Identification and validation of potential diagnostic signature and immune cell infiltration for NAFLD based on cuproptosis-related genes by bioinformatics analysis and machine learning

Abstract

Background and aimsCuproptosis has been identified as a key player in the development of several diseases. In this study, we investigate the potential role of cuproptosis-related genes in the pathogenesis of nonalcoholic fatty liver disease (NAFLD).MethodThe gene expression profiles of NAFLD were obtained from the Gene Expression Omnibus database. Differential expression of cuproptosis-related genes (CRGs) were determined between NAFLD and normal tissues. Protein–protein interaction, correlation, and function enrichment analyses were performed. Machine learning was used to identify hub genes. Immune infiltration was analyzed in both NAFLD patients and controls. Quantitative real-time PCR was employed to validate the expression of hub genes.ResultsFour datasets containing 115 NAFLD and 106 control samples were included for bioinformatics analysis. Three hub CRGs (NFE2L2, DLD, and POLD1) were identified through the intersection of three machine learning algorithms. The receiver operating characteristic curve was plotted based on these three marker genes, and the area under the curve (AUC) value was 0.704. In the external GSE135251 dataset, the AUC value of the three key genes was as high as 0.970. Further nomogram, decision curve, calibration curve analyses also confirmed the diagnostic predictive efficacy. Gene set enrichment analysis and gene set variation analysis showed these three marker genes involved in multiple pathways that are related to the progression of NAFLD. CIBERSORT and single-sample gene set enrichment analysis indicated that their expression levels in macrophages, mast cells, NK cells, Treg cells, resting dendritic cells, and tumor-infiltrating lymphocytes were higher in NAFLD compared with control liver samples. The ceRNA network demonstrated a complex regulatory relationship between the three hub genes. The mRNA level of these hub genes were further confirmed in a mouse NAFLD liver samples.ConclusionOur study comprehensively demonstrated the relationship between NAFLD and cuproptosis, developed a promising diagnostic model, and provided potential targets for NAFLD treatment and new insights for exploring the mechanism for NAFLD.

Identification and validation of potential diagnostic signature and immune cell infiltration for HIRI based on cuproptosis-related genes through bioinformatics analysis and machine learning

“…The combined datasets encompassed 75 cases of HIRI and 80 control cases. Thirty-eight CRGs were recovered from the previous literature ( ATP7A, ATP7B, ACO2, CDKN2A, DBT, DLAT, DLD, DLST, DPYD, FDX1, GCSH, GLRX5, GLS, ISCA2, LIAS, LIPA, LIPT1, LIPT2, LIPM, MTF1, NDUFA1, NDUFA8, NDUFB10, NDUFB2, NDUFB6, NLRP3, NDUFC1, NDUFC2, NDUFV2, NFE2L2, PDHA1, PLAT, PDHB, POLD1, PPAT, SLC31A1, SDHB, and TIMMDC1 ) ( 11 , 12 ). ATP7A mutations cause Menkes disease, Hence, ATP7A was excluded from further consideration.…”

“…This mutation has been reported to potentially involve cuproptosis ( 8 ). Some studies have also hinted at an underlying connection between cuproptosis and other liver diseases such as hepatocellular carcinoma and nonalcoholic fatty liver disease; cuproptosis has also attracted great interest in its therapy ( 11 , 12 ). However, research on the role of copper or cuproptosis in HIRI remains relatively limited.…”

Identification and validation of cuproptosis-related genes in acetaminophen-induced liver injury using bioinformatics analysis and machine learning

“…After merging the GSE51969 and GSE205201 data, the merged datasets contained 10 AILI and 10 control samples. Thirty-five CRGs were retrieved from previous literature (ATP7B, CDKN2A, DLD, DPYD, FDX1, GLRX5, GLS, ISCA2, LIPT1, MTF1, NDUFA1, NDUFA8, NDUFB10, NDUFB2, NDUFB6, NDUFC1, NDUFC2, NDUFV2, PDHA1, PLAT, POLD1, PPAT, SLC31A1, SDHB, TIMMDC1, DLAT, GCSH, DBT, DLST, LIAS, LIPM, LIPA, LIPT2, PDHB, ACO2, NLRP3, and NFE2L2) ( 11 , 13 , 14 ). The flowchart of this study is presented in Figure 1 .…”

“…Copper is mainly stored in the liver and is an essential cofactor for diverse biological processes. Aberrant copper concentrations are involved in many liver diseases ( 10 , 11 ). In addition, copper plays an important role in the immune response ( 12 ).…”

Examining the Pathogenesis of MAFLD and the Medicinal Properties of Natural Products from a Metabolic Perspective

“…Ferroptosis and cuproptosis overlap in pathways that regulate complex metabolic processes including mitochondrial respiration, the TCA cycle, and GSH synthesis [233]. Several studies to date have attempted to explore the potential involvement of cuproptosis in MAFLD [234][235][236]. Therefore, the maintenance of copper homeostasis is crucial for normal physiology of the liver, and regulating copper metabolism appears to be a novel therapeutic strategy for MAFLD.…”