590). Kamradt et al screened 20 primary prostate cancer samples and found that only IL-11RA was gained in 75% of the tumors, whereas only DCTN3 was not gained in any of the cases; both genes were gained together in 10% of the tumors.…”

Expression of the IL‐11 Gene in Metastatic Cells Is Supported by Runx2‐Smad and Runx2‐cJun Complexes Induced by TGFβ1

“…Potentially relevant to the osteoblastic lesions in PC tumors, IL-11 has been reported to have osteogenic properties in normal bone cells [Matsumoto et al, 2012]. Elevated levels of IL-11 and its receptor IL-11Rα have been observed in PC tumors [Campbell et al, 2001; Kamradt et al, 2007]. The cytokine is long known to be induced by TGFβ1 signaling, stimulating IL-11 gene transcription via induction of AP-1 factors [Kang et al, 2003; Matsumoto et al, 2012; Tang et al, 1998a].…”