Targeted Proteomics Quantitation of NRF2 and Predictive Biomarkers in HNSCC
  • Organism: Homo sapiens
  • Instrument: Orbitrap Eclipse
  • SpikeIn: No
  • Keywords: HNSCC, NRF2, IS-PRM
  • Lab head: Michael B. Major Submitter: Emily Wilkerson
The NFE2L2/NRF2 oncogene and transcription factor drives a gene expression program that promotes cancer progression, metabolic reprogramming, immune evasion and chemoradiation resistance. Patient stratification by NRF2 activity may guide treatment decisions to improve outcome. Here, we developed a mass spectrometry (MS)-based targeted proteomics assay based on internal standard triggered parallel reaction monitoring (IS-PRM) to quantify 69 NRF2 pathway components and targets as well as 21 proteins of broad clinical significance in head and neck squamous cell carcinoma (HNSCC). We improved the existing IS-PRM acquisition algorithm, called SureQuantâ„¢, to increase throughput, sensitivity, and precision. Testing the optimized platform on 27 lung and upper aerodigestive cancer cell models revealed 35 NRF2 responsive proteins. In formalin-fixed paraffin-embedded (FFPE) HNSCCs, NRF2 signaling intensity positively correlated with NRF2 activating mutations and with SOX2 protein expression. PD-L2/CD273 and protein markers of T-cell infiltration correlated positively with one another and with human papilloma virus (HPV) infection status. p16/CDKN2A protein expression positively correlated with the HPV oncogenic E7 protein, and confirmed the presence of translationally active virus. This work establishes a clinically actionable HNSCC protein biomarker assay capable of quantifying over 600 peptides from frozen or FFPE archived tissues in under 90 minutes.
Created on 6/22/23, 10:06 PM
Clustergrammer Heatmap
SCC90_SCC152_SCC154_2023-06-12_13-00-29.sky.zip2023-06-22 22:02:11882254502,68418
FFPE_NRF2_MUT_WT_2023-06-12_12-29-17.sky.zip2023-06-22 22:02:11882254502,68429
CELL_LINES_2023-06-12_12-06-35.sky.zip2023-06-22 22:02:11882254502,68447
FFPE_HPV_2023-06-12_11-58-29.sky.zip2023-06-22 22:02:11882254502,68430