Fragment-Based Discovery of Novel MUS81 Inhibitors.

MUS81 is a structure-selective endonuclease that cleaves various branched DNA structures arising from natural physiological processes such as homologous recombination and mitosis. Due to this, MUS81 is able to relieve replication stress, and its function has been reported to be critical to the survival of many cancers, particularly those with dysfunctional DNA-repair machinery. There is therefore interest in MUS81 as a cancer drug target, yet there are currently few small molecule inhibitors of this enzyme reported, and no liganded crystal structures are available to guide hit optimization. Here we report the fragment-based discovery of novel small molecule MUS81 inhibitors with sub-µM biochemical activity. These inhibitors were used to develop a novel crystal system, providing the first structural insight into the inhibition of MUS81 with small molecules.

Hypoxia-responsive gene F3 Promotes GBM Cell Proliferation and Migration through Activating NF-κB/p65 Signaling Pathway.

Background: Glioblastoma multiforme (GBM) is the most common malignant form of glioma, but the molecular mechanisms underlying the progression of GBM in hypoxic microenvironment remain elusive. This study aims to explore the pathological functions of hypoxia-responsive genes on GBM progression and its downstream signaling pathways. Methods: RNA-seq was performed in normoxic and hypoxic U87 cells to identify the differentially expressed genes (DEGs) under hypoxia. The mRNA expression levels of hypoxia-responsive gene F3 in glioma clinical samples were analyzed according to the transcriptional information from CGGA, TCGA and Rembrandt databases. EdU, transwell and wound-healing assays were conducted to evaluate the pathological functions of F3 on GBM proliferation and migration under hypoxia. RNA-seq and gene set enrichment analysis were conducted to analyze the enriched pathways in LN229 cells overexpressed F3 compared to controls. GBM cells were treated with NF-κB inhibitor PDTC, and cell experiments were performed to evaluate the effects of PDTC on OE-F3-LN229 and OE-F3-U87 cells. Western blot was performed to validate the downstream pathways. Results: F3 was identified as a hypoxia responsive gene in GBM cells. The mRNA expression level of F3 was negatively correlated with the overall survival of glioma patients, and significantly increased in grade IV and GBM than lower grade or other histology of glioma. Overexpression of F3 enhanced the proliferation and migration of hypoxic U87 and LN229 cells, while knockdown inhibited them. In OE-F3-LN229 cells, the NF-κB pathway was activated, with an increased level of phosphorylated p65. PDTC treatment effectively rescued the enhanced proliferation and migration of OE-F3-LN229 cells under hypoxia, indicating that the effect of F3 on GBM progression is probably dependent on the NF-κB pathway. Conclusion: Hypoxia-induced F3 activates NF-κB pathway through upregulation of the phosphorylated p65, thus promoting the proliferation and migration of GBM cells under hypoxia, which might be a potential therapeutic target for GBM treatment.

PCM1 conveys centrosome asymmetry to polarized endosome dynamics in regulating daughter cell fate.

Vertebrate radial glia progenitors (RGPs), the principal neural stem cells, balance self-renewal and differentiation through asymmetric cell division (ACD), during which unequal inheritance of centrosomes is observed. Mechanistically, how centrosome asymmetry leads to distinct daughter cell fate remains largely unknown. Here we find that the centrosome protein Pericentriolar Material 1 (Pcm1), asymmetrically distributed at the centrosomes, regulates polarized endosome dynamics and RGP fate. In vivo time-lapse imaging and nanoscale-resolution expansion microscopy of zebrafish embryonic RGPs detect Pcm1 on Notch ligand-containing endosomes, in a complex with the polarity regulator Par-3 and dynein motor. Loss of pcm1 disrupts endosome dynamics, with clonal analysis uncovering increased neuronal production at the expense of progenitors. Pcm1 facilitates an exchange of Rab5b (early) for Rab11a (recycling) endosome markers and promotes the formation of Par-3 and dynein macromolecular complexes on recycling endosomes. Finally, in human-induced pluripotent stem cell-derived brain organoids, PCM1 shows asymmetry and co-localization with PARD3 and RAB11A in mitotic neural progenitors. Our data reveal a new mechanism by which centrosome asymmetry is conveyed by Pcm1 to polarize endosome dynamics and Notch signaling in regulating ACD and progenitor fate.

