A comprehensive review of bioinformatics tools for chromatin loop calling.

Precisely calling chromatin loops has profound implications for further analysis of gene regulation and disease mechanisms. Technological advances in chromatin conformation capture (3C) assays make it possible to identify chromatin loops in the genome. However, a variety of experimental protocols have resulted in different levels of biases, which require distinct methods to call true loops from the background. Although many bioinformatics tools have been developed to address this problem, there is still a lack of special introduction to loop-calling algorithms. This review provides an overview of the loop-calling tools for various 3C-based techniques. We first discuss the background biases produced by different experimental techniques and the denoising algorithms. Then, the completeness and priority of each tool are categorized and summarized according to the data source of application. The summary of these works can help researchers select the most appropriate method to call loops and further perform downstream analysis. In addition, this survey is also useful for bioinformatics scientists aiming to develop new loop-calling algorithms.

Comprehensive Urinary Proteome Profiling Analysis Identifies Diagnosis and Relapse Surveillance Biomarkers for Bladder Cancer.

Bladder cancer (BCa) is the predominant malignancy of the urinary system. Herein, a comprehensive urine proteomic feature was initially established for the noninvasive diagnosis and recurrence monitoring of bladder cancer. 279 cases (63 primary BCa, 87 nontumor controls (NT), 73 relapsed BCa (BCR), and 56 nonrelapsed BCa (BCNR)) were collected to screen urinary protein biomarkers. 4761 and 3668 proteins were qualified and quantified by DDA and sequential window acquisition of all theoretical mass spectra (SWATH-MS) analysis in two discovery sets, respectively. Upregulated proteins were validated by multiple reaction monitoring (MRM) in two independent combined sets. Using the multi-support vector machine-recursive feature elimination (mSVM-RFE) algorithm, a model comprising 13 proteins exhibited good performance between BCa and NT with an AUC of 0.821 (95% CI: 0.675-0.967), 90.9% sensitivity (95% CI: 72.7-100%), and 73.3% specificity (95% CI: 53.3-93.3%) in the diagnosis test set. Meanwhile, an 11-marker classifier significantly distinguished BCR from BCNR with 75.0% sensitivity (95% CI: 50.0-100%), 81.8% specificity (95% CI: 54.5-100%), and an AUC of 0.784 (95% CI: 0.609-0.959) in the test cohort for relapse surveillance. Notably, six proteins (SPR, AK1, CD2AP, ADGRF1, GMPS, and C8A) of 24 markers were newly reported. This paper reveals novel urinary protein biomarkers for BCa and offers new theoretical insights into the pathogenesis of bladder cancer (data identifier PXD044896).

A deep learning model to identify gene expression level using cobinding transcription factor signals.

Gene expression is directly controlled by transcription factors (TFs) in a complex combination manner. It remains a challenging task to systematically infer how the cooperative binding of TFs drives gene activity. Here, we quantitatively analyzed the correlation between TFs and surveyed the TF interaction networks associated with gene expression in GM12878 and K562 cell lines. We identified six TF modules associated with gene expression in each cell line. Furthermore, according to the enrichment characteristics of TFs in these TF modules around a target gene, a convolutional neural network model, called TFCNN, was constructed to identify gene expression level. Results showed that the TFCNN model achieved a good prediction performance for gene expression. The average of the area under receiver operating characteristics curve (AUC) can reach up to 0.975 and 0.976, respectively in GM12878 and K562 cell lines. By comparison, we found that the TFCNN model outperformed the prediction models based on SVM and LDA. This is due to the TFCNN model could better extract the combinatorial interaction among TFs. Further analysis indicated that the abundant binding of regulatory TFs dominates expression of target genes, while the cooperative interaction between TFs has a subtle regulatory effects. And gene expression could be regulated by different TF combinations in a nonlinear way. These results are helpful for deciphering the mechanism of TF combination regulating gene expression.

Molecular Pathogenic Mechanisms of IgA Nephropathy Secondary to COVID-19 mRNA Vaccination.

