In breast cancer amplification of the HER-2/neu oncogene and over-expression of the protein product is associated with poor prognosis, predicts response to some chemotherapeutic regimens and is the target for Herceptin treatment. To date there are several methods to assess the amplification/overexpression of HER-2/neu with each having advantages and disadvantages. We have studied amplification and over-expression of HER-2/neu in 250 consecutive cases of breast cancer (220 invasive and 30 in situ carcinomas) presenting to the Department of Pathology at Women's College Campus of Sunnybrook and Women's College Health Sciences Center. Thirty percent of the invasive carcinomas were node positive. HER-2/neu protein overexpression was assessed by immunohistochemistry (IH) using antibody CB11 and amplification of the gene by differential PCR. The percentage of tumor cells showing CB11 staining was determined and the most significant cut off point for positivity was >10% moderate or strong complete membranous staining. The gene was considered amplified if the density score of the product was >2. There was 94% concordance between the two methods (P value .0001). Both methods were positive in 16% of cases and negative in 78% of cases. Discrepant cases were examined by FISH which confirmed the IH results in 9/11 invasive carcinomas. These results show that there is excellent concordance between IH and PCR. However, immunohistochemistry is easier to perform and cheaper than PCR and could be used in routine assessment of HER-2/neu in breast cancer patients.

Osteosarcoma (OS) is a primary bone malignancy with high incidence in children and young adults. It frequently occurs in patients with strong cancer history (Li-Fraumeni syndrome, retinoblastoma), but the etiology of sporadic OS is still uncertain. The present study is an intensive investigation on susceptibility to sporadic osteosarcoma by genome wide copy number analysis. We evaluated the hypothesis that germline copy number variants (CNVs) could act as a source of genetic susceptibility that may contribute to the development of sporadic osteosarcoma. We analyzed 78 sporadic pediatric OS cases and 2375 controls using Affymetrix SNP 6.0 Array. Two independent methods, Genotyping Console™ (Affymetrix) and Birdsuite (Broad Institute) were employed to call for CNVs. Outliers with large genomic alterations and TP53 mutations were flagged and filtered out. Both bioinformatics methods show similar distribution of CNVs per chromosome, with slightly higher range depicted by Genotyping Console™, with an enriched set of CNVs in the diseased data. Bioinformatics analysis predicts overlap of copy number variable regions with several candidate genes (PIK3CA, STK11, AKT3, ZMAT3, BAI1), for selected samples. We validated these findings by performing real time quantitative PCR experiments that not only verified most of the computational results, but also identified more amplifications, in an extended selection of samples and regions. The most affected candidate gene, showing gain in 66% of osteosarcoma samples tested, is ZMAT3 (Chr. 3q26.32). A very recent method, digital droplet PCR (BioRAD), with very high sensitivity, also confirms qPCR results, although for a smaller number of samples. In addition to calling for CNVs, pathways analyses have been also pursued, to address the hypothesis that disruption of multiple genes from the same pathway in the germline of a particular individual may cause susceptibility for developing osteosarcoma. DAVID software predicted several pathways that are enriched, p53 being one of them. Further investigations by KEGG suggest that several genes, including ZMAT3, are disrupted in the p53 signaling pathway. In order to validate these findings, functional assays on osteosarcoma derived lymphoblastoid cell lines are designed and currently in progress. In all, the current study suggests that ZMAT3 could represent a good candidate signature gene for susceptibility to sporadic osteosarcoma. Citation Format: Cristina Baciu, Rinnat Porat, Margaret Pienkowska, Noa Alon, Jonathan Wasserman, David Malkin. ZMAT3, a signature gene for sporadic osteosarcoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3163. doi:10.1158/1538-7445.AM2013-3163

Germline TP53 mutations are observed in ∼80% of patients with Li-Fraumeni syndrome (LFS) and a lesser frequency of patients meeting the revised Chompret criteria. A variety of studies are being conducted exploring the role of genetic modifiers on p53 function and their impact in refining the genotype:phenotype correlation of the TP53:LFS relationship. In this presentation, four classical pediatric-onset LFS tumors (choroid plexus carcinoma, medulloblastoma, adrenocortical carcinoma and rhabdomyosarcoma) will be used as examples to demonstrate the molecular nuances of this complex relationship. A spectrum of findings will be outlined that support the notion that presence of a germline TP53 mutation in the context of different modifying effects of intragenic TP53 polymorphism as well as variants in genes and proteins that play important roles in the p53 network confers certain biological features to the presentation of these tumors. Biological mechanisms will be discussed and strategies for early cancer detection will be presented. Citation Format: Jonathan Wasserman, Anita Villani, Nardin Samuel, Diana Merino, Ana Novokmet, Margaret Pienkowska, Badr IdSaid, David Malkin. Li-Fraumeni syndrome: p53 and beyond. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Susceptibility and Cancer Susceptibility Syndromes; Jan 29-Feb 1, 2014; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(23 Suppl):Abstract nr IA10. doi:10.1158/1538-7445.CANSUSC14-IA10