Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment

Abstract

Several databases have been published to predict alternative splicing of mRNAs by analysing the exon linkage relationship by alignment of expressed sequence tags (ESTs) to the genome sequence; however, little effort has been made to investigate the relationship between cancers and alternative splicing. We developed a program, Alternative Splicing Assembler (ASA), to look for splicing variants of human gene transcripts by genome-wide ESTs alignment. Using ASA, we constructed the biosino alternative splicing database (BASD), which predicted splicing variants for reference sequences from the reference sequence database (RefSeq) and presented them in both graph and text formats. EST clusters that differ from the reference sequences in at least one splicing site were counted as splicing variants. Of 4322 genes screened, 3490 (81%) were observed with at least one alternative splicing variants. To discover the variants associated with cancers, tissue sources of EST sequences were extracted from the UniLib database and ESTs from the same tissue type were counted. These were regarded as the indicators for gene expression level. Using Fisher's exact test, alternative splicing variants, of which EST counts were significantly different between cancer tissues and their counterpart normal tissues, were identified. It was predicted that 2149 variants, or 383 variants after Bonferroni correction, of 26 812 variants were likely tumor-associated. By reverse transcription-PCR, 11 of 13 novel alternative splicing variants and eight of nine variants' tissue specificity were confirmed in hepatocelluar carcinoma and in lung cancer. The possible involvement of alternative splicing in cancer is discussed.

Caffeine Regulates Alternative Splicing in a Subset of Cancer-Associated Genes: a Role for SC35

“…A recent analysis of more than 3 million transcripts in the EST database has demonstrated that 524 splice sites show statistically significant specificity to cancer tissues (57). These 524 cancer-specific splice sites derive from highly expressed splice isoforms, and many are being validated for use as reproducible molecular signatures of cancer (1,17). The TransExpress Cancer Human Splice Variant microarray (offered by ArrayIT, Sunnyvale, CA, as a test platform) includes 524 pairs of oligonucleotides optimized for splice variant profiling of these 524 genes.…”

Identification of RNA-binding proteins that regulate FGFR2 splicing through the use of sensitive and specific dual color fluorescence minigene assays

“…While the precise functional relevance of different spliced forms of specific transcripts has thus far been delineated in a limited number of cases, there is no question that alternative splicing yields variants with differential functions that are critical for development as well as for maintenance of normal cellular homeostasis and intercellular communication pathways (Matlin et al 2005). As such, it has also become evident that alterations in the regulation of splicing can have drastic consequences resulting in human diseases, including cancer (Xu and Lee 2003;Brinkman 2004;Hui et al 2004;Venables 2004;Relogio et al 2005).…”

Transposable elements in human cancers by genome-wide EST alignment

“…When bioinformatic analysis was conducted for the investigation of alternative splicing, singleton EST sequences were considered to be insufficient data (Brett et al, 2000) because of the sequencing errors or genomic DNA contamination present in the EST database. However, singleton EST sequences could pro- vide enough evidence for transcript variants (Hui et al, 2004). On the basis of this report, the singleton EST was included in our analysis of cancer-specific transposable element fusion transcripts and database construction.…”

“…Several genes showed tumorspecific alternative splicing by integration of TEs (Okumura et al, 2005). In addition, genome-wide expressed sequence tag (EST) alignment indicated that alternatively spliced mRNA variants were related to various human cancers (Hui et al, 2004). Those transposable elements have been assumed to be noninfectious replication-defective retroviral fossils passed on during primate evolution.…”