Impact of Electrospun Piezoelectric Core–Shell PVDFhfp/PDMS Mesh on Tenogenic and Inflammatory Gene Expression in Human Adipose-Derived Stem Cells: Comparison of Static Cultivation with Uniaxial Cyclic Tensile Stretching

Specific microenvironments can trigger stem cell tenogenic differentiation, such as specific substrates or dynamic cell cultivation. Electrospun meshes composed by core–shell fibers (random or aligned; PDMS core; piezoelectric PVDFhfp shell) were fabricated by coaxial electrospinning. Elastic modulus and residual strain were assessed. Human ASCs were seeded on such scaffolds either under static conditions for 1 week or with subsequent 10% dynamic stretching for 10,800 cycles (1 Hz, 3 h), assessing load elongation curves in a Bose® bioreactor system. Gene expression for tenogenic expression, extracellular matrix, remodeling, pro-fibrotic and inflammatory marker genes were assessed (PCR). For cell-seeded meshes, the E modulus increased from 14 ± 3.8 MPa to 31 ± 17 MPa within 3 h, which was not observed for cell-free meshes. Random fibers resulted in higher tenogenic commitment than aligned fibers. Dynamic cultivation significantly enhanced pro-inflammatory markers. Compared to ASCs in culture flasks, ASCs on random meshes under static cultivation showed a significant upregulation of Mohawk, Tenascin-C and Tenomodulin. The tenogenic commitment expressed by human ASCs in contact with random PVDFhfp/PDMS paves the way for using this novel highly elastic material as an implant to be wrapped around a lacerated tendon, envisioned as a functional anti-adhesion membrane.

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Multi-view feature selection for identifying gene markers: a diversified biological data driven approach

BMC Bioinformatics ◽

10.1186/s12859-020-03810-0 ◽

2020 ◽

Vol 21 (S18) ◽

Author(s):

Sudipta Acharya ◽

Laizhong Cui ◽

Yi Pan

Keyword(s):

Gene Expression ◽

Feature Selection ◽

Gene Selection ◽

Marker Gene ◽

Biological Data ◽

Protein Interaction Data ◽

Marker Genes ◽

Data Sets ◽

Gene Markers ◽

Multi Objective

Abstract Background In recent years, to investigate challenging bioinformatics problems, the utilization of multiple genomic and proteomic sources has become immensely popular among researchers. One such issue is feature or gene selection and identifying relevant and non-redundant marker genes from high dimensional gene expression data sets. In that context, designing an efficient feature selection algorithm exploiting knowledge from multiple potential biological resources may be an effective way to understand the spectrum of cancer or other diseases with applications in specific epidemiology for a particular population. Results In the current article, we design the feature selection and marker gene detection as a multi-view multi-objective clustering problem. Regarding that, we propose an Unsupervised Multi-View Multi-Objective clustering-based gene selection approach called UMVMO-select. Three important resources of biological data (gene ontology, protein interaction data, protein sequence) along with gene expression values are collectively utilized to design two different views. UMVMO-select aims to reduce gene space without/minimally compromising the sample classification efficiency and determines relevant and non-redundant gene markers from three cancer gene expression benchmark data sets. Conclusion A thorough comparative analysis has been performed with five clustering and nine existing feature selection methods with respect to several internal and external validity metrics. Obtained results reveal the supremacy of the proposed method. Reported results are also validated through a proper biological significance test and heatmap plotting.

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CdSe/ZnS Core-Shell-Type Quantum Dot Nanoparticles Disrupt the Cellular Homeostasis in Cellular Blood–Brain Barrier Models

International Journal of Molecular Sciences ◽

10.3390/ijms22031068 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1068

Author(s):

Katarzyna Dominika Kania ◽

Waldemar Wagner ◽

Łukasz Pułaski

Keyword(s):

