Genome-wide analysis of human bone marrow-derived MSC cells in comparision with MSC with EGR1 knockdown or EGR1 overexpressing cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE122831 | GEO | 2021/11/21
REPOSITORIES: GEO
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Project description:Genome-wide analysis of human bone marrow-derived MSC cells in comparision with MSC with EGR1 knockdown or EGR1 overexpressing cells
| PRJNA506451 | ENA
Project description:Human bone marrow stromal cells (BMSCs) are key elements of the hematopoietic environment and they play a central role in bone and bone marrow physiology. However, how key BMSC functions are regulated is largely unknown. We analyzed the role of the immediate early response transcription factor EGR1 as key BMSC regulator and found that EGR1 was highly expressed in prospectively-isolated primary BMSCs, downregulated upon culture, and lower in non-CFU-F-containing CD45neg BM cells. Furthermore, EGR1 expression was lower in proliferative regenerating adult and fetal primary cells compared to adult steady-state BMSCs. Accordingly, EGR1 overexpression markedly decreased BMSC proliferation but considerably improved hematopoietic stroma support function as indicated by an increased production of transplantable CD34+CD90+ hematopoietic stem cells in expansion co-cultures. The improvement of BMSC stroma support function was mediated by increased expression of hematopoietic supporting genes, such as VCAM1 and CCL28. On the other hand, EGR1 knockdown increased ROS-mediated BMSC proliferation, and clearly reduced BMSC hematopoietic stroma support potential. These findings thus show that EGR1 is a key BMSC transcription factor with a dual role in regulating proliferation and hematopoietic stroma support function that is controlling a genetic program to coordinate the specific functions of BMSC in their different biological contexts.
2019-06-27 | PXD011767 | Pride
Project description:Mesenchymal stromal cells (MSC) are ideal candidates for cell therapies, due to their immune-regulatory and regenerative properties. We have previously reported that lung-derived MSC are tissue-resident cells with lung-specific properties compared to bone marrow-derived MSC. Assessing relevant molecular differences between lung-MSC and bone marrow-MSC is important, given that such differences may impact their behavior and potential therapeutic use. Here, we present an in-depth mass spectrometry (MS) based strategy to investigate the proteomes of lung-MSC and bone marrow-MSC. The MS-strategy relies on label free quantitative data-independent acquisition (DIA) analysis and targeted data analysis using a MSC specific spectral library. We identified several significantly differentially expressed proteins between lung-MSC and bone marrow-MSC within the cell layer (352 proteins) and in the conditioned medium (49 proteins). Bioinformatics analysis revealed differences in regulation of cell proliferation, which was functionally confirmed by decreasing proliferation rate through Cytochrome P450 stimulation. Our study reveals important tissue-specific differences within proteome and matrisome profiles between lung- and bone marrow-derived MSC that may influence their behavior and affect the clinical outcome when used for cell-therapy.
2018-10-18 | PXD006419 | Pride
Project description:To investigate the function of EGR1 in HCC growth, we established EGR1 knock out MHCC97H cells by CRISPR/Cas9 system and EGR1-overexpressing PLC/PRF5 cells. We then performed gene expression profiling analysis using data obtained from RNA-seq of EGR1 knock out MHCC97H cells and parental MHCC97H cells, EGR1-overexpressing PLC/PRF5 cells and control PLC/PRF5 cells.
2024-02-07 | GSE238116 | GEO
Project description:Therapy-related myeloid neoplasms (t-MN) share many similarities with AML de novo in the elderly. One common factor is that they arise in the setting of chronic inflammation, likely due to advanced age or chemotherapy-induced senescence. Here, we examined the impact of haploinsufficient loss of the del(5q) tumor suppressor gene, EGR1, commonly deleted in high-risk MNs. In mice, under the exogenous inflammatory stress of either serial transplant or successive doses of the alkylating agent ENU, Egr1-haploinsufficient hematopoietic stem cells (HSCs) exhibit a clonal advantage. Complete loss of EGR1 function is incompatible with transformation; mutations of EGR1 are rare and are not observed in the remaining allele in del(5q) patients and complete knockout of Egr1 in mice leads to HSC exhaustion. Using chromatin immunoprecipitation sequencing (ChIP-seq), we identify EGR1 binding sites in human CD34+ cord blood-derived stem and progenitor cells (HSPCs) and show that EGR1 binds genes critical for stem cell differentiation, inflammatory signaling, and the DNA damage response. Notably, in the chromosome 5 sequences frequently deleted in patients, there is a significant enrichment of innate and inflammatory genes, which may confer a fitness advantage in an inflammatory environment. Short hairpin RNA (shRNA) mediated silencing of EGR1 biases HSPCs towards a self-renewal transcriptional signature. In the absence of EGR1, cells upregulate MYC-driven proliferative signals, downregulate CDKN1A (p21), disrupt the DNA damage response, and downregulate inflammation - adaptations anticipated to confer a relative fitness advantage for stem cells especially in an environment of chronic inflammation.