INTRODUCTION: Accumulating evidence has disclosed that IgA nephropathy (IgAN) could present shortly after the second dose of COVID-19 mRNA vaccine. However, the undying mechanism remains unclear and we aimed to investigate the potential molecular mechanisms. METHODS: We downloaded gene expression datasets of COVID-19 mRNA vaccination (GSE201535) and IgAN (GSE104948). Weighted Gene Co-Expression Network Analysis (WGCNA) was performed to identify co-expression modules related to the second dose of COVID-19 mRNA vaccination and IgAN. Differentially expressed genes (DEGs) were screened, and a transcription factor (TF)-miRNA regulatory network and protein-drug interaction were constructed for the shared genes. RESULTS: WGCNA identified one module associated with the second dose of COVID-19 mRNA vaccine and four modules associated with IgAN. Gene ontology (GO) analyses revealed enrichment of cell cycle-related processes for the COVID-19 mRNA vaccine hub genes and immune effector processes for the IgAN hub genes. We identified 74 DEGs for the second dose of COVID-19 mRNA vaccine and 574 DEGs for IgAN. Intersection analysis with COVID-19 vaccine-related genes led to the identification of two shared genes, TOP2A and CEP55. The TF-miRNA network analysis showed that hsa-miR-144 and ATF1 might regulate the shared hub genes. CONCLUSIONS: This study provides insights into the common pathogenesis of COVID-19 mRNA vaccination and IgAN. The identified pivotal genes may offer new directions for further mechanistic studies of IgAN secondary to COVID-19 mRNA vaccination.

Incarvine C and its analogues inhibit the formation of cell cytoskeleton by targeting Rac1.

Ras-related C3 botulinum toxin substrate 1 (Rac1) has emerged as a key regulator in the treatment of cancer metastasis because of its involvement in the formation of cell plate pseudopods and effects on cell migration. In this study, we found that incarvine C, a natural product isolated from Incarvillea sinensis, and its seven analogues exhibited antitumour activity by inhibiting cell cytoskeleton formation, with moderate cytotoxicity. Accordingly, these compounds inhibited the cytoskeleton-mediated migration and invasion of MDA-MB-231 cells, with inhibition rates ranging from 37.30 % to 69.72 % and 51.27 % to 70.90 % in vitro, respectively. Moreover, they induced G2/M phase cell cycle arrest in MDA-MB-231 cells. A pull-down assay revealed that the interaction between Rac1 and its downstream effector protein PAK1 was inhibited by these compounds and that the compound Ano-6 exhibited substantial activity, with an inhibition rate of more than 90 %. Molecular docking showed that incarvine C and its analogues could bind to the nucleotide-binding pocket of Rac1, maintaining high levels of inactivated Rac1. As Ano-6 exhibited significant activity in vitro, its anti-cancer activity was tested in vivo. Four weeks of oral treatment with Ano-6 was well-tolerated in mice, and it induced a potential anti-tumour response in xenografts of MDA-MB-231 cells. Further studies demonstrated that Ano-6 was enriched in tumour tissues after 2 h of administration and induced an increase in the number of dead tumour cells. In summary, these findings not only reveal the mechanism of incarvine C but also provide a new molecular template for Rac1 inhibitors and identify a promising candidate for breast cancer treatment.

Construction of hub transcription factor-microRNAs-messenger RNA regulatory network in recurrent implantation failure.

PURPOSE: Recurrent implantation failure (RIF) affects up to 10% of in vitro fertilization (IVF) patients worldwide. However, the pathogenesis of RIF remains unclear. This study was aimed at identifying hub transcription factors (TFs) of RIF in bioinformatics approaches. METHODS: The GSE111974 (mRNA), GSE71332 (miRNA), and GSE103465 (mRNA) datasets were downloaded from the Gene Expression Omnibus database from human endometrial tissue using R version 4.2.1 and used to identify differentially expressed TFs (DETFs), differentially expressed miRNAs, and differentially expressed genes for RIF, respectively. DETFs were subjected to functional enrichment analysis and the protein-protein interaction network analysis using the Search Tool for the Retrieval of Interacting Genes (version 11.5) database. Hub TFs were identified using the cytoHubb plug-in, after which a hub TF-miRNA-mRNA network was constructed using Cytoscape v3.8.2. RESULTS: Fifty-seven DETFs were identified, in which Gene Ontology analysis revealed to be mainly involved in the regulation of transcription. Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that DETFs were enriched in transcriptional misregulation in cancer, aldosterone synthesis and secretion, AMPK signaling pathway, and cGMP-PKG signaling pathway. EOMES, NKX2-1, and POU5F1 were identified as hub TFs, and a hub TF-miRNA-mRNA regulatory network was constructed using these three hub TFs, four miRNAs, and four genes. CONCLUSION: Collectively, we identified three promising molecular biomarkers for the diagnosis of RIF, which may further be potential therapeutic targets. This study provides novel insights into the molecular mechanisms underlying RIF. However, further experiments are required to verify these results.