Gene Expression ◽

Quantum Dot ◽

Blood Brain Barrier ◽

Protein Gene ◽

Brain Barrier ◽

Core Shell ◽

Cellular Homeostasis ◽

Blood Brain ◽

Shell Type ◽

The Impact

Two immortalized brain microvascular endothelial cell lines (hCMEC/D3 and RBE4, of human and rat origin, respectively) were applied as an in vitro model of cellular elements of the blood–brain barrier in a nanotoxicological study. We evaluated the impact of CdSe/ZnS core-shell-type quantum dot nanoparticles on cellular homeostasis, using gold nanoparticles as a largely bioorthogonal control. While the investigated nanoparticles had surprisingly negligible acute cytotoxicity in the evaluated models, a multi-faceted study of barrier-related phenotypes and cell condition revealed a complex pattern of homeostasis disruption. Interestingly, some features of the paracellular barrier phenotype (transendothelial electrical resistance, tight junction protein gene expression) were improved by exposure to nanoparticles in a potential hormetic mechanism. However, mitochondrial potential and antioxidant defences largely collapsed under these conditions, paralleled by a strong pro-apoptotic shift in a significant proportion of cells (evidenced by apoptotic protein gene expression, chromosomal DNA fragmentation, and membrane phosphatidylserine exposure). Taken together, our results suggest a reactive oxygen species-mediated cellular mechanism of blood–brain barrier damage by quantum dots, which may be toxicologically significant in the face of increasing human exposure to this type of nanoparticles, both intended (in medical applications) and more often unintended (from consumer goods-derived environmental pollution).

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Elevation of gene expression of Btg2, Gadd 153, and antioxidant markers in RONS-induced PC12 cells

Beni-Suef University Journal of Basic and Applied Sciences ◽

10.1186/s43088-020-00080-w ◽

2020 ◽

Vol 9 (1) ◽

Author(s):

Aravind P ◽

Sarojini R. Bulbule ◽

Hemalatha N ◽

Anushree G ◽

Babu R.L ◽

...

Keyword(s):

Gene Expression ◽

Endoplasmic Reticulum ◽

Protein Expression ◽

Pc12 Cells ◽

Expression Pattern ◽

High Glucose ◽

Nitrosative Stress ◽

Gene Expression Pattern ◽

Marker Genes ◽

Differential Stress

Abstract Background Free radicals generated in the biological system bring about modifications in biological molecules causing damage to their structure and function. Identifying the damage caused by ROS and RNS is important to predict the pathway of apoptosis due to stress in PC12 cells. The first defense mechanisms against them are antioxidants which act in various pathways through important cellular organelles like the mitochondria and endoplasmic reticulum. Specific biomarkers like Gadd153 which is a marker for endoplasmic reticulum stress, Nrf2 which responds to the redox changes and translocates the antioxidant response elements, and Btg2 which is an antioxidant regulator have not been addressed in different stress conditions previously in PC12 cells. Therefore, the study was conducted to analyze the gene expression pattern (SOD, Catalase, Btg2, Gadd153, and Nrf2) and the protein expression pattern (iNOS and MnSOD) of the antioxidant stress markers in differential stress-induced PC12 cells. Peroxynitrite (1 μM), rotenone (1 μM), H2O2(100 mM), and high glucose (33 mM) were used to induce oxidative and nitrosative stress in PC12 cells. Results The results obtained suggested that rotenone-induced PC12 cells showed a significant increase in the expression of catalase, Btg2, and Gadd153 compared to the control. Peroxynitrite-induced PC12 cells showed higher expression of Btg2 compared to the control. H2O2 and high glucose showed lesser expression compared to the control in all stress marker genes. In contrast, the Nrf2 gene expression is downregulated in all the stress-induced PC12 cells compared to the control. Further, MnSOD and iNOS protein expression studies suggest that PC12 cells exhibit a selective downregulation. Lower protein expression of MnSOD and iNOS may be resulted due to the mitochondrial dysfunction in peroxynitrite-, high glucose-, and H2O2-treated cells, whereas rotenone-induced cells showed lower expression, which could be the result of a dysfunction of the endoplasmic reticulum. Conclusion Different stress inducers like rotenone, peroxynitrite, H2O2, and high glucose increase the NO and ROS. Btg2 and Gadd153 genes were upregulated in the stress-induced cells, whereas the Nrf2 was significantly downregulated in differential stress-induced PC12 cells. Further, antioxidant marker genes were differentially expressed with different stress inducers.

