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Transcriptome analysis of mammospheres from MCF-7 and T47D cells

ABSTRACT: Transcriptome analysis of mammospheres from MCF-7 and T47D cells

PROVIDER: PRJNA902361 | ENA |

REPOSITORIES: ENA

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Project description:Purpose: The goals of this study is to compare and examine the transcriptional profile in the secondary mammospheres of control versus CIC-deficient T47D cells by mRNA sequencing and to understand the molecular basis of the CIC regulation of CSC-like properties in luminal type of breast cancer cells. Methods: DNA library for mRNA sequencing of secondary mammospheres derived from control and CIC-deficient T47D breast cancer cells was prepared using a TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) and their libraries sequenced on the NovaSeq sequencer accompanying the NovaSeq 6000 S4 Reagent Kit. The trimmed reads that passed quality filters were mapped to reference genome with HISAT2, followed by assembly of transcript with StringTie. Results: A total of 20377 genes were differentially expressed (10438 upregulated and 9939 downregulated) in the CIC-deficient T47D mammospheres when compared with control mammospheres. Approximately 5% of the transcripts showed differential expression between the control and CIC-deficient secondary mammospheres, with a fold change ≥1.2 and p value <0.05. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) analyses revealed that CIC-deficient mammospheres differentially expressed genes that are involved in processes associated with cancer progression such as cell cycle, cell proliferation, cell growth, and apoptotic process, as well as autoimmunity. Conclusions: Our results show the first comparative analysis of secondary mammospheres derived from control and CIC-deficient T47D breast cancer cells. The data reported here should also provide reference for expression profiles of CSC-like cells in ER+/PR+/HER2- luminal breast cancer cells. We conclude that CIC deficiency promotes CSC-like properties and thus breast cancer progression through controlling CSC-related pathways including focal adhesion and extracellular matrix (ECM)-receptor interactions, and may also regulate cell cycle, cell proliferation, and apoptosis.

Project description:Luminal A breast cancer, constituting 70 % of breast cancer cases, presents a challenge due to the development of resistance and recurrence caused by breast cancer stem cells (BCSC). Luminal breast tumors are characterized by TP53 expression, a tumor suppressor gene involved in maintaining stem cell attributes in cancer. Although a previous study successfully developed mammospheres (MS) from MCF-7 (with wild-type TP53) and T47D (with mutant TP53) luminal breast cancer cells for BCSC enrichment, their transcriptomic profiles remain unclear. We aimed to elucidate the transcriptomic disparities between MS of MCF-7 and T47D cells using bioinformatics analyses of differentially expressed genes (DEGs), including the KEGG pathway, Gene Ontology (GO), drug-gene association, disease-gene association, Gene Set Enrichment Analysis (GSEA), DNA methylation analysis, correlation analysis of DEGs with immune cell infiltration, and association analysis of genes and small-molecule compounds via the Connectivity Map (CMap). Upregulated DEGs were enriched in metabolism-related KEGG pathways, whereas downregulated DEGs were enriched in the MAPK signaling pathway. Drug-gene association analysis revealed that both upregulated and downregulated DEGs were associated with fostamatinib. The KEGG pathway GSEA results indicated that the DEGs were enriched for oxidative phosphorylation, whereas the downregulated DEGs were negatively enriched for the p53 signaling pathway. Examination of DNA methylation revealed a noticeable disparity in the expression patterns of the PKM2, ERO1L, SLC6A6, EPAS1, APLP2, RPL10L, and NEDD4 genes when comparing cohorts with low- and high-risk breast cancer. Furthermore, a significant positive correlation was identified between SLC6A6 expression and macrophage presence, as well as MSN, and AKR1B1 expression and neutrophil and dentritic cell infiltration. CMap analysis unveiled SA-83851 as a potential candidate to counteract the effects of DEGs, specifically in cells harbouring mutant TP53. Further research, including in vitro and in vivo validations, is warranted to develop drugs targeting BCSCs.

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Transcriptome analysis of mammospheres from MCF-7 and T47D cells

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