Scanning copy number and gene expression on the 18q21‐qter chromosomal region by the systematic multiplex PCR and reverse transcription‐PCR methods

Abstract

We examined differences in copy number and expression of 127 genes located on the 18q21-qter chromosomal region of the breast and prostate cancer cell lines, using the systematic multiplex PCR and reverse transcription-PCR (SM PCR and SM RT-PCR) methods that we developed. Semi-quantitative data were obtained that were comparable in quality, but not in quantity, to data from DNA microarray hybridization analysis. In the chromosomal region where losses are frequent in breast, prostate, and other cancers, we detected a homozygous deletion of the SMAD4 gene in the MDA-MB-468 breast cancer cell line. We also observed partial or entire loss of expression in genes such as CCBE1, CCDC11, CD226, NP_115536.1, NP_689683.2, RNF152, SERPINB8, and TCF4 in certain breast and/or prostate cancer cell lines. An increase in gene expression was rare, but found with the transcription factor ONECUT2 gene in all of the cancer cell lines examined. Real-time qRT-PCR experiments confirmed these SM RT-PCR results. Further analysis of clinical specimens of breast cancer by real-time qRT-PCR demonstrated that the gene expression of CCBE1, TCF4, NP_115536.1, and NP_689683.2 was downregulated in the majority of clinical cases of breast cancer.

Collagen and calcium-binding EGF domains 1 is frequently inactivated in ovarian cancer by aberrant promoter hypermethylation and modulates cell migration and survival

“…As earlier reported in primary breast cancers (Yamamoto and Yamamoto, 2007), we found that CCBE1 expression was downregulated in the majority of ovarian cancer cell lines tested and in primary ovarian carcinomas as compared with NOSE. Loss of CCBE1 expression was significantly associated with higher grade ovarian carcinomas and likely occurs early in ovarian carcinogenesis, with stage I carcinomas expressing lower levels of CCBE1 than NOSE, one predicted cellular origin of ovarian carcinomas.…”

“…Collagen and calcium-binding EGF domains 1 (CCBE1) is an earlier uncharacterised gene of unknown function that has recently been reported to be down-regulated in primary breast carcinomas as compared with matched normal breast tissue (Yamamoto and Yamamoto, 2007). CCBE1 maps to 18q21.32, a common region of loss of heterozygosity (LOH) in ovarian cancer (Takakura et al, 1999;Lambros et al, 2005) that is associated with malignant progression of ovarian cancer (Hauptmann et al, 2002) and high tumour grade and poor survival (Lassus et al, 2001).…”

RNF152, a novel lysosome localized E3 ligase with pro-apoptotic activities

“…The full ORF of RNF152 has been sequenced and confirmed by the Mammalian Gene Collection program (Strausberg et al, 2002). Decreased expression of RNF152 was reported in some cancer cell lines (Yamamoto and Yamamoto, 2007). Our studies showed for the first time that RNF152 is an E3 ligase and is self-polyubiqutinated.…”

“…Human RNF152 gene is located on 18q21.33 chromosomal region (Yamamoto and Yamamoto, 2007) and encodes a 203-amino-acid protein with predicted molecular weight of 22 kDa. RNF152 protein contains two predicted functional domains: a RING finger motif at N-terminus, with the sequence resembling a canonical RING motif (CX 2 CX 14 CX 1 HX 2 CX 2 CX 12 CX 2 C), and a transmembrane motif at the C-terminus (Fig.…”

Identification of potential key genes and high-frequency mutant genes in prostate cancer by using RNA-Seq data

“…Furthermore, the upregulated expression of transcription factor ONECUT2 was revealed in breast and prostate cancer cell lines (32), and increased IFI16 protein in normal human prostate epithelial cells was associated with cellular senescence-associated cell growth arrest (33). NEUROG3 was identified to be expressed in metastatic neuroendocrine prostate cancer cells (34).…”