Gene expression profile, population of macrophages and lymphocytes of the spleen in conditions of liver regeneration after 70% resection in mice
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE232531 | GEO | 2023/09/27
REPOSITORIES: GEO
Similar Datasets
Project description:In this work, the effect of splenectomy on liver regeneration was studied. For this purpose in 1 series of experiments the animals were reproduced splenectomy, and after 7 days 70% liver resection was performed. It was found that spleen removal leads to a decrease in the migration of Ly6C+ monocytes into the regenerating liver. Using transcriptional analysis it was shown that spleen and peripheral blood monocytes differ in the expression of genes associated with the synthesis of surface receptors necessary for cell migration. The obtained data explain the reason for the preferential migration of spleen monocytes rather than peripheral blood monocytes into the regenerating liver.
2024-04-16 | GSE263764 | GEO
Project description:The liver has the unique capacity to regenerate after surgical resection. However, the regulation of liver regeneration is not completely understood. We performed miRNA microarray analyses of liver tissue from Wistar rats at different time points after 70% partial hepatectomy (0, 2, 6, 12, 24, 48 hours, and 5 days) and after sham laparotomy (12, 24, and 48 hours). We demonstrate that miRNA expression patterns changed during liver regeneration and that these changes were most evident during the peak of DNA replication at 24 hours after resection. Expression of 13 miRNAs, including five members of the let-7 family, was significantly reduced 12-48 hours after resection, whereas 3 miRNAs were significantly upregulated (> 25% change). We provide a temporal miRNA expression dataset of the regenerating rat liver, which indicates a primary function for miRNA during the peak of DNA replication. These data will assist further functional studies on the role of miRNAs during liver regeneration.
2011-03-28 | GSE23696 | GEO
Project description:The liver has the unique capacity to regenerate after surgical resection. However, the regulation of liver regeneration is not completely understood. We performed miRNA microarray analyses of liver tissue from Wistar rats at different time points after 70% partial hepatectomy (0, 2, 6, 12, 24, 48 hours, and 5 days) and after sham laparotomy (12, 24, and 48 hours). We demonstrate that miRNA expression patterns changed during liver regeneration and that these changes were most evident during the peak of DNA replication at 24 hours after resection. Expression of 13 miRNAs, including five members of the let-7 family, was significantly reduced 12-48 hours after resection, whereas 3 miRNAs were significantly upregulated (> 25% change). We provide a temporal miRNA expression dataset of the regenerating rat liver, which indicates a primary function for miRNA during the peak of DNA replication. These data will assist further functional studies on the role of miRNAs during liver regeneration. This project analyzed the miRNA expression in 30 different sample types of the organism rattus norvegicus. The miRNA expression was compared at 7 different growth time points after liver resection (0, 2, 6, 12, 24, 48 hours, 5 days) and at 3 different time points after sham laparotomy (12, 24, and 48 hours). Three biological replicates were used per time point.
2011-03-28 | E-GEOD-23696 | biostudies-arrayexpress
Project description:Following parenchymal loss, the liver regenerates restoring normal mass and metabolic function. Prevailing theories on triggering events leading to regeneration include humoral, metabolic and flow-mediated mechanisms, the latter emphasizing the importance of shear stress mediated nitric oxide (NO) regulation. We aimed to investigate whether the grade of resection and hence the portal venous pressure and sinusoidal shear stress increase, would be reflected in the gene expression profiles in the liver remnant by employing a global porcine cDNA microarray chip with approximately 23 000 genes represented. Six pig livers were resected with 62% (Low Portal Pressure Resection, LPPR) and 75% (High Portal Pressure Resection) resulting in a portal venous pressure increase from a baseline of 6.1 mmHg to 8.2 and 12 mmHg respectively. By sampling consecutive biopsies from the liver remnants we found differentially expressed genes in the HPPR group to have functions related primarily to apoptosis, nitric oxide metabolism and oxidative stress, whereas differentially expressed genes in the LPPR group potentially regulate the cell cycle. Common to both groups was the upregulation of genes regulating inflammation, transport, cell proliferation and development and protein metabolism. Also common to both groups was both up- and downregulation of genes regulating cell-cell signaling, signal transduction, cell adhesion and translation. Genes regulating the metabolism of lipids, hormones, amines, and alcohol were downregulated in both groups. Conclusions: The genetic regenerative response in the liver remnant to varies according to the level of resection. Keywords: time course, treatment comparison Three pigs underwent a 62% liver resection (low-pressure resection, LPR) and three underwent a 75% resection (high-pressure resection, HPR). Biopsies from the liver remnant were taken from all animals at time points 1, 30, 90, minutes and 3, 4 and 6 hours after resection. Expression profiling was conducted by hybridising each sample against a common reference, consisting of liver RNA from an unrelated animal.
