AM in vivo and ex vivo RNAseq
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE194142 | GEO | 2022/01/23
REPOSITORIES: GEO
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Project description:Here we show that alveolar macrophage (AM) identity were conserved through culture expansion as determined by the analysis of epigenetic chromatin accessibility of core AM specific transcription markers and surface markers. Further, the adaptations to the culture environment were transient, reversible and fully restored to the in vivo status upon transplantation into the alveolar niche.
2022-01-23 | GSE194143 | GEO
Project description:Ex-vivo expanded mesenchymal stromal cells (MSCs) are increasingly used for paracrine support of hematopoietic stem cell (HSC) regeneration, but inconsistent outcomes have been the huddle for on-going clinical trials. Here, we hypothesized that the heterogeneity in the niche activity of manufactured MSCs can be a parameter for variable outcomes in MSC-based cell therapy. We first screened MSC culture medium and found that serum batches caused larger variations in colony forming unit-fibroblast (CFU-F) content of MSCs than individual donor variations. The culture conditions supporting high (stimulatory) and low (non-stimulatory) CFU-F caused distinct niche activity of MSCs; MSCs under stimulatory condition exhibited higher level expression of cross-talk molecules (Jagged-1 and CXCL-12) and higher support for HSCS during long-term culture than MSCs under non-stimulatory culture. Moreover, the effects of MSCs enhancing hematopoietic engraftment were only visible when HSCs were co-transplanted with MSCs expanded under stimulatory, but not non-stimulatory conditions. However, these differences of MSCs were readily reversed by switching the culture mediums, indicating their distinct functional state, rather than clonal heterogeneity. Accordingly, transcriptomic analysis showed distinct gene set enrichment between the different MSCs and revealed distinct upstream signaling pathways such as inhibition of P53 and activation of ATF4 for MSCs under stimulatory conditions. Taken together, our study shows that the heterogeneity in the niche activity of MSCs can be created during ex-vivo expansion to cause a difference in the hematopoietic engraftment and raise the possibility that MSCs can be pre-screened for more predictable outcomes in clinical trials of MSCs. Total RNA obtained from isolated human mesenchymal stromal cells. To compare stimulatory (SS) serum and non-stimulatory (NSS) serums, MSCs had been maintained in each serum media were sub-cultured for at least two passages before analysis.
2016-07-25 | E-GEOD-84754 | biostudies-arrayexpress
Project description:Ex-vivo expanded mesenchymal stromal cells (MSCs) are increasingly used for paracrine support of hematopoietic stem cell (HSC) regeneration, but inconsistent outcomes have been the huddle for on-going clinical trials. Here, we hypothesized that the heterogeneity in the niche activity of manufactured MSCs can be a parameter for variable outcomes in MSC-based cell therapy. We first screened MSC culture medium and found that serum batches caused larger variations in colony forming unit-fibroblast (CFU-F) content of MSCs than individual donor variations. The culture conditions supporting high (stimulatory) and low (non-stimulatory) CFU-F caused distinct niche activity of MSCs; MSCs under stimulatory condition exhibited higher level expression of cross-talk molecules (Jagged-1 and CXCL-12) and higher support for HSCS during long-term culture than MSCs under non-stimulatory culture. Moreover, the effects of MSCs enhancing hematopoietic engraftment were only visible when HSCs were co-transplanted with MSCs expanded under stimulatory, but not non-stimulatory conditions. However, these differences of MSCs were readily reversed by switching the culture mediums, indicating their distinct functional state, rather than clonal heterogeneity. Accordingly, transcriptomic analysis showed distinct gene set enrichment between the different MSCs and revealed distinct upstream signaling pathways such as inhibition of P53 and activation of ATF4 for MSCs under stimulatory conditions. Taken together, our study shows that the heterogeneity in the niche activity of MSCs can be created during ex-vivo expansion to cause a difference in the hematopoietic engraftment and raise the possibility that MSCs can be pre-screened for more predictable outcomes in clinical trials of MSCs.
