Targeted transcriptome analysis uncovers previously unknown isoform reprograming in colon cancer

Despite progress in massively parallel sequencing there remains a gap in our ability to characterize mRNA splicing in cancer due to read-length limitations of short-read sequencing and accuracy limitations of long-read sequencing. This has limited the use of RNA as a diagnostic marker and of mutated protein isoforms as drug targets.

In a new study, The University of Pittsburgh Medical Center and Loop Genomics describe a targeted synthetic long-read approach for sequencing mRNA isoforms with ultra-high accuracy.

rna-seq

Overview of the library preparation for isoform sequencing using LoopSeq, including an optional target enrichment step to focus the sequencing depth on genes or isoforms of interest.

Applied to mRNA isoforms in colon cancer, it uncovered large scale reprogramming of isoform expression in the progression of cancer. Much of novel isoform reprogramming has gone undetected using short read sequencing as it alters isoform expression without altering gene expression. Additionally, many SNP isoforms have gone undetected because ultra-low error rate long reads are required to distinguish real from false positive mutation isoforms. The study demonstrates that isoforms outperform genes in segregating tissue types by their cancer progression stage and that isoform specific mutations can define tissues along the cancer progression timeline.

“We are very excited with the results and look forward to seeing this methodology used in the next few years to discover new and potentially druggable protein isoforms targets in cancer,” says Jianhua Luo, MD, PhD, Director of the High Throughput Genome Center at the University of Pittsburgh Medical Center Department of Pathology.

Source – PR Newswire

Liu S, Wu I, Yu YP, Balamotis M, Ren B, Yehezkel TB, Luo JH. (2020) Targeted Transcriptome Analysis using Synthetic Long Read Sequencing Uncovers Isoform Reprograming in the Progression of Colon Cancer. bioRXiv [online preprint]. [abstract]

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