Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer
Open Access
- 22 January 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Genome Biology
- Vol. 22 (1), 1-24
- https://doi.org/10.1186/s13059-021-02261-x
Abstract
Deregulated gene expression is a hallmark of cancer; however, most studies to date have analyzed short-read RNA sequencing data with inherent limitations. Here, we combine PacBio long-read isoform sequencing (Iso-Seq) and Illumina paired-end short-read RNA sequencing to comprehensively survey the transcriptome of gastric cancer (GC), a leading cause of global cancer mortality. We performed full-length transcriptome analysis across 10 GC cell lines covering four major GC molecular subtypes (chromosomal unstable, Epstein-Barr positive, genome stable and microsatellite unstable). We identify 60,239 non-redundant full-length transcripts, of which > 66% are novel compared to current transcriptome databases. Novel isoforms are more likely to be cell line and subtype specific, expressed at lower levels with larger number of exons, with longer isoform/coding sequence lengths. Most novel isoforms utilize an alternate first exon, and compared to other alternative splicing categories, are expressed at higher levels and exhibit higher variability. Collectively, we observe alternate promoter usage in 25% of detected genes, with the majority (84.2%) of known/novel promoter pairs exhibiting potential changes in their coding sequences. Mapping these alternate promoters to TCGA GC samples, we identify several cancer-associated isoforms, including novel variants of oncogenes. Tumor-specific transcript isoforms tend to alter protein coding sequences to a larger extent than other isoforms. Analysis of outcome data suggests that novel isoforms may impart additional prognostic information. Our results provide a rich resource of full-length transcriptome data for deeper studies of GC and other gastrointestinal malignancies.Funding Information
- Kyowa Hakko Kirin (2016-1700)
- Khoo Postdoctoral Fellowship Award (Duke-NUS-KPFA/2019/0031)
- National Medical Research Council (NMRC/STaR/0026/2015, OF-LCG18May-0023)
- National Research Foundation Singapore
- Singapore Ministry of Education
This publication has 65 references indexed in Scilit:
- Sensitive detection of somatic point mutations in impure and heterogeneous cancer samplesNature Biotechnology, 2013
- STAR: ultrafast universal RNA-seq alignerBioinformatics, 2012
- Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genesNature Genetics, 2012
- RAF inhibitor resistance is mediated by dimerization of aberrantly spliced BRAF(V600E)Nature, 2011
- Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanomaNature Medicine, 2010
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- Model-based Analysis of ChIP-Seq (MACS)Genome Biology, 2008
- Protection from Fas-Mediated Apoptosis by a Soluble Form of the Fas MoleculeScience, 1994
- bcl-x, a bcl-2-related gene that functions as a dominant regulator of apoptotic cell deathCell, 1993