Modulation Of Transcription Factors Research Articles

Physiological and transcriptomic study reveal SeNPs-mediated AsIII stress detoxification mechanisms involved modulation of antioxidants, metal transporters, and transcription factors in Glycine max L. (Merr.) roots

Physiological changes and genome-wide alteration in gene expression were performed in soybean (Glycine max [L.] Merr.) roots exposed to AsⅢ (25 μmol/L) alone and supplemented with selenium nanoparticles (SeNPs) at the concentration of 10 and 25 μmol/L at the V2 growth stage. Excessive arsenic in the root zone poses a potential threat to soybean yield, particularly to roots, due to the limited translocation of AsIII from root to shoot in the case of soybean. We hypothesized that SeNPs can relieve AsⅢ toxicity to soybean root by reducing the AsⅢ uptake and regulating the internal tolerance mechanism of the plants. Results accomplished that SeNPs had positive impact on soybean dry weight and roots parameters under AsⅢ stress. Then, we further evaluated physiological indexes, whole genome transcriptomic analysis and quantitative real-time PCR to elucidate the underlying mechanism of AsⅢ tolerance under SeNPs supplementation. Under the condition of AsⅢ-stress, SeNPs exposure significantly reduced the electrolyte leakage, O2−•, H2O2 and MDA accumulation while increasing the antioxidants level. The RNA-seq dataset revealed total of 5819 up and 7231 down expressed DEGs across all libraries. The number of exclusively regulated genes were higher under As + SeNP10 (4909) treatment than in the AsⅢ-alone (4830) and As + SeNP25 (3311) treatments. The KEGG and GO analyses revealed that stress responsive DEGs such as glutathione S-transferase, glutathione peroxidase, ascorbate, glutaredoxin, thioredoxin, and phytochelatins synthase are responsible for AsⅢ tolerance under the SeNPs supplementation. Similarly, sulfate transporter, and ABC transporters (ATP-binding cassettes) expression were induced, and aquaporin channels related DEGs expression were reduced under SeNPs application in AsⅢ exposure condition. Furthermore, the expression of molecular chaperones (HSP) and transcription factors (MYB, bZIP, bHLH, and HSFs) were increased in SeNPs treatment groups. These results provide vital information of AsⅢ tolerance mechanism in response to SeNPs in soybean. We suggest that functional characterization of these genes will help us learn more about the SeNPs responsive arsenic tolerance mechanism in soybean.

TCDD alters essential transcriptional regulators of osteogenic differentiation in multipotent mesenchymal stem cells.

Differentiation of multipotent mesenchymal stem cells (MSCs) into bone-forming osteoblasts requires strict coordination of transcriptional pathways. Aryl hydrocarbon receptor ligands, such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), have been shown to alter osteoblast differentiation in vitro and bone formation in multiple developmental in vivo models. The goal of the present study was to establish a global transcriptomic landscape during early, intermediate, and apical stages of osteogenic differentiation in vitro in response to TCDD exposure. Human bone-derived mesenchymal stem cells (hBMSCs) were cultured in growth media (GM), osteogenic differentiation media (ODM), or ODM containing 10 nM TCDD (ODM + TCDD), thus enabling a comparison of the transcriptomic profiles of undifferentiated, differentiated, and differentiated-TCDD-exposed hBMSCs, respectively. In this test system, exposure to TCDD attenuated the differentiation of hBMSCs into osteoblasts as evidenced by reduced alkaline phosphatase activity and mineralization. At various timepoints, we observed altered expression of genes that play a role in the Wnt, fibroblast growth factor, bone morphogenetic protein/transforming growth factor beta developmental pathways, as well as pathways related to extracellular matrix organization and deposition. Reconstruction of gene regulatory networks with the interactive dynamic regulatory event miner (iDREM) analysis revealed modulation of transcription factors (TFs) including POLR3G, NR4A1, RDBP, GTF2B, POU2F2, and ZEB1, which may putatively influence osteoblast differentiation and the requisite deposition and mineralization of bone extracellular matrix. We demonstrate that the combination of RNA-Seq data in conjunction with the iDREM regulatory model captures the transcriptional dynamics underlying MSC differentiation under different conditions in vitro. Model predictions are consistent with existing knowledge and provide a new tool to identify novel pathways and TFs that may facilitate a better understanding of the osteoblast differentiation process, perturbation by exogenous agents, and potential intervention strategies targeting those specific pathways.

