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Fusion transcript detection using spatial transcriptomics
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Fusion transcripts are involved in tumourigenesis and play a crucial role in tumour heterogeneity, tumour evolution and cancer treatment resistance. However, fusion transcripts have not been studied at high spatial resolution in tissue sections due to the lack of full-length transcripts with spatial information. New high-throughput technologies like spatial transcriptomics measure the transcriptome of tissue sections on almost single-cell level. While this technique does not allow for direct detection of fusion transcripts, we show that they can be inferred using the relative poly(A) tail abundance of the involved parental genes.

We present a new method STfusion, which uses spatial transcriptomics to infer the presence and absence of poly(A) tails. A fusion transcript lacks a poly(A) tail for the 5´ gene and has an elevated number of poly(A) tails for the 3´ gene. Its expression level is defined by the upstream promoter of the 5´ gene. STfusion measures the difference between the observed and expected number of poly(A) tails with a novel C-score. 

We verified the STfusion ability to predict fusion transcripts on HeLa cells with known fusions. STfusion and C-sore applied to clinical prostate cancer data revealed the spatial distribution of the cis-SAGe SLC45A3-ELK4 in 12 tissue sections with almost single-cell resolution. The cis-SAGe occured in the centre or periphery of inflamed, prostatic intraepithelial neoplastic, or cancerous areas, and occasionally in normal glands.

Keywords [en]
Fusion transcript detection, Spatial Transcriptomics, gene fusion, cis-SAGE, oncogenes
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:su:diva-177919OAI: oai:DiVA.org:su-177919DiVA, id: diva2:1384889
Available from: 2020-01-12 Created: 2020-01-12 Last updated: 2020-01-12Bibliographically approved
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Friedrich, Stefanie
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