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A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis
Chunjiang He1, Fang Zhou, Zhixiang Zuo
1Department of Genetics and Center for Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, People's Republic of China.
Plos One
|March 7, 2009
Summary
Researchers discovered thousands of novel, cancer-specific alternative splicing variants in human tumors. This finding highlights the crucial role of alternative splicing in cancer development and offers potential new tools for cancer diagnosis and treatment.
Area of Science:
- Genomics
- Molecular Biology
- Cancer Research
Background:
- Alternative pre-mRNA splicing (AS) is vital for protein diversity and impacts disease.
- The role and regulation of AS in human cancer remain poorly understood.
Purpose of the Study:
- To systematically identify and characterize cancer-specific alternative splicing variants.
- To explore the global landscape of AS in human tumorigenesis.
Main Methods:
- Constructed a database of expressed sequence tags (ESTs) from human cancer and normal tissues.
- Identified alternatively spliced transcripts by aligning ESTs with genomic sequences.
- Cross-screened variants to identify tissue-specific and cancer-specific forms.
Main Results:
- Identified 15,093 cancer-specific variants from 9,989 genes across 27 cancer types.
- Identified 14,376 normal tissue-specific variants from 7,240 genes across 35 normal tissues.
- Approximately 70% of identified transcripts are novel; cancer-specific AS affects oncogenes and tumor suppressors.
Conclusions:
- Cancer-specific AS plays a significant and global role in human tumorigenesis.
- Novel splice forms in cancer-associated genes suggest AS is critical.
- Cancer-specific AS variants represent potential diagnostic, prognostic, and therapeutic targets.
