Intrinsic differentiation potential of human postnatal MSC, Mab and MAPC reflected in their transcriptome
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE23131 | GEO | 2011/07/12
SECONDARY ACCESSION(S): PRJNA131715
REPOSITORIES: GEO
Similar Datasets
Project description:We have employed whole genome microarray expression profiling to identify genes that characterize different populations of human postnatal stem cells and reflect their potency MSC, Mab and MAPC cultures were established from at least three different donors and their transcriptome was assayed using the Agilent 4x44k whole human genome microarray; furthermore, the H9 ESC line from U of Wisconsin and MSC from Lonza were added for comparison MSC = Mesenchymal Stem Cells, MAPC= Multipotent Adult Progenitor Cells, Mab= Mesoangioblasts, ESC= Embryonic Stem Cells
2011-07-12 | E-GEOD-23131 | biostudies-arrayexpress
Project description:Introduction: Overall survival of early-stage breast cancer (BC) patients is similar for those who undergo breast conserving therapy (BCT) and mastectomy, however, 10-15% of women undergoing BCT suffer ipsilateral breast tumor recurrence. The risk of recurrence may vary with age or breast cancer subtype. Understanding the gene expression of the cancer-adjacent tissue and/or stromal response to specific tumor subtypes is important for developing clinical strategies to reduce recurrence risk. Methods: We studied gene expression data in cancer-adjacent tissue from 158 BC patients. Complementary in vitro cocultures were used to study cell-cell communication between fibroblasts and specific breast cancer subtypes. Results: Our results suggest that intrinsic tumor subtypes are reflected in histologically normal cancer-adjacent tissue. Gene expression of cancer-adjacent tissues shows that triple negative (Claudin-low or Basal-like tumors) exhibit increased expression of genes involved in inflammation and immune response. While such changes could reflect distinct immune populations present in the microenvironment of different breast cancer subtypes, altered immune response gene expression was also observed in cocultures in the absence of immune cell infiltrates, emphasizing that these inflammatory mediators are secreted by breast-specific cells. In addition, while triple negative BCs are associated with upregulated immune response genes, Luminal breast cancers are more commonly associated with estrogen-response in adjacent tissues. Conclusions: Specific characteristics of BCs are reflected in the surrounding benign tissue. This commonality between tumor and surrounding tissue may underlie second primaries and local recurrences. Biomarkers derived from cancer-adjacent tissue may be helpful in defining personalized surgical strategies or in predicting recurrence risk. reference x sample
2014-04-30 | E-GEOD-50939 | biostudies-arrayexpress
Project description:GENES ASSOCIATED WITH THE CELL CYCLE, LINEAGE COMMITMENT AND IMMUNOMODULATORY POTENTIAL DISCRIMINATE HUMAN POSTNATAL STEM CELLS OF DIFFERENT ORIGIN. Stem cells hold great promise for future clinical use. Their intrinsic biological properties are, however, not fully understood and many of their therapeutic benefits still unclear. Better understanding of their genetic and biological properties is essential for the development of clinically relevant stem cell applications. The neonatal unrestricted somatic stem cell (USSC) from cord blood has the capacity to differentiate into cells from all three germ layers. Here we investigate the gene expression profile of USSC using the Affymetrix Exon Array platform and compare it with those of bone-marrow derived mesenchymal adult stem cells (BM-MSC) and adipose tissue-derived adult stem cells (AdAS). Extensive data analysis revealed limited variation in the expression profile of the different cell lines from the same origin, while stem cells from different origins showed distinct profiles, with the BM-MSC and AdAS being more closely related to each other than to USSC. Interestingly, USSC expressed genes involved in the cell cycle at much higher levels, indicative of their relatively higher cycling rate (~ 24 hrs as opposed to more than 2 days for BM-MSC and AdAS). They also show higher expression of genes involved in neurogenesis, consistent with their reported neuronal differentiation capacity. The BM-MSC signature indicates that they are primed towards developmental processes of tissues and organs derived from the mesoderm and endoderm. Remarkably, AdAS appear to be highly enriched in immune-related genes. Together, the data suggest that the different mesenchymal stem cell types have distinct gene expression profiles,that reflect their origin and differentiation potential. Keywords: Adult stem cells, developmental biology, gene expression, genomics, human cord blood, mesenchymal stem cells, cell type comparison
2009-10-22 | GSE18698 | GEO
