Selection of thermodynamic models for combinatorial control of multiple transcription factors in early differentiation of embryonic stem cells

<p>Abstract</p> <p>Background</p> <p>Transcription factors (TFs) have multiple combinatorial forms to regulate the transcription of a target gene. For example, one TF can help another TF to stabilize onto regulatory DNA sequence and the other TF may attract RNA polymerase (RNAP) to start transcription; alternatively, two TFs may both interact with both the DNA sequence and the RNAP. The different forms of TF-TF interaction have different effects on the probability of RNAP's binding onto the promoter sequence and therefore confer different transcriptional efficiencies.</p> <p>Results</p> <p>We have developed an analytical method to identify the thermodynamic model that best describes the form of TF-TF interaction among a set of TF interactions for every target gene. In this method, time-course microarray data are used to estimate the steady state concentration of the transcript of a target gene, as well as the relative changes of the active concentration for each TF. These estimated concentrations and changes of concentrations are fed into an inference scheme to identify the most compatible thermodynamic model. Such a model represents a particular way of combinatorial control by multiple TFs on a target gene.</p> <p>Conclusions</p> <p>Applying this approach to a time-course microarray dataset of embryonic stem cells, we have inferred five interaction patterns among three regulators, Oct4, Sox2 and Nanog, on ten target genes.</p

Myeloid-Derived Suppressor Cells Impair Alveolar Macrophages through PD-1 Receptor Ligation during Pneumocystis Pneumonia

Myeloid-derived suppressor cells (MDSCs) were recently found to accumulate in the lungs during Pneumocystis pneumonia (PcP). Adoptive transfer of these cells caused lung damage in recipient mice, suggesting that MDSC accumulation is a mechanism of pathogenesis in PcP. In this study, the phagocytic activity of alveolar macrophages (AMs) was found to decrease by 40% when they were incubated with MDSCs from Pneumocystis-infected mice compared to those incubated with Gr-1+ cells from the bone marrow of uninfected mice. The expression of the PU.1 gene in AMs incubated with MDSCs also was decreased. This PU.1 downregulation was due mainly to decreased histone 3 acetylation and increased DNA methylation caused by MDSCs. MDSCs were found to express high levels of PD-L1, and alveolar macrophages (AMs) were found to express high levels of PD-1 during PcP. Furthermore, PD-1 expression in AMs from uninfected mice was increased by 18-fold when they were incubated with MDSCs compared to those incubated with Gr-1+ cells from the bone marrow of uninfected mice. The adverse effects of MDSCs on AMs were diminished when the MDSCs were pretreated with anti-PD-L1 antibody, suggesting that MDSCs disable AMs through PD-1/PD-L1 ligation during PcP

Microglia in the aging brain: relevance to neurodegeneration

Microglia cells are the brain counterpart of macrophages and function as the first defense in the brain. Although they are neuroprotective in the young brain, microglia cells may be primed to react abnormally to stimuli in the aged brain and to become neurotoxic and destructive during neurodegeneration. Aging-induced immune senescence occurs in the brain as age-associated microglia senescence, which renders microglia to function abnormally and may eventually promote neurodegeneration. Microglia senescence is manifested by both morphological changes and alterations in immunophenotypic expression and inflammatory profile. These changes are likely caused by microinvironmental factors, but intrinsic factors cannot yet be completely excluded. Microglia senescence appears to underlie the switching of microglia from neuroprotective in the young brain to neurotoxic in the aged brain. The hypothesis of microglia senescence during aging offers a novel perspective on their roles in aging-related neurodegeneration. In Parkinson's disease and Alzheimer's disease, over-activation of microglia may play an active role in the pathogenesis because microglia senescence primes them to be neurotoxic during the development of the diseases