RNA Sequencing Addresses a 5’ UTR Variant Leading to X-Linked Agammaglobulinemia and Broader Immune Dysregulation

Pathogenic variants in BTK cause X-linked agammaglobulinemia (XLA), yet some cases remain undiagnosed despite extensive genetic testing. Additionally, autoimmune complications have been increasingly reported, but the underlying etiology is still unclear. This study aimed to use RNA sequencing (RNA-seq) to resolve an undiagnosed case and characterize transcriptomic features associated with disease mechanisms of XLA. We performed genome sequencing and RNA-seq, detected outliers against 89 controls to identify disease-causing variants, and validated functional consequences through RT-PCR. We further conducted gene set enrichment analysis (GSEA) to delineate the transcriptomic features of XLA. We recruited an 18-year-old male who experienced recurrent infections since infancy but developed idiopathic portal hypertension recently. He had received four noninformative genetic test results. RNA-seq enabled the identification of significantly decreased BTK expression caused by a de novo hemizygous variant (NM_000061.3:c.-32A > G) located in the 5’ UTR. Outlier analysis revealed reduced expression of genes critical for not only immunoglobulin synthesis, but also T-cell development and inflammation intensification, such as IGHM, TRBV24-1, and PLVAP. GSEA additionally revealed significant enrichment in pathways associated with immune response and inflammatory response, suggesting broader immune dysregulation. These findings align with the growing recognition of autoimmune complications in XLA. This study emphasizes the clinical utility of RNA-seq and provides a comprehensive expression profile of XLA. These findings can guide future molecular analyses in undiagnosed cases and enhance understanding of autoimmune complications in XLA, suggesting a Multidisciplinary Team approach in both diagnostic and treatment processes.