Temporal switching and cell-to-cell variability in Ca2+ release activity in mammalian cells

Genetically identical cells in a uniform external environment can exhibit different phenotypes, which are often masked by conventional measurements that average over cell populations. Although most studies on this topic have used microorganisms, differentiated mammalian cells have rarely been explored. Here, we report that only approximately 40% of clonal human embryonic kidney 293 cells respond with an intracellular Ca2+ increase when ryanodine receptor Ca2+ release channels in the endoplasmic reticulum are maximally activated by caffeine. On the other hand, the expression levels of ryanodine receptor showed a unimodal distribution. We showed that the difference in the caffeine sensitivity depends on a critical balance between Ca2+ release and Ca2+ uptake activities, which is amplified by the regenerative nature of the Ca2+ release mechanism. Furthermore, individual cells switched between the caffeine-sensitive and caffeine-insensitive states with an average transition time of approximately 65 h, suggestive of temporal fluctuation in endogenous protein expression levels associated with caffeine response. These results suggest the significance of regenerative mechanisms that amplify protein expression noise and induce cell-to-cell phenotypic variation in mammalian cells

On the Complexity of Tree Edit Distance with Variables

In this paper, we propose tree edit distance with variables, which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas. We analyze the computational complexity of several variants of this model. In particular, we show that the problem is NP-complete for ordered trees. We also show for unordered trees that the problem of deciding whether or not the distance is 0 is graph isomorphism complete but can be solved in polynomial time if the maximum outdegree of input trees is bounded by a constant. We also present parameterized and exponential-time algorithms for ordered and unordered cases, respectively

Phosphodiesterase Inhibitors Suppress Lactobacillus casei Cell-Wall-Induced NF-κB and MAPK Activations and Cell Proliferation through Protein Kinase A—or Exchange Protein Activated by cAMP-Dependent Signal Pathway

Specific strains of Lactobacillus have been found to be beneficial in treating some types of diarrhea and vaginosis. However, a high mortality rate results from underlying immunosuppressive conditions in patients with Lactobacillus casei bacteremia. Cyclic AMP (cAMP) is a small second messenger molecule that mediates signal transduction. The onset and progression of inflammatory responses are sensitive to changes in steady-state cAMP levels. L. casei cell wall extract (LCWE) develops arteritis in mice through Toll-like receptor-2 signaling. The purpose of this study was to investigate whether intracellular cAMP affects LCWE-induced pathological signaling. LCWE was shown to induce phosphorylation of the nuclear factor κB (NF-κB) and mitogen-activated protein kinase (MAPK) signaling pathways and cell proliferation in mice fibroblast cells. Theophylline and phosphodiesterase inhibitor increased intracellular cAMP and inhibited LCWE-induced cell proliferation as well as phosphorylation of NF-κB and MAPK. Protein kinase A inhibitor H89 prevented cAMP-induced MAPK inhibition, but not cAMP-induced NF-κB inhibition. An exchange protein activated by cAMP (Epac) agonist inhibited NF-κB activation but not MAPK activation. These results indicate that an increase in intracellular cAMP prevents LCWE induction of pathological signaling pathways dependent on PKA and Epac signaling

Genome-wide association study of individual differences of human lymphocyte profiles using large-scale cytometry data

Human immune systems are very complex, and the basis for individual differences in immune phenotypes is largely unclear. One reason is that the phenotype of the immune system is so complex that it is very difficult to describe its features and quantify differences between samples. To identify the genetic factors that cause individual differences in whole lymphocyte profiles and their changes after vaccination without having to rely on biological assumptions, we performed a genome-wide association study (GWAS), using cytometry data. Here, we applied computational analysis to the cytometry data of 301 people before receiving an influenza vaccine, and 1, 7, and 90 days after the vaccination to extract the feature statistics of the lymphocyte profiles in a nonparametric and data-driven manner. We analyzed two types of cytometry data: measurements of six markers for B cell classification and seven markers for T cell classification. The coordinate values calculated by this method can be treated as feature statistics of the lymphocyte profile. Next, we examined the genetic basis of individual differences in human immune phenotypes with a GWAS for the feature statistics, and we newly identified seven significant and 36 suggestive single-nucleotide polymorphisms associated with the individual differences in lymphocyte profiles and their change after vaccination. This study provides a new workflow for performing combined analyses of cytometry data and other types of genomics data

Protein kinase A and Epac activation by cAMP regulateS the expression of glial fibrillary acidic protein in glial cells

Cyclic adenosine monophosphate (cAMP) controls differentiation in several types of cells during brain development. However, the molecular mechanism of cAMP-controlled differentiation is not fully understood. We investigated the role of protein kinase A (PKA) and exchange protein directly activated by cAMP (Epac) on cAMP-induced glial fibrillary acidic protein (GFAP), an astrocyte marker, in cultured glial cells. B92 glial cells were treated with cAMP-elevating drugs, an activator of adenylate cyclase, phosphodiesterase inhibitor and a β adrenal receptor agonist. These cAMP-elevating agents induced dramatic morphological changes and expression of GFAP. A cAMP analog, 8-Br-cAMP, which activates Epac as well as PKA, induced GFAP expression and morphological changes, while another cAMP analog, 8-CPT-cAMP, which activates Epac with greater efficacy when compared to PKA, induced GFAP expression but very weak morphological changes. Most importantly, the treatment with a PKA inhibitor partially reduced cAMP-induced GFAP expression. Taken together, these results indicate that cAMP-elevating drugs lead to the induction of GFAP via PKA and/or Epac activation in B92 glial cells. © 2016 by the Serbian Biological Society

