Core Regulator Research Articles

Ferroptosis due to Cystathionine γ Lyase/Hydrogen Sulfide Downregulation Under High Hydrostatic Pressure Exacerbates VSMC Dysfunction.

Hydrostatic pressure, stretch, and shear are major biomechanical forces of vessels and play critical roles in genesis and development of hypertension. Our previous work demonstrated that high hydrostatic pressure (HHP) promoted vascular smooth muscle cells (VSMCs) two novel subsets: inflammatory and endothelial function inhibitory VSMCs and then exacerbated VSMC dysfunction. However, the underlying mechanism remains unknown. Here, we first identified that aortic GPX4 (a core regulator of ferroptosis) significantly downregulated association with VSMC novel phenotype elevation in SHR rats and hypertension patients. In primary VSMCs, HHP (200 mmHg) increased iron accumulation, ROS production, and lipid peroxidation compared with normal pressure (100 mmHg). Consistently, the ferroptosis-related gene (COX-2, TFRC, ACSL4, and NOX-1) expression was also upregulated. The ferroptosis inhibitor ferrostatin-1 (Fer-1) administration blocked HHP-induced VSMC inflammatory (CXCL2 expression) and endothelial function inhibitory (AKR1C2 expression) phenotyping switch association with elevation in the GPX4 expression, reduction in the reactive oxygen species (ROS), and lipid peroxidation production. In contrast, the ferroptosis inducer RLS3 increased HHP-induced CXCL2 and AKR1C2 expressions. These data indicate HHP-triggering ferroptosis contributes to VSMC inflammatory and endothelial function inhibitory phenotyping switch. In mechanism, HHP reduced the VSMC GSH content and cystathionine gamma-lyase (CSE)/hydrogen sulfide (H2S)—an essential system for GSH generation. Supplementation of the H2S donor-NaHS increased the VSMC GSH level, alleviated iron deposit, ROS and lipid peroxidation production. NaHS administration rescues both HHP- and RLS3-induced ferroptosis. Collectively, HHP downregulated VSMC CSE/H2S triggering GSH level reduction, resulting in ferroptosis, which contributed to the genesis of VSMC inflammation and endothelial function inhibitory phenotypes.

Noncanonical Wnt5a Signaling Suppresses Hippo/TAZ-Mediated Osteogenesis Partly Through the Canonical Wnt Pathway in SCAPs.

PurposeStem cells from the apical papilla (SCAPs) are promising seed cells for tissue regeneration medicine and possess the osteogenic differentiation potential. Wnt5a, a typical ligand of the noncanonical Wnt pathway, exhibits diverse roles in the regulation of osteogenesis. The transcriptional co-activator with PDZ-binding motif (TAZ, WWTR1) is a core regulator in the Hippo pathway and regulates stem behavior including osteogenic differentiation. This study aims to examine how Wnt5a regulates SCAPs osteogenesis and explore the precise mechanistic relationship between Wnt5a and TAZ.MethodsSCAPs were isolated from developing apical papilla tissue of extracted human immature third molars in vitro. ALP staining, ALP activity and Alizarin red staining were used to evaluate osteogenic capacity. Osteogenic-related factors were assessed by qRT-PCR or Western blotting. Additionally, the receptor tyrosine kinase-like orphan receptor 2 (ROR2) was detected by immunocytofluorescence staining and silenced by small interfering RNA to verify the function of Wnt5a/ROR2 in TAZ-mediated osteogenesis. And we constructed TAZ-overexpression and β-catenin-overexpression SCAPs generated by lentivirus to explore the precise mechanistic relationship between Wnt5a and TAZ.ResultsWnt5a (100ng/mL) significantly suppressed ALP activity, mineralization nodules formation, expression of osteogenic-related factors. Meanwhile, it decreased the expression of TAZ mRNA and protein. TAZ overexpression promoted osteogenesis of SCAPs while Wnt5a could block TAZ-mediated osteogenesis. Furthermore, ROR2 siRNA (siROR2) was found to upregulate TAZ and canonical Wnt pathway signaling related molecules such as β-catenin, GSK3β and p-GSK3β. The suppression of Wnt5a/ROR2 on osteogenesis was significantly reversed by β-catenin overexpression through Wnt5a/ROR2/β-catenin/TAZ pathway.ConclusionTaken together, the present study demonstrates that Wnt5a suppresses TAZ-mediated osteogenesis of SCAPs and there may be a Wnt5a/ROR2/β-catenin/TAZ pathway regulating osteogenesis of SCAPs. Moreover, Wnt5a could be a candidate for regulators in tissue regeneration.