Project description:Introduction: Overall survival of early-stage breast cancer (BC) patients is similar for those who undergo breast conserving therapy (BCT) and mastectomy, however, 10-15% of women undergoing BCT suffer ipsilateral breast tumor recurrence. The risk of recurrence may vary with age or breast cancer subtype. Understanding the gene expression of the cancer-adjacent tissue and/or stromal response to specific tumor subtypes is important for developing clinical strategies to reduce recurrence risk. Methods: We studied gene expression data in cancer-adjacent tissue from 158 BC patients. Complementary in vitro cocultures were used to study cell-cell communication between fibroblasts and specific breast cancer subtypes. Results: Our results suggest that intrinsic tumor subtypes are reflected in histologically normal cancer-adjacent tissue. Gene expression of cancer-adjacent tissues shows that triple negative (Claudin-low or Basal-like tumors) exhibit increased expression of genes involved in inflammation and immune response. While such changes could reflect distinct immune populations present in the microenvironment of different breast cancer subtypes, altered immune response gene expression was also observed in cocultures in the absence of immune cell infiltrates, emphasizing that these inflammatory mediators are secreted by breast-specific cells. In addition, while triple negative BCs are associated with upregulated immune response genes, Luminal breast cancers are more commonly associated with estrogen-response in adjacent tissues. Conclusions: Specific characteristics of BCs are reflected in the surrounding benign tissue. This commonality between tumor and surrounding tissue may underlie second primaries and local recurrences. Biomarkers derived from cancer-adjacent tissue may be helpful in defining personalized surgical strategies or in predicting recurrence risk.
2014-04-30 | GSE50939 | GEO
Project description:To gain an integrated view of the dynamic changes in gene expression during postnatal heart development at the organ level, time-series transcriptome analyses of the postnatal hearts of neonatal through adult mice (P1, P7, P14, P30, and P60) were performed using a newly developed bioinformatics pipeline. Additionally, the role of the transcription factor Sox6 in the postnatal maturation of cardiac muscle was investigated by differential transcriptome analyses between Sox6 knockout (KO) and control hearts.
2016-11-10 | GSE60958 | GEO
Project description:Tissue stem cells preserve a certain level of potency to maintain intact tissue integrity after various injury. Postnatal dermal fibroblasts lose differentiation potential for regenerative healing that recreates normal tissue including functional hair follicles (HFs), however, their intrinsic cellular changes are not understood yet. Here, we uncover a postnatal maturation process in papillary fibroblasts (PFs) mediated by Twist2-driven chromatin and transcriptional remodeling. Within 4 days after birth, dermal PFs lost WNT transcription factors (TFs) and target gene expressions accompanied by loss of H3K27ac expression. Through single-cell transcriptomics, ATAC-seq and ChIP-seq profiling, we define a postnatal maturation trajectory of PFs, in addition to loss of regenerative trajectory, triggered by decrease of H3K27ac and chromatic accessibility. In vivo inhibition of histone deacetylation delays the postnatal chromatin remodeling and maintains developmental signaling and differentiation potential in PFs. TF motif analysis on the chromatin regions losing accessibility identifies TWIST as a potential regulator specifying these regions. Using Twist2 conditional knock-out mouse model, we unearth a postnatal role of Twist2 TF as governing the postnatal maturation process resulting in switch-off of developmental pathways after birth. Together, our findings expose a comprehensive intracellular mechanism driving postnatal maturation in dermal fibroblasts with profound implications for regenerative medicine.
2022-05-17 | GSE181390 | GEO
Project description:Tissue stem cells preserve a certain level of potency to maintain intact tissue integrity after various injury. Postnatal dermal fibroblasts lose differentiation potential for regenerative healing that recreates normal tissue including functional hair follicles (HFs), however, their intrinsic cellular changes are not understood yet. Here, we uncover a postnatal maturation process in papillary fibroblasts (PFs) mediated by Twist2-driven chromatin and transcriptional remodeling. Within 4 days after birth, dermal PFs lost WNT transcription factors (TFs) and target gene expressions accompanied by loss of H3K27ac expression. Through single-cell transcriptomics, ATAC-seq and ChIP-seq profiling, we define a postnatal maturation trajectory of PFs, in addition to loss of regenerative trajectory, triggered by decrease of H3K27ac and chromatic accessibility. In vivo inhibition of histone deacetylation delays the postnatal chromatin remodeling and maintains developmental signaling and differentiation potential in PFs. TF motif analysis on the chromatin regions losing accessibility identifies TWIST as a potential regulator specifying these regions. Using Twist2 conditional knock-out mouse model, we unearth a postnatal role of Twist2 TF as governing the postnatal maturation process resulting in switch-off of developmental pathways after birth. Together, our findings expose a comprehensive intracellular mechanism driving postnatal maturation in dermal fibroblasts with profound implications for regenerative medicine.
