Gene expression of human bone marrow-derived stem cells on liquid crystalline self-assembed hydroxyapatite nanorods for bone regeneration
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ABSTRACT:
PROVIDER: PRJNA867161 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20958311_1.fastq.gz | Fastqsanger.gz | |||
| SRR20958311_2.fastq.gz | Fastqsanger.gz | |||
| SRR20958312_1.fastq.gz | Fastqsanger.gz | |||
| SRR20958312_2.fastq.gz | Fastqsanger.gz | |||
| SRR20958313_1.fastq.gz | Fastqsanger.gz |
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Project description:Liquid crystal-like, low-dimensional and long-range ordered structures (LC) are found in human tissues including bones. The excellent mechanical and biological functions of natural bones entail the well-orchestrated nano-scale hydroxyapatite (HAp) crystals within collagen fibres matrix. However, the understanding of the self-assembling of HAp nanocrystals and formation of hierarchically ordered bone structure are still elusive. Our study aims to develop an in situ traceable anisotropic HAp nanorods doped with citrate and terbium (Cit/Tb-HAp NRs), investigate their self-assembling behaviour and illuminate their potential and pathway of guiding ordered osteogenesis at multi-scale in vitro.
2024-08-23 | GSE210696 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE30178: Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling (rat lungs) GSE30180: Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling (A549 cells dataset 1) GSE30200: Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling (A549 cells dataset 2) GSE30213: Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling (A549 cells dataset 3) GSE30214: Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling (A549 cells dataset 4) GSE30215: Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling (A549 cells dataset 5) Refer to individual Series
2012-06-29 | E-GEOD-30216 | biostudies-arrayexpress
Project description:The effect, if any, of age on the pulmonary toxicity induced by Min-U-Sil 5 crystalline silica exposure was investigated in rats. As part of the study, the changes in global gene expression profiles in the blood and lungs of the animals were determined. To conduct these studies, to determine if age influences the pulmonary response to crystalline silica exposure, two different age groups of healthy, male F344 rats were used. In this study the young age group of rats (6 months old at the time of exposure) was exposed to either air or crystalline silica (Min-U-Sil 5) (15 mg/m3, 6 hours/day, 5 days) by whole body inhalation. The young age group of rats simulates a group of workers who would be 18 to 20 years old. At two crystalline silica post-exposure time periods (1-day and 6-months) animals were euthanized and pulmonary inflammatory, cytotoxic, and oxidant responses were determined. Analysis of bronchoalveolar lavage parameters of toxicity such as oxidant generation and inflammation revealed significant changes in pulmonary toxicity in the crystalline silica exposed rats compared with the time-matched, air exposed control rats. The blood gene expression profiles showed only minimal changes, at both the time points, in the crystalline silica exposed rats compared with the controls. Specifically, there were a total of 5 genes significantly differentially expressed (fold change >1.5 and FDR p<0.05) in the one-day post-exposure group and no significantly differentially genes in the 6-month post-exposure group. However, the lung gene expression profiles showed substantial changes in the crystalline silica exposed animals at both one-day and 6-month post-exposure. Specifically, there were a total of 385 genes significantly differentially expressed (fold change >1.5 and FDR p<0.05) at the one-day post-exposure group and 317 genes significantly differentially expressed at the 6-month post-exposure. The data obtained from the present study demonstrated that crystalline silica inhalation exposure, under the conditions employed in the present study, resulted in significant changes in lung toxicity parameters and lung gene expression profile in the rats at both 1-day and 6-month post-exposure.