Identification of Nanog as a novel inhibitor of Rad51

To develop inhibitors targeting DNA damage repair pathways is important to improve the effectiveness of chemo- and radiotherapy for cancer patients. Rad51 mediates homologous recombination (HR) repair of DNA damages. It is widely overexpressed in human cancers and overwhelms chemo- and radiotherapy-generated DNA damages through enhancing HR repair signaling, preventing damage-caused cancer cell death. Therefore, to identify inhibitors of Rad51 is important to achieve effective treatment of cancers. Transcription factor Nanog is a core regulator of embryonic stem (ES) cells for its indispensable role in stemness maintenance. In this study, we identified Nanog as a novel inhibitor of Rad51. It interacts with Rad51 and inhibits Rad51-mediated HR repair of DNA damage through its C/CD2 domain. Moreover, Rad51 inhibition can be achieved by nanoscale material- or cell-penetrating peptide (CPP)-mediated direct delivery of Nanog-C/CD2 peptides into somatic cancer cells. Furthermore, we revealed that Nanog suppresses the binding of Rad51 to single-stranded DNAs to stall the HR repair signaling. This study provides explanation for the high γH2AX level in unperturbed ES cells and early embryos, and suggests Nanog-C/CD2 as a promising drug candidate applied to Rad51-related basic research and therapeutic application studies.

Regulation of Virulence Factors Expression During the Intestinal Colonization of Vibrio parahaemolyticus.

Colonization and adhesion are the key steps for Vibrio parahaemolyticus to infect human body and cause seafood poisoning. However, at present, there is a lack of systematic review on the regulation of virulence factors expression during the intestinal colonization of V. parahaemolyticus. This review aims to describe the virulence factors associated with the colonization and adhesion of V. parahaemolyticus (multivalent adhesion molecule 7, enolase secretion, use of flagella, biofilm formation, and the action of secretion systems) and focuses on the aspects that affect these processes in V. parahaemolyticus, including secretion systems, quorum sensing (QS), and the human gastrointestinal tract. V. parahaemolyticus regulates the expression of virulence factors by forming a virulence regulation network through QS and the core regulator, ToxR, which contributes to the early colonization of the pathogen. In the virulence regulation network, the secretion systems, type III and type VI secretion systems, help V. parahaemolyticus adhere to the distal end of the small intestine by secreting effectors that induce the lysis of epithelial cells and change the shape of the intestinal lining, which provides nutrients and a suitable environment for its growth. This review summarizes the research progress in recent years on the virulence factors associated with the colonization and adhesion of V. parahaemolyticus, which provides valuable information for the safety control of marine food.

TmIKKε Is Required to Confer Protection Against Gram-Negative Bacteria, E. coli by the Regulation of Antimicrobial Peptide Production in the Tenebrio molitor Fat Body.

The inhibitor of nuclear factor-kappa B (NF-κB) kinase (IKK) is the core regulator of the NF-κB pathway against pathogenic invasion in vertebrates or invertebrates. IKKβ, -ε and -γ have pivotal roles in the Toll and immune deficiency (IMD) pathways. In this study, a homolog of IKKε (TmIKKε) was identified from Tenebrio molitor RNA sequence database and functionally characterized for its role in regulating immune signaling pathways in insects. The TmIKKε gene is characterized by two exons and one intron comprising an open reading frame (ORF) of 2,196 bp that putatively encodes a polypeptide of 731 amino acid residues. TmIKKε contains a serine/threonine protein kinases catalytic domain. Phylogenetic analysis established the close homology of TmIKKε to Tribolium castaneum IKKε (TcIKKε) and its proximity with other IKK-related kinases. The expression of TmIKKε mRNA was elevated in the gut, integument, and hemocytes of the last-instar larva and the fat body, Malpighian tubules, and testis of 5-day-old adults. TmIKKε expression was significantly induced by Escherichia coli, Staphylococcus aureus, and Candida albicans challenge in whole larvae and tissues, such as hemocytes, gut, and fat body. The knockdown of the TmIKKε messenger RNA (mRNA) expression significantly reduced the survival of the larvae against microbial challenges. Further, we investigated the induction patterns of 14 T. molitor antimicrobial peptides (AMPs) genes in TmIKKε gene-silencing model after microbial challenges. While in hemocytes, the transcriptional regulation of most AMPs was negatively regulated in the gut and fat body tissue of T. molitor, AMPs, such as TmTenecin 1, TmTenecin 4, TmDefensin, TmColeoptericin A, TmColeoptericin B, TmAttacin 1a, and TmAttacin 2, were positively regulated in TmIKKε-silenced individuals after microbial challenge. Collectively, the results implicate TmIKKε as an important factor in antimicrobial innate immune responses in T. molitor.