OR30-3 Direct and VGLL1-Mediated Gene Regulation by GRHL2 During Mesenchymal to Epithelial Transition in Breast Cancer

Abstract The transcription factor (TF) GRHL2 controls normal epithelial differentiation in different tissues. It is expressed in all breast cancer subtypes except those with a mesenchymal phenotype (claudin-low subtype), where its ectopic expression leads to induction of a mesenchymal-epithelial transition (MET) (1). Here we explored the mechanisms by which GRHL2 induces MET in claudin-low breast cancer cell lines using a combination of ChIP-seq and RNAseq analyses upon modulation of GRHL2 expression in mesenchymal and epithelial cell lines. Direct DNA binding by GRHL2 was enriched in proximity of genes positively regulated in mesenchymal cell lines, which include several epithelial TFs as well as an array of epithelial genes. Biotinylation and mass spectrometry analysis of membrane proteins confirmed surfaceome remodeling via induction of membrane proteins with roles in cell-cell contacts and adhesion. Repression of mesenchymal genes was mediated in part by direct induction of miRNAs targeting mesenchymal transcription factors. In addition, GRHL2 strongly induced expression of the cofactor VGLL1, whose expression is high in the triple-negative (TNBC) basal-like subtype. VGLL1 overexpression in mesenchymal cell lines and suppression in basal-like TNBC cells confirmed its role in mediating part of GRHL2 signaling, in particular via interaction with and modulation of TEAD transcription factors. In addition, GRHL2 also interacted with VGLL1 upon its induction in mesenchymal cells, recruiting it to some of its binding motifs, suggesting a multilayered cross-talk between GRHL2 and TEAD factors. Together, our results indicate that GRHL2 acts as a master regulator in the induction of TNBC epithelial differentiation via direct upregulation of epithelial transcription factors, miRNAs and TEAD cofactor VGLL1, resulting in both upregulation of epithelial genes and suppression of mesenchymal genes.(1) Cieply B. et al., Cancer Res. 2013 Oct. 1;73 (20): 6299-309 Presentation: Tuesday, June 14, 2022 10:15 a.m. - 10:30 a.m.

CRIT: Identifying RNA-binding protein regulator in circRNA life cycle via non-negative matrix factorization

Circular RNAs (circRNAs) are endogenous non-coding RNAs that regulate gene expression and participate in carcinogenesis. However, the RNA-binding proteins (RBPs) involved in circRNAs biogenesis and modulation remain largely unclear. We developed the circRNA regulator identification tool (CRIT), a non-negative matrix-factorization-based pipeline to identify regulating RBPs in cancers. CRIT uncovered 73 novel regulators across thousands of samples by effectively leveraging genomics data and functional annotations. We demonstrated that known RBPs involved in circRNA control are significantly enriched in these predictions. Analysis of circRNA-RBP interactions using two large cross-linking immunoprecipitation (CLIP) databases, we validated the consistency between CRIT prediction and the CLIP experiments. Furthermore, newly discovered RBPs are functionally connected with authentic circRNA regulators by various biological associations, such as physical interaction, similar binding motifs, common transcription factor modulation, and co-expression. When analyzing RNA sequencing (RNA-seq) datasets after short hairpin RNA (shRNA)/small interfering RNA (siRNA) knockdown, we found several novel RBPs that can affect global circRNA expression, which strengthens their role in the circRNA life cycle. The above evidence provided independent confirmation that CRIT is a useful tool to capture RBPs in circRNA processing. Finally, we show that authentic regulators are more likely the core splicing proteins and peripheral factors and usually harbor more alterations in the vast majority of cancers.

