Deciphering the role of tryptophan metabolism-associated genes ECHS1 and ALDH2 in gastric cancer: implications for tumor immunity and personalized therapy

Abstract

Background: Tryptophan Metabolism-associated Genes (TMGs), such as ECHS1 and ALDH2, are crucial in cancer progression through immunosuppressive mechanisms, particularly in Gastric Cancer (GC). This study explores their effects on the Tumor Microenvironment (TME). Additionally, it examines their potential as novel immunotherapy targets.

Methods: We utilized single-cell and bulk transcriptomic technologies to analyze the heterogeneity of GC. Non-negative Matrix Factorization (NMF) clustering identified key TMGs, and extensive RNA-seq analyses were performed to pinpoint prognostic genes and potential immunotherapy targets. Furthermore, through PCR analyses we found that ECHS1 and ALDH2 gene expression plays a regulatory role in the migration, invasion and inflammatory factor in AGS and SNU-1 cell lines. The interference effect of si-ECHS1 and ad-ALDH2 was validated using cell scratch assay in AGS and SNU-1 cell line.

Results: We observed a statistically significant correlation between ECHS1 and ALDH2 expression and increased TME heterogeneity. Our findings also revealed that ECHS1 down-regulation and ALDH2 up-regulation contribute to reduced TME heterogeneity, decreased inflammation, and inhibited AGS and SNU-1 tumor cells migration and proliferation. GSVA enrichment analysis highlighted the NF-kappa B(NF-κB) signaling pathway as specifically regulated by TMGs. Furthermore,ECHS1 and ALDH2 modulated CD8+ and CD4+ T cell activities, impacting GC progression. In vitro experiments further solidified our conclusions by showcasing the inhibitory effects of Si-ECHS1 and ad-ALDH2 on the invasive and proliferative capabilities of AGS and SNU-1 cells. Moreover, Si-ECHS1 and ad-ALDH2 gene expression effectively reduced the expression of inflammatory factors IL-10,IL-7,CXCL8 and IL-6, leading to a remarkable alleviation of chronic inflammation and the heterogeneous nature of the TME.

Conclusion: This research highlights the importance of ECHS1 and ALDH2 in GC progression and immune modulation, suggesting that targeted therapies focusing on these genes offer promising avenues for personalized immunotherapy in GC. These findings hold potential for improving patient survival and quality of life. Future studies on the NF-κB signaling pathway's role in this context are warranted to further elucidate the mechanisms underlying TMG-mediated immune modulation in GC.

Keywords: ALDH2; ECHS1; gastric cancer (GC); tryptophan metabolism-associated genes (TMGs); tumor microenvironment (TME).

Figure 1

ScRNA-seq analysis of GC and normal groups. (A, B) Identification of TME cells type expression in GC including T cells, Monocytes cells, B cells, Macrophages cells, Plasma cells, Epithelial cells, Fibroblasts cells, Mast cells and Stromal cells in GSE163558. (C) The network diagram illustrates the interaction of key cell types in the GC. Each point represents a cell cluster, with the size of the point indicating the weight of that cluster in the network. The thickness of each line corresponds to its strength. (D) The expression of tryptophan metabolism family genes in key cell type of GC.

Figure 2

HLA-A ligands mediate a stronger tumor microenvironment regulated by FOXF1 and ZNF384. (A, B) The different expression of receptor-ligand in cell type. (C) The expression and function of HLA-A ligands in relation to the receptor on epithelial cells. Red indicates positive regulation, blue indicates negative regulation, and gray has no regulatory significance. (D) The expression of transcription factors varies among cell types. Red indicates positive regulation, blue indicates negative regulation, and gray has no regulatory significance.

Figure 3

Identification of key tryptophan metabolism genes expression in GC. (A) The pseudo-time analysis the expression of TMGs-related genes, red indicates high expression and blue indicates low expression. (B)The process of extracting and visualizing epithelial cells through reclustering, which led to the identification of two distinct groups of epithelial cells, with epi-2 constituting the majority. The genes STAT1, ALDH2, and ECHS1 were specifically found to be expressed in the epi-2 group, as determined by NMF analysis. (C) The tSNE visualization displays the expression levels of STAT1, ALDH2, and ECHS1. (D) GSVA analysis highlights critical pathways in GC. (E)The tryptophan metabolism genes STAT1, ALDH2, and ECHS1 are significantly enriched in GC, with red indicating high expression levels.

Figure 4

The SVM algorithm model was constructed for the tryptophan metabolism family genes. (A) The various expressions of tryptophan metabolism family genes in the GC transcriptome were analyzed. Red indicates high expression, blue indicates low expression. (B) The correlation of tryptophan metabolism family genes. The higher the correlation, the darker the color. (C) The SVM-RFE machine algorithm model was constructed in GSE79973. (D, E) ROC and calibration curve analysis of machine algorithm model predictive value in GSE79973. *, P<0.05,**, P<0.01, ***, P<0.001.

Figure 5

Transcriptomic analysis of tryptophan metabolic family genes expressed in GC and normal groups. The positive expression of tryptophan metabolism family genes were screened by svm algorithm. (A) RF model showed the top 10 tryptophan metabolic key genes in terms of importance. This graph is the MeanDecreaseGini coefficient graph, with MeanDecreaseGini values on the horizontal axis. The larger the MeanDecreaseGini value, the better the classification of categories. The vertical axis represents the expression of positive genes, arranged in descending order according to the MeanDecreaseGini coefficient. (B, C) Decision curve analysis (DCA) and nomogram predict the key gene expression in GC patients. (D) The correlation between the ALDH2 and ECHS1 genes and inflammation. *, P<0.05, **, P<0.01, ***, P<0.001.

Figure 6

ALDH2 and ECHS1 ICB immunotherapy restrain the progress of GC. (A, B) Immune infiltration of ALDH2 and ECHS1 gene in GC. (C) To evaluate the key genes expression survival curves by Kaplan-Meier survival analysis. (D) Evaluation of the prognosis of ICB immunotherapy by TCGA-STAD, GSE79973, GSE62254, GSE54129, GSE34942 and GSE5118986. (E) bulk transcriptome analysis the expression of ALDH2 and ECHS1 and prognosis by TCGA-STAD, GSE54129 and GSE26253. *, P<0.05, **, P<0.01, ***, P<0.001.

Figure 7

si-ECHS1 and ad-ALDH2 transfections were inhibition of inflammatory expression. The expression of IL6, IL7, IL10, CXCL8 by qPCR assay in AGS and SNU-1 cells. *, P<0.05, **, P<0.01, ***, P<0.001.

Figure 8

Low levels of tryptophan metabolism were effective in slowing the progression of GC. (A) The transfection of si-ECHS1 and ad-ALDH2 into AGS and SNU-1 cells influenced the expression of TMGs and tryptophan metabolism. (B) The influence of cell migration by the transfection of si-ECHS1 and ad-ALDH2 in AGS and SNU-1 cells. **, P<0.01, ***, P<0.001, ****, P<0.0001.

Figure 9

A global landscape of tryptophan metabolism analysis.