LncRNA MAGI2-AS3 promotes fracture healing through downregulation of miR-223-3p.

BACKGROUND: Long non-coding RNAs (LncRNAs) are recognized as a pivotal element in the processes of fracture healing and the osteogenic differentiation of stem cells. This study investigated the molecular mechanism and regulatory significance of lncRNA MAGI2-AS3 (MAGI2-AS3) in fracture healing. METHODS: Serum levels of MAGI2-AS3 in patients with normal and delayed fracture healing were verified by RT-qPCR assays. The predictive efficacy of MAGI2-AS3 for delayed fracture healing was analyzed by ROC curve. Osteogenic markers were quantified by RT-qPCR assays. MC3T3-E1 cell viability was detected using CCK-8 assay, and flow cytometry was utilized to measure cell apoptosis. The dual-luciferase reporter gene assay was used to determine the targeted binding between MAGI2-AS3 and miR-223-3p. RESULTS: Serum MAGI2-AS3 expression was decreased in patients with delayed fracture healing compared with patients with normal healing. Elevated MAGI2-AS3 resulted in an upregulation of the proliferative capacity of MC3T3-E1 cells and a decrease in mortality, along with increased levels of both osteogenic markers. However, after transfection silencing MAGI2-AS3, the trend was reversed. Additionally, miR-223-3p was the downstream target of MAGI2-AS3 and was controlled by MAGI2-AS3. miR-223-3p mimic reversed the promoting effects of MAGI2-AS3 overexpression on osteogenic marker levels and cell growth, and induced cell apoptosis. CONCLUSION: The upregulation of MAGI2-AS3 may expedite the healing of fracture patients by targeting miR-223-3p, offering a novel biomarker for diagnosing patients with delayed healing.

CircVCAN promotes glioma progression through the miR-488-3p/MEF2C-JAGGED1 axis.

Gliomas are the most prevalent primary malignant brain tumors worldwide. Growing evidences indicate that circular RNAs (circRNAs) play an important role in the regulation of biological behavior of tumors. We aimed to investigate the role and mechanism of circVCAN in glioma. RNase R treatment was utilized to assess the cyclic properties of circVCAN. CircVCAN, miR-488-3p, and myocyte enhancer factor 2C (MEF2C) levels in glioma tissues and cells were detected by reverse transcription real-time polymerase chain reaction (RT-qPCR), and the localization of them in glioma cells was determined with fluorescence in situ hybridization. Furthermore, a variety of biologically functional assessments were used to validate the role of circVCAN in glioma. The regulatory mechanisms of circVCAN, miR-488-3p, and MEF2C were further confirmed by double luciferase reporter gene assay, RNA immunoprecipitation and RNA pull-down assay, and the binding of MEF2C to JAGGED1 was revealed by chromatin immunoprecipitation. Additionally, a xenograft tumor model was constructed to demonstrate the effect of circVCAN on tumor growth in vivo. Our results indicated that circVCAN was more stable than its linear RNA and was significantly upregulated in gliomas. CircVCAN overexpression stimulated glioma cells to proliferate and metastasize, but circVCAN silencing exerted the opposite effect. Meanwhile, silencing circVCAN inhibited tumor growth in vivo. Moreover, we found that circVCAN interacted with miR-488-3p to regulate MEF2C expression, and miR-488-3p inhibition or MEF2C overexpression reversed the inhibitory effect on malignant bio-behaviors mediated by circVCAN knockdown in glioma cells. MEF2C promoted the transcription of JAGGED1, and circVCAN knockdown reduced the binding between MEF2C and JAGGED1. Collectively, circVCAN is a carcinogenic circRNA in glioma, and the circVCAN/miR-488-3p/MEF2C-JAGGED1 axis could serve as a potential target for the management of glioma.

