Gene expression profile of patient with biallelic BRF2 mutation

We performed single-cell RNA sequencing (scRNA-seq) on whole blood cells from a patient with biallelic BRF2 variants (c.782C>T and c.379C>T), exhibiting defective RNA polymerase III activity. The patient presented with recurrent infections, hypogammaglobulinemia, and was later diagnosed with low-grade B cell lymphoma. Our scRNA-seq analysis revealed alterations in gene expression related to BRF2-dependent Pol III transcription, particularly affecting redox genes, including GPX1 and GPX4. Peripheral blood mononuclear cells (PBMCs) were isolated from a patient with biallelic BRF2 mutations and from four age-matched pediatric healthy controls obtained from an independent study. All samples were processed using the 10X Genomics Chromium platform (5' HT v2) for single-cell RNA sequencing. After sequencing, scRNA-seq data were aligned to the GRCh38 reference using Cell Ranger (v7.1.0). Demultiplexing was performed with Demuxafy based on SNP array data. Ambient RNA contamination was corrected using SoupX, and doublets were removed with DoubletFinder. Following quality control in Seurat, all samples were merged, batch-corrected with Harmony, and subjected to UMAP for dimensionality reduction and Louvain clustering. Differential expression and gene set enrichment analyses were performed to explore transcriptional signatures associated with BRF2 deficiency. *************************************************************** Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access. *************************************************************** UPDATE: [Aug-12-2025] The processed data were updated.