2008-01-14 | E-GEOD-6860 | biostudies-arrayexpress
Project description:Following parenchymal loss, the liver regenerates restoring normal mass and metabolic function. Prevailing theories on triggering events leading to regeneration include humoral, metabolic and flow-mediated mechanisms, the latter emphasizing the importance of shear stress mediated nitric oxide (NO) regulation. We aimed to investigate whether the grade of resection and hence the portal venous pressure and sinusoidal shear stress increase, would be reflected in the gene expression profiles in the liver remnant by employing a global porcine cDNA microarray chip with approximately 23 000 genes represented. Six pig livers were resected with 62% (Low Portal Pressure Resection, LPPR) and 75% (High Portal Pressure Resection) resulting in a portal venous pressure increase from a baseline of 6.1 mmHg to 8.2 and 12 mmHg respectively. By sampling consecutive biopsies from the liver remnants we found differentially expressed genes in the HPPR group to have functions related primarily to apoptosis, nitric oxide metabolism and oxidative stress, whereas differentially expressed genes in the LPPR group potentially regulate the cell cycle. Common to both groups was the upregulation of genes regulating inflammation, transport, cell proliferation and development and protein metabolism. Also common to both groups was both up- and downregulation of genes regulating cell-cell signaling, signal transduction, cell adhesion and translation. Genes regulating the metabolism of lipids, hormones, amines, and alcohol were downregulated in both groups. Conclusions: The genetic regenerative response in the liver remnant to varies according to the level of resection. Keywords: time course, treatment comparison
2008-01-14 | GSE6860 | GEO
Project description:The DNA double-strand breaks that initiate homologous recombination during meiosis are subject to extensive 5ʹ→3′ exonucleolytic processing. This resection is a central and conserved feature of recombination, yet its mechanism is poorly understood. Using a purpose-made deep-sequencing method, namely S1Seq, we mapped meiotic resection endpoints genome-wide at high spatial resolution in Saccharomyces cerevisiae. Generating full-length resection tracts requires Exo1 exonuclease activity and the DNA-damage responsive kinase Tel1, but not the helicase Sgs1. Tel1 is also required for efficient and timely initiation of resection. We find that distributions of resection endpoints at individual genomic loci display pronounced heterogeneity that reflects a tendency for nucleosomes to block Exo1 in vivo, yet modeling experiments indicate that Exo1 digests chromatin with high apparent processivity and at rates approaching those for naked DNA in vitro. This paradox points to nucleosome destabilization or eviction as a determining feature of the meiotic resection landscape.
2016-08-06 | GSE85253 | GEO
Project description:Resection, nucleolytic processing of DSB ends is necessary to generate 3' single-stranded DNA tails (ssDNA) for homologous recombination (HR). Meiotic recombination initiated by Spo11 induced double-strand breaks (DSBs) is essential for the accurate segregation of homologous chromosomes. After cleavage, Spo11 stays covalently linked to the DSB ends, which requires MRX/Sae2 incision on broken molecules to allow following Exo1-mediated resection. Exonuclease I activity is inhibited by nucleosome bound DNA in vitro. To ensure resection proceeds, resection machineries must overcome chromatin barrier. Here we show that in the absence of Fun30, an SNF2-like ATPase, resection tract lengths shortened, albeit less severe than exo1-nd (with more longer resection tracts than that in exo1nd), across all DSB hotspots, suggesting that Fun30 is required for meiotic resection. Additive resection defect in fun30Δ exo1-nd (nuclease dead) compared to exo1-nd mutant indicates that Fun30 regulates MRX/Sae2 nicking positions. We also observed extremely short resection tracts in the double mutants are mostly confined to NDR, suggesting initial nicking step is blocked by nucleosomes.