Roles of abscisic acid in regulating ripening and quality of strawberry, a model non-climacteric fruit.

Abscisic acid (ABA) is a dominant regulator of ripening and quality in non-climacteric fruits. Strawberry is regarded as a model non-climacteric fruit due to its extensive genetic studies and proven suitability for transgenic approaches to understanding gene function. Strawberry research has contributed to studies on color, flavor development, and fruit softening, and in recent years ABA has been established as a core regulator of strawberry fruit ripening, whereas ethylene plays this role in climacteric fruits. Despite this major difference, several components of the interacting genetic regulatory network in strawberry, such as MADS-box and NAC transcription factors, are similar to those that operate in climacteric fruit. In this review, we summarize recent advances in understanding the role of ABA biosynthesis and signaling and the regulatory network of transcription factors and other phytohormones in strawberry fruit ripening. In addition to providing an update on its ripening, we discuss how strawberry research has helped generate a broader and more comprehensive understanding of the mechanism of non-climacteric fruit ripening and focus attention on the use of strawberry as a model platform for ripening studies.

SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling.

Adult stem cells maintain regenerative tissue structure and function by producing tissue-specific progeny, but the factors that preserve their tissue identities are not well understood. The small and large intestines differ markedly in cell composition and function, reflecting their distinct stem cell populations. Here we show that SATB2, a colon-restricted chromatin factor, singularly preserves LGR5+ adult colonic stem cell and epithelial identity in mice and humans. Satb2 loss in adult mice leads to stable conversion of colonic stem cells into small intestine ileal-like stem cells and replacement of the colonic mucosa with one that resembles the ileum. Conversely, SATB2 confers colonic properties on the mouse ileum. Human colonic organoids also adopt ileal characteristics upon SATB2 loss. SATB2 regulates colonic identity in part by modulating enhancer binding of the intestinal transcription factors CDX2 and HNF4A. Our study uncovers a conserved core regulator of colonic stem cells able to mediate cross-tissue plasticity in mature intestines.

Feedback regulation of antioxidant transcription factor NFE2L1 and immunostimulatory factor 41BBL mediates the crosstalk between oxidative stress and tumor immunity

Targeting the immune checkpoint to inhibit tumor immune escape, which is one of the fundamental causes of cancer, has become an important strategy for cancer treatment. The molecular mechanism of tumor immune escape involved in the process of spontaneous hepatocellular carcinoma after specifically knocking out NFE2L1, the core regulator of redox homeostasis, in the mouse liver is still unclear. Transcriptome data showed that the immunostimulatory TNFSF9/41BBL was significantly reduced in NFE2L1 knockdown hepatocarcinoma HepG2 cells, and this suggests that 41BBL may be an oxidative stress-responsive immune checkpoint. The results of the promoter activity experiment showed that NFE2L1 can promote 41BBL gene transcription activation through the ARE element in the promoter region. In addition, cell biology experiments have found that overexpression of 41BBL can inhibit cell proliferation and promote senescence. Importantly, reactive oxygen species in cells significantly increased after overexpression of 41BBL, whereas NFE2L1 was inhibited, indicating that 41BBL has the effect of feedback regulating oxidative stress in cells. In conclusion, in this study, the transcriptional activation effect of NFE2L1 on 41BBL and the feedback inhibition relationship of 41BBL on NFE2L1 was clarified. The NFE2L1/41BBL axis might be an important pathway that mediates the crosstalk between oxidative stress and the tumor immune response.