Capsaicin partially mimics heat in mouse fibroblast cells in vitro

Capsaicin activates transient receptor potential vanilloid 1 (TRPV1), a cation channel in the transient receptor potential family, resulting in the transient entry of Ca2+ and Mg2+ and a warm sensation. However, the effects of capsaicin on cells have not fully elucidated in fibroblasts. In this study, we investigated whether capsaicin could induce signal transduction in mouse fibroblast cells and compared the effect with that of heat-induced signal transduction. The activation of the mitogen-activated protein kinases (MAPKs) ERK and p38 MAPK, expression levels of heat shock protein 70 (HSP70) and HSP90, actin assembly, and cell proliferation were analyzed in NIH3T3 mouse fibroblast cells. A 15-min stimulation with capsaicin (∼100 μM) phosphorylated ERK and p38 MAPK and induced actin assembly. A 2-day stimulation with capsaicin increased the level of HSP70, but not HSP90, and the 2-day stimulation with capsaicin (∼100 μM) did not affect cell proliferation. A 15-min exposure to moderate heat (39.5 °C) phosphorylated both ERK and p38 MAPK and induced actin assembly to similar degrees as stimulation with capsaicin. A 2-day exposure to moderate heat increased the levels of both HSP70 and HSP90 and prevented cell proliferation. However, the 2-day stimulation with capsaicin (100 μM) failed to prevent heat shock-induced cell death. Thus, our results suggest that the effects of capsaicin on fibroblast cells partially differ from those of heat. Notably, the 2-day stimulation with capsaicin was not sufficient to develop heat tolerance in fibroblast cells. © 2016 Springer-Verlag Berlin HeidelbergEmbargo Period 12 month

Lactobacillus casei cell wall extract directly stimulates the expression of COX2 independent of Toll-like receptor 2 in rat glial cells

Kawasaki disease is an acute illness of early childhood that is characterized by prolonged fever and vasculitis of unknown pathogenesis. Lactobacillus casei cell wall extract (LCWE)-induced vasculitis in mice is a well-validated model of Kawasaki disease. In the nervous system, glial cells play an important role in fever development. This study investigated whether LCWE directly stimulates glial cells, resulting in the induction of cyclooxygenase-2 (COX2), which is required for prostaglandin synthesis and fever development. We found that LCWE induced COX2 expression and activated the nuclear factor-κB signaling pathway in rat B92 glial cells, but Toll-like receptor-2, which is one of the receptors for LCWE, could not be detected in the cells. These results suggest that LCWE activates the nuclear factor-κB signaling pathway and induces COX2 in rat B92 glial cells through another LCWE receptor other than Toll-like receptor-2. © 2012

Activation of tumor suppressor protein PTEN and induction of apoptosis are involved in cAMP-mediated inhibition of cell number in B92 glial cells

金沢大学医薬保健研究域医学系During brain development, cAMP induces morphological changes and inhibits growth effects in several cell types. However, the molecular mechanisms underlying the growth inhibition remain unknown. Tumor suppressor protein phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is a lipid phosphatase that inhibits the phosphoinositide 3-kinase (PI3K) pathway. The phosphorylation of Akt, which is one of the key molecules downstream of PI3K, inhibits apoptosis. In this study, we investigated the role of PTEN in cAMP-mediated growth inhibition. B92 rat glial cells were treated with 2 different cAMP stimulatory agents, a phosphodiesterase (PDE) inhibitor and a β-adrenoceptor agonist. Both cAMP stimulatory agents induced marked morphological changes in the cells, decreased cell number, decreased Akt phosphorylation, activated PTEN, cleaved caspase-3, and induced the condensation and fragmentation of nuclei. These results indicate that the cAMP stimulatory agents induced apoptosis. Protein phosphatase inhibitor prevented cAMP-induced dephosphorylation of PTEN and Akt. In addition, cAMP analogs and Epac-selective agonists affected PTEN and Akt activities. These results suggested that cAMP-induced apoptosis may be mediated by PTEN activation and Akt inhibition through protein phosphatase in B92 cells. Our results provide new insight into the role of PTEN in cAMP-induced apoptosis in glial cells. © 2011 Elsevier Ireland Ltd

Hematopoietic cell-derived IL-15 supports NK cell development in scattered and clustered localization within the bone marrow

骨髄のNK細胞の分化に造血細胞が産生するIL-15が必須である --2種類の局在を示すNK細胞の新規分化モデル--. 京都大学プレスリリース. 2023-09-20.Natural killer (NK) cells are innate immune cells critical for protective immune responses against infection and cancer. Although NK cells differentiate in the bone marrow (BM) in an interleukin-15 (IL-15)-dependent manner, the cellular source of IL-15 remains elusive. Using NK cell reporter mice, we show that NK cells are localized in the BM in scattered and clustered manners. NK cell clusters overlap with monocyte and dendritic cell accumulations, whereas scattered NK cells require CXCR4 signaling. Using cell-specific IL-15-deficient mice, we show that hematopoietic cells, but not stromal cells, support NK cell development in the BM through IL-15. In particular, IL-15 produced by monocytes and dendritic cells appears to contribute to NK cell development. These results demonstrate that hematopoietic cells are the IL-15 niche for NK cell development in the BM and that BM NK cells are present in scattered and clustered compartments by different mechanisms, suggesting their distinct functions in the immune response