Different inhibitory mechanisms of flexible and rigid clay minerals on the transport of microplastics in marine porous media.

Colloidal interactions between clay minerals and microplastics (MPs) in high salinity seawater are crucial for determining MP fate in marine environments. Montmorillonite (MMT) forms thin and pliable films that tightly cover MPs, while the thick and rigid lamellae of kaolinite (KLT) have limited contact with MPs, resulting in unstable bonding. However, a small quantity of small-sized KLT can create relatively stable heteroaggregates by embedding into the interstitial spaces of MPs. Both MMT and KLT colloids can decrease the mobility of MPs in seawater-saturated sea sand, but their breakthrough curves (BTCs) show distinct phenomena of "blocking" and "ripening", respectively. The "blocking" phenomenon occurs when flexible MMT adheres to the sand surface, depleting attachment sites quickly and inhibiting the retention of subsequent heteroaggregates of MMT-wrapped MPs. The transport of single MMT also experiences colloid competition for attachment sites, but pre-equilibration experiments reveal no competition between MMT and bare MPs for attachment sites. Instead, the attached MMT provides additional attachment sites for MPs. These results suggest that the wrapping of MPs by MMT plays a dominant role in the "blocking" of cotransport. In contrast, rigid KLT forms a three-dimensional stack on the sand surface, offering more attachment sites for subsequent MPs and heteroaggregates.

Discovery and Optimization of Potent, Efficacious and Selective Inhibitors Targeting EGFR Exon20 Insertion Mutations.

Herein, we report the identification and optimization of a series of potent inhibitors of EGFR Exon20 insertions with significant selectivity over wild-type EGFR. A strategically designed HTS campaign, multiple iterations of structure-based drug design (SBDD), and tactical linker replacement led to a potent and wild-type selective series of molecules and ultimately the discovery of 36. Compound 36 is a potent and selective inhibitor of EGFR Exon20 insertions and has demonstrated encouraging efficacy in NSCLC EGFR CRISPR-engineered H2073 xenografts that carry an SVD Exon20 insertion and reduced efficacy in a H2073 wild-type EGFR xenograft model compared to CLN-081 (5), indicating that 36 may have lower EGFR wild-type associated toxicity.

Identification of PANoptosis-related predictors for prognosis and tumor microenvironment by multiomics analysis in glioma.

PANoptosis is a newly described inflammatory programmed cell death, that highlights coordination between pyroptosis, apoptosis and necroptosis. However, the functions of PANoptosis-related genes in glioma progression still remain to be explored. This study aims to identify PANoptosis-related predictors that may be utilized for prognosis prediction and development of new therapeutic targets. Firstly, bulk and single-cell RNA-seq (scRNA-seq) data of glioma patients were extracted from TCGA, CGGA and GEO database. Genetic analysis indicates a considerably high mutation frequency of PANoptosis-related genes (PANRGs) in glioma. Consensus clustering was applied to reveal different subtypes of glioma based on PANRGs. Two PANoptosis subtypes with distinct prognostic and TME characteristics were identified. Then, with LASSO-Cox regression analysis, four PANoptosis-related predictors (MYBL2, TUBA1C, C21orf62 and KCNIP2) were determined from bulk and scRNA-seq analysis. Predictive PANRG score model was established with these predictors and its correlation with tumor microenvironment (TME) was investigated. The results showed that patients with low PANRG score, had higher infiltration of anti-tumor immune cells, higher MSI score and lower TIDE score, which are more likely to benefit from immunotherapy. Further analysis identified 16 potential drugs associated with PANoptosis-related predictors. Moreover, the expression levels of four PANoptosis-related predictors were examined in clinical samples and the results were consistent with those analyzed in the database. Besides, we also confirmed the biological functions of two oncogenic predictors (MYBL2 and TUBA1C) by cell experiments, which revealed that knockdown of MYBL2 or TUBA1C could significantly inhibit the proliferation and migration of glioma cells. These findings highlight the prognostic value and biological functions of PANRGs in glioma, which may provide valuable insights for individualized treatment.

