RNA-seq identifies autophagy as the most prevalent upregulated pathway in dormant breast cancer cells

Purpose: The goal of this study is to evaluate the transcriptome profiling (RNA-seq) of dormant and proliferating breast cancer cells using an in vitro 3D model Methods: mRNA profiles of D2.0R cells growing either on basal membrane extracts (BME) (dormant phase) or BME + Collagen (COL) (proliferative phase) at days 1 or 5 of culture were generated by deep sequencing in triplicate with Ilumina HiSeq2500 using Illumina TruSeq V4. Aligned reads (BAM files) were analysed using PartekFlow software for differential expression and gene enrichment analysis. Comparisons used Partek Gene Specific Analysis (GSA) algorithm and multiple comparisons were corrected using False Discovery Rate (FDR), which was set at 0.05 Results: Using an optimized data analysis workflow, we mapped about 118 – 133 million reads per sample to the mouse genome (build mm9). Total alignment with reference genome is between 81-90%. RNA-seq identified 5,524 transcripts showing differential expression between the D2.0R cells cultured on BME + COL vs D2.0R cells cultured on BME matrices at day 5, with a fold change =1.5 or =-1.5 and p value <0.05. On the other hand, only 1,097 were found to be differentially expressed between D2.0R cells growing on BME matrices at day 5 and day 1, with a fold change =1.5 or =-1.5 and p value <0.05. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to breast cancer dormancy and identifies autophagy as a top biological process activated in dormant D2.0R cells. Conclusions: Our study represents a detailed analysis of the transcriptomes of dormant and proliferating D2.0R cells, with three biologic replicates, generated by RNA-seq technology. RNA-seq based transcriptome characterization identifies autophagy as the most prevalent upregulated pathway in dormant breast cancer cells. Overall design: mRNA profiles of D2.0R cells after culture on BME or BME + COL matrices for 1 or 5 days were generated by deep sequencing in triplicate with Ilumina HiSeq2500 using Illumina TruSeq V4.

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Vera-Ramirez L, Vodnala SK, Nini R, Hunter KW, Green JE