Project description:Macrophages play fundamental roles in regulation of inflammatory responses to pathogens, resolution of inflammation and tissue repair, and maintenance of tissue homeostasis. The long (L) and short (S) isoforms of SP-R210/MYO18A, a macrophage receptor for surfactant protein A (SP-A) and C1q, regulate basal and inflammatory macrophage phenotype at multiple gene expression, translational, and subcellular levels in addition to their SP-A and C1q-mediated functions; disruption of L renders macrophages hyper-inflammatory, although the underlying mechanism had previously been unexplored. We questioned whether disruption of the L isoform would alter the global genomic responses. RNA sequencing analysis of SP-R210L(DN) macrophages revealed basal and influenza induced upregulation of genes associated with inflammatory pathways, including TLR, RIG-I, NOD, and cytoplasmic DNA signaling, whereas knockdown of both SP-R210 isoforms (L and S) only resulted in increased RIG-I and NOD signaling. Chromatin immunoprecipitation sequencing (ChIP-seq) analysis showed increased genome-wide deposition of the pioneer transcription factor PU.1 in SP-R210L(DN) compared to WT cells. ChIP-seq analysis of histone H3 methylation showed alterations in both repressive (H3K9me3 and H3K27me3) and transcriptionally active (H3K9me3) histone marks. Influenza A virus (IAV) infection, which stimulates an array of cytosolic and TLR-mediated antiviral mechanisms, resulted in differential redistribution between proximal promoter and distal sites and decoupling of PU.1 binding from Toll-like receptor regulated gene promoters in SP-R210L(DN) cells. Our findings suggest that SP-R210L-deficient macrophages are poised with an open PU.1-primed chromatin conformation to rapidly respond to inflammatory and metabolic stimuli.
Project description:Np63+ve cells are multipotent and maintain all epithelial cell lineages of the embryonic and adult salivary gland (SG). However, the molecular mechanisms by which Np63 regulates stem/progenitor (SP) cell populations in the SG remains elusive. To better understand Np63 s role in directing cell fate choices, here we have utilized Np63-null adult mice and primary salivary cell cultures to probe alterations in SP cell differentiation and function. Specifically, we have generated bulk RNA-seq and scRNA-seq data from Np63-null adult mice and p63 and H3K27Ac ChIP-seq data from primary salivary cell cultures. These genomic and epigenomic data sets were leveraged to interrogate altered SG cellular identities and differentiation states resulting from the loss of Np63. Our studies reveal that ablation of Np63 results in a loss of the SP cell population and skewed SG differentiation that is modulated by dysregulated TGF- /Activin signaling. Our findings offer new molecular revelations into the SP cell gene regulatory networks that are likely to be relevant for normal or diseased SG states.
Project description:We integrated genomic and transcriptomic analysis of a newly isolated obligate Methylomonas sp. DH-1 grown on methane and methanol. Comparative transcriptomic analysis between methane and methanol as a sole carbon source revealed different transcriptional responses of Methylomonas sp. DH-1, especially in C1 assimilation, the secondary metabolites pathways and the oxidative stress related genes
Project description:Side population (SP) cells harbor malignant phenotypes, such as sphere forming capacity, single cell clonogenicity and in vivo tumorigenicity. These malignant phenotypes are related to a poor prognosis for women with ovarian cancer. The aim of this study was to identify key factor(s) that increase the proportion of ovarian cancer SP cells through a functional genomics screen. A library of 81 000 shRNAs targeting 15 000 genes was transfected into CH1 and SKOV3 cells, followed by SP analysis. We found that suppression of MSL3, ZNF691, VPS45, ITGB3BP, TLE2, and ZNF498 markedly increased the proportion of SP cells. Newly generated SP cells exhibit significantly greater capacity for sphere formation, single cell clonogenicity, and in vivo tumorigenicity. On the contrary, overexpression of MSL3, VPS45, ITGB3BP, TLE2, and ZNF498 significantly decreased the proportion of SP cells, sphere formation capacity and single cell clonogenicity. In ovarian cancer cases, low expression of MSL3, ZNF691 and VPS45 was related to poor prognosis. Suppression of these six genes tended to increase some stem cell-related pathways, and significantly enhanced activity of the hedgehog pathway. Cyclopamine, a hedgehog pathway inhibitor, significantly decreased the number of newly generated SP cells and their sphere forming ability. Our results provide new information regarding molecular mechanisms favoring SP cells and suggest that Hedgehog signaling may provide a viable target for improving ovarian cancer survival.