High-throughput transcriptome analysis for identification of Helicobacter pylori vaccine target antigens

Helicobacter pylori (Hp), a Gram-negative bacterium, establishes enduring colonization inthe human stomach by inducing immunoregulatory responses [۱]. Due to its involvement in chronicgastritis, peptic ulcers, and gastric cancer, researchers aim to prevent these conditions through novel,safe, and highly effective vaccines [۲]. Microarray and RNA-seq techniques play crucial roles in aidingvaccinologists to identify novel vaccine-targeted antigens contributing significantly to the pathogenesisof various pathogens. In this study, we analyze microarray (GSE۶۰۴۲۷ and GSE۱۲۳۶۲۳) and RNA-seq(GSE۱۶۴۲۱۶) datasets from the NCBI GEO database. After quality control using R programBioconductor packages, principal component analysis assesses sample uniformity within each dataset.The Limma package conducts statistical analysis, and a Venn diagram identifies common differentiallyexpressed virulence genes (DEVGs). Kaplan-Meier plotter assesses the correlation between geneexpression and survival outcomes.High-throughput transcriptome analysis of ۴۸ samples reveals ۲۴ significantly upregulated and ۲۳downregulated genes (adj.P.val < ۰.۰۱ and |log۲ FC| > ۲). Top less-annotated genes (HP۱۱۶۷ andHP۱۴۴۰) were identified in the upregulated list, and (HP۱۵۸۸ and HP۰۴۱۵) in the downregulated list,with predicted key roles in bacterial pathogenicity, proposing them as notable vaccine antigens. Geneslike dppA, gpsA, pdxJ, rnhB, tagD (downregulated), and flgK, flaA, cag۷, fliD, flag (upregulated) werediscovered as known antigens in bacterial invasion pathways. GeneCards and KEGG pathwaydatabases indicate their significant molecular function in pathogenicity-related pathways, suggestingthem as vaccine targets in subsequent in silico and experimental studies.This study not only provides valuable insights into the molecular signatures associated with Hp’spathogenicity but also highlights their potential for developing prophylactic interventions in clinicalsettings.

کلیدواژه ها:

Antigen ، Helicobacter pylori ، Microarray ، RNA-seq ، Transcriptome ، Vaccine