High-throughput assay confirmation of a T-cell receptor pre-mRNA fragment as a blood-based inflammatory breast cancer biomarker.

Previous TGIRT-seq analysis of RNAs in Inflammatory Breast Cancer (IBC) patient tumors, peripheral blood mononuclear cells (PBMCs) and plasma identified a short T-cell receptor mRNA fragment () as a potential IBC biomarker that was detected in plasma samples from IBC patients but not patients with non-inflammatory breast cancer or healthy donors. Here, we traced the origin of this RNA fragment to IBC patient PBMCs and used a high-throughput RT-PCR/Cas12a assay with larger numbers of samples to confirm its prevalence in IBC patient PBMCs. Detection of this RNA was enhanced by T4 polynucleotide kinase treatment, indicating the presence of a 2',3'-cyclic phosphate. Analysis of previous TGIRT-seq datasets revealed gene expression differences in IBC patient PBMCs that could contribute to RNA prevalence in IBC patient PBMCs and plasma. Our results support the identification of the RNA fragment as a novel, readily detectable blood-based RNA biomarker derived from IBC-patient immune cells, addressing a major unmet need for diagnosing IBC.