Multiple Time Delays Induced Dynamics of p53 Gene Regulatory Network

p53 dynamics plays an important role in determining cell arrest or apoptosis upon DNA damage response. In this paper, based on a p53 gene regulatory network composed of its core regulator ATM, Mdm2 and Wip1, the effect of multiple time delays in transcription and translation of Mdm2 and Wip1 gene expression on p53 dynamics are investigated through theoretical and numerical analyses. The stability of the positive equilibrium point and the existence of Hopf bifurcation are demonstrated through analyzing the associated characteristic equation of the corresponding linearized system in five cases. Detailed numerical simulations and bifurcation analyses are performed to support the theoretical results. The results show that with the increase of a time delay, the positive equilibrium point becomes unstable, and the p53 dynamics presents an oscillating state. These results reveal that time delay has a significant impact on p53 dynamics and may provide a useful insight into developing anti-cancer therapy.

The relationship between hippocampal volume and P3 event‐related potential in cognitively normal older adults without and with elevated amyloid: A pilot study

AbstractBackgroundThe P3 event‐related potential (ERP) is typically reduced and delayed in patients with Alzheimer’s disease (AD). The hippocampus is a core regulator of the P3 ERP. The aim of this study was to investigate the relationship between hippocampal volume and P3 peak amplitude and latency in cognitively normal older adults with (Aβ+) and without elevated amyloid (Aβ‐).MethodAβ was assessed using a Florbetapir F‐18A positron emission tomography scan. No participants showed cognitive impairments based on performance on neuropsychological tests. Hippocampal volume was measured from T1‐weighted magnetic resonance imaging using Freesurfer. 256‐channel high‐definition electroencephalography (EEG) was used to record brain activity while completing a working memory (1‐back) test. The 1‐back test consisted of 120 non‐targets and 60 targets and lasted about 7 minutes. P3 amplitude and latency of the task effect (non‐target – target) was extracted using EEGlab software. Midline (Fz, Cz, Pz) and frontal (F3, F4) were identified a priori as channels of interest.ResultWe assessed 12 Aβ‐ participants (age 75.0 ± 6.4; MOCA 27.8 ±1.4; 6 (50%) women) and 11 Aβ+ participants (age 71.8 ± 5.6; MOCA 27.7 ± 2.0; 8 (72% women). Pearson r correlations for the total group (n = 23) demonstrated significant and positive correlations between both left and right hippocampal volume (L/R HV) and peak P3 amplitude at Fz (L HV, r = 0.55, p = 0.006); R HV, r = 0.52, p = 0.01), Cz (L HV, r = 0.55, p = 0.006; R HV, r = 0.53, p = 0.01), F3 (L HV, r = 0.50, p = 0.01; R HV, r = 0.44, p = 0.03), F4 (L HV, r = 0.57, p = 0.004; R HV, r = 0.55, p = 0.007), but not with Pz (L HV, r = 0.24, p = 0.26; R HV, r = 0.33, p = 0.12). Hippocampal volume did not correlate with any P3 peak latencies.ConclusionOur preliminary findings suggest a relationship between hippocampal volume and P3 peak amplitude in the frontocentral channels in cognitively normal older adults. Further research will reveal the putative mechanisms of neurophysiological changes in preclinical AD.

Characterization of the sugarcane MYC gene family and the negative regulatory role of ShMYC4 in response to pathogen stress

As a core regulator of the jasmonic acid (JA) signaling pathway, myelocytomatosis (MYC) transcription factors play a significant role in plant stress responses. However, there are currently no report on the MYC genes in sugarcane (Saccharum spp.), an important sugar and energy crop worldwide. Here, 23 SsMYC genes in Saccharum spontaneum, 3 ShMYC genes in Saccharum spp. hybrid R570 and 8 SbMYC genes in Sorghum bicolor were identified and classified into four groups (A-1, A-2, B, and C). Synteny analysis showed a close relationship among the MYC genes of S. spontaneum, R570, and S. bicolor. The cis-regulatory elements (CREs) in the promoter regions of the MYC genes were related to light, plant growth/development, hormones, and stress. RNA sequencing and real-time quantitative polymerase chain reaction analysis demonstrated that MYC genes were differentially expressed in sugarcane tissues and under Sporisorium scitamineum stress. A novel ShMYC4 gene was cloned from Saccharum spp. hybrid ROC22 and validated to be a nuclear-localized group A-1 member without transcriptional self-activating activity. The decreased transcripts of ShMYC4 in six different sugarcane cultivars may have been associated with its negative response to S. scitamineum. Additionally, transient expression showed that ShMYC4 negatively regulated the defense response of Nicotiana benthamiana to Ralstonia solanacearum and Fusarium solani var. coeruleum by mediating the hypersensitive response, salicylic acid, JA and ethylene pathways. This study provided comprehensive information for the MYC gene family in sugarcane, which should be helpful for functional characterization of sugarcane MYC genes in the future.

