Next Generation Sequencing Analysis of livers from 2-month WT/12-month WT and 2-month HKO/12-month nontumor/12month- tumor.
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ABSTRACT: SRSF2 flanked with flox was specifically depleted in the livers by Alb-Cre(HKO),and took the intact ones as contorl(WT).Near 70% of the HKO livers spontaneously developed malignant tumors(took the tumor areas as tumor while the tumor-adjacent as nontumor).Then total RNAs of 2-month WT/HKO and 12-month WT/nontumor/tumor were isolated and performed the next generation sequencing. We profiled the gene expression regulated by Cre-loxp-mediated knockout system.
Project description:To look for age-related changes in the liver, we used RNAseq gene expression analysis to characterize mRNA expression profile in livers from 1-month vs. 6-month-old mice
Project description:To look for age-related changes in the liver that take place during DNA damage resolution, we used RNAseq gene expression analysis to characterize mRNA expression profile in livers from 1-month vs. 6-month-old mice either before or 2 days (representing the peak of DNA damage response) and 6 days (representing the resolution phase of DNA damage) after DEN treatment.
Project description:In cerebellar atrophy of 12-month-old ATM-null mice, transcriptome upregulations concern most neurotransmission and neuropeptide pathways, while downregulations affect prominently Itpr1, Usp2 and non-coding RNA In cerebellar atrophy of 12-month-old ATM-null mice, transcriptome upregulations concern most neurotransmission and neuropeptide pathways, while downregulations affect prominently Itpr1, Usp2 and non-coding RNA The autosomal recessive disorder Ataxia-Telangiectasia is caused by dysfunction of stress response protein ATM. In the nucleus of proliferating cells, ATM senses DNA double-strand breaks and coordinates their repair. This role explains T-cell dysfunction and tumor risk. However, it remains unclear whether this function is relevant for postmitotic neurons and underlies the cerebellar atrophy, since ATM is cytoplasmic in postmitotic neurons. Here, we used ATM-null mice that survived early immune deficits by bone-marrow transplantation, and reached initial neurodegeneration stages at 12 months of age. Global cerebellar transcriptomics demonstrated ATM depletion to trigger upregulations in most neurotransmission and neuropeptide systems. Downregulated transcripts were found for the ATM interactome component Usp2, many non-coding RNAs, ataxia genes Itpr1, Grid2, immediate early genes and immunity factors. Allelic splice changes affected prominently neuropeptide machinery, e.g. Oprm1. Validation experiments with stressors were performed in human neuroblastoma cells, where ATM localized only to cytoplasm, similar to brain. Effect confirmation in SH-SY5Y cells occurred better after ATM depletion and osmotic stress better than nutrient / oxidative stress, rather than ATM kinase inhibition or DNA stressor bleomycin. Overall, we provide pioneer observations from a faithful A-T mouse model, which suggest general changes in synaptic and dense-core vesicle stress adaptation.
Project description:As the central hub metabolic organ bodily, the liver is paramount to keep whole-body energy homeostasis. Further, mitochondria are the central metabolic hub within cells to connect the main catabolized, energy production, and hormonal signaling pathways. It is evident that mitochondrial dysfunction may play a critical role in the development of NASH. Accordingly, understanding the underlying mechanisms of mitochondrial dysfunction is of importance to develop therapies for NASH. Here, we report that mice with hepatocyte-specific deletion of Tid1, encoding a mitochondrial cochaperone, tended to develop NASH-dependent HCC. The hepatocellular nodules were developed in 3-month DEN-treated Tid1-/- mice. At the age of 6 months, the DEN-treated Tid1-/- mice showed a higher number of tumors and greater tumor size than the DEN-treated Tid1+/- mice, followed by the DEN-treated WT mice. To gain insights into the mRNA changes during NASH-HCC progress, we performed an RNA-seq analysis with livers collected from 6-month DEN-treated mice.
Project description:To investigate the potential mechanism by which RECS1 regulate metabolic disorder, we treated control mice and RECS1 HKO mice with HFD for 8 weeks, and performed microarray to identify the expression pattern and the potential important molecules regulated by RECS1. We used microarrays to detect the global gene expression in the livers of control mice and RECS1 HKO mice after treatment with HFD for 8 weeks and identified distinct classes of altered genes in the livers of mice upon HFD compared .
Project description:Whole body knockout mice lacking IQ-motif containing GTPase-activating protein 2 (IQGAP2) develop spontaneous hepatocellular carcinoma (HCC) at the age of 12 months and older (Schmidt et al., 2008). Hepatic transcript expression profiles were obtained for IQGAP2 knockout and wild-type control mice of two age groups, 6- and 24-month-old. Liver samples from 24-month-old IQGAP2 knockout mice were HCC tumors, livers from all other groups were tumor-free. Results provide insights into the potential role of IQGAP2 as a liver-specific tumor suppressor. Transcript profiles of four groups of mouse livers (N = 3 in each group) were compared using Affymetrix GeneChip® Mouse Genome 430 2.0 Array. The groups included livers from 6- and 24-month-old wild-type (WT) mice and 6- and 24-month-old (KO) Iqgap2-/- mice.
Project description:Purpose: The goal of this study is to compare transcriptome profilings of liver from Mettl3 flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice. Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from livers of Mettl3 flox/flox and HKO mice at 8 weeks old. mRNA profiles were generated by deep sequencing using an Illumina HiSeq X Ten platform. Paired-end clean reads were aligned to the mouse reference genome(Ensemble_GRCm38.90) with Hisat2 (version 2.0.4), and the aligned reads were used to quantify mRNA expression by using HTSeq (version 0.9.1). Conclusion: The hepatic mRNA profiles in Mettl3 flox/flox and HKO mice were characterized.