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Connectivity Map-based discovery of parbendazole reveals targetable human osteogenic pathway

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1501597112 ◽

2015 ◽

Vol 112 (41) ◽

pp. 12711-12716 ◽

Cited By ~ 41

Author(s):

Andrea M. Brum ◽

Jeroen van de Peppel ◽

Cindy S. van der Leije ◽

Marijke Schreuders-Koedam ◽

Marco Eijken ◽

...

Keyword(s):

Gene Expression ◽

Alkaline Phosphatase ◽

Osteoblast Differentiation ◽

Target Genes ◽

Focal Adhesions ◽

Bone Fragility ◽

Bone Morphogenetic Protein 2 ◽

Marker Genes ◽

Connectivity Map ◽

Morphogenetic Protein

Osteoporosis is a common skeletal disorder characterized by low bone mass leading to increased bone fragility and fracture susceptibility. In this study, we have identified pathways that stimulate differentiation of bone forming osteoblasts from human mesenchymal stromal cells (hMSCs). Gene expression profiling was performed in hMSCs differentiated toward osteoblasts (at 6 h). Significantly regulated genes were analyzed in silico, and the Connectivity Map (CMap) was used to identify candidate bone stimulatory compounds. The signature of parbendazole matches the expression changes observed for osteogenic hMSCs. Parbendazole stimulates osteoblast differentiation as indicated by increased alkaline phosphatase activity, mineralization, and up-regulation of bone marker genes (alkaline phosphatase/ALPL, osteopontin/SPP1, and bone sialoprotein II/IBSP) in a subset of the hMSC population resistant to the apoptotic effects of parbendazole. These osteogenic effects are independent of glucocorticoids because parbendazole does not up-regulate glucocorticoid receptor (GR) target genes and is not inhibited by the GR antagonist mifepristone. Parbendazole causes profound cytoskeletal changes including degradation of microtubules and increased focal adhesions. Stabilization of microtubules by pretreatment with Taxol inhibits osteoblast differentiation. Parbendazole up-regulates bone morphogenetic protein 2 (BMP-2) gene expression and activity. Cotreatment with the BMP-2 antagonist DMH1 limits, but does not block, parbendazole-induced mineralization. Using the CMap we have identified a previously unidentified lineage-specific, bone anabolic compound, parbendazole, which induces osteogenic differentiation through a combination of cytoskeletal changes and increased BMP-2 activity.

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The influence of apple- and red-wine pomace rich diet on mRNA expression of inflammatory and apoptotic markers in different piglet organs

Animal Science ◽

10.1017/asc200699 ◽

2006 ◽

Vol 82 (6) ◽

pp. 877-887 ◽

Cited By ~ 4

Author(s):

J. Sehm ◽

H. Lindermayer ◽

H. H. D. Meyer ◽

M. W. Pfaffl

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Mrna Expression ◽

Caspase 3 ◽

Red Wine ◽

Marker Genes ◽

Apoptotic Marker ◽

Mrna Gene ◽

Turn Over ◽

Mrna Gene Expression

Flavan-3-ols are a class of flavonoids that are widely distributed in fruits and beverages including red wine and apples. Consumption of flavanoid-rich food has been shown to exhibit anti-microbial, anti-oxidative, anti-inflammatory, and immune-modulating effects. To test the nutritional effects of flavanols on mRNA gene-expression of inflammatory and apoptotic marker genes, piglets were given two flavanoids-rich feeding regimens: a low flavanoid standard diet (SD) was compared with diets enriched with 3·5% apple pomace (APD) or 3·5% red-wine pomace (RWPD). The influence on mRNA expression levels was investigated in different immunological active tissues and in the gastro-intestinal tract (GIT). The investigation took place from 1 week prior weaning to 19 days post weaning in 78 piglets. The expression of expressed marker genes was determinate by one-step quantitative real-time (qRT-PCR): TNFα, NFκB as pro-inflammatory; IL10, as anti-inflammatory; caspase 3 as apoptosis; cyclin D1 as cell cycle marker; and nucleosome component histon H3 as reference gene.The feeding regimens result in tissue individual regulation of mRNA gene expression in all investigated organs. It was discovered that there were significant differences between the applied diets and significant changes during feeding time curse. Both pomace treatments caused a significant up-regulation of all investigated genes in liver. The effect on mesenterial lymph nodes and spleen was not prominent. In the GIT, the treatment groups showed a inhibitory effects on gene expression mainly in stomach and jejunum (NFκB, cyclin D1 and caspase 3). In colon the trend of caspase 3 was positive with the greatest change in the RWPD group.In jejunum and stomach the cell cycle turn over was reduced, whereas in liver the cell turn over was highly accelerate. The influence on inflammatory marker gene expression is mainly relevant in stomach. It is presume that both flavanoid rich feeding regimens have the potential to modulate the mRNA expressions of inflammatory, proliferation and apoptotic marker genes in the GIT and piglet organs.

