Abstract PD7-04: Transcriptomic Profiling Reveals PMSB8-AS1 and LINC00996 as Potential Prognostic Biomarkers in Triple-Negative Breast Cancer Treated with Neoadjuvant Docetaxel-Carboplatin

Abstract Background: The identification of prognostic biomarkers in triple-negative breast cancer (TNBC) is critical for optimizing therapeutic strategies in this aggressive subtype. Bulk RNA sequencing enables comprehensive transcriptomic profiling that encompasses both coding and non-coding regions, thereby offering a more integrative view of TNBC biology. Within the non-coding transcriptome, long non-coding RNAs (lncRNAs) have emerged as candidate biomarkers due to their roles in the regulation of gene expression. However, additional evidence is needed to validate their prognostic relevance specifically in the context of early-stage TNBC. Methods: Bulk RNA-seq analysis was performed on FFPE diagnostic core-biopsies from TNBC patients obtained prior to neoadjuvant systemic treatment with 6 cycles of docetaxel-carboplatin (NACT). Sequences annotation was conducted using STAR (v.2.7.9a) and SALMON (v.1.6.0) software, and data was analysed attending differential expression analysis associated with response to NACT in the surgical specimen. The analysis was performed using Wald test, and the regulatory expression associations between coding and non-coding elements were evaluated using Pearson’s correlation analysis. Results: Transcript biotype analysis in TNBC patients classified as responders (pCR, N=140) and non-responders (RCB I-II-III, N = 141) to NACT showed a high proportion of non-coding elements, with a predominance of lncRNAs and pseudogenes. Interestingly, the non-pCR group exhibited a marked absence of immunoglobulin (IG) and T-cell receptor (TCR) transcripts compared to the pCR group. Differential expression analysis identified 166 lncRNA significantly deregulated between groups, among which PMSB8-AS1 emerged as a candidate prognostic biomarker, showing significant association with event-free survival (EFS) in Kaplan Meier analysis (p