2016-07-25 | GSE84754 | GEO
Project description:Reprogramming of bone marrow microenvironments (BMMs) is a key process by which ALL cells gain resilience however the specific adaptations that facilitate primary disease and ALL survival after induction chemotherapy remain unclear. Using temporal analysis of clinical biopsies we identify that BM adipocytes are profoundly remodelled during ALL pathogenesis and treatment transitioning from cellular depletion within the primary leukaemia niche to a fully restored state upon remission treatment highlighting the specific and selective participation of adipocyte stroma in the chemotherapy context. The functional relevance of these dynamics was revealed through modelling studies demonstrating that adipocytes non- cell autonomously regulate ALL development by reducing proliferative capacity whilst simultaneously increasing leukaemia cell quiescence. Thus, adipocyte dynamics mark a transition in the functional organisation of BMM from one that favours emergent ALL to an adverse setting for chemotherapeutic effects. Mechanistically, we show that adipocyte induced tumour suppression, accompanies rapid but reversible non canonical translational arrest revealing a novel regulatory relationship that executes at the level of the leukaemia proteome to lower ALL expansion. Importantly, adipocyte remodelled ALL proteomes adopt a distinct, reversible, stress-resistant state which was independent of cell cycle status underscoring the importance of therapy emergent adipocyte niches in conferring global tumour cell protection. These studies reveal the critical contribution of adipocyte mediated repression of the ALL proteome as another mode of microenviromental intervention advantaging ALL tumours to prevent their elimination.
2021-05-25 | GSE151801 | GEO
Project description:Reprogramming of bone marrow microenvironments (BMMs) is a key process by which ALL cells gain resilience however the specific adaptations that facilitate primary disease and ALL survival after induction chemotherapy remain unclear. Using temporal analysis of clinical biopsies we identify that BM adipocytes are profoundly remodelled during ALL pathogenesis and treatment transitioning from cellular depletion within the primary leukaemia niche to a fully restored state upon remission treatment highlighting the specific and selective participation of adipocyte stroma in the chemotherapy context. The functional relevance of these dynamics was revealed through modelling studies demonstrating that adipocytes non- cell autonomously regulate ALL development by reducing proliferative capacity whilst simultaneously increasing leukaemia cell quiescence. Thus, adipocyte dynamics mark a transition in the functional organisation of BMM from one that favours emergent ALL to an adverse setting for chemotherapeutic effects. Mechanistically, we show that adipocyte induced tumour suppression, accompanies rapid but reversible non canonical translational arrest revealing a novel regulatory relationship that executes at the level of the leukaemia proteome to lower ALL expansion. Importantly, adipocyte remodelled ALL proteomes adopt a distinct, reversible, stress-resistant state which was independent of cell cycle status underscoring the importance of therapy emergent adipocyte niches in conferring global tumour cell protection. These studies reveal the critical contribution of adipocyte mediated repression of the ALL proteome as another mode of microenviromental intervention advantaging ALL tumours to prevent their elimination.
2021-05-25 | GSE150832 | GEO
Project description:Hematopoietic stem cells (HSCs) maintain lifelong hematopoiesis by remaining quiescent in the bone marrow niche. Recapitulation of a quiescent state in culture has not been achieved, as cells rapidly proliferate and differentiate in vitro. By modulating environmental factors mimicking physiological conditions, we were able to maintain engraftable quiescent HSCs for 1 month in culture under low cytokine concentrations, hypoxia, and high fatty acid concentration, the latter required due to suppression of intrinsic fatty acid synthesis. By contrast, high cytokine concentrations or normoxia induced HSC proliferation and differentiation. Our novel culture system provides a means to evaluate properties of steady state HSCs and test effects of defined factors in vitro under near-physiological conditions.
