Gene expression analysis of GzmB-/- hematopoietic stem cells (HSC).
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE56574 | GEO | 2014/04/11
SECONDARY ACCESSION(S): PRJNA244163
REPOSITORIES: GEO
Similar Datasets
Project description:This study aimed to compare the expression profile of GzmB deficient HSCs and their WT counterparts in order to understand their phenotype in bone marrow in vivo reconstitution assays. GzmB-/- HSC mRNA expression was compared to WT counterparts. Samples of 3 biological replicates (pool of 3 mice per replicate) of each group has been used for the array.
2014-04-11 | E-GEOD-56574 | biostudies-arrayexpress
Project description:During adult bone marrow hematopoiesis, extremely rare and dormant hematopoietic stem cells (HSCs) harbor the highest self-renewal activity within all blood cells. They give rise to active HSCs, which generate multipotent progenitors (MPPs) which differentiate into lineage-committed progenitors and subsequently mature cells. While HSCs are characterized by long-term self-renewal capacity, quiescence and multipotency, MPPs show steadily decreasing self-renewal activity, are cycling but are thought to maintain multipotency. To establish a comprehensive genome-wide landscape of expressed transcripts, we performed a quantitative transcriptome analysis by next-generation sequencing (RNA-seq) of seven ex vivo FACS-sorted mouse HSC/progenitor populations. Eleven-fold coverage of the genome was achieved, revealing quantification of > 27,000 mRNA species of which 589 long non-coding RNAs (lncRNAs) were quantified. A profile of 79 differentially expressed lncRNAs in HSC-MPPs was identified suggesting a role for these RNA species in HSC/progenitor biology. Expression clusters of transcription factors and cell adhesion molecules are identified between the different cell populations. Dormant HSCs, as identified by label-retaining assays, showed a highly differential expression profile compared to active HSCs. In addition to >200 differentially expressed cell surface receptors and lncRNAs, processes including metabolism, development, immune response, signaling (TGFb, Kit, senescence/autophagy) are distinct between the two types of HSCs. In addition, using whole cell proteome analysis of FACS-sorted HSCs and MPP1, >6,000 proteins were identified by quantitative tandem mass spectrometry. Quantification of these proteins confirmed the close relationship between these cell types also seen in their transcript profile and revealed processes such as energy metabolism, immune response and cell cycle to be modulated along early lineage progression. While MPP1/2 still show multilineage potential in reconstitution experiments, a strong lineage bias and low self-renewal potential is observed in mice reconstituted with MPP3/4. These functional differences are accompanied by complex changes in their transcriptome and is also revealed by principal component analysis. In summary, the global mRNA, lncRNA and proteome signatures uncovered here and which are complemented by functional assays, provide a comprehensive and searchable resource of the molecular make-up of the entire HSC/progenitor population present in the bone marrow. These data will provide the basis for a global understanding of stem cell biology in the adult blood system. The uploaded dataset corresponds to the quantitative proteomic comparison of HSC and MPP1, which was done in three biological replicates. Data analysis: MS raw data files were processed with MaxQuant (version 1.3.0.5) (Cox and Mann 2008). Enzyme specificity was set to trypsin/P and a maximum of two missed cleavages were allowed. Cysteine carbamidomethylation and methionine oxidation were selected as fixed and variable modifications, respectively. The derived peak list was searched using the built-in Andromeda search engine (version 1.3.0.5) in MaxQuant against the Uniprot mouse database (2013.02.20) containing 75,721 proteins to which 247 frequently observed contaminants as well as reversed sequences of all entries had been added. Initial maximal allowed mass tolerance was set to 20 ppm for peptide masses, followed by 6 ppm in the main search, and 0.5 Dalton for fragment ion masses. The minimum peptide length was set to six amino acid residues and three labeled amino acid residues were allowed. A 1% false discovery rate (FDR) was required at both the protein level and the peptide level. In addition to the FDR threshold, proteins were considered identified if they had at least one unique peptide. The protein identification was reported as an indistinguishable “protein group” if no unique peptide sequence to a single database entry was identified. The ‘match between runs’ was enabled for consecutive peptide fractions with a 2 minutes time window. The iBAQ algorithm was used for estimation of the abundance of different proteins within a single sample (proteome) (Schwanhausser 2011). For evaluation of differential protein expression between HSC and MPP1, statistical analysis was performed for the proteins quantified in all three replicates using the Limma package in R/Bioconductor (Gentleman 2004, Smyth 2004). After fitting a linear model to the data, an empirical Bayes moderated t-test was used for the protein ratios, which were weighted on log10(summed peptide intensities) in order to capture the effect that the statistical spread of unregulated proteins is much more focused for highly abundant proteins than for low abundance ones (Cox 2008). P-values were then adjusted for multiple testing with Benjamini and Hochberg's method and proteins with an adjusted p-value lower than 0.1 were considered to be differentially expressed between HSC and MPP1. Associated transcriptomics data has been deposited at ArrayExpress with accession E-MTAB-2262.
2014-08-21 | PXD000572 | Pride
Project description:We demonstrated that NK cell activity affects HSCs frequency in vitro as well as hematopoietic reconstitution in vivo. Gene expression and cytokine profile assays revealed the potential players of this HSC-NK cell regulation, such as IFNγ. Besides the known role of C/EBPg in NK cell differentiation, we demonstrated that it is also essential for NK-cytokine mediated HSC regulation. Finally, NK cell depletion from murine and human bone marrow favored transplant chimerism.