2022-09-01 | GSE184931 | GEO
Project description:To investigate the effects of TWIST1 expression on mesenchymal stem cells, we established a retrovirally transduced MSC line overexpressing TWIST1.
2023-08-01 | GSE220639 | GEO
Project description:We have demonstrated that DICER1 (a key enzyme of miRNA biogenesis) was underexpressed in myelodysplastic syndrome MSC. We hypothesize that those MSC harbored a deregulated pattern of miRNA versus healthy donors MSC.
2020-10-04 | GSE139471 | GEO
Project description:In the current study, we hypothesized that if bone-marrow derived MSC contribute to endometrial regeneration and are progenitors to hESF, their treatment with agents known to regulate hESF differentiation could promote their differentiation down the stromal fibroblast lineage. To this end, we treated bone marrow-derived MSC with estradiol (E2) and progesterone (P4), BMP2, and activators of the PKA pathway and investigated specific markers of hESF differentiation (decidualization). Furthermore, we investigated the transcriptome of these cells in response to cAMP and compared this to the transcriptome of hESF decidualized in response to activation of the PKA pathway. The data support that MSC can be differentiated down the hESF pathway, as evidenced by changes in cell shape and common expression of decidual markers and other genes important in hESF differentiation and function. Bone marrow-derived MSC were expanded in DMEM (high glucose) medium containing 10% fetal bovine serum, 1% penicillin and streptomycin. At 80% confluency MSC were trypsinized and plated at 5x103 cells/cm2 in 6cm plates. Nearly confluent cells were serumstarved overnight and thereafter treated for 0, 3, 7, 14 and 21 days in low-serum medium (2% FBS) with the following treatments: (a) 10nM E2/1mM P4; (b) 0.5mM or 1mM 8-Br-cAMP (cAMP); (c) 50nM or 100nM BMP-2; (d) 0.5mM and 1mM 8-Br-cAMP + BMP-2; (d) 0.5mM and 1mM 8-BrcAMP + BMP-2 + E2/P4; (e) 50nM or 100nM human FSH, with vehicle controls at each time point. Each experiment was conducted in duplicate and repeated at least 3 times. Media were changed every third day. Endpoints were prolactin (PRL) and IGF binding protein-1 (IGFBP1) mRNA, assessed by quantitative real-time RT-PCR, and protein in conditioned media, assessed by ELISA (see below), after 3, 7, 14 and 21 days of incubation. Immunostaining for vimentin, cytokeratin 7, and Oct-4 was performed before and after MSC treatments to assess the stromal lineage of MSC and their differentiation status. MSC expressed vimentin and did not express cytokeratin or Oct-4, independent of culture conditions or duration of culture or treatment. The morphological appearance of MSC under different treatment conditions was photographed using a Leica CTR 6500 microscope. Microarray analysis was performed with MSC, n=3, at t=0 (untreated, uncultured control), 14day vehicle control, and 14day treated with 8-Br-cAMP. Only high quality samples (RIN=9.1-10) were used for microarray analysis. Hybridization was performed with Affymetrix Human Gene 1.0 ST arrays.
2010-04-14 | E-GEOD-20631 | biostudies-arrayexpress
Project description:To gain insight into the function of DNA-PKcs within immune cells, we performed a quantitative phosphoproteomic screen in T cells to identify first order phosphorylation targets of DNA-PKcs. Results indicate that DNA-PKcs phosphorylates the transcription factor Egr1 (early growth response protein 1) at S301. Expression of Egr1 is induced early upon T cell activation and dictates T cell response by modulating expression of cytokines and key costimulatory molecules. Mutation of serine 301 to alanine via CRISPR-Cas9 resulted in increased proteasomal degradation of Egr1 and a decrease in Egr1-dependent transcription of IL2 (interleukin-2) in activated T cells. Our findings identify DNA-PKcs as a critical intermediary link between T cell activation and T cell fate and a novel phosphosite involved in regulating Egr1 activity.
2021-12-21 | PXD026352 | Pride
Project description:In the current study, we hypothesized that if bone-marrow derived MSC contribute to endometrial regeneration and are progenitors to hESF, their treatment with agents known to regulate hESF differentiation could promote their differentiation down the stromal fibroblast lineage. To this end, we treated bone marrow-derived MSC with estradiol (E2) and progesterone (P4), BMP2, and activators of the PKA pathway and investigated specific markers of hESF differentiation (decidualization). Furthermore, we investigated the transcriptome of these cells in response to cAMP and compared this to the transcriptome of hESF decidualized in response to activation of the PKA pathway. The data support that MSC can be differentiated down the hESF pathway, as evidenced by changes in cell shape and common expression of decidual markers and other genes important in hESF differentiation and function.
2010-03-31 | GSE20631 | GEO