Quantitative analysis of tyrosine phosphorylation from FFPE tissues reveals patient-specific signaling networks.

TitleQuantitative analysis of tyrosine phosphorylation from FFPE tissues reveals patient-specific signaling networks.
Publication TypeJournal Article
Year of Publication2021
AuthorsKohale IN, Burgenske DM, Mladek AC, Bakken KK, Kuang J, Boughey JC, Wang L, Carter JM, Haura EB, Goetz MP, Sarkaria JN, White FM
JournalCancer Res
Date Published2021 May 20
ISSN1538-7445
Abstract

Human tissue samples commonly preserved as formalin-fixed paraffin-embedded (FFPE) tissues after diagnostic or surgical procedures in the clinic represent an invaluable source of clinical specimens for in-depth characterization of signaling networks to assess therapeutic options. Tyrosine phosphorylation (pTyr) plays a fundamental role in cellular processes and is commonly dysregulated in cancer but has not been studied to date in FFPE samples. Additionally, pTyr analysis that may otherwise inform therapeutic interventions for patients has been limited by the requirement for large amounts of frozen tissue. Here we describe a method for highly sensitive, quantitative analysis of pTyr signaling networks, with hundreds of sites quantified from 1-2 10-┬Ám sections of FFPE tissue specimens. A combination of optimized magnetic bead-based sample processing, optimized pTyr enrichment strategies, and TMT multiplexing enabled in depth coverage of pTyr signaling networks from small amounts of input material. Phosphotyrosine profiles of flash frozen and FFPE tissues derived from the same tumors suggested that FFPE tissues preserve pTyr signaling characteristics in patient-derived xenografts and archived clinical specimens. pTyr analysis of FFPE tissue sections from breast cancer tumors as well as lung cancer tumors highlighted patient-specific oncogenic driving kinases, indicating potential targeted therapies for each patient. These data suggest the capability for direct translational insight from pTyr analysis of small amounts of FFPE tumor tissue specimens.

DOI10.1158/0008-5472.CAN-21-0214
Alternate JournalCancer Res
PubMed ID34016623
Grant ListP42 ES027707 / ES / NIEHS NIH HHS / United States
P30 CA014051 / CA / NCI NIH HHS / United States
U01 CA238720 / CA / NCI NIH HHS / United States
P50 CA116201 / CA / NCI NIH HHS / United States
U54 CA210180 / CA / NCI NIH HHS / United States