Gene Expression Analysis of CD4 T Cells in Autoimmune Pancreatitis: Treatment-Correlated Expression Profiles

Introduction: Autoimmune pancreatitis (AIP) is a rare inflammatory disease characterized by elevated serum IgG4, pancreatic fibrosis, and immune cell infiltration. Prednisolone (PSL) effectively induces remission; however, high relapse rates after treatment cessation highlight the need for reliable biomarkers to predict long-term outcomes. While T cells, particularly regulatory T cells (Tregs) and Th2 cells, are implicated in AIP pathogenesis, comprehensive immune profiling has been limited. Methods: Peripheral blood CD4+ T cells were isolated from AIP patients in the active phase (aAIP, n = 8), remission phase (tAIP, n = 14), and healthy controls (HC, n = 23). RNA sequencing was used to identify differentially expressed genes (DEGs) across groups, and PSL-responsive genes were determined through comparative analysis. Immune-related functions were analyzed via gene ontology (GO) enrichment. Overall design: This study investigates the gene expression profiles of CD4+ T cells in type 1 autoimmune pancreatitis (AIP) patients and healthy controls (HC). Peripheral blood samples were collected from participants and divided into three groups: (1) active AIP patients (aAIP) before steroid treatment, (2) treated AIP patients (tAIP) in remission, and (3) healthy controls (HC). RNA was extracted from CD4+ T cells isolated from these samples, and mRNA sequencing was performed using the Illumina HiSeq 2500 platform. Raw sequencing data were processed to generate gene-level read counts. Differential gene expression analysis was conducted using DESeq2, focusing on three pairwise comparisons: 'aAIP vs. HC,' 'tAIP vs. aAIP,' and 'tAIP vs. HC.' Genes with an adjusted p-value < 0.05 and |log2 fold change| > 0.75 were classified as differentially expressed genes (DEGs). This experimental design aims to identify transcriptional changes associated with AIP disease activity and treatment response.