Abstract 4118: Decoding the noncoding: An insight into the noncoding genome of breast cancers

Introduction: The PI3K/AKT pathway, a key oncogenic signalling pathway, is mutated in 70% of breast cancers (BC). PI3K/AKT coding mutations promote BC progression and are associated with poor survival. However, coding mutations represent <1% of the whole genome. Non-coding mutations (NCMs) can promote oncogenic gene expression in several cancers, including BC. Further study on NCMs can enhance our understanding of BC and help identify novel treatments targets. Experimental procedure: NCMs surrounding kinome genes were identified from whole genome sequencing of 915 BC tumours. NCMs were prioritised based on recurrence and analysed with the Activity by Contact (ABC) bioinformatic model, which estimates their likelihood to interact with transcription start sites (TSS) and indicates their enhancer potential. Epigenetic data (Hi-C and H3K27ac, ChIP Seq) from BC cell lines (n=12) was screened to identify BC subtype-specific epigenetic changes surrounding the prioritised NCMs. The NCMs’ regulatory effect over gene expression was confirmed by luciferase reporter assays. Results: We identified 3,546 recurrent NCMs surrounding kinome genes in BCs and observed an enrichment of NCMs in gene loci of PI3K/AKT pathway members (p=0.005). We discovered subtype-specific enrichment of NCMs around oncogenes, like AKT2 in HR+ BCs (29/398, 7.2%) or AKT3 for TNBC (21/444, 4.7%). Of the 152 NCMs analysed, 17 (11.2%) reported positive by ABC analysis. 6/17 NCMs were identified in the gene loci of AKT2 or AKT3 (ABC scores 0.023-0.1) and were predicted to interact with genes up to 75kb from the NCM. Epigenetic analysis of ER+ and TNBC cell lines reported peaks of enhancer activity near the AKT2 and AKT3 NCMs, thus supporting the ABC analysis. Luciferase assays confirmed a 1.6-fold increase in luciferase expression for an AKT2 gene loci NCM (AC_A, chr19:41858248) and a 3-fold increase in luciferase expression for an AKT3 gene loci NCM (-_AT, chr1:244065861), whilst we observed a 3-fold decrease for a NCM in AKT2 gene loci (CAG_C, chr19:39686510). Conclusions: We have identified that BCs have an enrichment of NCMs surrounding PI3K/AKT pathway genes. NCMs in the gene loci of AKT2 and 3 were predicted to interact with distal genes and luciferase reporter assays confirmed their regulatory effects in vitro. These results highlight the potential of NCMs to drive BC oncogenesis and potentially act as targets for drug development. Citation Format: Arnau Cuy Saques, Anita White, Kaneez Rabab, Philip Scarry, Francesca Matra, Craig Monger, Adrian Bracken, John Crown, Alexander Eustace. Decoding the noncoding: An insight into the noncoding genome of breast cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4118.