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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

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A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

Published on: April 18, 2025

Proteomic characterization identifies clinically relevant subgroups of soft tissue sarcoma.

Shaoshuai Tang¹, Yunzhi Wang¹, Rongkui Luo²

¹State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433, China.

Nature Communications

|February 15, 2024

Summary

This study reveals proteomic differences in soft tissue sarcoma subtypes, linking SHC1 to poor prognosis and identifying proliferation markers APEX1 and NPM1. Immune evasion markers correlate with metastasis.

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Last Updated: Jul 3, 2025

A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

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Published on: April 18, 2025

Isolation and Characterization of Tumor-initiating Cells from Sarcoma Patient-derived Xenografts

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Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors

Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors

Published on: February 27, 2015

Area of Science:

Oncology
Proteomics
Cancer Biology

Background:

Soft tissue sarcoma is a diverse group of mesenchymal tumors.
Understanding the molecular underpinnings of different subtypes is crucial for targeted therapies.

Purpose of the Study:

To comprehensively analyze the proteomic landscape of various soft tissue sarcoma subtypes.
To identify proteomic signatures associated with prognosis and clinical outcomes.
To explore immune microenvironment characteristics and their relation to metastasis.

Main Methods:

Proteomic profiling of 272 soft tissue sarcoma samples across 12 major subtypes.
Hierarchical classification and proteomic clustering for patient stratification.
Analysis of immune signatures and expression of immune evasion markers (PD-L1, CD80).

Main Results:

Proteomic similarity identified between angiosarcoma and epithelial sarcoma, with elevated SHC1 correlating to poor prognosis.
Three distinct proteomic clusters emerged, each with unique driven pathways and clinical outcomes.
High cell proliferation cluster showed APEX1 and NPM1 promoting cancer progression.
Three immune subtypes with distinct tumor microenvironments were defined.
Potential association between immune evasion markers and tumor metastasis was observed.

Conclusions:

Proteomic profiling provides insights into soft tissue sarcoma heterogeneity and relationships between subtypes.
Specific proteins (SHC1, APEX1, NPM1) and immune markers have prognostic and potentially therapeutic implications.
This proteomic atlas aids in understanding sarcoma biology and developing subtype-specific strategies.