Abstract 773: A global increase in miRNAs and a concomitant decrease in tumor suppressor pathways define preneoplastic transition in TNBC

Abstract

Abstract Introduction: The molecular changes that accompany the step wise progression to breast cancer are not well characterized. Recent studies have shown that histologically normal cells adjacent to cancer cells possess a large number of mutations suggesting that molecular aberrations often precede the development of histologic change. The goal of this study was to characterize the timing and extent of genomic changes across several well-defined histologic stages of progression to breast cancer and to identify downstream functional target pathways. Methods: We performed next generation small RNA & RNA seq using a cell line panel previously shown to replicate the multi-step progression from normal (MCF10A) to preneoplastic stage (hyperplastic/ atypia, MCF10.AT1), ductal carcinoma in situ (MCF10.DCIS), and invasive (MCF10.Ca1d) TNBC. Sequencing outputs were analyzed to identify aberrant miRNAs and their functional target pathways. Biological pathways from MSigDB were downloaded and parametric analysis of gene set enrichment were applied to RNA seq data to calculate pathway scores. K-means clustering algorithm was used to group miRNAs, mRNAs and pathways. Interesting groups were selected based on predefined tumor progression profiles. Target Scan was used to identify miRNA target genes, which were used to determine target pathways. The biological networks between miRNAs, target mRNAs and pathways were then created based on Pearson’s correlation. Highly correlated and robust target pathways were identified through Pathway Co-expression Network analysis. miRNA and mRNA expression were compared by ANOVA, and a FDR of <0.05 was considered to be statistically significant. Results: Approximately 70% of miRNA alterations occur during the initial progression from normal to preneoplastic stage. Interestingly, most of the early changes reflect a global upregulation of miRNAs. This was consistent with a global increase in miRNA processing enzyme-DICER and upregulation in XOP5 transcription, a gene involved in miRNA export. DICER upregulation is a direct result of loss of Let-7b-5p, which regulates DICER during TNBC progression and eventually leads to a global increase in miRNA expression. Consistent with early genome wide-increase in miRNA expression, we found a global (>60%) decrease in gene expression. Lastly, we noticed that compared to a relatively small number of miRNAs that change, a larger number of genes and pathways change during TNBC progression. Several oncogenic and tumor suppressor pathways including PI3K cascade, DNA damage check point & DNA damage response are found to be among these miRNAs mediated networks that change early. Conclusions: These data suggest that most of the genomic changes in the progression to TNBC occur in the very earliest stages of histologic progression, providing significant opportunities to develop targeted strategies for prevention. Citation Format: Anjana Bhardwaj, Zhenlin Ju, Harpreet Singh, Matthew Embury, Jing Wang, Isabelle Bedrosian. A global increase in miRNAs and a concomitant decrease in tumor suppressor pathways define preneoplastic transition in TNBC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 773.