Project description:Microarray analysis of gene expression in the olfactory epithelium of macrophage depleted mice to study the role of macrophages in regulating neurodegeneration, neuroprotection, and neurogenesis of olfactory sensory neurons Experiment Overall Design: Olfactory epithelium from LIp-C-treated and Lip-O-treated mice was microdissected for RNA extraction and hybridization on Affymetrix microarrays. We compared levels of gene expression in macrophage-depleted and non-depleted sham and 48 hr OBX mice using a 2x2 ANOVA and pairwise comparisons to identify molecular mechanisms of macrophage-mediated neurodegeneration, neuroprotection, and neurogenesis and to validate the gene expression patterns using real-time RT-PCR and immunohistochemistry
Project description:Microarray analysis of gene expression in the olfactory epithelium of macrophage depleted mice to study the role of macrophages in regulating neurodegeneration, neuroprotection, and neurogenesis of olfactory sensory neurons Keywords: comparison of gene expression level in sham and 48 hr OBX Lip-O mice versus Lip-C mice
Project description:Limited proteolysis combined with mass spectrometry of farrerol treated. Briefly, cell lysates containing approximately 500 μg of total protein sample were incubated with farrerol or vehicle (DMSO) for 10 min at 25 °C. Proteinase K (5 μg, Sigma–Aldrich) was added simultaneously to each sample for the following 10 min. Then, the reaction was stopped by heating at 98 °C for 3 min. The samples were subjected to limited proteolysis to generate structure-specific protein fragments. Complete digestion was performed with trypsin (Promega) at a 1:50 ratio (trypsin:protein, w:w) for 16 h at 37 °C, and then the reaction was stopped by adding formic acid to reach a pH less than 2. The polypeptide samples were dissolved in 0.1% formic acid and detected by Orbitrap mass spectrometry with label-free quantitation (LFQ) analysis to search for differential proteins on the MaxQuant platform via MS sensitivity.
Project description:snRNA-sequencing data for macaque LIP area. We isolated single nuclei from the LIP region. annotating the dataset with the canonical classification and integration with other datasets.
Project description:Lip is an anatomical junction between skin and mucosa and the squamous cell carcinoma (SCC) is the most frequent lip cancers. Lip SCC is frequently developed from actinic cheilitis, presented as ulcerative lesions. However, changes in transcriptomes and tumor microenvironment driving oncogenic transformation from actinic cheilitis to lip SCC and determinants of differentiation of lip SCC are largely unknown. This study aimed to investigate differences between lip SCC and its premalignant actinic cheilitis and factors related to tumor differentiation.
Project description:Macrophages are versatile immune cells, with the ability to respond to varied intrinsic and extrinsic cues, and transition between inflammatory and pro-reparative phenotypes. A complex network of epigenetic processes, such as DNA methylation, histone methylation, and acetylation, play key roles in modulating macrophage polarization and inflammatory gene expression. Transcriptional analysis in patients with respiratory failure, long COVID-19, and influenza revealed an augmented expression of chromatin-modifiers including histone demethylases, broadly defined as lysine demethylases (KDMs), in lung macrophages. Therefore, macrophage-specific pharmacological perturbation of these enzymes in vivo holds therapeutic promise in abating inflammation. To investigate the role of KDMs in inflammation, we screened a panel of small-molecule inhibitors of chromatin modifiers for their efficacy in inducing anti-inflammatory macrophage polarization in vitro. We demonstrate that pretreatment with the broad spectrum KDM inhibitor n-octyl-IOX1, KDM5-specific inhibitor PB-IT resulted in a significant decrease of lipopolysaccharide (LPS)-induced expression of the inflammatory genes Il1b, Il6, Tnfa, and iNos in bone marrow-derived macrophages (BMDM). Subsequent RNA sequencing and CUT&RUN analyses revealed that LPS activation led to distinct transcriptomic and epigenomic alterations including expression of master transcription factors (TFs) BLIMP-1 and GFI1 whereas n-octyl-IOX1 and PB-IT treatments rewired these regulatory networks, thereby impeding inflammatory gene expression and response. To further probe the merit of KDM inhibition in perturbing macrophage-mediated inflammation in vivo, we delivered n-octyl-IOX1 selectively to macrophages in mice using a cell-specific, targeted lipidoid nanoparticles. n-octyl-IOX1 loaded nanoparticles significantly diminished LPS-mediated peritoneal macrophage expansion and inflammatory gene expression in this cell population, underscoring the importance of macrophage-specific targeting of KDMs with small-molecule inhibitors in inflammatory disease.
