# Proteoform Patterns in Hepatocellular Carcinoma Tissues: Aspects of Oncomarkers

## TL;DR

This study identifies distinct proteoform patterns in liver cancer and non-cancerous tissues, highlighting potential oncomarkers for hepatocellular carcinoma.

## Contribution

The study introduces a comprehensive top-down proteomics approach to identify proteoform patterns as potential biomarkers in liver cancer.

## Key findings

- Over 2500 proteoform patterns were visualized per sample type, revealing distinct protein signatures in HCC and nonmalignant tissues.
- 38 proteins showed significant differences in proteoform patterns between cancerous and non-cancerous liver tissues.
- Most proteoform patterns were similar to theoretical unmodified proteins, but some showed altered patterns in cancer.

## Abstract

Background: Human proteins exist in numerous modifications—proteoforms—which are promising targets for biomarker studies. In this study, we aimed to generate comparative proteomics data, including proteoform patterns, from hepatocellular carcinoma (HCC) and nonmalignant liver tissues. Methods: To investigate protein profiles and proteoform patterns, we employed a panoramic, integrative top-down proteomics approach: two-dimensional gel electrophoresis (2DE) coupled with liquid chromatography–electrospray ionization–tandem mass spectrometry (LC-ESI-MS/MS). Results: We visualized over 2500 proteoform patterns per sample type, enabling the identification of distinct protein signatures and common patterns differentiating nonmalignant and malignant liver cells. Among these, 1270 protein patterns were uniformly observed across all samples. Additionally, 38 proteins—including pyruvate kinase PKM (KPYM), annexin A2 (ANXA2), and others—exhibited pronounced differences in proteoform patterns between nonmalignant and malignant tissues. Conclusions: Most proteoform patterns of the same protein were highly similar, with the dominant peak corresponding to theoretical (unmodified) protein parameters. However, certain proteins displayed altered proteoform patterns and additional proteoforms in cancer compared to controls. These proteins were prioritized for further characterization.