Predictive role of endothelial cell activation in cytokine release syndrome after chimeric antigen receptor T cell therapy for acute lymphoblastic leukaemia.

CD19‐target chimeric antigen receptor (CAR)‐T cell therapy is highly effective for relapsed/refractory (R/R) acute lymphoblastic leukaemia (ALL), but is often complicated by cytokine release syndrome (CRS), which is potentially life‐threatening. Endothelial cells are the core regulator of CRS in many infectious diseases and may also play a key role after CAR‐T cell therapy. We provided a detailed clinical, laboratory description and endothelial cell activation biomarkers in patients with CRS. Endothelial cell activation was associated with occurrence, development and severity of CRS, manifested by decreased serum angiopoietin (Ang)‐1 levels and increased levels of von Willebrand Factor (VWF), Ang‐2, Ang‐2:Ang‐1, sE‐selectin, soluble intercellular adhesion molecule (sICAM‐1) and soluble vascular cell adhesion molecule (sVCAM)‐1. Besides, the endothelial activation was correlated with the hepatic, kidney and hematopoietic dysfunction in CRS patients. After infusion of CAR‐T cells, we detected changes of endothelial activation‐related biomarkers within 36 hours in patients who subsequently developed CRS, especially severe CRS. Using top tree models, we could predict which patients would develop CRS, especially severe CRS, or identify the severity of CRS by certain biomarkers of endothelial activation. These data provide a new idea and will help identify new targets for early intervention and prevention of CRS.

Role of Plin5 Deficiency in Progression of Non-Alcoholic Fatty Liver Disease Induced by a High-Fat Diet in Mice

Characterized by steatosis, inflammation and fibrosis, non-alcoholic fatty liver disease (NAFLD) is a metabolic disorder. As a major lipid droplet-binding protein, Plin5 has been reported to have multiple effects on metabolism, but the effect of Plin5 deficiency on NAFLD is unknown. Plin5 knockout mice and wild-type mice were used to investigate the role of Plin5 in the progression of NAFLD by feeding a high-fat diet (HFD) for 20 weeks. Plin5 deficiency improved obesity induced by the HFD and altered glucose tolerance. Histological examination revealed that Plin5 deficiency alleviated hepatic steatosis and fibrosis induced by the HFD. Plin5 deficiency was also associated with a significant change in lipid metabolism-associated molecules. Further studies of these molecules indicated that Plin5 deficiency activated the expression of AMP-activated protein kinase and inhibited the core regulator of lipogenesis, sterol regulatory element binding protein 1 and its downstream lipid synthesis-related genes. These findings suggest that Plin5 deficiency ameliorates NAFLD by regulating lipid metabolism and inhibiting lipogenesis, and may provide a new strategy for the treatment of NAFLD.

Expression of cell proliferation regulatory factors bricd5, tnfrsf21, cdk1 correlates with expression of clock gene cry1 in testes of Hu rams during puberty.

Cryptochrome 1 (cry1), the core regulator of the circadian clock, is essential for ontogeny and mammalian reproduction. Unlike in other tissues, the cry1 gene have noncircadian functions in spermatogenesis, which implies the unique role of cry1 gene in the development of testis. The role of cry1 during the puberty has not been described yet. This study aimed to explore the relationship between cry1 expression and spermatogenic cell numbers. We analyzed testicular tissues from Hu sheep aged 0-180days by hematoxylin and eosin staining, measured cry1 and cell proliferation regulatory factors (bricd5, tnfrsf21, cdk1) expression by quantitative real-time PCR and characterized the transcription factor in the 5' flanking region of cry1 gene. The data revealed that the number of spermatocytes and early spermatocytes increased rapidly from 90 to 120 dpp (day postpartum). Correspondingly, there was a marked variation in the cry1 and cell proliferation related genes (bricd5, tnfrsf21, cdk1) mRNA expression in the testes from the age of 90days to 180days (p < 0.05). We also identified some transcription factors (tcfl5) related to cell proliferation. There is a significant causal relationship between the transcription level of cry1 gene in Hu sheep testes and the number of spermatogenic cells. It is speculated that cry1 gene may regulate the proliferation of spermatogenic cells by regulating the expression of cell proliferation related genes such as bricd5, tnfrsf21 and cdk1.