Empagliflozin alleviates diabetic cardiomyopathy via inhibiting excessive autophagy and adverse remodeling in type 1 diabetic mice

Abstract Sodium-glucose cotransporter 2 (SGLT2) inhibitors reduce cardiovascular mortality in patients with and without diabetes mellitus, but underlying mechanisms remain unclear. Autophagy is an important cardioprotective mechanism under acute stress conditions, but excessive autophagy can accelerate myocardial cell death leading to autosis. In this study we evaluated the role of empagliflozin (EMPA) against cardiac injury in streptozotocin (STZ)-induced diabetic mice, and assessed underlying mechanisms. EMPA (10 mg/kg/die)-treated diabetic male mice had a lower number of TUNEL-positive apoptotic cells (%TdT+ 4.9±2, p<0.05), lower percentage of SA-β-gal positive senescent cardiac area (%SA-β-gal 7.9±1, p<0.05), lower fibrotic area (%picrosirius red 0.15±0.06, p<0.05), lower autophagy (%green fluorescence 2.3±0.6, p<0.01), compared to diabetic mice (%TdT+ 4.9±2; %SA-β-gal 10±2; %picrosirius red fibrotic area 0.24±0.08; %green fluorescence autophagic area 3.98±0.5). Proteomics analysis of cardiac tissue showed downregulation of apoptosis, necrosis and 5' adenosine monophosphate-activated protein kinase (AMPK) pathways, along with upstream activation of vascular endothelial growth factor and sirtuins in the heart of EMPA+STZ treated mice compared to STZ mice. Since activation of sirtuins leads to modulation of cardiomyogenic transcription factors, we analyzed total expression of serum response factor (SRF), myocardin and myocardin-related transcription factor (MRTF), and DNA binding activity of SRF by electromobility shift assay. While EMPA only increased MRTF, EMPA (2.2±0.01, p<0.01) and EMPA+STZ (2.0±0.1, p<0.01) significantly increased SRF/SRE binding activity compared with STZ alone (0.5±0.01), which was paralleled by the increase in cardiac actin expression (4.06±0.1 vs 2.2±0.01, p<0.01). EMPA significantly reversed STZ-induced systolic cardiac dysfunction at echocardiography, and downregulation of pS368-connexin 43 active isoform (Table). In parallel in vitro experiments, EMPA inhibited excessive autophagy in high glucose-treated cardiomyocytes by inhibiting the autophagy inducer GSK3β, leading to reactivation of transcriptional complex for cardiomyocyte contractile genes. Our results indicate that EMPA plays a cardioprotective effect by inhibiting excessive autophagy through the mTOR/AMPK axis in the mouse model of STZ-induced type 1 diabetes. EMPA also promotes cardiac reverse remodeling by inhibiting fibrosis, activates cardiac Cx43 and the promyogenic transcriptional program through the sirtuins-SRF axis (Figure 1), in the context of diabetes. Funding Acknowledgement Type of funding sources: None.

Plant based polyphenol associations with protein: A prospective review

This review discusses the classes of plant polyphenols along with their binding mechanisms with protein molecules. Generally, polyphenols bind in covalent and non-covalent orientations with protein molecules. Their addition to the protein usually results in undesirable flavors and tastes inside the proteins. They also affect the color of the food. Plant polyphenols are found to act in a protective way against cardiovascular disease, neurodegenerative diseases, diabetes, and cancer. In addition to redox activity, their modes of action include the inhibition of key enzymes, modulation of transcription factors or cell receptors, and finally, perturbation of protein aggregates. Dietary polyphenols usually play a key role in protein digestion by forming covalent and non-covalent bonds with proteins. In addition, polyphenols and plant phenolics possess the scavenging ability of reactive oxygen species (ROS), including radical/non-radical oxygen species including HOC•, H2O2, HOCl, 1O2 (singlet oxygen), and oxidatively generated radicals derived from LDL biomolecules such as ROOC• and oligonucleic acids.

Protein arginine methyltransferase PRMT1 promotes adipogenesis by modulating transcription factors C/EBPβ and PPARγ

