Pervasive Enhanced Transcription in Inflammatory Breast Cancer Tumors and PBMCs Impacts RNA Splicing and Intronic RNAs in Plasma

ABSTRACT: Inflammatory breast cancer (IBC), the most aggressive and lethal breast cancer subtype, lacks unequivocal genomic differences or robust biomarkers that differentiate it from non-IBC. Here, Thermostable Group II Intron Reverse Transcriptase sequencing of RNA samples revealed myriad differences in tumors, PBMCs, and plasma that distinguished IBC from non-IBC patients and healthy donors across all tested non-IBC subtypes. By mapping reads to genome and transcriptome reference sequences and quantitating intron-to-exon read depth ratios, we developed methods for parallel analysis of transcriptional and post-transcriptional gene regulation. This analysis identified numerous protein-coding genes in IBC patient tumors and PBMCs with high intron-to-exon read depths, suggesting rate-limiting RNA splicing that negatively impacts mRNA production. Mirroring gene expression differences in tumors and PBMCs, over-represented protein-coding gene RNAs in IBC patient plasma were largely intron RNA fragments, while those in non-IBC patient and healthy donor plasma were largely mRNA fragments. Our findings provide new insights into IBC and should enable monitoring disease progression by liquid biopsy.

ORGANISM(S): Homo sapiens

PROVIDER: GSE325047 | GEO | 2026/05/01

REPOSITORIES: GEO