Puccinia suaveolens Causing Leaf Rust on Cirsium setosum in China.

Thistle, Cirsium setosum (Willd.) M. Bieb., is widely distributed in China as a common weed in fields. It is also used as a traditional Chinese medicine for cooling blood, stopping bleeding, dispelling stasis, detoxifying, and resolving carbuncle. In 2023, we found a rust disease on plants of Cirsium setosum in the experimental field of Hebei Agricultural University, Baoding, Hebei Province, China, with incidence of 15% - 25% (Fig. S1 A, B). The diseased leaves turned yellow, and the leaf edges were slightly rolled. The yellow, oil-like pycnia and pycniospores covered the baxial surface of leaves, and brown pustules were produced after 2-3 weeks. On the adaxial surface of the leaves, the brown rust pustules were mainly along the leaf veins. Stems were also be infected later, and dark pustules were scattered. The diseased plants were relatively short and small, and produced relatively small or no flowers compared to healthy plants. A total of 100 plants with typical leaf rust symptoms and signs were collected. To confirm the pathogenicity, healthy plants of thistle were sprayed with 5 ml of urediospores suspension (2.6×105/ml), and plants sprayed with sterile distilled water were treated as control. The sprayed plants were incubated under high moist conditions at 18°C for 24 h, and the inoculated plants were grown at 20°C in a greenhouse. Ten days after inoculation, the plants inoculated with urediniospores showed rust symptoms with uredinia and urediniospores on the leaves (Fig. S1 C), while the control plants were healthy. For morphological characterization, urediospores were picked from the naturally infected plants and placed in a drop of sterile water on a glass slide using a sterile needle, and observed and measured under a microscope. Urediospores were nearly spherical, brown-yellow, and measured 15 - 25 µm in diameter (n=100) (Fig. S1 D). Telia were scattered on the baxial surface of the naturally infected leaves, and teliospores were oval, yellow-brown, double-celled, with very short hyaline pedicels, and measured 15-20 × 15-30 µm (n=100) (Fig. S1 E). For molecular characterization, about 200 µg of urediniospores was collected and placed in a 1.5 ml sterile centrifuge tube, and genomic DNA was extracted using the cetyl-trimethylammonium bromide method (Gawel et al. 1991). The internal transcribed spacer (ITS) region of the rDNA and the D1/D2 domain were amplified using primer pairs ITS1/ITS4 (White et al. 1990) and NL1/NL4 (Borhani et al. 2013) in polymerase chain reaction (PCR), respectively. The PCR products were sequenced, and their sequences were aligned and compared with those deposited in GenBank. The obtained sequences were deposited in GenBank (OR600240 for ITS and OR598614 for D1/D2), which were 100% identical with 100% coverage to the ITS sequence (ON063373.1) and the D1/D2 sequence (ON063379.1) of Puccinia suaveolens (Menzies 1953). Based on the morphological characteristics and DNA sequences, the isolates were identified as P. suaveolens (Fig. S1 and Fig. S2). Thistle rust caused by Puccinia obtegens has been reported in some other parts of China (Zhang 2012). To the best of our knowledge, this is the first report of P. suaveolens causing leaf rust on C. setosum in China. This discovery is helpful for control of leaf rust on thistle grown for Chines medicine and other purposes, and the rust species could be used for biological control of thistle as a weed in crop fields.

Accurate Classification and Prediction of Acute Myocardial Infarction through an ARMD Procedure.