Protein arginine methyltransferase 1 (PRMT1) methylates a variety of histone and nonhistone protein substrates to regulate multiple cellular functions such as transcription, DNA damage response, and signal transduction. It has been reported as an emerging regulator of various metabolic pathways including glucose metabolism in the liver, atrophy in the skeletal muscle, and lipid catabolism in the adipose tissue. However, the underlying mechanisms governing how PRMT1 regulates adipogenesis remain elusive. Here, we delineate the roles of PRMT1 in mitotic clonal expansion and adipocyte differentiation. Gain and loss of functions demonstrate that PRMT1 is essential for adipogenesis of 3T3-L1 and C3H10T1/2 cells. Mechanistically, we show PRMT1 promotes the expression of transcription factor peroxisome proliferator-activated receptor-γ (PPARγ) by catalyzing histone modification H4R3me2a and impedes the activation of Wnt/β-catenin signaling by increasing the level of Axin to accelerate adipogenic differentiation. In addition, we demonstrate mitotic clonal expansion is suppressed by PRMT1 deficiency. PRMT1 interacts with transcription factor CCATT enhancer-binding protein β (C/EBPβ), and the absence of PRMT1 leads to the depressed phosphorylation of C/EBPβ. Interestingly, we discover PRMT1 acts as a positive regulator of C/EBPβ protein stability through decreasing the level of E3 ubiquitin ligase Smurf2, which promotes the ubiquitination and degradation of C/EBPβ, thus facilitating adipogenesis. Collectively, these discoveries highlight a critical role of PRMT1 in adipogenesis and provide potential therapeutic targets for the treatment of obesity.

Integrated RNA-sequencing and network pharmacology approach reveals the protection of Yiqi Huoxue formula against idiopathic pulmonary fibrosis by interfering with core transcription factors

BackgroundIdiopathic pulmonary fibrosis (IPF) is a refractory disease. Therefore, developing effective therapies for IPF is the need of the hour. PurposeYiqi Huoxue Formula (YQHX) is an herbal formula comprising three herbal medicines: Ligusticum chuanxiong Hort. (Chuanxiong Rhizoma, CR), Panax notoginseng (Burk.) F. H. Chen (Notoginseng Radix Et Rhizoma, NR) and Panax ginseng C. A. Mey. (Ginseng Radix Et Rhizoma, GR). This study aims to determine the anti-pulmonary fibrosis effect of YQHX and explore its mechanism of action. StudyDesign and Methods: The chemical components in the GR, CR and NR extracts were identified by High Performance Liquid Chromatography. A TGF-β1-induced myofibroblast cell model was used to test the anti-fibrosis effect of GR, CR, NR and YQHX. RNA-sequencing was used to identify the differentially expressed genes (DEGs) after YQHX treatment. Subsequently, gene enrichment analysis and key transcription factors (TFs) prediction for YQHX-regulated DEGs was performed. The active constituents of GR, CR and NR were obtained from the Traditional Chinese Medicine Database and Analysis Platform. Targets of the active constituents were predicted using the similarity ensemble approach search server and Swiss Target Prediction tool. YQHX-targeted key TFs that transcribed the DEGs were screened out. Then, the effect of YQHX on the bleomycin-induced pulmonary fibrosis mouse model was studied. Finally, one of the predicted TFs, STAT3, was selected to validate the prediction accuracy. ResultsSeven, two, and five compounds were identified in the GR, CR, and NR extracts, respectively. YQHX and its constituents-GR, CR and NR-inhibited the expression of fibrotic markers, including α -SMA and fibronectin, indicating that YQHX inhibited TGF-β1-induced myofibroblast activation. RNA-sequencing identified 291 genes that were up-regulated in the TGF-β1 group but down-regulated after YQHX treatment. In total, 55 key TFs that transcribed YQHX-regulated targets were predicted. A regulatory network of 24 active ingredients and 232 corresponding targets for YQHX was established. Among YQHX's predicted targets, 20 were TFs. On overlapping YQHX-targeted TFs and DEGs’ key TFs, six key TFs, including HIF1A, STAT6, STAT3, PPARA, DDIT3 and AR, were identified as the targets of YQHX. Additionally, YQHX alleviated bleomycin-induced pulmonary fibrosis in a mouse model by inhibiting the phosphorylation of STAT3 in the lungs of pulmonary fibrosis mice. ConclusionsThis study provides pharmacological support for the use of YQHX in the treatment of IPF. The potential mechanism of action of YQHX is speculated to involve the modulation of core TFs and inhibition of pathogenetic gene expressions in IPF.

Unveiling the Molecular Mechanisms Driving the Capsaicin-Induced Immunomodulatory Effects on PD-L1 Expression in Bladder and Renal Cancer Cell Lines.

