High‐resolution analysis of 16q22.1 in breast carcinoma using DNA amplifiable probes (multiplex amplifiable probe hybridization technique) and immunohistochemistry

Abstract

Loss of the chromosomal material at 16q22.1 is one of the most frequent genetic aberrations found in both lobular and low-grade nonlobular invasive carcinoma of the breast, indicating the presence of a tumour suppressor gene (TSG) at this region in these tumours. However, the TSG (s) at the 16q22.1 in the more frequent nonlobular carcinomas is still unknown. Multiplex Amplifiable Probe Hybridisation (MAPH) is a simple, accurate and a high-resolution technique that provides an alternative approach to DNA copy-number measurement. The aim of our study was to examine the most likely candidate genes at 16q22.1 using MAPH assay combined with protein expression analysis by immunohistochemistry. We identified deletion at 16q22.1 that involves some or all of these genes. We also noticed that the smallest region of deletion at 16q22.1 could be delineated to a 3 Mb region centromeric to the P-cadherin gene. Apart from the correlation between E-cadherin protein expression and its gene copy number, no correlation was detected between the expression of E2F-4, CTCF, TRF2 or P-cadherin with their gene's copy number. In the malignant tissues, no significant loss or decrease of protein expression of any gene other than E-cadherin was seen in association with any specific tumour type. No expression of VE-cadherin or Ksp-cadherin was detected in the normal and/or malignant tissues of the breast in these cases. However, there was a correlation between increased nuclear expression of E2F-4 and tumours with higher histological grade (p ‫؍‬ 0.04) and positive lymph node disease (p ‫؍‬ 0.02), suggesting that it may have an oncogenic rather than a tumour suppressor role. The malignant breast tissues also showed abnormal cytoplasmic cellular localisation of CTCF, compared to its expression in the normal parenchymal cells. In conclusion, we have demonstrated that MAPH is a potential technique for assessment of genomic imbalances in malignant tissues. Although our results support E-cadherin as the TSG in invasive lobular carcinoma, they argue against the candidacy of E2F-4, CTCF, TRF2, P-cadherin, Ksp-cadherin and VE-cadherin as TSGs in breast cancer.

Allelic Losses of Chromosome 10 in Glioma Tissues Detected by Quantitative Single-Strand Conformation Polymorphism Analysis

“…This reproducibility is comparable to that of the bacterial artificial chromosome-based comparative genomic hybridization array (32,33 ) and better than the reproducibility of other methods such as multiplex ligation-dependent probe amplification analysis (34,35 ), multiplex amplification and probe hybridization analysis (36 ), and SYBR Green I-based real-time PCR analysis (30 ).…”

Infrequent mutation of ATBF1 in human breast cancer

“…Several genes including E-cadherin, CBFA2T3, CTCF, and WWOX have been evaluated as the candidates for the 16q tumor suppressor gene, although none of them has been convincingly established as the 16q gene (Berx et al 1996;Cleton-Jansen 2002;Cowin et al 2005;Rakha et al 2005;Watanabe et al 2003;van Wezel et al 2005). Recently, the ATmotif Binding Factor (ATBF1) gene was identiWed as a reasonable candidate for the 16q22 tumor suppressor gene based on its frequent mutations and functional inhibition of cell proliferation in prostate cancer (Sun et al 2005).…”

Microarray comparative genomic hybridization analysis of tubular breast carcinoma shows recurrent loss of the CDH13 locus on 16q

“…Using mCGH, Buerger et al [10] showed that lowgrade DCIS, TBC, and lobular invasive carcinoma can genetically be related (gain on 1q, loss on 16q), whereas high-grade ductal invasive carcinomas are more likely related to high-grade DCIS (gain on 11q13 and 17q12). 16q has been studied thoroughly in breast cancer, and many genes were suspected to be important tumor suppressor genes in IDCs [34,35]. In lobular invasive carcinoma, the loss on 16q clearly affects CDH1.…”