ArticleBMC genomics2014
Transcriptome instability as a molecular pan-cancer characteristic of carcinomas.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion.Genome research · 2024Article
- Alternative RNA Splicing as a Potential Major Source of Untapped Molecular Targets in Precision Oncology and Cancer Disparities.Clinical cancer research : an official journal of the American Association for Cancer Research · 2019Article
- Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing.Blood cells, molecules & diseases · 2018Article
- Important molecular genetic markers of colorectal cancer.Oncotarget · 2016Review
- CLASS2: accurate and efficient splice variant annotation from RNA-seq reads.Nucleic acids research · 2016Article
- Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes.Oncogene · 2016Review
- ELF5 isoform expression is tissue-specific and significantly altered in cancer.Breast cancer research : BCR · 2016Article
- Novel RNA variants in colorectal cancers.Oncotarget · 2015Article
- Triple-layer dissection of the lung adenocarcinoma transcriptome: regulation at the gene, transcript, and exon levels.Oncotarget · 2015Article
- Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.Database : the journal of biological databases and curation · 2015Article
- TIN: An R Package for Transcriptome Instability Analysis.Cancer informatics · 2015Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWe have previously proposed transcriptome instability as a genome-wide, pre-mRNA splicing-related characteristic of colorectal cancer. Here, we explore the hypothesis of transcriptome instability being a general characteristic of cancer.
resultsExon-level microarray expression data from ten cancer datasets were analyzed, including breast cancer, cervical cancer, colorectal cancer, gastric cancer, lung cancer, neuroblastoma, and prostate cancer (555 samples), as well as paired normal tissue samples from the colon, lung, prostate, and stomach (93 samples). Based on alternative splicing scores across the genomes, we calculated sample-wise relative amounts of aberrant exon skipping and inclusion. Strong and non-random (P < 0.001) correlations between these estimates and the expression levels of splicing factor genes (n = 280) were found in most cancer types analyzed (breast-, cervical-, colorectal-, lung- and prostate cancer). This suggests a biological explanation for the splicing variation. Surprisingly, these associations prevailed in pan-cancer analyses. This is in contrast to the tissue and cancer specific patterns observed in comparisons across healthy tissue samples from the colon, lung, prostate, and stomach, and between paired cancer-normal samples from the same four tissue types.
conclusionBased on exon-level expression profiling and computational analyses of alternative splicing, we propose transcriptome instability as a molecular pan-cancer characteristic. The affected cancers show strong and non-random associations between low expression levels of splicing factor genes, and high amounts of aberrant exon skipping and inclusion, and vice versa, on a genome-wide scale.
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