RNA Sequencing of WT Aged Vehicle vs. HPBCD Infarcts
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA726821 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14385626_1.fastq.gz | Fastqsanger.gz | |||
| SRR14385626_2.fastq.gz | Fastqsanger.gz | |||
| SRR14385627_1.fastq.gz | Fastqsanger.gz | |||
| SRR14385627_2.fastq.gz | Fastqsanger.gz | |||
| SRR14385628_1.fastq.gz | Fastqsanger.gz |
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Project description:RNA Sequencing of WT Aged Vehicle vs. HPBCD
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Project description:We systematically characterized the transcriptomes of stroke infarcts in vehicle- and HPβCD-treated aged (18-month-old) mice by performing bulk RNA-Seq on infarcted brain tissue collected 7 weeks after distal middle cerebral artery occlusion + hypoxia (DH) stroke. The DE analysis revealed 991 upregulated genes and 1,876 downregulated genes. HPβCD treatment upregulated intracellular cholesterol transporters, lipoproteins, and lipoprotein receptors, such as Npc1, Npc2, Apoe, Trem2, Abca1, Vldlr, and Hdlbp, and downregulated Ffar1, Lrpb1, and Dgkb. These alterations in lipid metabolism suggest that HPβCD aids in the restoration of lipid homeostasis by 7 weeks after stroke. In addition, the DE analysis revealed a downregulation of genes involved in chemotaxis, including Cx3cr1, Cxcl5, and Ccr6, and innate and adaptive immune responses, including Mmd2, Mzb1, Btla, Jchain, and Igkv5-48. Correspondingly, there was an upregulation of anti-inflammatory genes, such as Tgfb1, Tgfb2, P2ry2, and Il18bp. Next, we performed genome-wide expression analysis of the RNA-Seq data using GSEA, which revealed significant enrichment of various biological processes in infarcts of HPβCD-treated aged mice, including (i) collagen formation, (ii) regulation of angiogenesis, (iii) lipid catabolic process, (iv) regulation of autophagy, and (v) regulation of apoptotic process. These results indicate that HPβCD treatment promotes lipid metabolism and angiogenesis and dampens chronic inflammation in infarcts of aged mice at 7 weeks after stroke.
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Project description:Prior to assessing the impact of repeated HPβCD administration on the peri-infarct region of the brain, we first compared the transcriptome of the peri-infarct region to the equivalent region of the contralateral hemisphere in aged (18-month-old) mice at 7 weeks after distal middle cerebral artery occlusion + hypoxia (DH) stroke. The peri-infarct region was characterized by 3,910 differentially expressed genes. Of these, 2,123 were upregulated, many of which were also upregulated in infarcts at 7 weeks after stroke. For instance, the infarct and peri-infarct regions were both defined by the upregulation of degradative enzymes, TLRs, and scavenger receptors. In addition, the upregulation of Lpl, Lrp2, Ch25h, Apoe, Trem2, and Abca1 signified a divergence from lipid homeostasis. These alterations in innate immunity coincided with corresponding perturbations in adaptive immunity. The upregulation of Cd3d, Cd3e, Cd3g, Blnk, Sdc1 and Jchain suggests that chronic inflammation persists in peri-infarct regions for at least 7 weeks after stroke. Conversely, the DE analysis revealed that 1,787 genes were downregulated in peri-infarct regions compared to equivalent regions of the contralateral hemisphere. These genes were primarily involved in mitochondrial respiration and neuronal function. Together, these results demonstrate that the transcriptome of the peri-infarct region is characterized by the upregulation of genes involved in inflammation and lipid metabolism and the downregulation of genes involved in mitochondrial respiration and neuronal function. To evaluate the impact of HPβCD treatment on the transcriptome of the peri-infarct region, we also performed bulk RNA-Seq on brain tissue collected 7 weeks after DH stroke. For this analysis, we compared the peri-infarct regions of vehicle- and HPβCD-treated aged mice. The peri-infarct region of HPβCD-treated mice was characterized by 5,385 differentially expressed genes. The DE analysis revealed that peri-infarct regions of HPβCD-treated mice were characterized by the downregulation of multiple degradative enzymes, chemokine receptors, and scavenger receptors. In addition, the transcriptomic analysis demonstrated a restoration of lipid homeostasis in peri-infarct regions of HPβCD-treated mice compared to vehicle-injected mice, as evidenced by the downregulation of Lipa, Apoe, Lamp1, Npc1, and Npc2 and upregulation of Nceh1 and Ldlr. Reductions in innate and adaptive immune responses characterized peri-infarct regions of HPβCD-treated mice; these alterations are consistent with the attenuated chronic inflammation that characterized infarcts of the HPβCD-treated aged mice. These results demonstrate that HPβCD treatment after stroke attenuates chronic inflammation and promotes lipid metabolism in peri-infarct regions of aged mice. Additionally, the DE analysis revealed an upregulation of genes involved in myelin sheath structural integrity, such as Ina, Omg, and Nefl, and synaptic plasticity and neuroplasticity, such as Syn1, Bdnf, Nrg1, Negr1, and Nsg1. These results suggest that HPβCD treatment improves the structure and function of neurons in peri-infarct regions of aged mice after stroke.
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