β-Hydroxybutyrate impairs neutrophil migration distance through activation of a protein kinase C and myosin light chain 2 signaling pathway in ketotic cows

Ketosis in dairy cows often occurs in the peripartal period and is accompanied by immune dysfunction. High concentrations of β-hydroxybutyrate (BHB) in peripheral blood during ketosis are closely related to the impairment of polymorphonuclear neutrophil (PMN) chemotaxis and contribute to immune dysfunction. The specific effect of BHB on PMN chemotaxis in dairy cows and the underlying molecular mechanisms are unclear. Here, 30 multiparous cows (within 3 wk postpartum) classified based on serum BHB as control (n = 15, BHB <0.6 mM) or clinically ketotic (n = 15, BHB >3.0 mM) were used. Blood samples were collected before feeding, and the isolated PMN were treated with platelet-activating factor for 0.5 h to activate their migration. Scanning electron microscopy revealed a longer tail in PMN of ketotic cows. In addition, the phosphorylation and transcription levels of myosin light chain 2 (MLC2) increased in PMN of ketotic cows. Polymorphonuclear neutrophils from control dairy cows were incubated with 3.0 mM BHB for different times in vitro, and 6 h was selected as the proper duration of BHB stimulation according to its inhibition effect on PMN migration using an under-agarose PMN chemotaxis model. Similarly, BHB stimulation in vitro resulted in inhibition of migration distance and deviation of migration direction of PMN, as well as a longer tail in morphology in the scanning electron microscope data, suggesting that BHB-induced PMN migration inhibition may be mediated by impairing the trailing edge contraction. To confirm this hypothesis, sotrastaurin (Sotra)-a specific inhibitor of protein kinase C (PKC), which is the core regulator of cell contraction-was used with or without BHB treatment in vitro. Sotra was pretreated 0.5 h before BHB treatment. Accordingly, BHB treatment increased the phosphorylation level of PKC and MLC2, the protein abundance of RhoA and rho-kinase 1 (ROCK1), and the mRNA abundance of PRKCA, MYL2, RHOA, and ROCK1 in PMN. In contrast, these effects of BHB on PMN were dampened by Sotra. As demonstrated by immunofluorescence experiments in vitro, the BHB-induced inhibition of trailing edge contraction of PMN was relieved by Sotra. In addition, Sotra also dampened the effects of BHB on PMN migration in vitro. Furthermore, as verified by in vivo experiments, compared with the control cows, both abundance and activation of PKC signaling were enhanced in PMN of ketotic cows. Overall, the present study revealed that high concentrations of blood BHB impaired PMN migration distance through inhibition of the trailing edge contraction, mediated by enhancing the activation of PKC-MLC2 signaling. These findings help explain the dysfunctional immune state in ketotic cows and provide information on the pathogenesis of infectious diseases secondary to ketosis.

In silico identification of natural product inhibitors against Octamer-binding transcription factor 4 (Oct4) to impede the mechanism of glioma stem cells.

Octamer-binding transcription factor 4 (Oct4) is a core regulator in the retention of stemness, invasive, and self-renewal properties in glioma initiating cells (GSCs) and its overexpression inhibits the differentiation of glioma cells promoting tumor cell proliferation. The Pit-Oct-Unc (POU) domain comprising POU-specific domain (POUS) and POU-type homeodomain (POUHD) subdomains is the most critical part of the Oct4 for the generation of induced pluripotent stem cells from somatic cells that lead to tumor initiation, invasion, posttreatment relapse, and therapeutic resistance. Therefore, the present investigation hunts for natural product inhibitors (NPIs) against the POUHD domain of Oct4 by employing receptor-based virtual screening (RBVS) followed by binding free energy calculation and molecular dynamics simulation (MDS). RBVS provided 13 compounds with acceptable ranges of pharmacokinetic properties and good docking scores having key interactions with the POUHD domain. More Specifically, conformational and interaction stability analysis of 13 compounds through MDS unveiled two compounds ZINC02145000 and ZINC32124203 which stabilized the backbone of protein even in the presence of linker and POUS domain. Additionally, ZINC02145000 and ZINC32124203 exhibited stable and strong interactions with key residues W277, R242, and R234 of the POUHD domain even in dynamic conditions. Interestingly, ZINC02145000 and ZINC32124203 established communication not only with the POUHD domain but also with the POUS domain indicating their incredible potency toward thwarting the function of Oct4. ZINC02145000 and ZINC32124203 also reduced the flexibility and escalated the correlations between the amino acid residues of Oct4 evidenced by PCA and DCCM analysis. Finally, our examination proposed two NPIs that can impede the Oct4 function and may help to improve overall survival, diminish tumor relapse, and achieve a cure not only in deadly disease GBM but also in other cancers with minimal side effects.

