Comparative analysis of gene expression under cold acclimation, deacclimation and reacclimation in Arabidopsis.

Cold acclimated plants show an elevated tolerance against subsequent cold stress. Such adaptation requires alterations in gene expression as well as physiological changes. We were interested in gene expression changes at the transcriptional level during adaptation processes. The patterns of transcriptional changes associated with cold acclimation, deacclimation and reacclimation in Arabidopsis leaves were characterized using the Coldstresschip. Gene expression profiles were further analyzed by 'coexpressed gene sets' using gene set enrichment analysis (GSEA). Genes involved in signal transduction through calcium, and cascades of kinases and transcription factor genes, were distinctively induced in the early response of cold acclimation. On the other hand, genes involved in antioxidation, cell wall biogenesis and sterol synthesis were upregulated in the late response of cold acclimation. After the removal of cold, the expression patterns of most genes rapidly returned to the original states. However, photosynthetic light-harvesting complex genes and lipid metabolism-related genes stayed upregulated in cold deacclimated plants compared to non-treated plants. It is also notable that many well-known cold-inducible genes are slightly induced in reacclimation and their expression remains at relatively low levels in cold reacclimation compared to the expression during the first cold acclimation. The results in this study show the dynamic nature of gene expression occurring during cold acclimation, deacclimation and reacclimation. Our results suggest that there is a memory of cold stress and that the 'memory of cold stress' is possibly due to elevated photosynthetic efficiency, modified lipid metabolism, increased calcium signaling, pre-existing defense protein made during first cold acclimation and/or modified signal transduction from pre-existing defense protein.

Systemic analysis of heat shock response induced by heat shock and a proteasome inhibitor MG132.

The molecular basis of heat shock response (HSR), a cellular defense mechanism against various stresses, is not well understood. In this, the first comprehensive analysis of gene expression changes in response to heat shock and MG132 (a proteasome inhibitor), both of which are known to induce heat shock proteins (Hsps), we compared the responses of normal mouse fibrosarcoma cell line, RIF-1, and its thermotolerant variant cell line, TR-RIF-1 (TR), to the two stresses. The cellular responses we examined included Hsp expressions, cell viability, total protein synthesis patterns, and accumulation of poly-ubiquitinated proteins. We also compared the mRNA expression profiles and kinetics, in the two cell lines exposed to the two stresses, using microarray analysis. In contrast to RIF-1 cells, TR cells resist heat shock caused changes in cell viability and whole-cell protein synthesis. The patterns of total cellular protein synthesis and accumulation of poly-ubiquitinated proteins in the two cell lines were distinct, depending on the stress and the cell line. Microarray analysis revealed that the gene expression pattern of TR cells was faster and more transient than that of RIF-1 cells, in response to heat shock, while both RIF-1 and TR cells showed similar kinetics of mRNA expression in response to MG132. We also found that 2,208 genes were up-regulated more than 2 fold and could sort them into three groups: 1) genes regulated by both heat shock and MG132, (e.g. chaperones); 2) those regulated only by heat shock (e.g. DNA binding proteins including histones); and 3) those regulated only by MG132 (e.g. innate immunity and defense related molecules). This study shows that heat shock and MG132 share some aspects of HSR signaling pathway, at the same time, inducing distinct stress response signaling pathways, triggered by distinct abnormal proteins.

Role of MyD88 in TLR agonist-induced functional alterations of human adipose tissue-derived mesenchymal stem cells.

Toll-like receptors (TLRs) sense microorganism components and are critical host mediators of inflammation during infection. Recently, TLRs have been reported to be involved in cell proliferation and differentiation. We previously reported that TLR agonists might affect proliferation and differentiation of human adipose tissue-derived mesenchymal stem cells (hASCs). In this study, we sought to determine whether TLR signaling is dependent on MyD88 in hASCs. The hASCs were downregulated using LV-GFP-miR-MyD88, a lentiviral construct inserted siRNA against human MyD88 that significantly inhibited cell proliferation. MyD88 downregulation reduced NF-kappaB activation and enhancement of osteogenic differentiation induced by peptidoglycan (PGN) more significantly than that induced by lipopolysaccharide (LPS). Although LPS- and PGN-induced cytokine secretions were decreased greatly by MyD88 downregulation, IFN-gamma-induced protein-10 (IP10) and IFNbeta expression were enhanced by LPS irrespective of the downregulation of MyD88. These results suggest that TLR signaling is mediated via MyD88-independent pathways as well as MyD88-dependent pathways in hASCs and that MyD88 contributes to the regulation of cell proliferation and differentiation in hASCs.

Role of CD9 in proliferation and proangiogenic action of human adipose-derived mesenchymal stem cells.

CD9 belongs to the tetraspanin family and is involved in cell motility, osteoclastogenesis, metastasis, neurite outgrowth, myotube formation, and sperm-egg fusion. CD9 also promotes juxtacrine signaling involved in proliferation and attachment. Varying degrees of CD9 expression have been found in human mesenchymal stem cells. In this study, we determined the functional roles of CD9 in human adipose-derived mesenchymal stem cells (hASCs). The CD9 expression in hASCs was down-regulated during culture expansion. A colony-forming unit assay revealed that the clonal expandability of hASCs was directly correlated with the CD9 expression level of the colony. The CD9(high) cells exhibited an increased ability to proliferate, increased cell adhesiveness, and better in vitro tube formation than the CD9(low) cells. The cellular proliferation and attachment of the CD9(high) cells were inhibited upon treatment with a blocking antibody against CD9 and the transduction of a CD9 miRNA lentivirus. The CD9(high) cells showed higher NF-kappaB promoter activity and higher levels of intercellular adhesion molecule 1 than the CD9(low) cells. Reverse transcription-polymerase chain reaction analysis revealed higher endothelial nitric oxide synthase expression in the CD9(high) cells than in the CD9(low) cells. The engraftment and the proangiogenic action of hASCs in a murine model of hindlimb ischemia were significantly higher in the CD9(high) cells than in the CD9(low) cells. This study indicates that CD9 plays roles in cell proliferation and attachment in vitro as well as in in vivo engraftment and that it can be considered as a useful marker to predict the in vivo efficacy of hASCs.

Systemic analysis of tyrosine phosphorylated proteins in angiopoietin-1 induced signaling pathway of endothelial cells.

Angiogenesis is an essential process in physiological and pathological processes and is well-regulated to maintain the cellular homeostasis by balancing the endothelial cells in proliferation and apoptosis. Angiopoietin-1 (Ang1) regulates angiogenesis as a ligand of Tie 2 receptor tyrosine kinase. However, the regulation pathways are not well-understood. To date, only a few of the signaling molecules involved in the Tie 2 receptor tyrosine kinase-mediated angiogenesis have been identified. In this study, we systematically identified tyrosine-phosphorylated proteins in Ang1-induced signaling cascade in human umbilical vein endothelial cells (HUVECs), employing proteomic analyses combining two-dimensional gel electrophoresis, Western analysis using phosphotyrosine antibody and mass spectrometry (MALDI-TOF MS and nanoLC-ESI-q-TOF tandem MS). We report here the identification, semiquantitative analysis, and kinetic changes of tyrosine-phosphorylated proteins in response to Ang1 in HUVECs and identified 66 proteins among 69 protein spots showing significant changes. Of these, p54nrb was validated as a molecule involved in cell migration. These results suggest that Ang1 induces stabilization of neo-vessel network by regulating the phosphorylations of metabolic and structural proteins.