Abstract B2-15: Functional enrichment and pathway analysis of the transcriptome related to lymphovascular invasion and recurrence in axillary-node negative breast cancer
Authors: Blais Mathieu , Pinnaduwage Dushanthi , Bull Shelley B. , Andrulis Irene L. 
Published: May 2016

Abstract
We previously reported that the presence of Lymphovascular invasion (LVI) is an independent predictor of recurrence in axillary node-negative breast cancer (ANNBC). We produced a unique set of gene expression microarrays specifically designed to identify genes with altered expression in LVI+ tumors (n= 37) compared to LVI- tumors (n = 68). We further examined expression differences in a second analysis designed to discover, within LVI+ tumors alone, clinically relevant genes involved in early recurrence (n = 4, smaller than 4 years) vs. no recurrence for at least 10 years (n = 41). To identify genes and pathways involved in LVI and recurrence in ANNBC, we performed a functional analysis of the expression data. We used the publicly available database tool via WebGestalt to perform a web-based enrichment analysis including Gene ontology, KEGG and the Cytogenetic band. In parallel, using Ingenuity pathway® (IPA), we identified networks, upstream regulators and canonical pathways. IPA provides the probability that the association between the genes in the dataset and the canonical pathways could be explained by chance alone through a right-tailed Fisher's exact test p-value. IPA use a z-score algorithm for predicting activation which reduces the chance that random data will generate significant predictions. In LVI+ vs LVI- analysis, the top IPA activated biofunctions are related to proliferation and migration. In LVI+REC+ vs LVI+REC- analysis, they are related to cell survival and migration as well as lipid synthesis and metabolism. The subset of genes identified in both comparisons include those involved in polarization of cells, oxidation of lipids, cellular homeostasis and growth of the lymphatic system component, with decreased cell death and apoptosis biofunctions. Our bioinformatics analyses are consistent with a migratory phenotype for cancer cells associated with LVI. In addition, we observed that inflammation related pathways are enriched in the LVI+ subgroup that undergoes early recurrence. In the upstream regulator IPA analysis, TGFb NFKb and PI3K are involved in the LVI+ in respect to LVI tumors as well as in LVI+REC+ tumors in respect to LVI+REC- tumors. The results suggest important pathways as well as upstream regulators associated with LVI and recurrence that are involved in invasion and cell fate biofunctions. The findings are currently being evaluated through mRNA and protein validation as well as functional studies.
Citation Format: Mathieu Blais, Dushanthi Pinnaduwage, Shelley B. Bull, Irene L. Andrulis. Functional enrichment and pathway analysis of the transcriptome related to lymphovascular invasion and recurrence in axillary-node negative breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-15.