The risk stratification of acute myocardial infarction (AMI) patients is of prime importance for clinical management and prognosis assessment. Thus, we propose an ensemble machine learning analysis procedure named ADASYN-RFECV-MDA-DNN (ARMD) to address sample-unbalanced problems and enable stratification and prediction of AMI outcomes. The ARMD analysis procedure was applied to the NMR data of sera from 534 AMI-related subjects in four categories with an extremely imbalanced sample proportion. Firstly, the adaptive synthetic sampling (ADASYN) algorithm was used to address the issue of the original sample imbalance. Secondly, the recursive feature elimination with cross-validation (RFECV) processing and random forest mean decrease accuracy (RF-MDA) algorithm was performed to identify the differential metabolites corresponding to each AMI outcome. Finally, the deep neural network (DNN) was employed to classify and predict AMI events, and its performance was evaluated by comparing the four traditional machine learning methods. Compared with the other four machine learning models, DNN presented consistent superiority in almost all of the model parameters including precision, f1-score, sensitivity, specificity, area under the receiver operating characteristic curve (AUC), and classification accuracy, highlighting the potential of deep learning in classification and stratification of clinical diseases. The ARMD analysis procedure was a practical analysis tool for supervised classification and regression modeling of clinical diseases.

Multi-omics profiling of cholangiocytes reveals sex-specific chromatin state dynamics during hepatic cystogenesis in polycystic liver disease.

BACKGROUND & AIMS: Cholangiocytes transit from quiescence to hyperproliferation during cystogenesis in polycystic liver disease (PLD), the severity of which displays prominent sex differences. Epigenetic regulation plays important roles in cell state transition. We aimed to investigate the sex-specific epigenetic basis of hepatic cystogenesis and to develop therapeutic strategies targeting epigenetic modifications for PLD treatment. METHODS: Normal and cystic primary cholangiocytes were isolated from wild-type and PLD mice of both sexes. Chromatin states were characterized by analyzing chromatin accessibility (ATAC sequencing) and multiple histone modifications (chromatin immunoprecipitation sequencing). Differential gene expression was determined by transcriptomic analysis (RNA sequencing). Pharmacologic inhibition of epigenetic modifying enzymes was undertaken in PLD model mice. RESULTS: Through genome-wide profiling of chromatin dynamics, we revealed a profound increase of global chromatin accessibility during cystogenesis in both male and female PLD cholangiocytes. We identified a switch from H3K9me3 to H3K9ac on cis-regulatory DNA elements of cyst-associated genes and showed that inhibition of H3K9ac acetyltransferase or H3K9me3 demethylase slowed cyst growth in male, but not female, PLD mice. In contrast, we found that H3K27ac was specifically increased in female PLD mice and that genes associated with H3K27ac-gained regions were enriched for cyst-related pathways. In an integrated epigenomic and transcriptomic analysis, we identified an estrogen receptor alpha-centered transcription factor network associated with the H3K27ac-regulated cystogenic gene expression program in female PLD mice. CONCLUSIONS: Our findings highlight the multi-layered sex-specific epigenetic dynamics underlying cholangiocyte state transition and reveal a potential epigenetic therapeutic strategy for male PLD patients. IMPACT AND IMPLICATIONS: In the present study, we elucidate a sex-specific epigenetic mechanism underlying the cholangiocyte state transition during hepatic cystogenesis and identify epigenetic drugs that effectively slow cyst growth in male PLD mice. These findings underscore the importance of sex difference in the pathogenesis of PLD and may guide researchers and physicians to develop sex-specific personalized approaches for PLD treatment.

CYP3A4 and CYP3A5 Expression is Regulated by CYP3A4*1G in CRISPR/Cas9-Edited HepG2 Cells.

