Unknown

Dataset Information

0

Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts.


ABSTRACT: BACKGROUND: Alternative splicing (AS) is a central mechanism in the generation of genomic complexity and is a major contributor to transcriptome and proteome diversity. Alterations of the splicing process can lead to deregulation of crucial cellular processes and have been associated with a large spectrum of human diseases. Cancer-associated transcripts are potential molecular markers and may contribute to the development of more accurate diagnostic and prognostic methods and also serve as therapeutic targets. Alternative splicing-enriched cDNA libraries have been used to explore the variability generated by alternative splicing. In this study, by combining the use of trapping heteroduplexes and RNA amplification, we developed a powerful approach that enables transcriptome-wide exploration of the AS repertoire for identifying AS variants associated with breast tumor cells modulated by ERBB2 (HER-2/neu) oncogene expression. RESULTS: The human breast cell line (C5.2) and a pool of 5 ERBB2 over-expressing breast tumor samples were used independently for the construction of two AS-enriched libraries. In total, 2,048 partial cDNA sequences were obtained, revealing 214 alternative splicing sequence-enriched tags (ASSETs). A subset with 79 multiple exon ASSETs was compared to public databases and reported 138 different AS events. A high success rate of RT-PCR validation (94.5%) was obtained, and 2 novel AS events were identified. The influence of ERBB2-mediated expression on AS regulation was evaluated by capillary electrophoresis and probe-ligation approaches in two mammary cell lines (Hb4a and C5.2) expressing different levels of ERBB2. The relative expression balance between AS variants from 3 genes was differentially modulated by ERBB2 in this model system. CONCLUSIONS: In this study, we presented a method for exploring AS from any RNA source in a transcriptome-wide format, which can be directly easily adapted to next generation sequencers. We identified AS transcripts that were differently modulated by ERBB2-mediated expression and that can be tested as molecular markers for breast cancer. Such a methodology will be useful for completely deciphering the cancer cell transcriptome diversity resulting from AS and for finding more precise molecular markers.

SUBMITTER: Ferreira EN 

PROVIDER: S-EPMC3045797 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

altmetric image

Publications

Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts.

Ferreira Elisa N EN   Rangel Maria C R MC   Galante Pedro F PF   de Souza Jorge E JE   Molina Gustavo C GC   de Souza Sandro J SJ   Carraro Dirce M DM  

BMC genomics 20101222


<h4>Background</h4>Alternative splicing (AS) is a central mechanism in the generation of genomic complexity and is a major contributor to transcriptome and proteome diversity. Alterations of the splicing process can lead to deregulation of crucial cellular processes and have been associated with a large spectrum of human diseases. Cancer-associated transcripts are potential molecular markers and may contribute to the development of more accurate diagnostic and prognostic methods and also serve a  ...[more]

Shared Molecules

Only show the datasets with similarity scores above: 0.5
     

Similar Datasets

| S-EPMC2911965 | biostudies-literature
| S-EPMC10020087 | biostudies-literature
| S-EPMC3891505 | biostudies-literature
| S-EPMC6288254 | biostudies-literature
| S-EPMC4597910 | biostudies-literature
| S-EPMC3728142 | biostudies-literature
| S-EPMC3118787 | biostudies-literature
| S-EPMC4164538 | biostudies-literature
| S-EPMC5070939 | biostudies-literature
| S-EPMC7052373 | biostudies-literature