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Transcriptome sequencing analysis of Cyp4f3b gene interference in human gallbladder carcinoma cells gbc-sd

ABSTRACT: This study aimed to investigate the molecular mechanism underlying the effects of Cyp4f3b gene interference on the biological behaviors of human gallbladder carcinoma cells gbc-sd. Three replicate cell samples from each group (sh-NC control group and sh-Cyp4f3b interference group) were subjected to total RNA extraction and quality control, sequencing library construction and evaluation, RNA-seq sequencing and filtering, reference sequence alignment, gene expression level analysis, and differential expression analysis. Differentially expressed genes and significantly enriched signaling pathways were systematically identified to provide molecular evidence for clarifying the role of Cyp4f3b in gallbladder carcinogenesis and progression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE325472 | GEO | 2026/03/25

REPOSITORIES: GEO

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Project description:Introduction: Gallbladder cancer (GBC) is a highly aggressive malignancy with limited therapeutic options, particularly in underrepresented populations, including South Africa. Understanding the molecular landscape of GBC may provide novel insights into its pathogenesis and potential therapeutic targets. Molecular changes are known to be associated with GBC, however, there is a paucity of this information especially in African populations. Furthermore, within the tumour microenvironment, different immune cells contribute to GBC progression. We investigated gene expression patterns in GBC tumours and their association with different immune cells in a cohort of South African patients. Methods: RNA sequencing was conducted on 2 normal and 8 gallbladder cancer tissues from South African patients (Ethics: M160640) to identify differentially expressed genes. Bioinformatics tools were used for pathway analysis, while immune cell quantification was performed using the quanTIseq software and presented as median [IQR]. Verification studies were further carried out using real-time PCR on an independent cohort comprising 7 gallstone samples and 26 gallbladder tumour samples. Results: A total of 65 genes were found to be significantly differentially expressed between the gallbladder tumours and gallstone controls. We also identified 37 upregulated and 28 downregulated genes in this cohort. Among the most upregulated genes, MUC16 was confirmed to be significantly overexpressed in tumours. Normal tissues exhibited a significantly higher proportion of dysregulated genes associated with B cells (17.132 [14.866–18.483], p<0.0001) and M1 macrophages (18.943 [1.097–36.790], p<0.0001) compared to tumours. In contrast, tumours showed a greater association with dysregulated genes linked to regulatory T cells (Tregs) (14.373 [9.696–20.162]) relative to normal tissues. Pathway analysis further revealed the upregulation of defective GALNT12, defective GALNT3, defective C1GALT1C1 and termination of O-glycan biosynthesis, highlighting key mechanisms potentially involved in tumour progression. Conclusion: The study has shown the dysregulation of key genes in South African gallbladder cancer patients. Specifically, MUC16 was verified to be significantly elevated in tumour samples. Furthermore, the association of these dysregulated genes with key immune cells in this patient group may further highlight their roles in dysfunctional immune processes linked with tumourigenesis.

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Transcriptome sequencing analysis of Cyp4f3b gene interference in human gallbladder carcinoma cells gbc-sd

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