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Abstract 74: The Nox4 Inhibitor GKT137831, Prevents Aldosterone Production by Adipocytes and Protects Against Adipose Tissue Inflammation and Fibrosis in Obese Mice

Hypertension ◽

10.1161/hyp.62.suppl_1.a74 ◽

2013 ◽

Vol 62 (suppl_1) ◽

Author(s):

Sarah Even ◽

Aurelie Nguyen Dinh Cat ◽

Francisco J Rios ◽

Antunes T Tayze ◽

Ying He ◽

...

Keyword(s):

Gene Expression ◽

Adipose Tissue ◽

Culture Media ◽

Inflammatory Marker ◽

High Dose ◽

Obese Mice ◽

Cardiovascular Damage ◽

Aldosterone Production ◽

Inflammatory Phenotype ◽

Sirius Red

Aldosterone (aldo) plays an important role in obesity-associated cardiovascular risk. We demonstrated that aldo is produced by adipocytes, an effect associated with increased generation of reactive oxygen species (ROS). These processes are exaggerated in obesity. The relationship between adipocyte aldosterone and ROS is unclear. We postulated that Nox4-derived ROS is important for aldo production in adipocytes and leads to a pro-inflammatory phenotype in obesity. Studies were performed in db/m (lean) and db/db (obese) mice, treated with low (20mg/kg/day) or high dose (60mg/kg/day) GKT137831 (GKT, Nox4 inhibitor, 16 weeks). Epididymal (EVAT) and perivascular (PVAT) fat were collected. Plasma and adipocyte aldo were measured by ELISA. Adipose tissue fibrosis was evaluated by picro Sirius red staining and inflammatory mediators by immunostudies. Body weight was increased in db/db mice (61.8g vs control 33.5g), with no effect of GKT. Epididymal adiposity was increased in db/db mice (0.098g vs. 0.067g, p<0.05). Plasma aldo levels in db/db (pg/mL: 518 vs. 272g) and aldo levels in culture media from db/db adipocytes were increased (pg/mL/μg RNA: 1964 vs. 388), p<0.05. All effects decreased by high dose GKT. In PVAT, CYP11B2 gene expression was increased in db/db (2.6±0.8 vs control 1.1±0.1, p<0.05), an effect blocked by Nox4 inhibition. Gene expression of adipocyte differentiation marker, AP2, was increased (3.5±1.1 vs control 1.4±0.4) while anti-inflammatory marker adiponectin was decreased (0.7±0.1 vs control 1.3±0.2, p<0.05)) in obese mice. GKT decreased AP2 levels. Adipocyte-derived TNFα was increased in db/db (4.9±1.8 vs control 1.6±0.6, p<0.05), an effect blocked by GKT. Pro-collagen I, marker of fibrosis, was increased in db/db mice (132±11 vs control 87±4, p<0.05). Sirius red staining was exaggerated in EVAT from db/db mice, and decreased by Nox4 inhibition. In conclusion, Nox4 plays a role in regulating adipocyte-derived aldosterone and promotes a pro-inflammatory and profibrotic adipose phenotype in obese db/db mice. These findings suggest that adipocyte Nox4 links hyperaldosteronism and inflammation/fibrosis in adiposity and as such may be a putative therapeutic target for obesity-associated cardiovascular damage.

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Protein phosphatase 2A potentiates activity of promoters containing AP-1-binding elements

Molecular and Cellular Biology ◽

10.1128/mcb.13.4.2104-2112.1993 ◽

1993 ◽

Vol 13 (4) ◽

pp. 2104-2112

Author(s):

A S Alberts ◽

T Deng ◽

A Lin ◽

J L Meinkoth ◽

A Schönthal ◽

...