Whole transcriptome sequencing identifies a competitive endogenous RNA network that regulates the immunity of bladder cancer.

Several types of non-coding RNAs such as circRNAs, lncRNAs, and miRNAs have been identified to regulate mRNAs through the mechanism known as the competitive endogenous RNA (ceRNA) network. To explore the role of the ceRNA regulatory network in the immune microenvironment of bladder cancer, whole-transcriptome sequencing of bladder tumor and its peritumoral tissues from 38 bladder cancer patients, with a total of 63 samples, was performed to screen differentially expressed circ-, lnc-, mi-, and mRNAs to construct a circ/lnc-mi-mRNA regulatory network with pruning algorithms. We excavated a key immune-related gene BDNF to build the final ceRNA network as hsa-miR-107 sponged by hsa-circ-000211, AC108488.1, and LINC00163. Finally, a meta-analysis of 7 public datasets demonstrated that low expression of BDNF and high expression of hsa-miR-107 were associated with longer survival. Our study identified a ceRNA regulatory network as a potentially new prognostic marker and molecular therapeutic target of bladder cancer.

Urea Coated with Polyaspartic Acid-Chitosan Increases Foxtail Millet (Setaria italica L. Beauv.) Grain Yield by Improving Nitrogen Metabolism.

Innovative measures of nitrogen (N) fertilization to increase season-long N availability is essential for gaining the optimal foxtail millet (Setaria italica L. Beauv.) productivity and N use efficiency. A split plot field experiment was conducted using the foxtail millet variety Huayougu 9 in 2020 and 2021 in Northeast China to clarify the physiological mechanism of a novel polyaspartic acid-chitosan (PAC)-coated urea on N assimilation and utilization from foxtail millet. Conventional N fertilizer (CN) and the urea-coated -PAC treatments were tested under six nitrogen fertilizer application levels of 0, 75, 112.5, 150, 225, and 337.5 kg N ha-1. The results showed that compared to CN, PN increased the foxtail millet yield by 5.53-15.75% and 10.43-16.17% in 2020 and 2021, respectively. PN increased the leaf area index and dry matter accumulation by 7.81-18.15% and 12.91-41.92%, respectively. PN also enhanced the activities of nitrate reductase, glutamine synthetase, glutamic oxaloacetic transaminase, and glutamic-pyruvic transaminase, thereby increasing the soluble protein in the leaf, plant, and grain N content at harvest compared to CN. Consequently, partial factor productivity from applied N, the agronomic efficiency of applied N, recovery efficiency of applied N, and physiological efficiency of applied N of foxtail millet under PN treatments compared to CN were increased. The improvement effect of the items above was more noticeable under the low-middle N application levels (75, 112.5, and 150 kg N ha-1). In conclusion, the PAC could achieve the goal of high yield and high N use efficiency in foxtail millet under the background of a one-time basic fertilizer application.

Large language models assisted multi-effect variants mining on cerebral cavernous malformation familial whole genome sequencing.

Cerebral cavernous malformation (CCM) is a polygenic disease with intricate genetic interactions contributing to quantitative pathogenesis across multiple factors. The principal pathogenic genes of CCM, specifically KRIT1, CCM2, and PDCD10, have been reported, accompanied by a growing wealth of genetic data related to mutations. Furthermore, numerous other molecules associated with CCM have been unearthed. However, tackling such massive volumes of unstructured data remains challenging until the advent of advanced large language models. In this study, we developed an automated analytical pipeline specialized in single nucleotide variants (SNVs) related biomedical text analysis called BRLM. To facilitate this, BioBERT was employed to vectorize the rich information of SNVs, while a deep residue network was used to discriminate the classes of the SNVs. BRLM was initially constructed on mutations from 12 different types of TCGA cancers, achieving an accuracy exceeding 99%. It was further examined for CCM mutations in familial sequencing data analysis, highlighting an upstream master regulator gene fibroblast growth factor 1 (FGF1). With multi-omics characterization and validation in biological function, FGF1 demonstrated to play a significant role in the development of CCMs, which proved the effectiveness of our model. The BRLM web server is available at http://1.117.230.196.

