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Transcriptome analysis of T-cell subsets before and under lenalidomide treatment sorted from the blood of 6 first-line follicular lymphoma (FL) patients

ABSTRACT: Transcriptome analysis of T-cell subsets before and under lenalidomide treatment sorted from the blood of 6 first-line follicular lymphoma (FL) patients

PROVIDER: PRJNA665225 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12698453_1.fastq.gz	Fastqsanger.gz
	SRR12698453_2.fastq.gz	Fastqsanger.gz
	SRR12698454_1.fastq.gz	Fastqsanger.gz
	SRR12698454_2.fastq.gz	Fastqsanger.gz
	SRR12698455_1.fastq.gz	Fastqsanger.gz

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Transcriptome analysis of T-cell subsets before and under lenalidomide treatment sorted from the blood of 6 first-line follicular lymphoma (FL) patients

Project description:Purpose: the goal of this study is to analyze the effect of lenalidomide on CD4pos PD-1pos, CD4pos PD-1neg, CD8pos PD-1neg and CD8pos PD-1pos subsets Methods: genome-wide mRNA profiles of 6 first-line follicular lymphoma patients (GALEN protocol) were generated using deep sequencing before and after one-week lenalidomide, using Illumina HiSEq4000. All paired-end sequence reads passed quality filters.and were analyzed at the gene level with STAR followed by Featurecount. Results: Important differences in functional biological pathways related to proliferation, immune system, metabolism and immune synapse in PD-1pos T-cells triggered by lenalidomide were highlighted by the experiment.

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Project description:Follicular lymphoma is the most common indolent non-Hodgkin's lymphoma involving germinal centre B cells, with a subset of patients undergoing transformation to a diffuse large B-cell lymphoma (DLBCL) morphology for which the clinical outcomes are poor. To elucidate the differences in copy number profiles between FL and tFL groups, we performed Affymetrix SNP 6.0 Array analysis on 31 paired FL-tFL cases. We wanted to identify and compare recurrent somatic copy number alterations (CNAs) between the two groups (FL vs. tFL). In addition, the concordance and discordance in the copy neutral loss of heterozygosity (cnLOH) between the two groups were also investigated to identify recurrent target gene regions. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from follicular lymphoma (FL), transformed follicular lymphoma (tFL) and matching germline (GL) sample (if available). Copy number analysis of Affymetrix SNP 6.0 Array were performed on 91 DNA samples, consisting of 31 patients. Among the 31 patients, 19 had matching germline samples, while 12 had no germline samples. The Log R Ratio (LRR) values and the B Allele Frequency (BAF) values were subsequently calculated to search for copy number aberrations and copy neutral (CN)-LOH in the FL and tFL samples. Paired and unpaired analyses were performed accordingly.

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