Combined Analysis of Nucleic Acids and Protein for Cancer Research

摘要

This study was undertaken to determine the feasibility of isolation of RNA, DNA and Protein from a single formaldehyde fixed paraffin embedded (FFPE) section to detect lung cancer biomarkers. Correlation of RNA expression and DNA mutations by Next Generation Sequencing (NGS) and Protein expression by liquid chromatography mass spectrometry (LC-MS) from the same tissue section is expected to empower researchers with confirmatory, quantitative data. A proprietary Unified Method (UM) (Thermo Fisher Scientific, Kalamazoo, MI) for isolating RNA, DNA and Proteins from a single FFPE section was developed and used to analyze RNA expression, DNA mutations and Protein expression from a clinical sample. The RNA and DNA were analyzed using the Thermo Scientific Ion AmpliSeq NGS platform and the Proteins were analyzed on a Thermo Scientific LC-MS system. A Proprietry Integrated Bioinformatics Software (PIBS) (Thermo Fisher Scientific, Kalamazoo, MI) was developed to correlate RNA expression, DNA mutations and Protein Expression. The PIBS correlates RNA and Protein Quantification, DNA mutations and morphological information, and it is scalable to handle replicate datasets from Proteogenomics workflows. Researchers will be able to correlate data across profiles and identify differentially expressed markers. Proteogenomics data can be analyzed with histological subtype as well as the presence of drug targets for research use. Development of targeted LC-MS research methods is expected to increase the correspondence between FF and FFPE datasets as well as the detection of future biomarkers of interest.