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ScRNAseq demonstrates distinct transcriptional response to IL-1B in mIDH2 cells as compared to wtIDH cells

ABSTRACT: scRNAseq demonstrates distinct transcriptional response to IL-1B in mIDH2 cells as compared to wtIDH cells

PROVIDER: PRJNA777647 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16766821_1.fastq.gz	Fastqsanger.gz
	SRR16766821_2.fastq.gz	Fastqsanger.gz
	SRR16766822_1.fastq.gz	Fastqsanger.gz
	SRR16766822_2.fastq.gz	Fastqsanger.gz
	SRR16766823_1.fastq.gz	Fastqsanger.gz

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scRNAseq demonstrates distinct transcriptional response to IL-1B in mIDH2 cells as compared to wtIDH cells

Project description:We report the results of scRNA sequencing of parental and mIDH2R140Q TF-1 cell lines following exposure to PBS (control) and IL-1B. We obtained 1 million cells of each cell line for each condition and incubated them with either PBS or IL-1B. Following treatment, cells were processed using previously described inDrop protocols (Wolock et al., 2019 Cell Reports). Samples were split into 3,000 single-cell transcriptomes and one library per sample was prepared and sequenced on NextSeq 500. Data was prepared for analysis as described in our methods and gene expression was normalized and quantified. Gene set enrichment, differential gene expression and UMAP visualization was performe dusing SEurat 3.0. Ultimately, we compared the cellular response of parental and mIDH2 cells to IL-1B and our results indicate that mIDH2 cells have augmented expression of NF-κB target transcripts . This component of our study demonstrates a dynamic response of both cell lines to IL-1B with an exaggerated response seen in mIDH2 cells.

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Project description:Growth Factor Independence-1B (Gfi-1B) is a transcriptional repressor essential for erythropoiesis and megakaryopoiesis. Targeted gene disruption of Gfi-1B in mice leads to embryonic lethality due to failure to produce definitive erythrocytes, hindering the study of Gfi-1B function in adult hematopoiesis. We here show that, in humans, Gfi-1B controls the development of erythrocytes and megakaryocytes by regulating the proliferation and differentiation of bipotent erythro-megakaryocytic progenitors (MEP). We further identify in this cell population the type III transforming growth factor-? receptor gene, TGFBR3, as a direct target of Gfi-1B. Knock down of Gfi-1B results in altered TGF? signaling as shown by the increase in Smad2 phosphorylation and its inability to associate to the Transcription Intermediary Factor 1? (TIF1?). Because Smad2/TIF1? complex is known to specifically regulate erythroid differentiation, we propose that, by repressing the transforming growth factor-? receptor III (T?R?II) expression, Gfi-1B favors the Smad2/TIF1? interaction downstream of TGF? signaling, allowing immature progenitors to differentiate toward the erythroid lineage.

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