Bioinformatics analysis of potential key ferroptosis-related genes involved in tubulointerstitial injury in patients with diabetic nephropathy

Abstract

Diabetic nephropathy (DN) is the primary complication of diabetes mellitus. Ferroptosis is a form of cell death that plays an important role in DN tubulointerstitial injury, but the specific molecular mechanism remains unclear. Here, we downloaded the DN tubulointerstitial datasets GSE104954 and GSE30529 from the Gene Expression Omnibus database. We examined the differentially expressed genes (DEGs) between DN patients and healthy controls, and 36 ferroptosis-related DEGs were selected. Pathway-enrichment analyses showed that many of these genes are involved in metabolic pathways, phosphoinositide 3-kinase/Akt signaling, and hypoxia-inducible factor-1 signaling. Ten of the 36 ferroptosis-related DEGs (CD44, PTEN, CDKN1A, DPP4, DUSP1, CYBB, DDIT3, ALOX5, VEGFA, and NCF2) were identified as key genes. Expression patterns for six of these (CD44, PTEN, DDIT3, ALOX5, VEGFA, and NCF2) were validated in the GSE30529 dataset. Nephroseq data indicated that the mRNA expression levels of CD44, PTEN, ALOX5, and NCF2 were negatively correlated with the glomerular filtration rate (GFR), while VEGFA and DDIT3 mRNA expression levels were positively correlated with GFR. Immune infiltration analysis demonstrated altered immunity in DN patients. Real-time quantitative PCR (qPCR) analysis showed that ALOX5, PTEN, and NCF2 mRNA levels were significantly upregulated in high-glucose-treated human proximal tubular (HK-2) cells, while DDIT3 and VEGFA mRNA levels were significantly downregulated. Immunohistochemistry analysis of human renal biopsies showed positive staining for ALOX5 and NCF2 protein in DN samples but not the controls. These key genes may be involved in the molecular mechanisms underlying ferroptosis in patients with DN, potentially through specific metabolic pathways and immune/inflammatory mechanisms.

Keywords:

• Diabetic nephropathy
• tubulointerstitial injury
• ferroptosis
• key gene
• key pathways

Acknowledgments

The authors thank Dr. Wei Chen from the experimental and translational center of Beijing Friendship Hospital for their kind suggestions. We also thank Susan Furness, PhD, and J. Iacona, PhD, from Liwen Bianji (Edanz) (www.liwenbianji.cn) for editing the English text of a draft of this manuscript.

Ethical approval

This study was approved by the Ethics Committee of Beijing Friendship Hospital affiliated with Capital Medical University (2023-P2-017-01). All subjects provided written informed consent in accordance with the World Medical Association Declaration of Helsinki.

Author contributions

WHL and ZLD conceived and designed the study. LLM and YB performed the bioinformatics and correlation analyses. LLM wrote the first draft. ZLD and YB revised the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The datasets used or analyzed during the current study are available from the corresponding author upon reasonable request. These data were derived in the public domain GEO.

Additional information

Funding

This work was supported by the Construction of Wu Jieping Medical Foundation under Grant code [32067502021-11-26]; the Beijing Municipal Administration of Hospitals Incubating Program under Grant code [PX2022003]; the Beijing Natural Science Foundation under Grant [7232036]; and the Beijing Natural Science Foundation under Grant [7232030].