Multiple Alternative Splicing Markers for Ovarian Cancer

Abstract

Intense efforts are currently being directed toward profiling gene expression in the hope of developing better cancer markers and identifying potential drug targets. Here, we present a sensitive new approach for the identification of cancer signatures based on direct high-throughput reverse transcription-PCR validation of alternative splicing events. This layered and integrated system for splicing annotation (LISA) fills a gap between high-throughput microarray studies and high-sensitivity individual gene investigations, and was created to monitor the splicing of 600 cancer-associated genes in 25 normal and 21 serous ovarian cancer tissues. Out of >4,700 alternative splicing events screened, the LISA identified 48 events that were significantly associated with serous ovarian tumor tissues. In a further screen directed at 39 ovarian tissues containing cancer pathologies of various origins, our ovarian cancer splicing signature successfully distinguished all normal tissues from cancer. High-volume identification of cancer-associated splice forms by the LISA paves the way for the use of alternative splicing profiling to diagnose subtypes of cancer.

Tumor microenvironment–associated modifications of alternative splicing

“…The results indicate that differences between normal and cancer tissues are much smaller than previously thought. Analyzing the expression of a subset of the RefSeq alternative splicing events in RNA extracted from whole ovarian tumors identified 336 cancer-associated ASEs (Klinck et al 2008;Venables et al 2009), while comparison of normal and cancer epithelial or stromal tissues identified a total of 17 cancer-specific ASEs (Supplemental Tables S2, S3, S9). Most of the 336 whole tumor markers affected celltype-specific genes including those linked to cell plasticity (MAP3K7) and cell movement (CEACAM1) (Venables et al 2009).…”

“…Gene expression and, more recently, alternative splicing, a highly regulated and cell-type-specific process, have been found to be globally altered in cancer cells (Sotiriou et al 2006;Klinck et al 2008;Venables et al 2009). Profiling the global expression resulted in several sets of biomarkers capable of detecting cancer subtypes and was particularly successful in differentiating between different breast cancer subtypes (Munirah et al 2011;Prat et al 2012).…”

“…However, most expression profiling techniques focus on changes in the levels of gene expression and simply ignore changes in the transcript architecture due to alternative splicing. Profiling the 4 expression of splicing isoforms identified potential markers for ovarian and breast cancers, and some of these were shown to be required for cell survival in vitro (Klinck et al 2008;Venables et al 2008a;Prinos et al 2011). Hundreds of splicing isoforms associated with the cell cytoskeleton and other tissue-specific genes were associated with ovarian cancer when RNA extracted from whole tumor tissues was compared with that extracted from normal ovaries (Venables et al 2009).…”

Guider et intégrer pour un épissage diversifié

“…Comme ces décisions sont souvent altérées dans certaines pathologies comme le cancer, l'application des connaissances qui expliquent comment les différences d'expression, les mutations et les polymorphismes entre individus contribuent au déve-loppement des maladies et à leur évolution chez l'homme représente un enjeu important au plan médical. Force est de constater que l'incroyable diversité créée par l'épissage alternatif contribue actuellement à l'identification de nouveaux biomarqueurs à potentiel clinique [44]. Il est maintenant permis d'espérer qu'une meilleure caractérisation des isoformes d'épissage et des mécanismes régulant leur production mènera à des traitements innovateurs en vue d'améliorer la santé humaine.…”

Alternative Splicing in Prostate and Breast Cancer

“…Other published techniques to determine AS include high throughput RT-PCR [13][14][15] and deep sequencing or RNASeq (short-read high-throughput sequencing) [16][17][18]. Venables et al described a RT-PCR based system that used two sets of primers specific to each identified exon-exon junction and AS events in 600 cancer associated genes [15].…”