Simple SummaryOver time, capsaicin (CPS) has been considered both a potential anti-cancer and pro-cancer molecule. Hence, the diversity of CPS functioning has already been established. Now, exploration of its application with immunotherapies might open up a new avenue in cancer therapy. Herein, the application of CPS as an immunoadjuvant to overcome the tumor’s immune-escaping mechanisms or to increase immune checkpoint therapy has been approached. In bladder cancer, the interaction of CPS with its receptor TRPV1 increases PD-L1 expression, promoting a tumorigenic effect and also providing a target for anti-PD-1/PD-L1 immunotherapy. On the contrary, in renal cell carcinoma, CPS downregulates PD-L1 expression in a TRPV1-independent manner, suggesting a potential application of CPS as an immune-adjuvant in this type of cancer.The blockade of the PD-L1/PD-1 immune checkpoint has promising efficacy in cancer treatment. However, few patients with bladder cancer (BC) or renal cell carcinoma (RCC) respond to this approach. Thus, it is important to implement a strategy to stimulate the immune anti-tumor response. In this scenario, our study evaluated the effects of a low capsaicin (CPS) dose in BC and RCC cell lines. Western blot, qRT-PCR and confocal microscopy were used to assess PD-L1 mRNA and protein expression. Alterations to the cellular oxidative status and changes to the antioxidant NME4 levels, mRNA modulation of cytokines, growth factors, transcriptional factors and oncogene, and the activation of Stat1/Stat3 pathways were examined using Western blot, cytofluorimetry and qRT-PCR profiling assays. In BC, CPS triggers an altered stress oxidative-mediated DNA double-strand break response and increases the PD-L1 expression. On the contrary, in RCC, CPS, by stimulating an efficient DNA damage repair response, thus triggering protein carbonylation, reduces the PD-L1 expression. Overall, our results show that CPS mediates a multi-faceted approach. In modulating PD-L1 expression, there is a rationale for CPS exploitation as a stimulus that increases BC cells’ response to immunotherapy or as an immune adjuvant to improve the efficacy of the conventional therapy in RCC patients.

Silibinin downregulates the expression of the Th1 and Th17 profiles by modulation of STATs and transcription factors in pregnant women with preeclampsia

Preeclampsia (PE) is a multifactorial disease that is characterized by inflammation. Some of the factors responsible for this inflammation are the cells of the innate and adaptive immune systems and their interactions. The use of natural products, such as silibinin (SB), can contribute to the control of this inflammation and gestational success. The present study evaluated whether the flavonoid SB has an in vitro immunomodulatory effect on the signal transducers and transcription activators (STATs) signaling pathway and transcription factors of CD4+ T cell subsets obtained from preeclamptic and normotensive (NT) pregnant women. Peripheral blood mononuclear cells (PBMCs) from 18 preeclamptic and 18 NT pregnant women were cultured with and without SB to analyze the expression of STATs and transcription factors by flow cytometry, and cytokines were measured in the culture supernatant by ELISA. The results showed that treating cells with SB decreased STAT1/ STAT4/T-bet and STAT3/RORγt, which characteristic of Th1 and Th17 inflammatory profiles, as well as increased STAT6/GATA-3 and STAT5/FoxP3 of anti-inflammatory and regulatory profiles, respectively. In addition, PBMCs from preeclamptic women treated with SB released lower concentrations of inflammatory cytokines and higher levels of IL-10 and TGF-β. Therefore, SB plays an immunomodulatory role on CD4+ T cell subsets in PE, leading to the downregulation of inflammatory profiles and upregulation of anti-inflammatory and regulatory profiles. More studies are necessary to better understand the modulation of CD4+ T cell subsets by the JAK/STAT and NF-κB pathways in this gestational pathology.