Keyword(s):

Gene Expression ◽

Reporter Gene ◽

Protein Phosphatase ◽

Signal Transduction Pathways ◽

Marker Genes ◽

Direct Mechanism ◽

Phosphatase 2A ◽

Beta Galactosidase ◽

Regulatory Sites

The involvement of serine/threonine protein phosphatases in signaling pathways which modulate the activity of the transcription factor AP-1 was examined. Purified protein phosphatase types 1 (PP1) and 2A (PP2A) were microinjected into cell lines containing stably transfected lacZ marker genes under the control of an enhancer recognized by AP-1. Microinjection of PP2A potentiated serum-stimulated beta-galactosidase expression from the AP-1-regulated promoter. Similarly, transient expression of the PP2A catalytic subunit with c-Jun resulted in a synergistic transactivation of an AP-1-regulated reporter gene. PP2A, but not PP1, potentiated serum-induced c-Jun expression, which has been previously shown to be autoregulated by AP-1 itself. Consistent with these results, PP2A dephosphorylated c-Jun on negative regulatory sites in vitro, suggesting one possible direct mechanism for the effects of PP2A on AP-1 activity. Microinjection of PP2A had no effect on cyclic AMP (cAMP)-induced expression of a reporter gene containing a cAMP-regulated promoter, while PP1 injection abolished cAMP-induced gene expression. Taken together, these results suggest a specific role for PP2A in signal transduction pathways that regulate AP-1 activity and c-Jun expression.

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Shear stress induces hepatocyte PAI-1 gene expression through cooperative Sp1/Ets-1 activation of transcription

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.00467.2005 ◽

2006 ◽

Vol 291 (1) ◽

pp. G26-G34 ◽

Cited By ~ 30

Author(s):

Hideki Nakatsuka ◽

Takaaki Sokabe ◽

Kimiko Yamamoto ◽

Yoshinobu Sato ◽

Katsuyoshi Hatakeyama ◽

...

Keyword(s):

Gene Expression ◽

Shear Stress ◽

Consensus Sequence ◽

Early Gene ◽

Immediate Early ◽

Mrna Levels ◽

Consensus Sequences ◽

Static Conditions ◽

Stress Dependent ◽

Pai 1

Partial hepatectomy causes hemodynamic changes that increase portal blood flow in the remaining lobe, where the expression of immediate-early genes, including plasminogen activator inhibitor-1 (PAI-1), is induced. We hypothesized that a hyperdynamic circulatory state occurring in the remaining lobe induces immediate-early gene expression. In this study, we investigated whether the mechanical force generated by flowing blood, shear stress, induces PAI-1 expression in hepatocytes. When cultured rat hepatocytes were exposed to flow, PAI-1 mRNA levels began to increase within 3 h, peaked at levels significantly higher than the static control levels, and then gradually decreased. The flow-induced PAI-1 expression was shear stress dependent rather than shear rate dependent and accompanied by increased hepatocyte production of PAI-1 protein. Shear stress increased PAI-1 transcription but did not affect PAI-1 mRNA stability. Functional analysis of the 2.1-kb PAI-1 5′-promoter indicated that a 278-bp segment containing transcription factor Sp1 and Ets-1 consensus sequences was critical to the shear stress-dependent increase of PAI-1 transcription. Mutations of both the Sp1 and Ets-1 consensus sequences, but not of either one alone, markedly prevented basal PAI-1 transcription and abolished the response of the PAI-1 promoter to shear stress. EMSA and chromatin immunoprecipitation assays showed binding of Sp1 and Ets-1 to each consensus sequence under static conditions, which increased in response to shear stress. In conclusion, hepatocyte PAI-1 expression is flow sensitive and transcriptionally regulated by shear stress via cooperative interactions between Sp1 and Ets-1.

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Gene Expression in RET/PTC3 and E7 Transgenic Mouse Thyroids: RET/PTC3 But Not E7 Tumors Are Partial and Transient Models of Human Papillary Thyroid Cancers

Endocrinology ◽

10.1210/en.2008-0531 ◽

2008 ◽

Vol 149 (10) ◽

pp. 5107-5117 ◽

Cited By ~ 14

Author(s):

Agnès Burniat ◽

Ling Jin ◽

Vincent Detours ◽

Natacha Driessens ◽

Jean-Christophe Goffard ◽

...

