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Differential transcription in cell sorted paired TLR9hi and TLR9lo CLL samples

ABSTRACT: Differential transcription in cell sorted paired TLR9hi and TLR9lo CLL samples

PROVIDER: PRJNA615364 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11427541.fastq.gz	Fastqsanger.gz
	SRR11427542.fastq.gz	Fastqsanger.gz
	SRR11427543.fastq.gz	Fastqsanger.gz
	SRR11427544.fastq.gz	Fastqsanger.gz
	SRR11427545.fastq.gz	Fastqsanger.gz

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Differential transcription in cell sorted paired TLR9hi and TLR9lo CLL samples

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Calcitriol induces a distinctive transcriptional program in Chronic Lymphocytic Leukemia (CLL) cells

Project description:Purpose: It has been proposed that vitamin D may play a role in prevention and treatment of cancer while epidemiological studies have linked vitamin D insufficiency to adverse disease outcome in chronic lymphocytic leukemia (CLL). However, the underlying mechanisms have not yet been revealed. In this study, we sought to identify key signaling pathways and molecules that are altered after calcitriol, the biologically active form of vitamin D, supplementation of CLL cells in vitro. Methods: An RNA-Sequencing analysis was performed in primary CLL cells that were treated in vitro with calcitriol. Total RNA was extracted from calcitriol-treated and non-treated CLL cells, while mRNA selection was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module. Library preparation for RNA-Sequencing (RNA-Seq) analysis was conducted with the NEBNext Ultra II Directional RNA Library Prep Kit. The libraries were paired-end sequenced on the NextSeq 500 Illumina platform. Differential expression analysis was performed using DESeq2; genes with log2FC>|1| and P≤0.05 were considered as differentially expressed. Results: Differential expression analysis revealed 85 differentially expressed genes (DEGs) (log2FC≥|1| and p≤0.05), of which 28 (32.9%) were overexpressed in calcitriol-treated cells versus unstimulated CLL cells, thus, contrasting the remaining 57 (67.1%) which showed the opposite pattern. Supervised hierarchical clustering analysis, based on the differentially expressed genes, was performed and revealed distinct gene expression patterns between calcitriol-treated and control CLL cells. Moreover, pathway enrichment analysis revealed that calcitriol-regulated genes are implicated in signaling pathways known to be deregulated in CLL biology. Conclusions: Transcriptome analysis highlighted the possible impact of calcitriol on the regulation of immune signaling pathways relevant to CLL pathophysiology.

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