Onion Vinegar Quality Evaluation and its Alleviate Oxidative Stress Mechanism in Caenorhabditis elegans Via SKN-1

Recently, there has been renewed interest in biorefining of agricultural onion into functional products. In this study, onion vinegar (OV) are prepared by a two-stage semi-continuous fermentation method, and its content of total flavonoids (3.01 mg/mL) and polyphenols (976.76 μg/mL) is superior to other commercial vinegars. OV possesses a high radical scavenging activity and enhances the antioxidant enzyme activities in vivo, alleviating intracellular oxidative stress in Caenorhabditis elegans. Treated by OV, the 1,1-diphenyl-2-picryl-hydrazyl radical (DPPH·), diammonium 2,2′-azino-bis (3-ethylbenzo thiazoline-6-sulfonic acid) (ABTS+·) and 2-phenyl-4,4,5,5- tetramethylimidazoline-1-oxyl 3-Oxide (PTIO·) free radicals clearance rates are 88.76, 98.76 and 90.54%, respectively in vitro. Whereas the glutathione peroxidase (GSH-Px), superoxide dismutase (SOD) and catalase (CAT) enzyme activities in C. elegans reach 271.57, 129.26, and 314.68%, respectively. Using RNAi and RT-PCR, it has been further confirmed that OV modulates transcription factor SKN-1, the nuclear factor erythroid 2-related factor 2 (Nrf2) homologous, in C. elegans, enhancing the resistance of C. elegans against sodium arsenite stress. Lifespan analysis reveals that 1 mL OV extends the maximum lifespan of the nematode to 26 days. Evidence is presented which shows that OV increases the lifespan of C. elegans by activating the SKN-1 signaling pathway. Overall, the OV is a well functional condiment, enhancing the value-added of onion.

Dendritic cell activation and screening for key molecular signatures required for the induction of allergic responses.

The chain of events that leads to the sensitization of the immune system to environmental antigens, resulting in the onset of allergic disease, has been studied in great detail over the past 30 years. However, during this time, the rate of allergic diseases has increased exponentially, indicating the need to concentrate our studies on host-environmental factors that contribute to the onset of disease. Monocyte-derived dendritic cells (DCs) play a key role in driving localized and systemic immune responses. In this study, we developed a platform for screening the molecular signature and phenotypic profile of DCs activated by allergenic stimuli, including TSLP, IL-25, IL-33, IL-1a, Vit-D3 (1α,25-Dihydroxyvitamin D3), PAR1-AP Peptide, Papain, and recombinant human DerP1 protein to induce a type II associated inflammatory signature. Following activation with allergenic stimuli, modulated DCs are subjected to deep phenotyping via flow cytometry for surface and intracellular markers to detect and/or validate immunomodulatory properties. RNA sequencing is further used to compare the gene expression profiles of DCs responding to either allergenic or microbial stimuli, including the TLR3 agonist dsRNA Poly I:C and TLR4 agonist LPS. In our study, we aimed to identify key molecular signatures of DCs involved in the development of asthma and allergy based on their comparative activation with this broad panel of allergens. We expect to determine central control modules of transcription factors in DCs associated with Th2 induction.

Advances in Cell Engineering of the Komagataella phaffii Platform for Recombinant Protein Production.

Komagataella phaffii (formerly known as Pichia pastoris) has become an increasingly important microorganism for recombinant protein production. This yeast species has gained high interest in an industrial setting for the production of a wide range of proteins, including enzymes and biopharmaceuticals. During the last decades, relevant bioprocess progress has been achieved in order to increase recombinant protein productivity and to reduce production costs. More recently, the improvement of cell features and performance has also been considered for this aim, and promising strategies with a direct and substantial impact on protein productivity have been reported. In this review, cell engineering approaches including metabolic engineering and energy supply, transcription factor modulation, and manipulation of routes involved in folding and secretion of recombinant protein are discussed. A lack of studies performed at the higher-scale bioreactor involving optimisation of cultivation parameters is also evidenced, which highlights new research aims to be considered.

Multigenomic modifications in human circulating immune cells in response to consumption of polyphenol rich extract of yerba mate (Ilex paraguariensis A. St.-Hil.) are suggestive of cardiometabolic protective effects.