Keyword(s):

Gene Expression ◽

Fusion Gene ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Human Thyroid ◽

Matrix Remodeling ◽

Biological Processes ◽

Papillary Thyroid ◽

Thyroid Cancers ◽

Transient Models

We studied gene expression profiles in two mouse models of human thyroid carcinoma: the Tg-RET/PTC3 (RP3) and Tg-E7 mice. RP3 fusion gene is the most frequent mutation found in the first wave post-Chernobyl papillary thyroid cancers (PTCs). E7 is an oncoprotein derived from the human papillomavirus 16 responsible for most cervical carcinoma in women. Both transgenic mice develop thyroid hyperplasia followed by solid differentiated carcinoma in older animals. To understand the different steps leading to carcinoma, we analyzed thyroid gene expression in both strains at different ages by microarray technology. Important biological processes were differentially regulated in the two tumor types. In E7 thyroids, cell cycle was the most up-regulated process, an observation consistent with the huge size of these tumors. In RP3 thyroids, contrary to E7 tumors, several human PTC characteristics were observed: overexpression of many immune-related genes, regulation of human PTC markers, up-regulation of EGF-like growth factors and significant regulation of angiogenesis and extracellular matrix remodeling-related genes. However, similarities were incomplete; they did not concern the overall gene expression and were not conserved in old animals. Therefore, RP3 tumors are partial and transient models of human PTC. They constitute a good model, especially in young animals, to study the respective role of the biological processes shared with human PTC and will allow testing drugs targeting these validated variables.

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Analysis of brain atrophy and local gene expression in genetic frontotemporal dementia

Brain Communications ◽

10.1093/braincomms/fcaa122 ◽

2020 ◽

Vol 2 (2) ◽

Cited By ~ 1

Author(s):

Andre Altmann ◽

David M Cash ◽

Martina Bocchetta ◽

Carolin Heller ◽

Regina Reynolds ◽

...

Keyword(s):

Gene Expression ◽

Frontotemporal Dementia ◽

Cell Function ◽

Neurodegenerative Disorder ◽

Positive Association ◽

Negative Association ◽

Marker Genes ◽

Gene Set ◽

Genetic Groups ◽

Cortical Regions

Abstract Frontotemporal dementia is a heterogeneous neurodegenerative disorder characterized by neuronal loss in the frontal and temporal lobes. Despite progress in understanding which genes are associated with the aetiology of frontotemporal dementia, the biological basis of how mutations in these genes lead to cell loss in specific cortical regions remains unclear. In this work, we combined gene expression data for 16 772 genes from the Allen Institute for Brain Science atlas with brain maps of grey matter atrophy in symptomatic C9orf72, GRN and MAPT mutation carriers obtained from the Genetic Frontotemporal dementia Initiative study. No significant association was seen between C9orf72, GRN and MAPT expression and the atrophy patterns in the respective genetic groups. After adjusting for spatial autocorrelation, between 1000 and 5000 genes showed a negative or positive association with the atrophy pattern within each individual genetic group, with the most significantly associated genes being TREM2, SSBP3 and GPR158 (negative association in C9Orf72, GRN and MAPT respectively) and RELN, MXRA8 and LPA (positive association in C9Orf72, GRN and MAPT respectively). An overrepresentation analysis identified a negative association with genes involved in mitochondrial function, and a positive association with genes involved in vascular and glial cell function in each of the genetic groups. A set of 423 and 700 genes showed significant positive and negative association, respectively, with atrophy patterns in all three maps. The gene set with increased expression in spared cortical regions was enriched for neuronal and microglial genes, while the gene set with increased expression in atrophied regions was enriched for astrocyte and endothelial cell genes. Our analysis suggests that these cell types may play a more active role in the onset of neurodegeneration in frontotemporal dementia than previously assumed, and in the case of the positively associated cell marker genes, potentially through emergence of neurotoxic astrocytes and alteration in the blood–brain barrier, respectively.

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