Identification of Key Disulfidptosis-Related Genes and Their Association with Gene Expression Subtypes in Crohn's Disease

Abstract

Background: Crohn's disease (CD) is a persistent inflammatory condition that impacts the gastrointestinal system and is characterized by a multifaceted pathogenesis involving genetic, immune, and environmental components. This study primarily investigates the relationship between gene expression and immune cell infiltration in CD, focusing on disulfidptosis-a novel form of cell death caused by abnormal disulfide accumulation-and its impact on various immune cell populations. By identifying key disulfidptosis-related genes (DRGs) and exploring their association with distinct gene expression subtypes, this research aims to enhance our understanding of CD and potentially other autoimmune diseases.

Methods: Gene expression data from intestinal biopsy samples were collected from both individuals with CD and healthy controls, and these data were retrieved from the GEO database. Through gene expression level comparisons, various differentially expressed genes (DEGs) were identified. Subsequently, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to reveal the biological processes and pathways linked to these DEGs. Later, immune cell infiltration was evaluated. Hub candidate DRGs were identified using machine learning algorithms. Validation of the expression of hub DRGs was carried out using quantitative real-time polymerase chain reaction. The hub DRGs were subjected to unsupervised hierarchical clustering to classify CD patients into subtypes. The characteristics of each subtype were then analyzed.

Results: Two hub DRGs (NDUFA11 and LRPPRC) were identified. NDUFA11 showed a significantly positive association with the abundance of Th17 cells. Conversely, higher expression levels of LRPPRC were associated with a reduced abundance of various immune cells, particularly monocytes. CD patients were classified into two disulfidptosis-related subtypes. Cluster B patients exhibited lower immune infiltration and milder clinical presentation.

Conclusion: LRPPRC and NDUFA11 are identified as hub DRGs in CD, with potential roles in disulfidptosis and immune regulation. The disulfidptosis subtypes provide new insights into disease progression.

Keywords: Crohn’s disease; disulfidptosis; expression pattern; immune cell infiltration; machine learning.

Figure 1

Integration of GEO datasets and identification of differentially expressed genes (DEGs). (A and B) illustrate principal component analysis demonstrating batch effects before and after de-batching the integrated datasets. (C) Depicts the volcano plot displaying DEGs related to Crohn’s disease. (D) Presents a clustered heatmap exhibiting expression levels of DEGs. (E) Shows enriched Gene Ontology (GO)analysis items. (F) Shows enriched items from the Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis items; “BP”, biological processes; “MF”, molecular functions; “CC”, cellular component.

Figure 2

Immune cell infiltration analysis in merging GEO datasets. (A) comparing 23 immune cell subtypes between CD patients and controls, with circle size and color representing Pearson correlation coefficients. (B) Presents a correlation matrix illustrating the compositions of all 23 immune cell subtypes. “ns” denotes no significance, while “*”, “**”, and “***” correspond to p-values of <0.05, <0.01, and <0.001, respectively.

Figure 3

Determination of disulfidptosis-related genes (DRGs) in merging GEO datasets. (A) Demonstrates the gene overlap between DEGs and DRGs. (B) Depicts an overall expression histogram of differentially expressed DEGs in CD patients. “**”,“***”, and “****” correspond to p-values of <0.01, <0.001, and <0.0001, respectively.

Figure 4

The mRNA levels of NDUFA11 (A), MYL6 (B), DSTN (C), LRPPRC (D), FLNA (E) and SLC7A11 (F) measured from collected samples. “*” represents p-values of <0.05.

Figure 5

Correlation analysis of immune infiltrating cells and gene set enrichment analysis with NDUFA11 and LRPPRC in merging GEO datasets (A–D).

Figure 6

Characteristics of the disulfidptosis-related subtype. (A) Volcano plot showing DEGs. (B) Shows enriched GO analysis items. (C) Shows enriched KEGG analysis items. (D) Association between the disulfidptosis-related subtype and Simple Endoscopic Score for 253 CD patients (GSE112366). The shape of each violin plot indicates the density and distribution of scores within each subtype, with wider sections showing a higher density of data points. The box within each violin shows the interquartile range, and the line within the box indicates the median score. (E) Matrix depicting the correlation among all 23 immune cell subtypes within distinct clusters. “BP”, biological processes; “MF”, molecular functions; “ns” denotes no significance, while “*”, “**”, and “***” correspond to p-values of <0.05, <0.01, and <0.001, respectively.

Figure 7

Gene set enrichment analysis based on the KEGG (A), Reactome (B) and HALLMARK (C) pathway.