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USP15 deubiquitinase safeguards hematopoiesis and genome integrity in hematopoietic stem cells and leukemia cells

ABSTRACT: To decipher the role of USP15 in DNA damage in leukemia cells, endogenous USP15 was immunoprecipitated from MV4-11 and Kasumi-1 cell lines under naive and DNA stress conditions (Mitomycin C, 30nM, 1h). 355 candidates co-immunoprecipitated with USP15 in all the conditions, in 4 independent experiments.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Leukocyte, Cell Culture

DISEASE(S): Acute Leukemia

SUBMITTER: Oliver Popp

LAB HEAD: Gaetano Gargiulo

PROVIDER: PXD020612 | Pride | 2021-01-04

REPOSITORIES: pride

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			Action	DRS
	Results_Two-sample_PRIDE_submission.xlsx	Xlsx
	Rowlf_20191031_OP_HS_MaPiSaBa_Kasumi_BTZ_MMC_IgG_01.raw	Raw
	Rowlf_20191031_OP_HS_MaPiSaBa_Kasumi_BTZ_MMC_IgG_02.raw	Raw
	Rowlf_20191031_OP_HS_MaPiSaBa_Kasumi_BTZ_MMC_IgG_03.raw	Raw
	Rowlf_20191031_OP_HS_MaPiSaBa_Kasumi_BTZ_MMC_IgG_04.raw	Raw

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Project description:Purpose: the goal of this study is to investigate the consequences of ubiquitin specific protease 15 (USP15) deletion on gene expression in mouse LSK hematopoietic progenitors. Methods: mRNA profiles of 8 weeks-old wild-type (WT) and ubiquitin specific protease 15 knockout (Usp15−/−) mice were generated by deep sequencing using Illumina Hiseq2500. The sequence reads that passed quality filters Alignments of the sequence reads that passed quality filters were performed using TopHat2.1, Genome build 38 and Ensembl gtf version 77 and genecounts have been generated using Itreecount. https://github.com/NKI-GCF/itreecount Results: We assigned about 30 million reads per sample uniquely to a gene of the mouse reference genome (mm10) We identified 21,219 genes in the LSKs of WT and Usp15−/− mice using TopHat2.1 in combination with Itreecount. https://github.com/NKI-GCF/itreecount. Distinct LSK-specific expressed genes (such as Eng, Tek, the MlI receptor and the Kit receptor) are identified. Comparison of normalized gene expression data for Usp15-/- versus WT LSK confirmed the loss of Usp15. Apart from Usp15, almost no other significantly deregurated genes were detected using a treshold of fold change ≥1.5 and p value <0.05, suggesting the maintenance of an overall stable identity of the cellular compartment in Usp15-/- mice. Conclusions: Our results represent the first detailed analyis of the consequences of USP15 deletion on gene expression in hematopoietic populations such as LSKs progenitors by genome wide expression profiling in WT and Usp15-/- mice. RNAseq of two freshly isolated biological replicas of sorted LSKs from 8 weeks old Usp15-/- animals confirmed the loss of Usp15, while showing almost no significant other up or down regulated genes among the 21,219 genes identified in Usp15-/- LSKs. We conclude that young adult hematopoietic stem and progenitor cells (LSKs) perpetuated a stable gene expression program regardless of the homozygous deletion of USP15.

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USP15 deubiquitinase safeguards hematopoiesis and genome integrity in hematopoietic stem cells and leukemia cells

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