Project description:Macrophages are versatile immune cells, with the ability to respond to varied intrinsic and extrinsic cues, and transition between inflammatory and pro-reparative phenotypes. A complex network of epigenetic processes, such as DNA methylation, histone methylation, and acetylation, play key roles in modulating macrophage polarization and inflammatory gene expression. Transcriptional analysis in patients with respiratory failure, long COVID-19, and influenza revealed an augmented expression of chromatin-modifiers including histone demethylases, broadly defined as lysine demethylases (KDMs), in lung macrophages. Therefore, macrophage-specific pharmacological perturbation of these enzymes in vivo holds therapeutic promise in abating inflammation. To investigate the role of KDMs in inflammation, we screened a panel of small-molecule inhibitors of chromatin modifiers for their efficacy in inducing anti-inflammatory macrophage polarization in vitro. We demonstrate that pretreatment with the broad spectrum KDM inhibitor n-octyl-IOX1, KDM5-specific inhibitor PB-IT resulted in a significant decrease of lipopolysaccharide (LPS)-induced expression of the inflammatory genes Il1b, Il6, Tnfa, and iNos in bone marrow-derived macrophages (BMDM). Subsequent RNA sequencing and CUT&RUN analyses revealed that LPS activation led to distinct transcriptomic and epigenomic alterations including expression of master transcription factors (TFs) BLIMP-1 and GFI1 whereas n-octyl-IOX1 and PB-IT treatments rewired these regulatory networks, thereby impeding inflammatory gene expression and response. To further probe the merit of KDM inhibition in perturbing macrophage-mediated inflammation in vivo, we delivered n-octyl-IOX1 selectively to macrophages in mice using a cell-specific, targeted lipidoid nanoparticles. n-octyl-IOX1 loaded nanoparticles significantly diminished LPS-mediated peritoneal macrophage expansion and inflammatory gene expression in this cell population, underscoring the importance of macrophage-specific targeting of KDMs with small-molecule inhibitors in inflammatory disease.
Project description:Two long and one truncated isoforms (termed LAP*, LAP, and LIP, respectively) of the transcription factor CCAAT enhancer binding protein beta (C/EBPβ) are expressed from a single intronless Cebpb gene by alternative translation initiation. Isoform expression is sensitive to mammalian target of rapamycin (mTOR)-mediated activation of the translation initiation machinery and relayed through an upstream open reading frame (uORF) on the C/EBPβ mRNA. The truncated C/EBPβ LIP, initiated by high mTOR activity, has been implied in neoplasia, but it was never shown whether endogenous C/EBPβ LIP may function as an oncogene. In this study, we examined spontaneous tumor formation in C/EBPβ knockin mice that constitutively express only the C/EBPβ LIP isoform from its own locus. Our data show that deregulated C/EBPβ LIP predisposes to oncogenesis in many tissues. Gene expression profiling suggests that C/EBPβ LIP supports a protumorigenic microenvironment, resistance to apoptosis, and alteration of cytokine/chemokine expression. The results imply that enhanced translation reinitiation of C/ EBPβ LIP promotes tumorigenesis. Accordingly, pharmacological restriction of mTOR function might be a therapeutic option in tumorigenesis that involves enhanced expression of the truncated C/EBPβ LIP isoform.