Discovery of Novel and Clinically Relevant Markers in Formalin-Fixed Paraffin-Embedded Esophageal Cancer Specimen

Abstract

Due to the ineffectiveness of chemoradiation and targeted therapy in esophageal anticancer care and the subsequent low survival rates, we constructed a high throughput method to discover and investigate new markers with prognostic, diagnostic, and therapeutic clinical utility. This was accomplished by developing a quick, inexpensive, and dependable platform to simultaneously quantify thousands of proteins which subsequently revealed novel markers involved in the pathogenesis of esophageal adenocarcinoma (EAC) via discovery mass spectrometry paired with conservative biostatistics. Our method uncovered a perfect storm of tumor suppressors being downregulated, proliferation markers ramped up, and chemoresistance markers overexpressed—many of which could serve as new therapy targets for EAC. The 12 markers discovered by this method are novel regarding their involvement in the pathogenesis of EAC. The molecular oncology arena now has a dozen new proteomic targets suitable for validation and elucidation of their clinical utility via gene knockdown in cellular and animal models. This new method can be replicated and applied to other cancers or disease states for research and development and discovery-based investigations. Our findings, which serve as a proof of concept, will hopefully motivate research groups to further expound on the molecular processes involved in the aggressiveness of EAC and other solid tumor diseases, ultimately leading to improved patient management strategies.

The Risk of Barrett’s Esophagus Transforming to Esophageal Cancer

“…With advancements in technology, proteomics analysis can be another tool for risk stratification in BE. The feasibility in formalin-fixed clinical specimens has been demonstrated 42 but needs further validation in larger cohorts before clinical application.…”

Current state of prognostication, therapy and prospective innovations for Barrett’s-related esophageal adenocarcinoma: a literature review

“…Mass spectrometry has recently been used to investigate and identify BE relevant biomarkers (83). An early study used matrix-assisted laser desorption/ionization mass spectrometry to attempt to identify protein peak differences, but the technology was not compatible with formalinfixed, paraffin-embedded tissue, serving as a problem for general use as the majority of patients are surveilled through biopsies in which the tissue is fixed as such, and an effective mass spectrometry approach would aim to make use of this tissue.…”

“…The SWATH-MS platform was used to identify proteomic expression trends related to EAC treatment resistance, in particular, cisplatin, 5-FU and taxanes (HMGB1, IL-1RA, LGALS3BP, PRMT1, S100A8, SFN, and TXN) (15). The use of mass spectrometry is novel within the BE diagnosis landscape but proves promising due to the high-throughput nature of the technology itself using original biopsy tissue and having the ability to use antibody free detection and quantification of multiple biomarkers simultaneously (83).…”

Biomarkers for Early Detection, Prognosis, and Therapeutics of Esophageal Cancers

“…Early-stage disease and complete resection of the lesion are favorable prognostic markers [ 13 ]. However, the ineffectiveness of chemotherapy, radiation therapy, immunotherapy, and targeted therapy contributing to low survival rates warrants the establishment of early-stage diagnostic biomarkers and novel therapeutics to improve clinical outcomes and decrease morbidity and mortality [ 14 , 15 ]. This notion is further supported by the asymptomatic nature of EC in its early stages, its extremely aggressive nature, and its poor survival rate.…”