Identification of the genome-wide binding sites of OCT2 in Reg-1fl/fl- and Reg-1ΔNK-NK cells. [ChIP-Seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA996085 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25336435_1.fastq.gz | Fastqsanger.gz | |||
| SRR25336435_2.fastq.gz | Fastqsanger.gz | |||
| SRR25336436_1.fastq.gz | Fastqsanger.gz | |||
| SRR25336436_2.fastq.gz | Fastqsanger.gz | |||
| SRR25336437_1.fastq.gz | Fastqsanger.gz |
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Project description:The expression of OCT2 was also increased in NK cells from Reg-1fl/fl in response to IL-12/18 stimulation implying that OCT2 has an intrinsic function not only in Regnase-1-deleted NK cells but also in wild-type NK cells. To identify the genome-wide binding sites of OCT2, we performed chromatin immunoprecipitation sequencing (ChIP-seq) for OCT2 in Reg-1fl/fl- and Reg-1ΔNK-NK cells.
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Project description:Differential expression was used to access gene differences after Entamoeba histolytica infection. Entamoeba histolytica is an important diarrheal pathogen worldwide, and induces apoptosis of the intestinal epithelium as part of its disease process. Regenerating (REG) 1 protein is anti-apoptotic. We investigated the involvement of REG 1 in E. histolytica colitis. Colonic biopsy samples were obtained from 8 subjects with acute E. histolytica colitis, and again 60 day later during convalescence. Gene expression in the human colon during acute and convalescent E. histolytica disease was evaluated using microarray and confirmed by polymerase chain reaction (PCR). REG 1 protein expression was evaluated with immunohistochemistry. The mechanism of REG 1 involvement in E. histolytica disease was subsequently investigated with a mouse model. REG 1A and REG 1B were the most upregulated genes in the human intestine in acute versus convalescent E. histolytica disease (p=0.003 and p=0.006 respectively). PCR confirmed the microarray results (p=<0.001 and p=0.001 respectively). Increased REG 1A and REG 1B protein expression was similarly observed by immunohistochemistry. REG 1 -/-mice were found to be significantly more susceptible to E. histolytica infection than wild type mice.
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Project description:The requirement for the B cell transcription factor OCT2 (encoded by Pou2f2) in germinal center B cells has proved controversial. Here, we report that germinal center B cells are formed normally after depletion of OCT2 in a conditional knockout mouse but that their proliferation is reduced and in vivo differentiation to antibody-secreting plasma cells is blocked. This led us to examine the role of OCT2 in germinal center derived lymphomas. ShRNA knockdown showed that almost all DLBCL cell lines are addicted to the expression of OCT2 and its co-activator OCA-B. Genome-wide chromatin Immunoprecipitation analysis and gene expression profiling revealed the broad transcriptional program regulated by OCT2 that includes the expression of STAT3, IL10, ELL2, XBP1, MYC, TERT and ADA. Importantly, genetic alteration of OCT2 is not a requirement for cellular addiction in DLBCL. However, we detected amplifications of the POU2F2 locus in DLBCL tumor biopsies as well as a recurrent mutation of threonine 223 in the DNA binding domain of OCT2. This neomorphic mutation subtly alters the DNA binding preference of OCT2 leading to the transactivation of novel target genes including HIF1a and FCRL3. Finally, by introducing mutations designed to disrupt the OCT2-OCA-B interface we reveal a requirement for this protein-protein interface that might ultimately be exploited therapeutically. Our findings, combined with the predominantly B cell restricted expression of OCT2 and the absence of systemic phenotype in our knockout mice, suggest that an OCT2-targeted therapeutic strategy would be efficacious in both major subtypes of DLBCL whilst avoiding systemic toxicity.
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Project description:The requirement for the B cell transcription factor OCT2 (encoded by Pou2f2) in germinal center B cells has proved controversial. Here, we report that germinal center B cells are formed normally after depletion of OCT2 in a conditional knockout mouse but that their proliferation is reduced and in vivo differentiation to antibody-secreting plasma cells is blocked. This led us to examine the role of OCT2 in germinal center derived lymphomas. ShRNA knockdown showed that almost all DLBCL cell lines are addicted to the expression of OCT2 and its co-activator OCA-B. Genome-wide chromatin Immunoprecipitation analysis and gene expression profiling revealed the broad transcriptional program regulated by OCT2 that includes the expression of STAT3, IL10, ELL2, XBP1, MYC, TERT and ADA. Importantly, genetic alteration of OCT2 is not a requirement for cellular addiction in DLBCL. However, we detected amplifications of the POU2F2 locus in DLBCL tumor biopsies as well as a recurrent mutation of threonine 223 in the DNA binding domain of OCT2. This neomorphic mutation subtly alters the DNA binding preference of OCT2 leading to the transactivation of novel target genes including HIF1a and FCRL3. Finally, by introducing mutations designed to disrupt the OCT2-OCA-B interface we reveal a requirement for this protein-protein interface that might ultimately be exploited therapeutically. Our findings, combined with the predominantly B cell restricted expression of OCT2 and the absence of systemic phenotype in our knockout mice, suggest that an OCT2-targeted therapeutic strategy would be efficacious in both major subtypes of DLBCL whilst avoiding systemic toxicity.
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