Mate is a traditional drink obtained from the leaves of yerba mate and rich in a diversity of plant bioactive compounds including polyphenols, particularly chlorogenic acids. Studies, even though limited, suggest that consumption of mate is associated with health effects, including prevention of cardiometabolic disorders. Molecular mechanisms underlying the potential health properties are still largely unknown, especially in humans. The aim of this study was to investigate nutrigenomic effects of mate consumption and identify regulatory networks potentially mediating cardiometabolic health benefits. Healthy middle-aged men at risk for cardiovascular disease consumed a standardized mate extract or placebo for 4 weeks. Global gene expression, including protein coding and non-coding RNAs profiles were determined using microarrays. Biological function analyses were performed using integrated bioinformatic tools. Comparison of global gene expression profiles showed significant change following mate consumption with 2635 significantly differentially expressed genes, among which 6 are miRNAs and 244 are lncRNAs. Functional analyses showed that these genes are involved in regulation of cell interactions and motility, inflammation or cell signaling. Transcription factors, such as MEF2A, MYB or HNF1A, could have their activity modulated by mate consumption either by direct interaction with polyphenol metabolites or by interactions of metabolites with cell signaling proteins, like p38 or ERK1/2, that could modulate transcription factor activity and regulate expression of genes observed. Correlation analysis suggests that expression profile is inversely associated with gene expression profiles of patients with cardiometabolic disorders. Therefore, mate consumption may exert cardiometabolic protective effects by modulating gene expression towards a protective profile.

Nuclear receptor coactivator-6 is essential for the morphological change of human uterine stromal cell decidualization via regulating actin fiber reorganization.

Nuclear receptor coactivator 6 (Ncoa6), a modulator of several nuclear receptors and transcription factors, is essential for the decidualization of endometrial stromal cells in mice. However, the function of Ncoa6 in the human endometrium remains unclear. We investigated its function in the decidualization of human endometrial stromal cells (HESCs) isolated from resected uteri. Knockdown of Ncoa6 was performed using two independent small interfering RNAs. Decidualization was induced in vitro via medroxyprogesterone and cyclic adenosine monophosphate. We compared decidualized cellular morphology between the Ncoa6 knockdown cells and control cells. Messenger RNA (mRNA) sequencing was performed to determine the Ncoa6 target genes in undecidualized HESCs. We found that the knockdown of Ncoa6 caused the failure of morphological changes in decidualized HESCs compared to that in the control cells. mRNA sequencing revealed that Ncoa6 regulates the expression of genes associated with the regulation of actin fibers. Ncoa6 knockdown cells failed to reorganize actin fibers during the decidualization of HESCs. Ncoa6 was shown to play an essential role in decidualization via the appropriate regulation of actin fiber regulation in HESCs. Herein, our in vitro studies revealed a part of the mechanisms involved in endometrial decidualization. Future research is needed to investigate these mechanisms in women with implantation defects.

Hsp70 in Redox Homeostasis.

Cellular redox homeostasis is precisely balanced by generation and elimination of reactive oxygen species (ROS). ROS are not only capable of causing oxidation of proteins, lipids and DNA to damage cells but can also act as signaling molecules to modulate transcription factors and epigenetic pathways that determine cell survival and death. Hsp70 proteins are central hubs for proteostasis and are important factors to ameliorate damage from different kinds of stress including oxidative stress. Hsp70 members often participate in different cellular signaling pathways via their clients and cochaperones. ROS can directly cause oxidative cysteine modifications of Hsp70 members to alter their structure and chaperone activity, resulting in changes in the interactions between Hsp70 and their clients or cochaperones, which can then transfer redox signals to Hsp70-related signaling pathways. On the other hand, ROS also activate some redox-related signaling pathways to indirectly modulate Hsp70 activity and expression. Post-translational modifications including phosphorylation together with elevated Hsp70 expression can expand the capacity of Hsp70 to deal with ROS-damaged proteins and support antioxidant enzymes. Knowledge about the response and role of Hsp70 in redox homeostasis will facilitate our understanding of the cellular knock-on effects of inhibitors targeting Hsp70 and the mechanisms of redox-related diseases and aging.

Activation and negative feedback regulation of SlHY5 transcription by the SlBBX20/21-SlHY5 transcription factor module in UV-B signaling.

