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ChIP-Seq of IRF4, BATF, and vIRF3 in BC-3 cells

ABSTRACT: The Kaposi's sarcoma-associated herpesviruses causes several cancers including Kaposi's sarcoma and primary effusion lymphoma (PEL). Our work reveals that the cellular transcription factors interferon regulatory factor 4 (IRF4) and basic leucine zipper ATF-like transcription factor (BATF), as well as the viral interferon regulatory factor 3 (vIRF3) are critical oncogenic dependencies specific to PEL cell lines. To understand the functions of these transcription factors, we performed ChIP-Seq on these proteins in BC-3 PEL cell line. Our results reveal that these oncogenic factors may cooperate to regulate the expression of the same mRNAs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE132777 | GEO | 2020/08/13

REPOSITORIES: GEO

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mRNA-Seq of BC-3 IRF4 KO, BATF KO, and vIRF3 KD

Project description:The Kaposi's sarcoma-associated herpesviruses causes several cancers including Kaposi's sarcoma and primary effusion lymphoma (PEL). Our work reveals that the cellular transcription factors interferon regulatory factor 4 (IRF4) and basic leucine zipper ATF-like transcription factor (BATF), as well as the viral interferon regulatory factor 3 (vIRF3) are critical oncogenic dependencies specific to PEL cell lines. To understand the functions of these transcription factors, we performed mRNA-Seq on the PEL BC-3 cell lines that have been targeted for CRISPR/Cas9 IRF4 KO, BATF KO and MDM4 KO (as unrelated negative control) and CRISPRi-mediated vIRF3 KD. Our results reveal that these oncogenic factors may cooperate to regulate the expression of the same mRNAs.

2020-08-13 | GSE132707 | GEO

Genome-wide maps of chromatin modifications in KSHV-transformed primary effusion lymphoma cell lines

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2018-10-11 | GSE116650 | GEO

mRNA Sequencing of BC-1 Cells

Project description:Kaposi’s sarcoma-associated herpesvirus (KSHV) causes the B cell malignancy primary effusion lymphoma (PEL). Here we performed mRNA sequencing to characterize the mRNA expression profile of the primary effusion lymhoma (PEL) cell line BC-1.

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Genome-wide mapping of RTA binding sites in KSHV+ PEL cells during KSHV reactivation.

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Knockdown of KSHV viral interferon-regulatory factor 3 (vIRF-3) in primary effusion lymphoma (PEL) cells by RNA-Interference

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A Computational Profiling of Changes in Gene Expression and Transcription Factors Induced by vFLIP K13 in Primary Effusion Lymphoma

Project description:Infection of Kaposi's sarcoma associated herpes virus (KSHV) has been linked to the development of primary effusion lymphoma (PEL), which is characterized by the loss of expression of B cell markers and effusions in the body cavities. This unique clinical feature of PEL has been attributed to their distinctive gene expression profile which shows overexpression of genes in various signaling pathways. KSHV-encoded latent protein vFLIP K13 has been shown to promote the survival and proliferation of PEL cells. In this study, we have employed gene array analysis followed by bioinformatics analysis of coordinated transcriptional factors network as well as biological pathways to characterize the effect of K13 on PEL-derived BCBL1 cells. We observed that genes associated with Cytokine signaling, Cell death, NF-kappaB and Cell adhesion pathways were differentially regulated by K13. We used computational approach complemented with microarrays to detail the global gene expression and identified distinct classes of differentially regulated genes in various cellular processes. We employed gene array analysis followed by bioinformatics analyses of coordinated transcriptional factors network as well as biological pathways to characterize the effect of K13 on in PEL-derived BCBL1 cells.

2012-05-20 | E-GEOD-37355 | biostudies-arrayexpress

Knockdown of KSHV viral interferon-regulatory factor 3 (vIRF-3) in primary effusion lymphoma (PEL) cells by RNA-Interference

Project description:KaposiM-bM-^@M-^Ys sarcoma-associated hepesvirus (KSHV) encodes four genes with homology to human interferon regulatory factors (IRFs). One of these IRFs, the viral interferon regulatory factor 3 (vIRF-3) is expressed in latently infected PEL cells and required for their continuous proliferation. Moreover, vIRF-3 is known to be involved in modulation of the type I interferon response. In order to identify cellular genes regulated by vIRF-3, cells from the PEL cell line BC-3 (KSHV positive) were transfected with either siRNAs targeted at vIRF-3 (si463 or si716s) or a negative control siRNA without homology to a known gene (siN, siNs). A total of 4 samples were analyzed. This includes two samples with silencing of vIRF-3 expression via RNA-interference (si463 or si716s) and two samples transfected with a negative-control siRNA (siN, siNs). Expression of vIRF-3 was reduced by approximately 75% as estimated by Western blot analysis.

2011-01-19 | E-GEOD-26661 | biostudies-arrayexpress

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