Transcriptome profiling of human bone marrow stem cells (HBMSC) and tumorigenic sublines
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE128418 | GEO | 2022/11/04
REPOSITORIES: GEO
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Project description:Direct transcriptomics comparison corroborated by functional and gene network analyses of pre-weaned bovine mammary parenchyma and fat pad shed light on potential cross-talk between these developing tissues. Transcriptomic characterization of mammary parenchyma and fat pad and their interaction is still incomplete. In the present experiment, the molecular epithelial-fat pad cross-talk during mammary development was assessed by transcript profiling and functional analyses. Background: Interactions between bovine mammary parenchyma (PAR) and fat pad (MFP) during neonatal tissue development are still not fully understood. It is thought that the MFP surrounding the parenchymal tissue exerts proliferative effects on the PAR through secretion of local modulators of growth induced by systemic hormones. Main objectives in the present study were to use bioinformatics tools to characterize differences in transcript profiles between mammary PAR and MFP from Holstein heifers at ca. 65 d age and uncover potential cross-talk between the two tissues via the analyses of signaling molecules (e.g., cytokines and growth factors) preferentially expressed in one tissue relative to the other. Results: Over 9,000 differentially expressed genes (DEG; False discovery rate ≤ 0.05) were found of which 1,478 had a ≥1.5-fold difference. Within these DEG in PAR vs. MFP (n = 736) we noted enrichment of functions related to cell cycle, structural organization, signaling, and DNA/RNA metabolism. Few canonical pathways were among DEG and were mostly involved in cell cycle and tissue organization (p53 signaling). Enriched among DEG more highly-expressed in MFP vs. PAR (n = 742) were genes involved in lipid metabolism, signaling, cell movement, and immune-related functions. Canonical pathways associated with metabolism (fatty acid metabolism) and signaling, particularly immune- (acute phase response) and metabolism-related (cAMP signaling), were significantly enriched. Network analysis uncovered a central role of MYC, TP53, and CTNNB1 in controlling expression of DEG highly-expressed in PAR vs. MFP. Similar analysis revealed a central role of PPARG, KLF2, EGR2, and EPAS1 in regulating expression of highly-expressed DEG in MFP vs. PAR. Analyses revealed putative crosstalk between tissues via differential expression of cytokines and growth factors highly-expressed in PAR (angiopoietin-1, osteopontin, interleukin-1β) or in MFP (adiponectin, interleukin-13, fibroblast growth factor-2, leptin) during bovine mammary development. Conclusions: We uncovered specific transcriptomic signatures characterizing MFP and PAR tissue. Not surprisingly, the expression profile of the MFP is characteristic of adipose tissue, and the one of PAR is characteristic of an epithelial tissue undergoing expansion and remodeling. Overall, our data highlighted a large degree of interaction between the two tissues and allowed envisaging a reciprocal influence in determining the biological features (and perhaps the fate) of each of the two tissues during this stage of development. This is strongly suggested by the potential effect that the signaling molecules released preferentially by PAR have on lipid metabolism-related pathways, which from our data was what most distinguished the MFP from PAR. Similarly, the cytokines and growth factors largely expressed in MFP potentially affect the pathways related to cell cycle, development, and proliferation in PAR, which our data highlighted as the main functions represented among the genes highly expressed in PAR vs. MFP. Based on the current analysis, the number of cytokines and growth factors that potentially are secreted by each tissue and affect molecules in the other underscores the concept of crosstalk. Ultimately, these bidirectional interactions might be required to coordinate mammary tissue development under normal circumstances or in response to environmental stimuli, such as nutrition.
2010-06-01 | GSE20363 | GEO
Project description:To better understand the impact of integrin beta3 signaling in myeloid cells on the tumor microenvironment, we compared the gene expression profiles of FACS isolated GFP+ PyMT-BO1 MFP tumor cells and also M2 TAMs (CD11b+Gr1-F4/80+CD206+) from tumor tissue of WT mice and b3ÎÎÎ mice. PyMT-BO1-GFP-Luc tumor cells (100,000) were injected into mammary fat pad (MFP) tissue from WT and b3KOM mice. PyMT-BO1-GFP-Luc cells and CD206hi tumor-associated macrophages (TAMs) were FACS-sorted from day 10 MFP tumor tissue. FACS-sorted cells directly used for RNA extraction and hybridization on Affymetrix microarrays.
