Identification of novel alternative splicing biomarkers for breast cancer with LC/MS/MS and RNA-Seq

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dc.creatorZhang, Fan
dc.creatorDeng, Chris K.
dc.creatorWang, Mu
dc.creatorDeng, Bin
dc.creatorBarber, Robert C.
dc.creatorHuang, Gang
dc.creator.orcid0000-0001-6857-0286 (Barber, Robert C.)
dc.date.accessioned2022-06-29T17:06:30Z
dc.date.available2022-06-29T17:06:30Z
dc.date.issued2020-12-03
dc.description.abstractBackground: Alternative splicing isoforms have been reported as a new and robust class of diagnostic biomarkers. Over 95% of human genes are estimated to be alternatively spliced as a powerful means of producing functionally diverse proteins from a single gene. The emergence of next-generation sequencing technologies, especially RNA-seq, provides novel insights into large-scale detection and analysis of alternative splicing at the transcriptional level. Advances in Proteomic Technologies such as liquid chromatography coupled tandem mass spectrometry (LC-MS/MS), have shown tremendous power for the parallel characterization of large amount of proteins in biological samples. Although poor correspondence has been generally found from previous qualitative comparative analysis between proteomics and microarray data, significantly higher degrees of correlation have been observed at the level of exon. Combining protein and RNA data by searching LC-MS/MS data against a customized protein database from RNA-Seq may produce a subset of alternatively spliced protein isoform candidates that have higher confidence. Results: We developed a bioinformatics workflow to discover alternative splicing biomarkers from LC-MS/MS using RNA-Seq. First, we retrieved high confident, novel alternative splicing biomarkers from the breast cancer RNA-Seq database. Then, we translated these sequences into in silico Isoform Junction Peptides, and created a customized alternative splicing database for MS searching. Lastly, we ran the Open Mass spectrometry Search Algorithm against the customized alternative splicing database with breast cancer plasma proteome. Twenty six alternative splicing biomarker peptides with one single intron event and one exon skipping event were identified. Further interpretation of biological pathways with our Integrated Pathway Analysis Database showed that these 26 peptides are associated with Cancer, Signaling, Metabolism, Regulation, Immune System and Hemostasis pathways, which are consistent with the 256 alternative splicing biomarkers from the RNA-Seq. Conclusions: This paper presents a bioinformatics workflow for using RNA-seq data to discover novel alternative splicing biomarkers from the breast cancer proteome. As a complement to synthetic alternative splicing database technique for alternative splicing identification, this method combines the advantages of two platforms: mass spectrometry and next generation sequencing and can help identify potentially highly sample-specific alternative splicing isoform biomarkers at early-stage of cancer.
dc.description.sponsorshipThis work was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103449. This work was also supported by the NIH Grant 5P30GM114737, the NIH Grant P20GM103466 and the NIH Grant U54 MD007584 and the NIH Grant 2U54MD007601. The funding bodies had no role in the design of the study, collection, analysis, interpretation of data, or in the writing of the manuscript. Publication costs are funded by Vermont Genetics Network.
dc.identifier.citationZhang, F., Deng, C. K., Wang, M., Deng, B., Barber, R., & Huang, G. (2020). Identification of novel alternative splicing biomarkers for breast cancer with LC/MS/MS and RNA-Seq. BMC bioinformatics, 21(Suppl 9), 541. https://doi.org/10.1186/s12859-020-03824-8
dc.identifier.issn1471-2105
dc.identifier.issueSuppl 9
dc.identifier.urihttps://hdl.handle.net/20.500.12503/31213
dc.identifier.volume21
dc.publisherBioMed Central Ltd.
dc.relation.urihttps://doi.org/10.1186/s12859-020-03824-8
dc.rights.holderCopyright © The Author(s) 2020
dc.rights.licenseAttribution 4.0 International (CC BY 4.0)
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.sourceBMC Bioinformatics
dc.subjectalternative splicing
dc.subjectbiomarker discovery
dc.subjectbreast cancer
dc.subjectmass spectrometry
dc.subjectpathway analysis
dc.subject.meshAlgorithms
dc.subject.meshAlternative Splicing
dc.subject.meshAmino Acid Sequence
dc.subject.meshBiomarkers, Tumor
dc.subject.meshBreast Neoplasms
dc.subject.meshChromatography, Liquid
dc.subject.meshDatabases, Protein
dc.subject.meshFemale
dc.subject.meshHumans
dc.subject.meshPeptides
dc.subject.meshProtein Isoforms
dc.subject.meshProteome
dc.subject.meshRNA-Seq
dc.subject.meshTandem Mass Spectrometry
dc.titleIdentification of novel alternative splicing biomarkers for breast cancer with LC/MS/MS and RNA-Seq
dc.typeArticle
dc.type.materialtext

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