Differential genomic and transcriptomic analysis of invasive lobular and ductal carcinomas.

Abstract

579 Background: Invasive lobular carcinoma (ILC) is more aggressive than hormone receptor (HR)-positive invasive ductal carcinoma (IDC). However, in practice, ILC and IDC are often treated in a similar fashion with endocrine therapy and chemotherapy. Identifying novel biomarkers, genetic alterations, transcriptomic features, and tumor microenvironment (TME) variations could initiate the development of personalized treatment plans for patients with ILC. Methods: We collected ILC and luminal (non-basal/non-HER2) IDC samples from four datasets (TCGA, METABRIC, RATHER PMC4700448, and UQCCR PMC31263747) and performed differential expression and gene set enrichment analyses, revealing novel genomic, transcriptomic, and TME differences. Using methods from Bagaev et al., we quantified the activity of 29 functional gene expression signatures with single sample gene set enrichment analysis before clustering the samples into five TME subtypes; statistical significance was measured with the Mann-Whitney U test. Differential expression analysis of RNA-Seq data was completed using DESeq2. Further, we analyzed the frequency of specific biomarkers to identify potential therapeutic options. Mutations and biomarker enrichment were assessed using the chi-squared test. Results: We analyzed 1,735 samples (1,442 luminal IDCs and 293 ILCs). CDH1 mutations were more prevalent in ILC samples (56%) compared to IDC samples (6%). Of the 44% of ILC samples with wild-type CDH1, 90% had low CDH1 expression. Inference models showed differences in transcription factors expression between ILC and IDC. ILC had significantly higher expression of TFAP2B, SOCS2, NOSTRIN, THBS4, SCUBE2, and GDF9 and lower expression of CDCA4, PSMG1, LMOD1, and SLC7A5 (adj p < 0.0001 for all genes). Analysis of the TME showed that 44% of ILC samples were immune enriched with high PDL1, CTLA4, and LAG3 expression. In comparison, approximately 30% of ILC samples contained enhanced vascularization and expressed high VEGFA, PDGFRA, and PDGFRB. Finally, compared to luminal IDC, ILC tend to have a statistically significant higher TROP2 expression, similar to that seen in basal subtype. Conclusions: ILC and IDC expressed distinct genomic alterations, gene expression, transcriptomic features, TMEs, and biomarkers. These differences can be used as a blueprint to tailor ILC phenotype-specific interventional clinical trials.