2023-05-01 | GSE221377 | GEO
Project description:Chromosomal double-strand breaks (DSBs) are resected by 5’-nucleases to form 3’ single-strand DNA (ssDNA) substrates for binding by homologous recombination and DNA damage checkpoint proteins. Two redundant pathways of extensive resection were described both in cells and in vitro, one relying on Exo1 exonuclease and the other on Sgs1 helicase and Dna2 nuclease. However, it remains unknown how resection proceeds within the context of chromatin where histones and histone-bound proteins represent barriers for resection enzymes. Here, we have identified the yeast nucleosome remodeling enzyme Fun30 as novel factor promoting DSB end resection. Fun30 is the major nucleosome remodeler promoting extensive Exo1- and Sgs1-dependent resection of DSBs while the RSC and INO80 chromatin remodeling complexes play redundant roles with Fun30 in resection adjacent to DSB ends. ATPase and helicase domains of Fun30, which are needed for nucleosome remodeling, are also required for resection. Fun30 is robustly recruited to DNA breaks and spreads around the DSB coincident with resection. Fun30 becomes less important for resection in the absence of the histone-bound Rad9 checkpoint adaptor protein known to block 5’ strand processing and in the absence of either histone H3 K79 methylation or γ-H2A, which mediate recruitment of the Rad9 . Together these data suggest that Fun30 helps to overcome the inhibitory effect of Rad9 on DNA resection.
2012-10-04 | GSE38601 | GEO
Project description:The DNA double-strand breaks that initiate homologous recombination during meiosis are subject to extensive 5ʹâ??3â?² exonucleolytic processing. This resection is a central and conserved feature of recombination, yet its mechanism is poorly understood. Using a purpose-made deep-sequencing method, namely S1Seq, we mapped meiotic resection endpoints genome-wide at high spatial resolution in Saccharomyces cerevisiae. Generating full-length resection tracts requires Exo1 exonuclease activity and the DNA-damage responsive kinase Tel1, but not the helicase Sgs1. Tel1 is also required for efficient and timely initiation of resection. We find that distributions of resection endpoints at individual genomic loci display pronounced heterogeneity that reflects a tendency for nucleosomes to block Exo1 in vivo, yet modeling experiments indicate that Exo1 digests chromatin with high apparent processivity and at rates approaching those for naked DNA in vitro. This paradox points to nucleosome destabilization or eviction as a determining feature of the meiotic resection landscape. 36 samples total: two biological replicate S1Seq maps of S.cerevisiae for each genetic background and time point in meiosis
2016-08-06 | E-GEOD-85253 | biostudies-arrayexpress
Project description:At critically short telomeres TERRA RNA-DNA hybrids become stabilized and drive homology-directed repair (HDR) to delay replicative senescence. However, even at long- and intermediate-length telomeres, not subject to HDR, transient TERRA RNA-DNA hybrids form, suggestive of additional roles. Here, we report that hybrids at telomeres prevent resection by the Exo1 nuclease when telomeres become non-functional. We employed the well-characterized cdc13-1 allele, where telomere resection can be induced in a temperature dependent manner, to demonstrate that ssDNA generation at telomeres is either prevented or augmented when RNA-DNA hybrids are stabilized or destabilized, respectively. The viability of cdc13-1 cells is affected by the presence or absence of hybrids accordingly. These results give insights into an additional role of TERRA at dysfunctional telomeres suggesting that it not only affects replicative senescence rates through HDR activation at critically short telomeres, but may also affect resection rates at intermediate length telomeres in pre-senescent cells.
2023-01-18 | PXD034986 | Pride