Molecular alterations in oral cancer using high-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue

Varshasnata Mohanty, Yashwanth Subbannayya, Shankargouda Patil, Vinuth N. Puttamallesh, Mohd Altaf Najar, Keshava K. Datta, Sneha M. Pinto, Sameera Begum, Neeta Mohanty, Samapika Routray, Riaz Abdulla, Jay Gopal Ray, David Sidransky, Harsha Gowda, T. S.Keshava Prasad, Aditi Chatterjee

Research output: Contribution to journalArticlepeer-review


Loss of cell differentiation is a hallmark for the progression of oral squamous cell carcinoma (OSCC). Archival Formalin-Fixed Paraffin-Embedded (FFPE) tissues constitute a valuable resource for studying the differentiation of OSCC and can offer valuable insights into the process of tumor progression. In the current study, we performed LC–MS/MS-based quantitative proteomics of FFPE specimens from pathologically-confirmed well-differentiated, moderately-differentiated, and poorly-differentiated OSCC cases. The data were analyzed in four technical replicates, resulting in the identification of 2376 proteins. Of these, 141 and 109 were differentially expressed in moderately-differentiated and poorly differentiated OSCC cases, respectively, compared to well-differentiated OSCC. The data revealed significant metabolic reprogramming with respect to lipid metabolism and glycolysis with proteins belonging to both these processes downregulated in moderately-differentiated OSCC when compared to well-differentiated OSCC. Signaling pathway analysis indicated the alteration of extracellular matrix organization, muscle contraction, and glucose metabolism pathways across tumor grades. The extracellular matrix organization pathway was upregulated in moderately-differentiated OSCC and downregulated in poorly differentiated OSCC, compared to well-differentiated OSCC. PADI4, an epigenetic enzyme transcriptional regulator, and its transcriptional target HIST1H1B were both found to be upregulated in moderately differentiated and poorly differentiated OSCC, indicating epigenetic events underlying tumor differentiation. In conclusion, the findings support the advantage of using high-resolution mass spectrometry-based FFPE archival blocks for clinical and translational research. The candidate signaling pathways identified in the study could be used to develop potential therapeutic targets for OSCC.

Original languageEnglish (US)
Pages (from-to)447-459
Number of pages13
JournalJournal of Cell Communication and Signaling
Issue number3
StatePublished - Sep 2021


  • Cancer grade
  • Cancer pathology
  • Molecular medicine
  • Pressure cycling technology
  • Quantitative proteomics
  • Tumor differentiation

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology


Dive into the research topics of 'Molecular alterations in oral cancer using high-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue'. Together they form a unique fingerprint.

Cite this