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The NEAT1/miR-124-3p/CCL2 axis in chronic kidney disease progression: integrated bioinformatics analysis and

Guanting Chen1,2, Linqi Zhang1,2, Yaoxian Wang2

  • 1Department of Nephrology, First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan Province, China.

Epigenomics
|August 21, 2025
PubMed
Abstract

Insights

Researchers identified key genes, including CCL2, as potential biomarkers and therapeutic targets for chronic kidney disease (CKD). A regulatory axis involving NEAT1, miR-124-3p, and CCL2 was found to be crucial in CKD progression.

Area of Science:

  • Nephrology
  • Molecular Biology
  • Genomics

Background:

  • Chronic kidney disease (CKD) represents a significant global health challenge with limited effective treatments.
  • Renal interstitial fibrosis (RIF) is a primary driver of CKD progression.
  • The study sought to discover novel diagnostic biomarkers and therapeutic targets for CKD.

Purpose of the Study:

  • To identify differentially expressed genes (DEGs) and key regulatory pathways in CKD.
  • To validate potential biomarkers and therapeutic targets using various experimental models and clinical samples.
  • To elucidate the role of the NEAT1/miR-124-3p/CCL2 axis in CKD pathogenesis.

Main Methods:

  • Analysis of the GEO dataset GSE137570 to identify DEGs.
  • Construction of protein-protein interaction (PPI) networks to screen Hub Genes.
  • Prediction of a competing endogenous RNA (ceRNA) network and validation through single-cell sequencing, in vitro EMT models, clinical samples, and dual-luciferase reporter assays (DLRA).

Main Results:

  • Five Hub Genes (EGF, VCAN, CXCL1, MMP7, CCL2) were identified, with CCL2 being the most central.
  • Enrichment analyses indicated a link between these genes and immune/inflammatory responses.
  • The NEAT1/miR-124-3p/CCL2 axis was confirmed, with serum CCL2 increasing and miR-124-3p and NEAT1 decreasing with CKD progression; these factors demonstrated diagnostic accuracy for staging.

Conclusions:

  • CCL2, alongside EGF, VCAN, CXCL1, and MMP7, shows promise as a CKD biomarker and therapeutic target.
  • The NEAT1/miR-124-3p/CCL2 axis is a critical regulatory pathway implicated in CKD.
  • Moderate sample sizes in bioinformatics and clinical cohorts represent key limitations for future research.
Keywords:
BioinformaticsCCL2NEAT1chronic kidney diseasemiR-124-3prenal interstitial fibrosis

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