2024-12-01 | GSE247344 | GEO
Project description:The effect, if any, of age on the pulmonary toxicity induced by Min-U-Sil 5 crystalline silica exposure was investigated in rats. As part of the study, the changes in global gene expression profiles in the blood and lungs of the animals were determined. To conduct these studies, to determine if age influences the pulmonary response to crystalline silica exposure, two different age groups of healthy, male F344 rats were used. In this study the old age group of rats (12 months old at the time of exposure) was exposed to either air or crystalline silica (Min-U-Sil 5) (15 mg/m3, 6 hours/day, 5 days) by whole body inhalation. The old age group of rats simulates a group of workers who would be 45 to 50 years old. At two crystalline silica post-exposure time periods (1-day and 6-months) animals were euthanized and pulmonary inflammatory, cytotoxic, and oxidant responses were determined. Analysis of bronchoalveolar lavage parameters of toxicity such as oxidant generation and inflammation revealed significant changes in pulmonary toxicity in the crystalline silica exposed rats compared with the time-matched, air exposed control rats. The blood gene expression profiles showed only minimal changes, at both the time points, in the crystalline silica exposed rats compared with the controls. Specifically, no genes were significantly differentially expressed (fold change >1.5 and FDR p<0.05) in the one-day post-exposure group and only 6 genes were significantly differentially expressed in the 6-month post-exposure group. However, the lung gene expression profiles showed substantial changes in the crystalline silica exposed animals at both one-day and 6-month post-exposure. Specifically, there were a total of 325 genes significantly differentially expressed (fold change >1.5 and FDR p<0.05) at the one-day post-exposure group and 3348 genes significantly differentially expressed at the 6-month post-exposure. The data obtained from the present study demonstrated that crystalline silica inhalation exposure, under the conditions employed in the present study, resulted in significant changes in lung toxicity parameters and lung gene expression profile in the rats at both 1-day and 6-month post-exposure.
2024-12-01 | GSE250537 | GEO
Project description:Introduction: Bone healing is a well-orchestrated process involving various bone cells and signaling pathways, where disruptions can result in delayed or incomplete healing. MicroRNAs (miRNAs) are small non-coding RNAs capable of influencing various cellular processes, including bone remodeling. Due to their biological relevance and stable presence in biofluids, miRNAs may serve as candidates for diagnosis and prognosis of delayed bone healing. The aim of this study was to investigate changes in miRNAs circulating in the blood during the healing of rat calvaria defects as biomarkers of successful bone regeneration. Methods: Standardized calvaria defects were created in 36 Wistar rats with a trephine drill and treated with collagen hydroxyapatite (CHA) scaffolds. The treatment groups included CHA scaffolds only, CHA scaffolds containing a plasmid coding for bone morphogenetic protein 2 (BMP2) and miR-590-5p, CHA scaffolds containing mesenchymal stromal cell-derived extracellular vesicles, and empty defects as a control group. After 1, 4 and 8 weeks of healing, the animals were evaluated by microcomputed tomography (microCT), as well as subjected to histological analyses. Blood was sampled from the tail vein prior to surgeries and after 1, 4, and 8 weeks of healing. miRNAs circulating in the plasma were determined using next generation sequencing. Results: Variability of bone regeneration within the four groups was unexpectedly high and did not result in significant differences between the groups, as indicated by the microCT and histological analyses of the newly formed bone tissue. However, irrespective of the treatment group and regenerative activity, we identified miRNAs with distinct expression patterns of up- and downregulation at different time points. Furthermore, rats with high and low regenerative activity were characterized by distinct circulating miRNA profiles. miR-133-3p was identified as the top up-regulated miRNA and miR-375-3p was identified as the top down- regulated miRNA in animals exhibiting good regeneration over all time points evaluated. Conclusion: Our study indicates that regardless of the treatment group, success or lack of bone regeneration is associated with a distinct expression pattern of circulating microRNAs. While for some of these microRNAs functional association with skeletal regeneration has previously been reported, further research is needed to evaluate whether their levels in the blood can be used as predictive factors of successful bone regeneration. Keywords: gene-activated scaffold; osteogenesis; bone regeneration, biomarkers, circulating microRNAs
2025-03-27 | GSE279239 | GEO
