Association between genomic alterations and response of triple-negative breast cancers (TNBC) to talimogene laherparepvec (TVEC) in combination with neoadjuvant chemotherapy (NACT).

Abstract

598 Background: TVEC is an engineered oncolytic virus (OVs) approved for the treatment of melanoma. We published a phase 1/2 trial combining TVEC with NACT in early stage TNBC demonstrating increased pathologic complete response (pCR) compared to expected rates with NACT. RNAseq was performed on 37 pretreatment samples from enrolled patients to identify potential predictive genomic alterations. Methods: Transcriptomic RNA sequencing analysis was performed on macrodissected tumor tissue through the Moffitt Molecular Genomics core using Illumina Truseq RNA exome kits. Read adapters were detected using BBMerge (v37.88) and removed with cutadapt (v1.8.1). For gene expression analysis, processed raw reads were aligned to human genome HG19 using STAR (v2.5.3a). Gene expression was evaluated as read count at gene level with HTSeq (v0.6.1) and Gencode gene model v19. Gene expression data were normalized and differential expression between experimental groups were evaluated using DEseq2 (v 1.38.2). Ensembl was used for SNP data search. Results: Tumor mutation burden was not significantly different between pCR and non-pCR samples (median 227 vs 222 mut/MB, p = .11). Top 5 upregulated non-immunoglobulin genes associated with pCR in baseline samples were MYBL1, DNAH8, NR2E1, FGFR2, and SLC12A1 (FDR < 1%). A single nucleotide polymorphism (SNP) of the EIF2A gene (c.C290G, p.T97S) was the top variant associated with response present in 21/37 samples (non-pCR = 17/21 vs. pCR = 4/21, FDR = < 1%). This exon 4 coding region SNP is present in 17% of Black, 35% of White, and 46% of Asian individuals but its biologic or clinical significance is unknown. Lower EIF2A pathway activation was associated with inferior response to therapy. Additional data will be presented at the meeting. Conclusions: Genomic alterations including a EIF2A SNP were correlated with response to OV plus NAC in TNBC. EIF2A is an important mediator of cellular responses to OV and may play a role in susceptibility to oncolysis. Additional investigation and validation of these variations in experimental models of OV susceptibility may provide predictive biomarkers for TNBC patients treated with OV plus NAC therapy. Clinical trial information: NCT02779855 .