Green synthesis of iron nanoparticles using mulberry leaf extract: characterization, identification of active biomolecules, and catalytic activity.

The synthesis of iron-based nanoparticles (Fe NPs) using traditional preparation methods suffered from the disadvantages of high cost, environmental harm, and easy agglomeration. In this study, a novel eco-friendly method was proposed for the synthesis of iron nanomaterials (ML-Fe NPs): using antioxidant components extracted from mulberry leaf to reduce divalent iron (II). The preparation conditions of ML-Fe NPs were optimized by orthogonal tests. The prepared ML-Fe NPs exhibited an amorphous core-shell structure, displaying excellent dispersion and stability. During the synthesis process of ML-Fe NPs, the polyphenol molecules in mulberry leaf extract played a dominant role. A possible synthetic mechanism involving complexation, reduction, and encapsulation was proposed. Furthermore, the ML-Fe NPs were utilized to construct an ML-Fe NPs/peroxymonosulfate catalytic system for the degradation of Rhodamine B dye wastewater. The ML-Fe NPs demonstrated remarkable catalytic potential, achieving a 99% degradation efficiency for Rhodamine B within a span of 40 min.

FOXO3a-interacting proteins' involvement in cancer: a review.

Due to its role in apoptosis, differentiation, cell cycle arrest, and DNA damage repair in stress responses (oxidative stress, hypoxia, chemotherapeutic drugs, and UV irradiation or radiotherapy), FOXO3a is considered a key tumor suppressor that determines radiotherapeutic and chemotherapeutic responses in cancer cells. Mutations in the FOXO3a gene are rare, even in cancer cells. Post-translational regulations are the main mechanisms for inactivating FOXO3a. The subcellular localization, stability, transcriptional activity, and DNA binding affinity for FOXO3a can be modulated via various post-translational modifications, including phosphorylation, acetylation, and interactions with other transcriptional factors or regulators. This review summarizes how proteins that interact with FOXO3a engage in cancer progression.

Establishment of a prognosis prediction model for lung squamous cell carcinoma related to PET/CT: basing on immunogenic cell death-related lncRNA.

BACKGROUND: Immunogenic cell death (ICD) stimulates adaptive immunity and holds significant promise in cancer therapy. Nevertheless, the influence of ICD-associated long non-coding RNAs (lncRNAs) on the prognosis of patients with lung squamous cell carcinoma (LUSC) remains unexplored. METHODS: We employed data from the The Cancer Genome Atlas (TCGA)database to identify ICD-related lncRNAs associated with the prognosis of LUSC using univariate Cox regression analysis. Subsequently, we utilized the LOSS regression model to construct a predictive risk model for assessing the prognosis of LUSC patients based on ICD-related lncRNAs. Our study randomly allocated187 TCGA patients into a training group and 184 patients for testing the predictive model. Furthermore, we conducted quantitative polymerase chain reaction (qPCR) analysis on 43 tumor tissues from LUSC patients to evaluate lncRNA expression levelsPearson correlation analysis was utilized to analyze the correlation of risk scores with positron emission tomography/computed tomography (PET/CT) parameters among LUSC patients. RESULTS: The findings from the univariate Cox regression revealed 16 ICD-associated lncRNAs linked to LUSC prognosis, with 12 of these lncRNAs integrated into our risk model utilizing the LOSS regression. Survival analysis indicated a markedly higher overall survival time among patients in the low-risk group compared to those in the high-risk group. The area under the Receiver operating characteristic (ROC) curve to differentiate high-risk and low-risk patients was 0.688. Additionally, the overall survival rate was superior in the low-risk group compared to the high-risk group. Correlation analysis demonstrated a positive association between the risk score calculated based on the ICD-lncRNA risk model and the maximum standard uptake value (SUVmax) (r = 0.427, P = 0.0043) as well as metabolic volume (MTV)of PET-CT (r = 0.360, P = 0.0177) in 43 LUSC patients. CONCLUSION: We have successfully developed a risk model founded on ICD-related lncRNAs that proves effective in predicting the overall survival of LUSC patients.