Functional CYP3A4*1G (G>A, rs2242480) in cytochrome P450 3A4 (CYP3A4) regulates the drug-metabolizing enzyme CYP3A4 expression. The objective of this study was to investigate whether CYP3A4*1G regulates both basal and rifampicin (RIF)-induced expression and enzyme activity of CYP3A4 and CYP3A5 in gene-edited human HepG2 cells. CYP3A4*1G GG and AA genotype HepG2 cells were established using the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) single nucleotide polymorphism technology and homology-directed repair in the CYP3A4*1G GA HepG2 cell line. In CYP3A4*1G GG, GA, and AA HepG2 cells, CYP3A4*1G regulated expression of CYP3A4 and CYP3A5 mRNA and protein in an allele-dependent manner. Of note, significantly decreased expression level of CYP3A4 and CYP3A5 was observed in CYP3A4*1G AA HepG2 cells. Moreover, the results after RIF treatment showed that CYP3A4*1G decreased the induction level of CYP3A4 and CYP3A5 mRNA expression in CYP3A4*1G AA HepG2 cells. At the same time, CYP3A4*1G decreased CYP3A4 enzyme activity and tacrolimus metabolism, especially in CYP3A4*1G GA HepG2 cells. In summary, we successfully constructed CYP3A4*1G GG and AA homozygous HepG2 cell models and found that CYP3A4*1G regulates both basal and RIF-induced expression and enzyme activity of CYP3A4 and CYP3A5 in CRISPR/Cas9 CYP3A4*1G HepG2 cells. SIGNIFICANCE STATEMENT: Cytochrome P450 (CYP) 3A4*1G regulates both basal and rifampicin (RIF)-induced expression and enzyme activity of CYP3A4 and CYP3A5. This study successfully established CYP3A4*1G (G>A, rs2242480), GG, and AA HepG2 cell models using CRISPR/Cas9, thus providing a powerful tool for studying the mechanism by which CYP3A4*1G regulates the basal and RIF-induced expression of CYP3A4 and CYP3A5.

Geranylgeranylacetone-induced heat shock protein70 expression reduces retinal ischemia-reperfusion injury through PI3K/AKT/mTOR signaling.

Retinal ischemia-reperfusion (I/R) injury is a common pathophysiological stress state connected to various diseases, including acute glaucoma, retinal vascular obstruction, and diabetic retinopathy. Recent studies have suggested that geranylgeranylacetone (GGA) could increase heat shock protein70 (HSP70) level and reduce retinal ganglion cells (RGCs) apoptosis in a rat retinal I/R model. However, the underlying mechanism remains unclear. Moreover, the injury caused by retinal I/R includes not only apoptosis but also autophagy and gliosis, and the effects of GGA on autophagy and gliosis have not been reported. Our study established a retinal I/R model by anterior chamber perfusion pressuring to 110 mmHg for 60 min, followed by 4 h of reperfusion. The levels of HSP70, apoptosis-related proteins, GFAP, LC3-II, and PI3K/AKT/mTOR signaling proteins were determined by western blotting and qPCR after treatment with GGA, HSP70 inhibitor quercetin (Q), PI3K inhibitor LY294002, and mTOR inhibitor rapamycin. Apoptosis was evaluated by TUNEL staining, meanwhile, HSP70 and LC3 were detected by immunofluorescence. Our results demonstrated that GGA-induced HSP70 expression significantly reduced gliosis, autophagosome accumulation, and apoptosis in retinal I/R injury, indicating that GGA exerted protective effects on retinal I/R injury. Moreover, the protective effects of GGA mechanistically relied on the activation of PI3K/AKT/mTOR signaling. In conclusion, GGA-induced HSP70 overexpression has protective effects on retinal I/R injury by activating PI3K/AKT/mTOR signaling.

Exosomes from human urine-derived stem cells carry NRF1 to alleviate bladder fibrosis via regulating miR-301b-3p/TGFßR1 pathway.

Bladder outlet obstruction (BOO) is a common disease that always make the bladder develops from inflammation to fibrosis. This study was to investigate the effect of exosomes from human urine-derived stem cells (hUSCs) on bladder fibrosis after BOO and the underlying mechanism. The BOO mouse model was established by inserting a transurethral catheter, ligation of periurethral wire, and removal of the catheter. Mouse primary bladder smooth muscle cells (BSMCs) were isolated and treated with TGFß1 to mimic the bladder fibrosis model in vitro. Exosomes from hUSCs (hUSC-Exos) were injected into the bladder of BOO mice and added into the culture of TGFß1-induced BSMCs. The associated factors in mouse bladder tissues and BSMCs were detected. It was confirmed that the treatment of hUSC-Exos alleviated mouse bladder fibrosis and down-regulated fibrotic markers (a-SMA and collagen III) in bladder tissues and TGFß1-induced BSMCs. Overexpression of NRF1 in hUSC-Exos further improved the effects of hUSC-Exos on bladder fibrosis both in vivo and in vitro. TGFßR1 was a target of NRF1 and miR-301b-3p, and miR-301b-3p was a target of NRF1. It was next characterized that hUSC-Exos carried NRF1 to up-regulate miR-301B-3p, thereby reducing TGFßR1level. Our results illustrated that hUSC-Exos carried NRF1 to alleviate bladder fibrosis through regulating miR-301b-3p/TGFßR1 pathway.

