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Proteomics01:33

Proteomics

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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.
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Multi-Site Proteomics Reveals Distinct Molecular Patterns Within Functional Dyspepsia.

Ruiqi Ma1, Qianjun Zhuang1, Zhanye Zhang1

  • 1Department of Gastroenterology and Hepatology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.

Neurogastroenterology and Motility
|April 29, 2026
PubMed
Summary
This summary is machine-generated.

Functional dyspepsia (FD) has distinct molecular subtypes in the stomach and duodenum, independent of symptom classification. Identifying these subtypes is crucial for developing targeted therapies for this common gastrointestinal disorder.

Keywords:
ferroptosisfunctional dyspepsiamolecular subtypingprecision medicineproteomics

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Area of Science:

  • Gastroenterology
  • Molecular Biology
  • Proteomics

Background:

  • Functional dyspepsia (FD) is a prevalent gastrointestinal disorder with limited molecular targets.
  • Current symptom-based classifications (epigastric pain syndrome and postprandial distress syndrome) often do not predict treatment response.

Purpose of the Study:

  • To uncover molecular subtypes of functional dyspepsia (FD) using advanced proteomics.
  • To elucidate the underlying molecular heterogeneity of FD for improved therapeutic strategies.

Main Methods:

  • 4D-DIA proteomics was employed on gastric and duodenal biopsies from 47 FD patients and 10 controls.
  • Unsupervised clustering via non-negative matrix factorization identified distinct molecular subtypes.
  • Subtypes were characterized by clinical data, pathway analysis, and immune cell infiltration.

Main Results:

  • Two gastric (G1, G2) and three duodenal (D1, D2, D3) molecular subtypes of FD were identified.
  • Gastric subtypes were associated with immune activation (H. pylori) or metabolic pathways.
  • Duodenal subtypes revealed distinct inflammatory (eosinophils, mast cells) and oxidative stress (ROS, ferroptosis) mechanisms linked to pain.

Conclusions:

  • Functional dyspepsia exhibits significant molecular heterogeneity across gastric and duodenal tissues.
  • Duodenal molecular profiling identified key immune and oxidative pathways relevant to FD.
  • Current symptom-based subtyping is insufficient; mechanism-based stratification is needed for personalized FD treatment.