2015-12-11 | E-GEOD-75882 | biostudies-arrayexpress
Project description:Human embryonic stem (ES) cell lines acquire recurrent karyotypic abnormalities that may promote growth and survival in long-term culture. Cells with these abnormalities are often present at low levels in human ES cell cultures, requiring subcloning for isolation and analyses. We have developed a rapid method to isolate either abnormal or normal clones from karyotypically mosaic human ES cell cultures that we call Genetic Diagnosis at Passage (G-DAP). We have used this technique to isolate three distinct abnormal sublines from H9 human ES cells in continuous culture. These sublines were characterized by G-banding, fluorescence in situ hybridization (FISH), spectral karyotyping (SKY), and array comparative genomic hybridization (aCGH). One subline (H9.DT) has, as it’s only abnormality, a duplication of 12p capped by a 5q subtelomere. A related subline (H9.TSF) has an additional copy of the derivative chromosome 12, partial trisomy of 17q, and trisomy 14. The third subline (H9.DE) has an interstitial deletion of 18q as the sole anomaly. Despite these karyotypic abnormalities, all three sublines retain markers of the undifferentiated state. The subline H9.TSF demonstrated the ability to form embryoid bodies consisting of all three germ layers. Significantly, H9.DT and H9.TSF sublines show a classic karyotype progression that mirrors that seen in both hematopoietic and solid tumors. This progression was accompanied by an impressive increase in growth potential. The isolation of human ES cell sublines with clonal cytogenetic abnormalities provides a valuable tool for study of factors that promote in vitro genetic changes and for analysis of mechanisms of aneuploidy related to genetic progression found in human cancers.
2008-07-18 | GSE12119 | GEO
Project description:Introduction: There is a clinical need for developing systemic transplantation protocols for use of human skeletal stem cells (also known bone marrow stromal stem cells) (hBMSC) in tissue regeneration. In systemic transplantation studies, only a limited number of hBMSC home to injured tissues suggesting that only a subpopulation of hBMSC possess âhomingâ capacity. Thus, we tested the hypothesis that a subpopulation of hBMSC defined by ability to form heterotopic bone in vivo, is capable of homing to injured bone. Methods: We tested ex vivo and in vivo homing capacity of a number of clonal cell populations derived from telomerized hBMSC (hBMSC-TERT) with variable ability to form heterotopic bone when implanted subcutaneously in immune deficient mice. In vitro transwell migration assay was used and in vivo homing ability to bone fractures in mice was visualized by bioluminescence imaging (BLI). In order to identify the molecular phenotype associated with enhanced migration, we carried out comparative DNA microarray analysis of gene expression of hBMSC-derived high bone forming (HBF) clones versus low bone forming (LBF) clones. Results: In this study, clonal cell populations forming in vivo bone were shown to exhibit higher ex vivo transwell migration and following intravenous infusion, enhanced in vivo homing ability to bone fractures. Comparative microarray analysis of LBF versus HBF clones identified a significant enrichment of gene categories of cell chemo-attraction, adhesion and migration. Among these genes, platelet-derived growth factor receptor (PDGF-R) α and β were highly expressed in HBF clones. Further studies showed that the chemoattractive effects of PDGF in vitro was more enhanced in HBF clones compared to LBF clones and this effect was abolished in presence of a PDGFR-β-specific inhibitor: SU-16f. Sorted PDGFR-β+ cells from LBF clones showed that the PDGFR-β+ enriched cell population exhibited strong chemoattractance towards PDGF. Conclusion: Our data demonstrate phenotypic and molecular association between in vivo bone formation and migratory capacity of hBMSC. PDGFR-β can be used as a potential marker for the prospective selection of hBMSC populations with high migration and bone formation capacities suitable for clinical trials for enhancing bone regeneration. Total RNA obtained from telomerized human bone marrow derived mesenchymal stromal cells (T4P38a) with high in vivo bone forming capacity and (T4P74a) with low bone forming capacity and three single cell clones with high bone forming capacities (DD8, AD10 and BB10) and three clones with low bone forming capacities (CF1, CB4 and CD4). All cells were cultured under standard conditions and RNAs were isolated at baseline with no induction. each sample was represented in doublicate as a and b.
2016-06-01 | E-GEOD-69358 | biostudies-arrayexpress
Project description:Gene expression profiles of in vitro selected highly metastatic MKN45-GFP sublines. The results were compared with MKN45-GFP control cell line to determine the metastasis associated genes. Four pairs compared experiment. Each pair was used MKN45-GFP cells as correlated control. Determining on the gene expression trends were by various metastatic ability of each subline.
2011-11-10 | E-GEOD-33570 | biostudies-arrayexpress
Project description:Expression data from 4T1 subclones derived from mammary fat pad tumors (MFP), axillary lymph node tumors (AxLN), and axillary lymph node-derived lung metastases (AxLN-LuM). In parallel, expression data, in the same subclones, of tail vein-derived (TV) lung metastases. The mechanism of how lymph node metastases seed distant metastases is unknown. We used the 4T1 breast cancer cell line, which is an immune competent model of triple negative breast cancer and spontaneously metastasizes in balb/c mice. 4T1-GFP/fLuc cells were injected into MFP to form tumors and 4T1-mCherry/rLuc cells were injected into axillary lymph nodes to form tumors and then allowed to metastasize to lung. TV cells were allowed to metastasize in the lung. Cells were harvested at different time intervals after the injection. Tumors were extracted, dissociated, and then expanded in vitro to obtain MFP, AxLN, AxLN-LuM and TV-LuM subclones isolated after different time lags with respect to the injection.
