TY - JOUR
T1 - Novel alternative splicing isoform biomarkers identification from high-throughput plasma proteomics profiling of breast cancer
AU - Zhang, Fan
AU - Wang, Mu
AU - Michael, Tran
AU - Drabier, Renee
N1 - Funding Information:
We thank Hoosier Oncology Group for collecting breast cancer plasma samples. The proteomics study for biomarker discovery was supported by the National Cancer Institute Clinical Proteomics Technology Assessment for Cancer program (U24 CA126480). We also thank the support of Bioinformatics Program at University of North Texas Health Science Center.
PY - 2013/12/9
Y1 - 2013/12/9
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84889641098&partnerID=8YFLogxK
U2 - 10.1186/1752-0509-7-S5-S8
DO - 10.1186/1752-0509-7-S5-S8
M3 - Article
C2 - 24565027
AN - SCOPUS:84889641098
SN - 1752-0509
VL - 7
JO - BMC Systems Biology
JF - BMC Systems Biology
IS - SUPPL 5
M1 - S8
ER -