Dynamic network biomarker analysis discovers IbNAC083 in the initiation and regulation of sweet potato root tuberization.

The initiation and development of storage roots (SRs) are intricately regulated by a transcriptional regulatory network. One key challenge is to accurately pinpoint the tipping point during the transition from pre-swelling to SRs and to identify the core regulators governing such a critical transition. To solve this problem, we performed a dynamic network biomarker (DNB) analysis of transcriptomic dynamics during root development in Ipomoea batatas (sweet potato). First, our analysis identified stage-specific expression patterns for a significant proportion (>9%) of the sweet potato genes and unraveled the chronology of events that happen at the early and later stages of root development. Then, the results showed that different root developmental stages can be depicted by co-expressed modules of sweet potato genes. Moreover, we identified the key components and transcriptional regulatory network that determine root development. Furthermore, through DNB analysis an early stage, with a root diameter of 3.5 mm, was identified as the critical period of SR swelling initiation, which is consistent with morphological and metabolic changes. In particular, we identified a NAM/ATAF/CUC (NAC) domain transcription factor, IbNAC083, as a core regulator of this initiation in the DNB-associated network. Further analyses and experiments showed that IbNAC083, along with its associated differentially expressed genes, induced dysfunction of metabolism processes, including the biosynthesis of lignin, flavonol and starch, thus leading to the transition to swelling roots.

Decreased Mitochondrial Membrane Potential Activates the Mitochondrial Unfolded Protein Response.

Mitochondria are ATP-producing organelles that also signal throughout the cell. Mitochondrial protein homeostasis is regulated through membrane potential-dependent protein import and quality control signaling. The mitochondrial unfolded protein response (UPRmt) is a specific program that responds to imbalances in nuclear and mitochondrial gene expression. Mounting evidence suggests that the electrochemical gradient that powers mitochondrial function, the mitochondrial membrane potential (Δψm), is a core regulator of the UPRmt. Here we tested this notion directly by pharmacologically dissipating Δψm and monitoring UPRmt activation. We found that chemical dissipation of Δψm using FCCP indeed activated UPRmt dose-dependently in C. elegans assayed by the HSP-60::GFP reporter strain.

Sequestosome 1/p62: A multitasker in the regulation of malignant tumor aggression (Review).

Sequestosome 1 (SQSTM1)/p62 is an adapter protein mainly involved in the transportation, degradation and destruction of various proteins that cooperates with components of autophagy and the ubiquitin-proteasome degradation pathway. Numerous studies have shown that SQSTM1/p62 functions at multiple levels, including involvement in genetic stability or modification, post-transcriptional regulation and protein function. As a result, SQSTM1/p62 is a versatile protein that is a critical core regulator of tumor cell genetic stability, autophagy, apoptosis and other forms of cell death, malignant growth, proliferation, migration, invasion, metastasis and chemoradiotherapeutic response, and an indicator of patient prognosis. SQSTM1/p62 regulates these processes via its distinct molecular structure, through which it participates in a variety of activating or inactivating tumor-related and tumor microenvironment-related signaling pathways, particularly positive feedback loops and epithelial-mesenchymal transition-related pathways. Therefore, functioning as a proto-oncogene or tumor suppressor gene in various types of cancer and tumor-associated microenvironments, SQSTM1/p62 is capable of promoting or retarding malignant tumor aggression, giving rise to immeasurable effects on tumor occurrence and development, and on patient treatment and prognosis.

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and the core regulator of cellular signaling. Despite this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here, we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, and these were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between the species, this study offers insights into Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq and identified significant similarities between Sbi and Ssp. Moreover, coexpression networks allowed inference of a core structure of kinase interactions with specific key elements. This study provides the first categorization of the allelic specificity of a kinome and offers a wide reservoir of molecular and genetic information, thereby enhancing the understanding of Sbi and Ssp PK evolutionary history.