Identification of Alternative Splicing Markers for Breast Cancer

Abstract

Breast cancer is the most common cause of cancer death among women under age 50 years, so it is imperative to identify molecular markers to improve diagnosis and prognosis of this disease. Here, we present a new approach for the identification of breast cancer markers that does not measure gene expression but instead uses the ratio of alternatively spliced mRNAs as its indicator. Using a high-throughput reverse transcription-PCR-based system for splicing annotation, we monitored the alternative splicing profiles of 600 cancer-associated genes in a panel of 21 normal and 26 cancerous breast tissues. We validated 41 alternative splicing events that significantly differed in breast tumors relative to normal breast tissues. Most cancer-specific changes in splicing that disrupt known protein domains support an increase in cell proliferation or survival consistent with a functional role for alternative splicing in cancer. In a blind screen, a classifier based on the 12 best cancer-associated splicing events correctly identified cancer tissues with 96% accuracy. Moreover, a subset of these alternative splicing events could order tissues according to histopathologic grade, and 5 markers were validated in a further blind set of 19 grade 1 and 19 grade 3 tumor samples. These results provide a simple alternative for the classification of normal and cancerous breast tumor tissues and underscore the putative role of alternative splicing in the biology of cancer. [Cancer Res 2008;68(22):9525-31]

Dysregulation of splicing proteins in head and neck squamous cell carcinoma

“…Recent studies have shown an association between altered splicing machinery and cancers. 19,20 Dysregulation of splicing has been reported as an important factor in leukemia. [21][22][23] Alterations in spliceosome associated genes/proteins can significantly impact alternative splicing events like exon skipping or intron retention as reported in breast cancer, lung adenocarcinoma and chronic lymphocytic leukemia.…”

Emerging roles for Sam68 in adipogenesis and neuronal development

“…previously identified 36 were also observed to display changes in the inclusion in 3/5 patient-matched pairs. However, the RBPs contributing to these events remain to be elucidated.…”

Next-generation biobanking of metastases to enable multidimensional molecular profiling in personalized medicine

“…16,17 RNA (25 ng) extracted from the biopsies was amplified using the Transplex Whole Transcriptome Amplification Kit (Sigma-Aldrich, Oakville, ON, Canada). Relative expression levels of a panel of reference genes were determined in each sample by qPCR to normalize the amplification of all RNA samples analyzed.…”