2018-07-24 | GSE117516 | GEO
Project description:Successful ex vivo expansion of hematopoietic stem cells (HSCs) would greatly benefit the treatment of disease and the understanding of critical questions of stem cell biology. Microarray studies showed that the HSC supportive mouse fetal liver CD3+ cells specifically expressed angiopoietin-like 2 (Angptl2) and angiopoietin-like 3 (Angptl3). When highly enriched HSCs were cultured in the presence of Angptl2 or Angptl3 together with saturating levels of other growth factors for 10 days, a 24 or 30 fold net expansion of long-term HSCs was observed by reconstitution analysis. The coiled-coil domain of Angptl2 mediated the effects of Angptl2 on HSC expansion. Furthermore, angiopoietin-like 5, angiopoietin-like 7, and microfibril-associated glycoprotein 4 also supported expansion of HSCs in culture. Keywords: Cell type comparison
2006-03-01 | GSE3609 | GEO
Project description:Ex vivo activation and expansion of natural killer (NK) cells is a strategy to produce sufficient numbers of these effector cells for adoptive immunotherapy. Therefore we aimed at the development of an automated, clinical scale NK cell expansion process and compared NK cells after manual and automated expansion.We found only a small subset of 124 genes that significantly varied between both sample groups. These genes were associated with movement of leukocytes were identified including a group of genes for NK cell movement (CMKLR1, CX3CR1, S1PR5, GNLY and CXCR1) which were slightly higher expressed after automated compared to manual expansion. Nevertheless, the expansion profiles of NK cells after automated or manual expansion were rather similar in comparison to the remarkable difference between primary and expanded NK cells in general represented by the vast majority of regulated genes between the analyzed sample groups. Pathway analysis revealed that most of regulated genes upon expansion were associated with cell cycle regulation, DNA replication, DNA recombination and DNA repair, regulation of apoptosis and cell survival as well as cytokine signaling. Furthermore, the expression of many NK cell relevant markers was changed upon expansion with the strongest effects on up regulation of TRAIL and FASL, inhibitory TIGIT and chemokine receptors CCR2, CCR5 and CXCR6. In addition, granzyme M was down regulated but other important effector molecules like TNFa, perforin and granzymes A, B and K were up regulated. In summary we could show that manual and automatically expanded NK cells show a similar expansion profile while the differ significantly from primary NK cells. Up regulation of many NK cell relevant markers indicate for an enhanced NK cell functionaility after ex vivo activation and expansion. 24 samples were analyzed in total. 6 biological replicates represented by cells from different donors. 4 different samples per donor: freshly isolated NK cells (d0) and NK cells expanded for 14 days under 3 different conditions: in co-culture with EBV-LCL feeder cells and 500 U/mL IL2 either cultivated manually in T75 flasks (T) or automatically using the CliniMACS Prodigy system (P); NK cells cultured with 500 U/ml IL2 without feeder cells (I)
2015-04-23 | E-GEOD-62654 | biostudies-arrayexpress
Project description:We studied whether Vγ9Vδ2-T cells can exploited as autologous effector lymphocytes in chronic lymphocytic leukemia (CLL). Healthy controls (HC) Vγ9Vδ2-T cells were activated by and had potent cytolytic activity against CLL cells, however CLL-derived Vγ9Vδ2-T cells proved dysfunctional with respect to effector cytokine production and cytotxicity. Dysfunction of Vγ9Vδ2-T cells was reversible upon activation with autologous monocyte-derived dendritic cells (mODCs). RNA sequencing confirmed that Vγ9Vδ2-T cells from CLL patients have a transcriptional profile that is distinct from HC Vγ9Vδ2-T cells prior to ex vivo expansion, although the profile after ex vivo expansion is similar between CLL and HC Vγ9Vδ2-T cells. Gene expression profiling implicated alterations in both synapse formation and exhaustion as conceivable contributors to compromised Vγ9Vδ2-T cell function in CLL patients. Taken together, CLL-mediated dysfunction of autologous Vγ9Vδ2-T cells is fully reversible, resulting in potent cytotoxicity towards CLL cells.
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