In tomato (Solanum lycopersicum) and other plants, the photoreceptor UV-RESISTANCE LOCUS 8 regulates plant UV-B photomorphogenesis by modulating the transcription of many genes, the majority of which depends on the transcription factor ELONGATED HYPOCOTYL 5 (HY5). HY5 transcription is induced and then rapidly attenuated by UV-B. However, neither the transcription factors that activate HY5 transcription nor the mechanism for its attenuation during UV-B signaling is known. Here, we report that the tomato B-BOX (BBX) transcription factors SlBBX20 and SlBBX21 interact with SlHY5 and bind to the SlHY5 promoter to activate its transcription. UV-B-induced SlHY5 expression and SlHY5-controlled UV-B responses are normal in slbbx20 and slbbx21 single mutants, but strongly compromised in the slbbx20 slbbx21 double mutant. Surprisingly, UV-B responses are also compromised in lines overexpressing SlBBX20 or SlBBX21. Both SlHY5 and SlBBX20 bind to G-box1 in the SlHY5 promoter. SlHY5 outcompetes SlBBX20 for binding to the SlHY5 promoter in vitro, and inhibits the association of SlBBX20 with the SlHY5 promoter in vivo. Overexpressing 35S:SlHY5-FLAG in the WT background inhibits UV-B-induced endogenous SlHY5 expression. Together, our results reveal the critical role of the SlBBX20/21-SlHY5 module in activating the expression of SlHY5, the gene product of which inhibits its own gene transcription under UV-B, forming an autoregulatory negative feedback loop that balances SlHY5 transcription in plants.

Silent Hypoxia in COVID-19 Pneumonia: State of Knowledge, Pathophysiology, Mechanisms, and Management.

Patients with COVID-19 often present with life-threatening hypoxemia without dyspnea or signs of respiratory distress. Termed silent or happy hypoxia, it has puzzled clinicians and challenged and defied our understanding of normal respiratory physiology. A range of host- and pathogen-related factors appears to contribute to its development, including SARS-CoV-2's ability to produce different COVID-19 phenotypes; induce endothelial damage and elicit a vascular distress response; invade cells of the central nervous system and disrupt normal interoception and response; and modulate transcription factors involved in hypoxic responses. Because hypoxemia in COVID-19 is associated with increased mortality risk and poorer survival, early detection and prompt treatment is essential to prevent potential complications. Interventions to prevent hypoxemia and improve oxygen delivery to the blood and the tissues include home pulse-oximetry monitoring, optimization of patient positioning, judicious use of supplemental oxygen, breathing control exercises, and timely and appropriate use of ventilatory modalities and adjuncts.

Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification.

SummaryElucidating regulatory relationships between transcription factors (TFs) and target genes is fundamental to understanding how cells control their identity and behavior. Unfortunately, existing computational gene regulatory network (GRN) reconstruction methods are imprecise, computationally burdensome, and fail to reveal dynamic regulatory topologies. Here, we present Epoch, a reconstruction tool that uses single-cell transcriptomics to accurately infer dynamic networks. We apply Epoch to identify the dynamic networks underpinning directed differentiation of mouse embryonic stem cells (ESCs) guided by multiple signaling pathways, and we demonstrate that modulating these pathways drives topological changes that bias cell fate potential. We also find that Peg3 rewires the pluripotency network to favor mesoderm specification. By integrating signaling pathways with GRNs, we trace how Wnt activation and PI3K suppression govern mesoderm and endoderm specification, respectively. Finally, we identify regulatory circuits of patterning and axis formation that distinguish in vitro and in vivo mesoderm specification.

Profiling transcription factor activity dynamics using intronic reads in time-series transcriptome data.

Activities of transcription factors (TFs) are temporally modulated to regulate dynamic cellular processes, including development, homeostasis, and disease. Recent developments of bioinformatic tools have enabled the analysis of TF activities using transcriptome data. However, because these methods typically use exon-based target expression levels, the estimated TF activities have limited temporal accuracy. To address this, we proposed a TF activity measure based on intron-level information in time-series RNA-seq data, and implemented it to decode the temporal control of TF activities during dynamic processes. We showed that TF activities inferred from intronic reads can better recapitulate instantaneous TF activities compared to the exon-based measure. By analyzing public and our own time-series transcriptome data, we found that intron-based TF activities improve the characterization of temporal phasing of cycling TFs during circadian rhythm, and facilitate the discovery of two temporally opposing TF modules during T cell activation. Collectively, we anticipate that the proposed approach would be broadly applicable for decoding global transcriptional architecture during dynamic processes.