Research on integrated inventory transportation optimization of inbound logistics via a VMI-TPL model of an existing enterprise.

Third-party logistics companies face a challenging task in minimizing inventory transportation costs due to the complexities of managing numerous suppliers. Effectively optimizing costs becomes a formidable problem for such companies. This empirical research has yielded strategies for minimizing the inventory transportation cost specifically for company D. Through a rigorous optimization process, the findings presented in this paper demonstrate an average reduction of 7.18% in company D's inventory transportation cost. By jointly optimizing inbound logistics inventory transportation under VMI-TPL mode, this study extends the theory of supplier managed inventory and improves the inbound logistics mode. The results of this study can provide quantitative support and decision-making references for the project operation management of company D and similar enterprises.

Overexpression of Glutathione S-Transferases in Human Diseases: Drug Targets and Therapeutic Implications.

Glutathione S-transferases (GSTs) are a major class of phase II metabolic enzymes. Besides their essential role in detoxification, GSTs also exert diverse biological activities in the occurrence and development of various diseases. In the past few decades, much research interest has been paid to exploring the mechanisms of GST overexpression in tumor drug resistance. Correspondingly, many GST inhibitors have been developed and applied, solely or in combination with chemotherapeutic drugs, for the treatment of multi-drug resistant tumors. Moreover, novel roles of GSTs in other diseases, such as pulmonary fibrosis and neurodegenerative diseases, have been recognized in recent years, although the exact regulatory mechanisms remain to be elucidated. This review, firstly summarizes the roles of GSTs and their overexpression in the above-mentioned diseases with emphasis on the modulation of cell signaling pathways and protein functions. Secondly, specific GST inhibitors currently in pre-clinical development and in clinical stages are inventoried. Lastly, applications of GST inhibitors in targeting cell signaling pathways and intracellular biological processes are discussed, and the potential for disease treatment is prospected. Taken together, this review is expected to provide new insights into the interconnection between GST overexpression and human diseases, which may assist future drug discovery targeting GSTs.

Dynamic RBM47 ISGylation confers broad immunoprotection against lung injury and tumorigenesis via TSC22D3 downregulation.

ISGylation is a well-established antiviral mechanism, but its specific function in immune and tissue homeostasis regulation remains elusive. Here, we reveal that the RNA-binding protein RBM47 undergoes phosphorylation-dependent ISGylation at lysine 329 to regulate immune activation and maintain lung homeostasis. K329R knockin (KI) mice with defective RBM47-ISGylation display heightened susceptibility to LPS-induced acute lung injury and lung tumorigenesis, accompanied with multifaceted immunosuppression characterized by elevated pro-inflammatory factors, reduced IFNs/related chemokines, increased myeloid-derived suppressor cells, and impaired tertiary lymphoid structures. Mechanistically, RBM47-ISGylation regulation of the expression of TSC22D3 mRNA, a glucocorticoid-inducible transcription factor, partially accounts for the effects of RBM47-ISGylation deficiency due to its broad immunosuppressive activity. We further demonstrate the direct inhibitory effect of RBM47-ISGylation on TSC22D3 expression in human cells using a nanobody-targeted E3 ligase to induce site-specific ISGylation. Furthermore, epinephrine-induced S309 phosphorylation primes RBM47-ISGylation, with epinephrine treatment exacerbating dysregulated cytokine expression and ALI induction in K329R KI mice. Our findings provide mechanistic insights into the dynamic regulation of RBM47-ISGylation in supporting immune activation and maintaining lung homeostasis.