RNA-sequencing of cells derived from dermis and postmortem dura mater from the same subject
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA741512 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14916215_1.fastq.gz | Fastqsanger.gz | |||
| SRR14916215_2.fastq.gz | Fastqsanger.gz | |||
| SRR14916216_1.fastq.gz | Fastqsanger.gz | |||
| SRR14916216_2.fastq.gz | Fastqsanger.gz | |||
| SRR14916217_1.fastq.gz | Fastqsanger.gz |
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Project description:Patient-derived cells hold great promise for precision medicine approaches in human health. Fibroblast cells have been a major source of human cells for reprogramming and differentiating into specific cell types for disease modeling. Such cells can be isolated at various stages during life (presymptomatic, symptomatic, and advanced disease) and thus can potentially be used to model different phases of disease progression. In certain circumstances, however, tissues are not collected during life and only postmortem tissues are the only available source of fibroblasts. Fibroblasts cultured from postmortem human dura mater of individuals with neurodegenerative diseases have been suggested as a primary source of cells for in vitro modeling of neurodegenerative diseases. Although fibroblast-like cells from human and mouse dura mater have been previously described, their utility for reprogramming and direct differentiation protocols requires further characterization. In this study, cells derived from dermal biopsies of living subjects were compared to cells derived from postmortem dura mater. In two instances, we have isolated and compared dermal and dural cell lines from the same subject. Notably, such striking differences were observed between cells of dermal and dural origin that their fibroblast nature was brought into question. Compared to dermal fibroblasts, postmortem dura mater-derived cells demonstrated different morphology, slower growth rates, and a higher rate of karyotype abnormality. Dura mater-derived cells also failed to express fibroblast protein markers. When dermal fibroblasts and dural-derived cells from the same subject were compared, they exhibited significant differences in gene expression profiles. Ultimately, dura mater-derived cells were found to originate from a mixed mural lineage consisting of smooth muscle cells and pericytes. Our study argues for rigorous karyotyping of all postmortem derived cell lines and highlights significant limitations of postmortem human dura mater-derived cells for modeling normal biology or disease-associated pathobiology.
2021-12-01 | GSE178933 | GEO
Project description:BACKGROUND: Although reossification of large calvarial defects is possible in children, adults lack this tissue engineering capacity. In this study, the authors compared the differences in gene expression between juvenile and adult dura mater using a mouse cDNA microarray with 42,000 unique elements. METHODS: Non-suture-associated parietal bone was harvested from 6-day-old and 60-day-old mice. The dura mater was carefully dissected from the calvarial disk and snap-frozen. RNA was extracted from pooled dura mater for microarray analysis. The 25 most differentially expressed genes were listed, as were selected bone-related genes. In addition, quantitative real-time reverse-transcriptase polymerase chain reaction confirmation of selected genes-BMP-2, BMP-4, and BMP-7; and osteopontin (OP), osteocalcin (OC), and FGFR-1-was performed. : Juvenile dura mater expressed significantly greater amounts of BMP-2 and OP. Minimal difference in OC expression was observed between juvenile and adult dura mater. Extracellular matrix proteins (Col3a1, 5a1, 6a1, and fibronectin 1), osteoblast differentiation markers (Runx2/Cbfa1, Itm2a, and FGFR-1), and the growth factor Ptn were among other genes with greater expression in juvenile dura mater. Markers of osteoclasts (Acp5, MMP9, Ctsk) and the multiple candidate gene Ntrk2 were also expressed at higher levels in the juvenile dura mater. CONCLUSIONS: These findings suggest a more differentiated osteoprogenitor population to exist along with a greater presence of osteoclasts in the juvenile dura mater relative to adults. In addition to establishing a baseline difference in gene expression between juvenile and adult dura mater, new genes potentially critical to the regenerative potential of juvenile calvaria were identified. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
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Project description:To further elucidate fundamental molecular differences between dura mater and brain ECs, we performed RNA-sequencing of primary dura mater or brain ECs isolated from adult mice
2020-05-18 | GSE138561 | GEO
Project description:BACKGROUND: Although reossification of large calvarial defects is possible in children, adults lack this tissue engineering capacity. In this study, the authors compared the differences in gene expression between juvenile and adult dura mater using a mouse cDNA microarray with 42,000 unique elements. METHODS: Non-suture-associated parietal bone was harvested from 6-day-old and 60-day-old mice. The dura mater was carefully dissected from the calvarial disk and snap-frozen. RNA was extracted from pooled dura mater for microarray analysis. The 25 most differentially expressed genes were listed, as were selected bone-related genes. In addition, quantitative real-time reverse-transcriptase polymerase chain reaction confirmation of selected genes-BMP-2, BMP-4, and BMP-7; and osteopontin (OP), osteocalcin (OC), and FGFR-1-was performed. RESULTS: Juvenile dura mater expressed significantly greater amounts of BMP-2 and OP. Minimal difference in OC expression was observed between juvenile and adult dura mater. Extracellular matrix proteins (Col3a1, 5a1, 6a1, and fibronectin 1), osteoblast differentiation markers (Runx2/Cbfa1, Itm2a, and FGFR-1), and the growth factor Ptn were among other genes with greater expression in juvenile dura mater. Markers of osteoclasts (Acp5, MMP9, Ctsk) and the multiple candidate gene Ntrk2 were also expressed at higher levels in the juvenile dura mater. CONCLUSIONS: These findings suggest a more differentiated osteoprogenitor population to exist along with a greater presence of osteoclasts in the juvenile dura mater relative to adults. In addition to establishing a baseline difference in gene expression between juvenile and adult dura mater, new genes potentially critical to the regenerative potential of juvenile calvaria were identified.
