To discriminate the patient subpopulations with different clinical outcomes within each breast cancer (BC) subtype, we introduce a robust, clinical-practical, activity-based proteogenomic method that identifies, in their oncogenically active states, candidate biomarker genes bearing patient-specific transcriptomic/genomic alterations of prognostic value. First, we used the intronic splicing enhancer (ISE) probes to sort ISE-interacting trans-acting protein factors (trans-interactome) directly from a tumor tissue for subsequent mass spectrometry characterization. In the retrospective, proteogenomic analysis of patient datasets, we identified those ISE trans-factor-encoding genes showing interaction-correlated expression patterns (iCEPs) as new BC-subtypic genes. Further, patient-specific co-alterations in mRNA expression of select iCEP genes distinguished high-risk patient subsets/subpopulations from other patients within a single BC subtype. Function analysis further validated a tumor-phenotypic trans-interactome contained the drivers of oncogenic splicing switches, representing the predominant tumor cells in a tissue, from which novel personalized biomarkers were clinically characterized/validated for precise prognostic prediction and subsequent individualized alignment of optimal therapy. The interpatient tumor-phenotypic heterogeneity hinders discovery of biomarkers for individualized prognosis. Wang and colleagues introduce an alternative splicing activity-based proteogenomic method that dissects tumor heterogeneity for de novo discovery of individualized prognostic biomarkers. The resulting biomarkers distinguish high-risk patient subpopulations from other patients within each single breast cancer subtype.
CITATION STYLE
Wang, L., Wrobel, J. A., Xie, L., Li, D. X., Zurlo, G., Shen, H., … Chen, X. (2018). Novel RNA-Affinity Proteogenomics Dissects Tumor Heterogeneity for Revealing Personalized Markers in Precision Prognosis of Cancer. Cell Chemical Biology, 25(5), 619-633.e5. https://doi.org/10.1016/j.chembiol.2018.01.016
Mendeley helps you to discover research relevant for your work.