2022-05-17 | GSE181394 | GEO
Project description:IntroductionOverall survival of early-stage breast cancer patients is similar for those who undergo breast-conserving therapy (BCT) and mastectomy; however, 10% to 15% of women undergoing BCT suffer ipsilateral breast tumor recurrence. The risk of recurrence may vary with breast cancer subtype. Understanding the gene expression of the cancer-adjacent tissue and the stromal response to specific tumor subtypes is important for developing clinical strategies to reduce recurrence risk.MethodsWe utilized two independent datasets to study gene expression data in cancer-adjacent tissue from invasive breast cancer patients. Complementary in vitro cocultures were used to study cell-cell communication between fibroblasts and specific breast cancer subtypes.ResultsOur results suggest that intrinsic tumor subtypes are reflected in histologically normal cancer-adjacent tissue. Gene expression of cancer-adjacent tissues shows that triple-negative (Claudin-low or basal-like) tumors exhibit increased expression of genes involved in inflammation and immune response. Although such changes could reflect distinct immune populations present in the microenvironment, altered immune response gene expression was also observed in cocultures in the absence of immune cell infiltrates, emphasizing that these inflammatory mediators are secreted by breast-specific cells. In addition, although triple-negative breast cancers are associated with upregulated immune response genes, luminal breast cancers are more commonly associated with estrogen-response pathways in adjacent tissues.ConclusionsSpecific characteristics of breast cancers are reflected in the surrounding histologically normal tissue. This commonality between tumor and cancer-adjacent tissue may underlie second primaries and local recurrences.ImpactBiomarkers derived from cancer-adjacent tissue may be helpful in defining personalized surgical strategies or in predicting recurrence risk.
| S-EPMC4437571 | biostudies-literature
Project description:Personality describes persistent human behavioral responses to broad classes of environmental stimuli. Investigating how personality traits are reflected in the brain's functional architecture is challenging, in part due to the difficulty of designing appropriate task probes. Resting-state functional connectivity (RSFC) can detect intrinsic activation patterns without relying on any specific task. Here we use RSFC to investigate the neural correlates of the five-factor personality domains. Based on seed regions placed within two cognitive and affective 'hubs' in the brain--the anterior cingulate and precuneus--each domain of personality predicted RSFC with a unique pattern of brain regions. These patterns corresponded with functional subdivisions responsible for cognitive and affective processing such as motivation, empathy and future-oriented thinking. Neuroticism and Extraversion, the two most widely studied of the five constructs, predicted connectivity between seed regions and the dorsomedial prefrontal cortex and lateral paralimbic regions, respectively. These areas are associated with emotional regulation, self-evaluation and reward, consistent with the trait qualities. Personality traits were mostly associated with functional connections that were inconsistently present across participants. This suggests that although a fundamental, core functional architecture is preserved across individuals, variable connections outside of that core encompass the inter-individual differences in personality that motivate diverse responses.
| S-EPMC3227579 | biostudies-literature
Project description:Genome-wide mRNA expression in brains of wild-type and eIF2B-R132H/R132H mutant mice (Geva et al., BRAIN 133 (8), 2010) profiled at postnatal (P) days 1, 18 and 21 to reflect the early proliferative stage prior to white matter establishment (P1) and the peak of oligodendrocye differentiation and myelin synthesis (P18 and P21). 3 biological replicates (whole brain without the cerebellum) from each wild-type and eIF2B-R132H/R132H mutant mice at 3 postnatal (P) days 1, 18 and 21 were used for RNA extraction and hybridization on Affymetrix microarrays.
2011-11-14 | E-GEOD-32201 | biostudies-arrayexpress