2006-11-06 | E-SMDB-3845 | biostudies-arrayexpress
Project description:To further elucidate molecular differences in immune cells and identify potential sources of Vegfa in response to photothrombotic injury, we performed single-cell RNA-sequencing of CD45+ cells isolated from the mouse dura mater or brain after photothrombotic injury.
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Project description:Purpose: Studies on gene expression changes in joint and heart tissues of laboratory mice have provided insights into the localized host responses to Borrelia burgdorferi colonization; however, gene expression changes in the CNS of mice during B. burgdorferi infection remain unclear. Therefore, we took an unbiased approach to examine potential changes in the dura mater as well as the brain cortex and hippocampus at day 7 post-infection using RNA sequencing (RNA-seq). Methods: Dura mater, brain cortex, and hippocampal mRNA profiles of 6-8 week old C3H/HeN mice infected with B. burgdorferi strain 297 or mock infected (n=4 per group) were generated by paired-end sequencing using the Illumina HiSeq 4000. The sequence reads were aligned using STAR aligner followed by DESeq2 for differential expression analysis. qRT–PCR validation was performed using SYBR Green assays. Results: In the dura mater, the presence of B. burgdorferi is associated with upregulation of genes consistent with TLR/NF-κB signalling and associated inflammatory cytokines and chemokines in addition to upregulation of interferon stimulated genes. In contrast, the brain parenchyma exhibits mainly an increase in interferon stimulated genes in response to B. burgdorferi infection without an associated cytokine response. Conclusion: Overall, the findings reported in this study are significant, as the lack of a tractable animal model has hindered our understanding of host-pathogen interactions in the CNS. Our results describe a model system that will allow for future studies evaluating the bacterial, host, and environmental factors that can contribute to the severity of CNS involvement during B. burgdorferi infection, as well as evaluating potential novel prophylactic and therapeutic interventions for this important disease.
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Project description:The arachnoid barrier delineates the border between the central nervous system and dura mater. Although the arachnoid barrier creates a partition, communication between the central nervous system and the dura mater is crucial for waste clearance and immune surveillance. How the arachnoid barrier balances separation and communication is poorly understood. Leveraging transcriptomic data, we developed novel transgenic mice to examine specific anatomical structures that serve as routes across the arachnoid barrier. Bridging veins create discontinuities where they cross the arachnoid barrier, forming structures that we termed arachnoid cuff exit (ACE) points. The openings that ACE points create allow the exchange of fluids and molecules between the subarachnoid space and the dura, enabling the drainage of cerebrospinal fluid and limited entry of molecules from the dura to the subarachnoid space. In healthy human volunteers, MRI tracers transit along bridging veins in a similar fashion to access the subarachnoid space. Interestingly, in neuroinflammatory conditions such as experimental autoimmune encephalomyelitis, ACE points also allow cellular trafficking, representing a previously unknown route for immune cells to directly enter the subarachnoid space from the dura mater. Collectively, our results indicate that ACE points are a critical part of the anatomy of neuroimmune communication in both mice and humans that links the central nervous system with the dura and its immunological diversity and waste clearance systems.
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Project description:The arachnoid barrier delineates the border between the central nervous system and dura mater. Although the arachnoid barrier creates a partition, communication between the central nervous system and the dura mater is crucial for waste clearance and immune surveillance. How the arachnoid barrier balances separation and communication is poorly understood. Leveraging transcriptomic data, we developed novel transgenic mice to examine specific anatomical structures that serve as routes across the arachnoid barrier. Bridging veins create discontinuities where they cross the arachnoid barrier, forming structures that we termed arachnoid cuff exit (ACE) points. The openings that ACE points create allow the exchange of fluids and molecules between the subarachnoid space and the dura, enabling the drainage of cerebrospinal fluid and limited entry of molecules from the dura to the subarachnoid space. In healthy human volunteers, MRI tracers transit along bridging veins in a similar fashion to access the subarachnoid space. Interestingly, in neuroinflammatory conditions such as experimental autoimmune encephalomyelitis, ACE points also allow cellular trafficking, representing a previously unknown route for immune cells to directly enter the subarachnoid space from the dura mater. Collectively, our results indicate that ACE points are a critical part of the anatomy of neuroimmune communication in both mice and humans that links the central nervous system with the dura and its immunological diversity and waste clearance systems.
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Project description:The arachnoid barrier delineates the border between the central nervous system and dura mater. Although the arachnoid barrier creates a partition, communication between the central nervous system and the dura mater is crucial for waste clearance and immune surveillance. How the arachnoid barrier balances separation and communication is poorly understood. Leveraging transcriptomic data, we developed novel transgenic mice to examine specific anatomical structures that serve as routes across the arachnoid barrier. Bridging veins create discontinuities where they cross the arachnoid barrier, forming structures that we termed arachnoid cuff exit (ACE) points. The openings that ACE points create allow the exchange of fluids and molecules between the subarachnoid space and the dura, enabling the drainage of cerebrospinal fluid and limited entry of molecules from the dura to the subarachnoid space. In healthy human volunteers, MRI tracers transit along bridging veins in a similar fashion to access the subarachnoid space. Interestingly, in neuroinflammatory conditions such as experimental autoimmune encephalomyelitis, ACE points also allow cellular trafficking, representing a previously unknown route for immune cells to directly enter the subarachnoid space from the dura mater. Collectively, our results indicate that ACE points are a critical part of the anatomy of neuroimmune communication in both mice and humans that links the central nervous system with the dura and its immunological diversity and waste clearance systems.
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