Personalized therapy for head and neck squamous carcinoma (HNSCC) utilizing tissue proteomics profiling.

person Sheeno P. Thyparambil mProbe Inc., Rockville, MD info_outline Sheeno P. Thyparambil, Wei-Li Liao, Amanda Strasbaugh, Marya Abebe Melkie, Negin Ghafourian, Robert Heaton, Xuefeng Ling

Authors person Sheeno P. Thyparambil mProbe Inc., Rockville, MD info_outline Sheeno P. Thyparambil, Wei-Li Liao, Amanda Strasbaugh, Marya Abebe Melkie, Negin Ghafourian, Robert Heaton, Xuefeng Ling Organizations mProbe Inc., Rockville, MD, mProbe, Rockville, MD, Stanford University, Stanford, CA Abstract Disclosures Research Funding Pharmaceutical/Biotech Company mProbe Background: Chemotherapy is widely used in the treatment of HNSCC, yet no biomarkers for chemotherapy is used for selection of the chemo agent in the treatment of HNSCC. We examined 143 HNSCC cancer using targeted proteomics for the protein expression levels of several chemo agents. These include markers of resistance to platinum agents (ERCC1), anti-tubulin inhibitors (TUBB3) and sensitivity markers for topoisomerase inhibitors (Topo1 – irinotecan, topotecan; Topo2A – doxorubicin, etoposide). We also measured markers for several antibody-drug conjugates (EGFR, Her2, Trop2, FR-alpha, Mesothelin). Methods: Tumor areas from Formalin-fixed, paraffin-embedded (FFPE) tumor tissues from clinical samples of HNSCC that were received at our CLIA certified laboratory were microdissected and a selected reaction monitoring mass spectrometry (SRM-MS) quantitative proteomic analysis of 72 protein biomarkers were conducted concurrently from 2-3 sections of FFPE tissue. Results: Platinum agents are widely agent in HNSCC cancer. ERCC1, a resistance marker for platinum agents was expressed in 44% of HNSCC. Similarly, TUBB3, a resistance marker for Paclitaxel, docetaxel was also expressed in ~45% of HNSCC. These indicate that ~45% of HNSCC could potentially be refractory to platinum and paclitaxel-based therapy. Additionally, ALDH1A1, a marker for resistance of cyclophosphamide, was expressed in 78% of HNSCC. Temozolomide, an alkylating agent used in other cancer type could be beneficial in 14% of HNSCC because of the lack of resistance marker MGMT. On the other hand, 88% of HNSCC expressed Topo1, which is a sensitivity marker for irinotecan or topotecan based therapy. Additionally, Top1 is also the target for the payload of several ADCs (e.g. trastuzumab deruxtecan and sacituzumab govitecan). Similarly, 55% of HNSCC expressed Topo2A, a target for etoposide and doxorubicin. Additionally, 57% of HNSCC expressed hENT1, a transporter of gemcitabine. HNSCC also expressed various targets for targeted and ADC agents. These include EGFR (86% detected with 37x range of distribution), Her3 (11%), IGF1R (16%), MET (13%), Folate receptor- alpha (18%), Mesothelin (13%), and Trop2 (89% with 134x range of distribution). Her2 was overexpressed ( > 750 amol/ug) in 11% of HNSCC, however, it was observed in 46% of HNSCC with a 53x range (276 – 14705 amol/ug), indicating that a significant population of HNSCC might be eligible for low Her2 clinical trials. Conclusions: Every cancer is unique, and the ability to analyze 72 protein biomarkers from 2-3 FFPE sections simultaneously at the same time provides a wealth of actionable information for clinical treatment or patient stratification for clinical trials.