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Genome-wide CRISPR inactivation based resistance screens using IMiDs in Primary Effusion Lymphoma (PEL) cells

ABSTRACT: Genome-wide CRISPR inactivation based resistance screens using IMiDs in Primary Effusion Lymphoma (PEL) cells

PROVIDER: PRJNA503251 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8142670.fastq.gz	Fastqsanger.gz
	SRR8142680.fastq.gz	Fastqsanger.gz
	SRR8142671.fastq.gz	Fastqsanger.gz
	SRR8142681.fastq.gz	Fastqsanger.gz
	SRR8142672.fastq.gz	Fastqsanger.gz

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CRISPR screens for synthetic rescue of cFLIP depletion in primary effusion lymphoma cell lines

Project description:Kaposi’s sarcoma-associated herpesvirus (KSHV) causes the B cell malignancy primary effusion lymphoma (PEL). We have previously shown that cultured PEL cell lines require expression of the cellular FLICE inhibitory protein (cFLIP) for survival (Manzano et al., Nat Comm 2018), although KSHV encodes a viral homolog of this protein (vFLIP). Here we employed genome-wide CRISPR/Cas9 synthetic rescue screens to identify loss of function perturbations that can compensate for cFLIP knockout/knockdown.

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Genome-wide CRISPR inactivation based resistance screens using IMiDs in Primary Effusion Lymphoma (PEL) cells

Project description:We report the application of genome-wide CRISPR-Cas9 inactivation based screening technology to identify genes whose inactivation can confer resistance to the IMiD compounds Lenalidomide, Pomalidomide and Avadomide (CC-122) in Kaposi's sarcoma-associated herpesvirus-transformed primary effusion lymphoma cell line BC-3. Cas9 expressing BC-3 cells were transduced with a lentiviral genome-wide targeting sgRNA library (Brunello, Doench et al, Nature Biotechnology, 2016) and subsequently treated with lethal concentrations (5uM Lenalidomide, 1uM Pomalidomide and 1uM CC-122) of the IMiD compounds mentioned above or DMSO vehicle. gDNA from resistant cells and matched DMSO treated control cells was harvested and the lentiviral sgRNA inserts in each sample were PCR amplified, barcoded and subjected to next gen sequencing on the Illumina HiSeq 4000 platform. This study provides a candidate list of genes whose inactivation can confer resistance to one or more IMiD compounds in BC-3 cells.

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Affymetrix 500K SNP array data for Primary Effusion Lymphoma samples

Project description:Affymetrix 500K array was used to determine gross genomic aberrations in a panel of Primary Effusion Lymphoma (PEL) cell lines, specifically focusing on chromosome 10, which includes the Phosphatase and Tensin Homolog (PTEN) locus. 10 PEL cell lines were hybridized to the Affymetrix 500K array where non-PEL B-cell lymphoma cell lines BJAB and DG75 were used as controls. The data was analyzed using Partek Genomic Suite software and compared to normal tonsil controls.

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