Project description:Tissue macrophages derive from bone marrow monocytes, and recent studies using mice have revealed that they also derive from yolk sac precursors or fetal liver monocytes. However, embryo-derived macrophages are supposed to be more important to maintain tissue macrophage pool because they can self-renew. Here, we show that adult bone marrow-derived macrophages (MDM) also retain the ability of self-renewal. Where they were readily obtained by a long-term culture: mouse bone marrow cells were cultured with macrophage colony-stimulating factor (M-CSF). After several passages, most MDM died owing to their limited life span with survival and expansion of self-renewing macrophages resided in a small fraction. Self-renewing macrophages were not tumorigenic, but proliferate for a long period in almost unlimited numbers. Despite being distinct from MDM, they were phenotypically and functionally differentiated macrophages, and could differentiate into dendritic cells or osteoclasts. Moreover, Krüppel-like Factor 2 (KLF2) involved in self-renewal of embryonic stem cells, was markedly up-regulated by M-CSF-stimulation in self-renewing macrophages, which was accompanied with a gradual down-regulation of MafB, a suppressor of KLF2 expression. Importantly, knockdown of KLF2 as well as c-Myc caused cell cycle arrest, apoptosis, and diminished cell growth. Our culture method results suggest the presence of precursor(s) for self-renewing macrophages in adult bone marrow that can be used to describe discrepancy of adult- and embryo-derived macrophages. Microarray data from both monocyte-derived and bone marrow-derived mouse macrophages are used to detail the global gene expression profile underlying phenotype, function and self-renewal capacity in order to unravel difference/similarity in phenotype/function and mechanism/degree of self-renewal between the two distinct macrophages.
2019-12-27 | GSE142619 | GEO
Project description:Bone matrix exhibits exceptional mechanical properties due to its unique nanocomposite structure of type I collagen fibrils and hydroxyapatite (HAp) nanoparticles in hierarchical liquid crystalline (LC) order. However, the regeneration mechanism of this LC structure is elusive. This study investigates the role of the LC structure of HAp nanorods in guiding aligned mineralization and its underlying molecular mechanism. A unidirectionally oriented LC phase of HAp nanorods is developed through engineering-assisted self-assembling. This is used to study the growth direction of long-range aligned extracellular matrix (ECM) and calcium deposit formation during the osteogenic differentiation of human bone marrow-derived mesenchymal stem cells. It is found that 2 key regulatory genes, COL1A1 and COL4A6, lead to the formation of aligned ECM. Activation of the PI3K-Akt pathway enhances osteogenesis and promotes ordered calcium deposits. This study provides evidence for elucidating the mechanism of LC-induced ordered calcium deposition at hierarchical levels spanning from the molecular to macro-scale, as well as the switch from ordered to disordered mineralization. These findings illuminate bone regeneration, contribute to the development of biomimetic artificial bone with long-range ordered structures, and suggest a basis for therapeutic targeting of microstructure-affected bone disorders and the broader field of cell-ECM interactions.
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Project description:Flexible construction of permanently stored supramolecular chirality with stimulus-responsiveness remains a big challenge. Herein, we describe an efficient method to realize the transfer and storage of chirality in intrinsically achiral films of a side-chain polymeric liquid crystal system by combining chiral doping and cross-linking strategy. Even the helical structure was destroyed by UV light irradiation, the memorized chiral information in the covalent network enabled complete self-recovery of the original chiral superstructure. These results allowed the building of a novel chiroptical switch without any additional chiral source in multiple types of liquid crystal polymers, which may be one of the competitive candidates for use in stimulus-responsive chiro-optical devices.
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Project description:Previous studies have shown that smoking induces oxidative stress and inflammation, known factors that coincide with the development and progression of lung toxicity in response to crystalline silica exposure. Nevertheless, the precise role of tobacco smoke exposure on the lung response to tobacco smoke exposure and the underlying mechanisms remain largely elusive. Therefore, the objective of the present study was to determine the effect of smoking, if any, on silica-induced pulmonary toxicity and the underlying molecular mechanisms. Pulmonary toxicity and lung gene expression profiles were determined in rats exposed to air, crystalline silica, tobacco smoke, or crystalline silica plus tobacco smoke. Silica exposure resulted in significant pulmonary toxicity which was further exacerbated by tobacco smoke exposure in the rats. Significant differences in the gene expression profiles were detected in the lungs of the rats exposed to tobacco smoke, silica or a combination of both compared with the air exposed control rats.
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