2019-08-20 | GSE136031 | GEO
Project description:Comparison of L1 high metastatic subline (C10F4) to low metastatic subline (C9F6) and normal lung cells from mouse
2021-02-07 | E-MTAB-6512 | biostudies-arrayexpress
Project description:Introduction: There is a clinical need for developing systemic transplantation protocols for use of human skeletal stem cells (also known bone marrow stromal stem cells) (hBMSC) in tissue regeneration. In systemic transplantation studies, only a limited number of hBMSC home to injured tissues suggesting that only a subpopulation of hBMSC possess “homing” capacity. Thus, we tested the hypothesis that a subpopulation of hBMSC defined by ability to form heterotopic bone in vivo, is capable of homing to injured bone. Methods: We tested ex vivo and in vivo homing capacity of a number of clonal cell populations derived from telomerized hBMSC (hBMSC-TERT) with variable ability to form heterotopic bone when implanted subcutaneously in immune deficient mice. In vitro transwell migration assay was used and in vivo homing ability to bone fractures in mice was visualized by bioluminescence imaging (BLI). In order to identify the molecular phenotype associated with enhanced migration, we carried out comparative DNA microarray analysis of gene expression of hBMSC-derived high bone forming (HBF) clones versus low bone forming (LBF) clones. Results: In this study, clonal cell populations forming in vivo bone were shown to exhibit higher ex vivo transwell migration and following intravenous infusion, enhanced in vivo homing ability to bone fractures. Comparative microarray analysis of LBF versus HBF clones identified a significant enrichment of gene categories of cell chemo-attraction, adhesion and migration. Among these genes, platelet-derived growth factor receptor (PDGF-R) α and β were highly expressed in HBF clones. Further studies showed that the chemoattractive effects of PDGF in vitro was more enhanced in HBF clones compared to LBF clones and this effect was abolished in presence of a PDGFR-β-specific inhibitor: SU-16f. Sorted PDGFR-β+ cells from LBF clones showed that the PDGFR-β+ enriched cell population exhibited strong chemoattractance towards PDGF. Conclusion: Our data demonstrate phenotypic and molecular association between in vivo bone formation and migratory capacity of hBMSC. PDGFR-β can be used as a potential marker for the prospective selection of hBMSC populations with high migration and bone formation capacities suitable for clinical trials for enhancing bone regeneration.
2016-06-01 | GSE69358 | GEO
Project description:E0771 tumors were implanted either subcutaneously on the left flank or orthotopically in the mammary fat pad and treated with either PBS or FEC + oHSV-1 Mice were sacrificed 5 days after the start of treatment and whole tumour digests were used for RNA extraction
2021-10-01 | GSE183864 | GEO
Project description:The aim of the project was to obtain murine hepatoma MH22a [1] cell subline, resistant to anticancer agent 3-amino-1,2,4-benzotriazine-1,4-dioxide (tirapazamine, TPZ), and examine the changes of the protein expression as compared with parental cells, with the main emphasis on the changes of redox proteins. MH22a cells obtained from the Institute of Cytology of the Russian Academy of Sciences (St. Petersburg, Russia), were grown at 37°C in DMEM medium, supplemented with 10% fetal bovine serum and antibiotics in T25 flasks until reaching 70-80% confluence. The medium is then changed to an analogous medium with 5.0 μM TPZ, and, depending on cell viability, 50% of the medium with TPZ is changed 1-2 times a week, repeating that procedure for 3.5 months to form a stable monolayer. The resulting monolayer is inoculated 1:2 and further grown by changing 50% of the culture medium twice a week until re-inoculation. 20 passages were made over 2.5 months in total. We were unable to obtain a cell subline in a stepwise fashion by growing the cells in increasing concentrations of TPZ, because its concentration increase up to 10 μM caused cell death after 1 month. For analysis, one flask per each sample, 3 samples of parental cell line and 3 samples of TPZ-resistant cell line (between 15th and 20th passages), were selected. Cells were rinsed three times with PBS, detached with TrypLE Express (ThermoFisher Scientific, Waltham, MA, USA) and cell concentration and viability was determined with Trypan blue and Countess 2 (ThermoFisher Scientific, Waltham, MA, USA) automated cell counter. Cells were rinsed by centrifuging 500xg for 5 min and suspending in PBS three times. Finally, cells were flash frozen in liquid nitrogen and transferred to -86°C freezer for storage. [1] European Collection of Authenticated Cell Cultures (ECACC), Catalogue No. 96121721.
2023-05-10 | PXD039876 | Pride