Protocol for proteogenomic dissection of intronic splicing enhancer interactome for prediction of individualized cancer prognosis

STAR Protoc. 2021 Feb 11;2(1):100338. doi: 10.1016/j.xpro.2021.100338. eCollection 2021 Mar 19.

Abstract

Inter- or intra-patient tumor heterogeneity hinders the discovery of biomarkers for predicting individualized prognosis. Here, we present a protocol for an alternative splicing activity-based proteogenomic approach for identification of candidate prognostic markers in cancer cell lines and human breast cancer specimens. The pull-down of protein complexes with intronic splicing enhancer (ISE) probes is followed by tandem mass spectrometry (MS/MS) peptide sequencing. The proteogenomic analysis of data from these ISE-MS/MS assays identifies new prognostic markers that can be utilized to stratify patients with poor prognosis. For complete details on the use and execution of this protocol, please refer to Wang et al. (2018).

Keywords: Cancer; Genomics; Mass spectrometry; Molecular/chemical probes; Proteomics.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Alternative Splicing*
  • Enhancer Elements, Genetic*
  • Humans
  • Introns*
  • MCF-7 Cells
  • Neoplasms / diagnosis
  • Neoplasms / genetics*
  • Neoplasms / metabolism*
  • Predictive Value of Tests
  • Prognosis
  • Proteogenomics*
  • RNA, Neoplasm* / genetics
  • RNA, Neoplasm* / metabolism

Substances

  • RNA, Neoplasm