Novel alternative splicing isoform biomarkers identification from high-throughput plasma proteomics profiling of breast cancer

Fan Zhang, Mu Wang, Tran Michael, Renee Drabier

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Background: In the biopharmaceutical industry, biomarkers define molecular taxonomies of patients and diseases and serve as surrogate endpoints in early-phase drug trials. Molecular biomarkers can be much more sensitive than traditional lab tests. Discriminating disease biomarkers by traditional method such as DNA microarray has proved challenging. Alternative splicing isoform represents a new class of diagnostic biomarkers. Recent scientific evidence is demonstrating that the differentiation and quantification of individual alternative splicing isoforms could improve insights into disease diagnosis and management. Identifying and characterizing alternative splicing isoforms are essential to the study of molecular mechanisms and early detection of complex diseases such as breast cancer. However, there are limitations with traditional methods used for alternative splicing isoform determination such as transcriptome-level, low level of coverage and poor focus on alternative splicing.Results: Therefore, we presented a peptidomics approach to searching novel alternative splicing isoforms in clinical proteomics. Our results showed that the approach has significant potential in enabling discovery of new types of high-quality alternative splicing isoform biomarkers.Conclusions: We developed a peptidomics approach for the proteomics community to analyze, identify, and characterize alternative splicing isoforms from MS-based proteomics experiments with more coverage and exclusive focus on alternative splicing. The approach can help generate novel hypotheses on molecular risk factors and molecular mechanisms of cancer in early stage, leading to identification of potentially highly specific alternative splicing isoform biomarkers for early detection of cancer.

Original languageEnglish
Article numberS8
JournalBMC Systems Biology
Volume7
Issue numberSUPPL 5
DOIs
StatePublished - Dec 9 2013

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Alternative Splicing
Proteomics
Biomarkers
Profiling
Breast Cancer
High Throughput
Protein Isoforms
Plasma
Throughput
Breast Neoplasms
Plasmas
Taxonomies
Microarrays
Cancer
Coverage
Surrogate Endpoint
DNA
DNA Microarray
Risk Factors
Disease Management

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology
  • Applied Mathematics
  • Modeling and Simulation
  • Computer Science Applications

Cite this

Novel alternative splicing isoform biomarkers identification from high-throughput plasma proteomics profiling of breast cancer. / Zhang, Fan; Wang, Mu; Michael, Tran; Drabier, Renee.

In: BMC Systems Biology, Vol. 7, No. SUPPL 5, S8, 09.12.2013.

Research output: Contribution to journalArticle

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