2018-01-02 | E-MTAB-5604 | biostudies-arrayexpress
Project description:Stem cell division is linked to tumorigenesis by yet-elusive mechanisms. The hematopoietic system reacts to stress by triggering stem and progenitor cell (HSPC) proliferation, which can be accompanied by chromosomal breakage in activated haematopoietic stem cells (HSCs). However, whether these lesions persist in their downstream progeny and induce a canonical DNA damage response (DDR) remained unclear. Inducing HSPC proliferation by simulated viral infection, we report that the associated DNA damage is restricted to HSCs and that proliferating HSCs rewire their DDR upon endogenous and clastogen-induced damage. Combining transcriptomics, single-cell and single-molecule assays on murine bone marrow cells, we found accelerated fork progression in stimulated HSPCs, reflecting engagement of Primpol-dependent repriming, at the expense of replication fork reversal. Ultimately, competitive bone marrow transplantation revealed the requirement of Primpol for efficient HSC amplification and bone marrow reconstitution. Hence, fine-tuning replication fork plasticity is essential to support stem cell functionality upon proliferation stimuli.
2023-06-14 | GSE212580 | GEO
Project description:This study aimed at identifying the differences in expression levels between HSCs isolated from PBS or IFNa treated mice to determine the mechanism of activation of HSCs by IFNa.
2016-08-17 | GSE72812 | GEO
Project description:Bone marrow transplantation therapy relies on the life-long regenerative capacity of hematopoietic stem cells (HSCs). HSCs present a wide complexity of regenerating behaviours at the clonal level, but the mechanisms underlying this diversity are still unclear. Recent advances in single cell sequencing have described transcriptional differences amongst HSCs, providing a possible explanation for their functional heterogeneity. However, the destructive nature of sequencing assays prevents simultaneous observation of stem cell functions. Thus, it is unclear to what extent transcriptome states carry information about stem cell outcomes. Here, we applied expressible barcodes to simultaneously recover lineages and transcriptomes from single adult HSCs, and investigated their clonal trajectories during bone marrow reconstitution in vivo. Using clonal readouts, we unveiled a previously underappreciated subset of quiescent HSCs that cell-autonomously retains native-like behaviours. Transcriptome enrichment using clonal information identified a distinct molecular signature that characterizes functional long-term repopulating HSCs. Probing this signature through in vivo CRISPR screening, we described the transcription factor Tcf15 to be required, and sufficient, to drive HSC quiescence and long-term self-renewal. In situ, Tcf15 labels the subset of native multipotent HSCs and its expression is inherited in a hierarchical fashion. In conclusion, our work elucidates molecular programs associated with stem cell function, and identifies a mechanism for the maintenance of the native-like quiescent state.
2020-03-23 | GSE134242 | GEO
Project description:Insulin-like growth factor-1 (IGF-1) is known as a hematopoietic factor which impacts hematopoietic reconstitution and facilitates thrombopoiesis, although its direct effect on hematopoietic stem cells (HSCs) remains unclear. Here, we show that IGF-1 rapidly prompts megakaryocyte (Mk)-lineage differentiation of HSCs by enhancing mitochondrial activity in HSCs. To identify the phenotype switching and function variation in HSCs with IGF-1 treatment, we performed RNA-seq of HSCs from the bone marrow of mice with single-dose IGF-1 treatment (IGF-1) and their age-matched control mice (Ctrl).
2024-06-05 | GSE229985 | GEO
Project description:This study aimed at identifying the differences in expression levels between wt and Mant4-/- HSCs after transplantation, to determine the mechanism through which Mant4-/- gain a proliferative advantage.
2016-08-17 | GSE72813 | GEO
Project description:Aged hematopoietic stem cells (HSCs) exhibit compromised reconstitution capacity. In this study, we observed that the expression of FUS is increased in aged HSCs. We aimed to analysis the changes of chromatin structure and gene expression signatures in FUS low and FUS high expressed hematopoietic stem cell (lineage-, c-kit+ Sca-1+ CD34-) using tagHi-C and RNA-seq .We also conducted CTCF CUT&RUN experiment in Young(2 months) and Aged(30 months) hematopoietic stem cell (lineage-, c-kit+ Sca-1+ CD34-) to analysis CTCF signal changes. These hematopoietic stem cell (HSC) were purified from the bone marrow of mice with fus-gtp or different ages. Results provide insight how aberrant FUS mobility effects chromatin structure and promotes HSC aging .
2024-06-06 | GSE209715 | GEO
Project description:Aged hematopoietic stem cells (HSCs) display myeloid-biased differentiation and reduced regenerative potential. In this study, we uncover that P-selectin (Selp) marks a subset of aged HSCs with reduced repopulation capacity. This population of HSCs expresses a prominent aging transcriptome. Overexpression of Selp in young HSCs impaired long-term reconstitution potential and repressed erythropoiesis. We show that IL-1β is elevated in aged bone marrow and administration of IL-1β induces expression of Selp and other aging-associated genes in HSCs. Finally, we demonstrate that transplantation of aged HSCs into young recipients restores a young-like transcriptome, specifically by repressing pro-inflammatory pathways, highlighting the important role of the bone marrow microenvironment in HSC aging.
2023-01-02 | GSE194273 | GEO