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Postnatal Subventricular Zone Injury Predicts Motor Impairment in Preterm Infants Following Intestinal Disease

ABSTRACT: Following intestinal perforation in neonatal mice there is an injury to the subventrcular zone stem cell niche. These files are the raw data from mouse brain sections, transecting SVZ in controls and mice with modeled instestinal perforation.

ORGANISM(S): Mus musculus

PROVIDER: GSE254087 | GEO | 2024/01/24

REPOSITORIES: GEO

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Project description:Histone 3 lysine 4 trimethylation (H3K4me3) is known to be associated with transcriptionally active or poised genes and required for postnatal neurogenesis within the subventricular zone (SVZ) in the rodent model. Previous comparisons have shown significant correlation between baboon (Papio anubis) and human brain. In this study, we demonstrate that chromatin activation mark H3K4me3 is present in undifferentiated progenitor cells within the SVZ of adult baboon brain. To identify the targets and regulatory role of H3K4me3 within the baboon SVZ, we developed a technique to purify undifferentiated SVZ cells while preserving the endogenous nature without introducing culture artifact to maintain the in vivo chromatin state for genome-wide studies (ChIP-Seq and RNA-Seq). We identified that H3K4me3 is significantly enriched for genes involved in cell cycle, cell signaling, nervous system development, metabolism, and ribosomal biogenesis. Among these genes, RNA-Seq identified that genes associated with cellular signaling/maintenance, DNA replication, metabolism, and protein synthesis are expressed. We found that 72% of H3K4me3-enriched genes in undifferentiated SVZ cells are expressed (1913 genes are detectable by RNA-Seq; 2663 genes enriched with H3K4me3 by ChIP-Seq). On the other hand, 750 out of total 2663 H3K4me3-enriched genes are not detectable by RNA-Seq, suggesting 28% of genes in SVZ are poised for activation. RNA-seq profiles were generated from adult baboon subventricular zone primary cells by paired-end deep sequencing with an Illumina HiSeq 2000. RNA-Seq Analysis: Total RNA was extracted from purified baboon SVZ cells using TRIzol reagent, and sequencing libraries were generated with the Illumina RNA-Seq library kit. Paired-end RNA-deepSeq (76 base pair; >300 million tag reads; 269,081,636 mapped reads) were aligned to hg19. DESeq was used to normalize raw read counts, and Cufflink reports read counts and estimated FPKM (fragments per kilobase of exon per million fragments mapped; http://cufflinks.cbcb.umd.edu/faq.html#fpkm). Genes with expression values >1 FPKM were considered for subsequent analyses.

Project description:Throughout postnatal life in mammals, neural stem cells (NSCs) are located in the subventricular zone (SVZ) of the lateral ventricles. The greatest diversity of neuronal and glial lineages they generate occurs during early postnatal life in a region-specific manner. In order to evaluate potential heterogeneity in the NSC pool, we microdissected the dorsal and lateral SVZ at different postnatal ages and isolated NSCs and their immediate progeny based on their expression of Hes5-EGFP/Prominin1 and Ascl1-EGFP, respectively. Whole genome comparative transcriptome analysis revealed transcriptional regulators as major hallmarks that sustain postnatal SVZ regionalization. Manipulation of single genes encoding for locally enriched transcription factors influenced NSC specification indicating that the fate of regionalized postnatal SVZ NSCs can be readily modified . These findings reveal functional heterogeneity of NSCs in the postnatal SVZ and provide targets to recruit region-specific lineages in regenerative contexts. Microarrays of neural stem cells, early progenitors and the tissue from subregions of the subventricular zone were compiled to screen for the full extent of heterogeneity in this region during postnatal life. Spatially distinct regions of the developing forebrain subventricular zone (SVZ) aged at P4, P8 and P11 were microdissected in RNAse free/sterile conditions. Mice expressing Ascl1-EGFP in the SVZ were used to aid accurate microdissection of the dorsal and lateral wall of each of the studied time points as per our previous publications characterizing this method. As well as at the whole microdomain level, additionally, NSCs (Hes5-EGFP+/Prom1+) and early progenitors (Ascl1-EGFP+) from each microdomain were further isolated by FAC sorting methods. This was to provide a comprehensive gene expression analysis at the tissue level and at the cellular level. Generally, 1 litter was used to yield 1 'n' number of replicates. A total of 23 affymetrix analysis were performed.

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Postnatal Subventricular Zone Injury Predicts Motor Impairment in Preterm Infants Following Intestinal Disease

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