Three Robust Isoreticular Metal-Organic Frameworks with High-Performance Selective CO2 Capture and Separation.

Based on the hard-soft acid base (HSAB) theory, three robust isoreticular metal-organic frameworks (MOFs) with nia topology were successfully synthesized by solvothermal reaction {[In3O(BHB)(H2O)3]NO3·3DMA (JLU-MOF110(In)), [Fe3O(BHB)(H2O)3]NO3 (JLU-MOF110(Fe)), and [Fe2NiO(BHB)(H2O)3] (JLU-MOF110(FeNi)) (DMA = N,N-dimethylacetamide, H6BHB = 4,4″-benzene-1,3,5-triyl-hexabenzoic acid)}. Both JLU-MOF110(In) and JLU-MOF110(Fe) are cationic frameworks, and their BET surface areas are 301 and 446 m2/g, respectively. By modification of the components of metal clusters, JLU-MOF110(FeNi) features a neutral framework, and the BET surface area is increased up to 808 m2/g. All three MOF materials exhibit high chemical and thermal stability. JLU-MOF110(In) remains stable for 24 h at pH values ranging from 1 to 11, while JLU-MOF110(Fe) and JLU-MOF110(FeNi) persist to be stable for 24 h at pH from 1 to 12. JLU-MOF110(In) exhibits thermal stability up to 350 °C, whereas JLU-MOF110(Fe) and JLU-MOF(FeNi) can be stable up to 300 °C. Thanks to the microporous cage-based structure and abundant open metal sites, JLU-MOF110(In), JLU-MOF110(Fe), and JLU-MOF110(FeNi) have excellent CO2 capture capacity (28.0, 51.5, and 99.6 cm3/g, respectively, under 298 K and 1 bar). Interestingly, the ideal adsorption solution theory results show that all three MOFs exhibit high separation selectivity toward CO2 over N2 (35.2, 43.2, and 43.2 for CO2/N2 = 0.15/0.85) and CO2 over CH4 (14.4, 11.5, and 10.1 for CO2/CH4 = 0.5/0.5) at 298 K and 1 bar. Thus, all three MOFs are potential candidates for CO2 capture and separation. Among them, JLU-MOF110(FeNi) displays the best separation potential, as revealed by dynamic column breakthrough experiments.

Syntheses, crystal structure, and photoelectric properties of two Zn-based chalcogenidoantimonates Zn-Sb-Q (Q = S, Se).

Metal chalcogenides are a special class of semiconducting materials characterized by their rich structures and compositions, making them a promising option for a broad range of applications in the field of inorganic chemistry. However, the path forward is not without its challenges, notably in the realms of interface management and enhancing carrier concentration. To address these issues, we solvothermally synthesized two novel chalcogenidoantimonates [Zn(tren)]2Sb2Se5 (1) [tren = tris (2-aminoethyl) amine] and [Zn(tepa)H]2Sb2S6 (2) (tepa = tetraethylenepentamine) utilizing transition metal Zn by band gap optimization strategy in the visible region. Both compounds exhibited distinct zero-dimensional cluster structures, with transition metal complex cations acting as structure-directing agents. A comprehensive analysis of the electronic structure, band gap, and photocurrent response of these crystals was undertaken, revealing significantly enhanced photocatalytic properties compared to preceding studies. This research underscores the potential of antimony chalcogenides in the realm of photoelectric properties and promotes the applications of chalcogenides.

Recent development of multi-target VEGFR-2 inhibitors for the cancer therapy.

Vascular epidermal growth factor receptor-2 (VEGFR-2), as an important tyrosine transmembrane protein, plays an important role in regulating endothelial cell proliferation and migration, regulating angiogenesis and other biological functions. VEGFR-2 is aberrantly expressed in many malignant tumors, and it is also related to the occurrence, development, and growth of tumors and drug resistance. Currently, there are nine VEGFR-2 targeted inhibitors approved by US.FDA for clinical use as anticancer drugs. Due to the limited clinical efficacy and potential toxicity of VEGFR inhibitors, it is necessary to develop new strategies to improve the clinical efficacy of VEGFR inhibitors. The development of multitarget therapy, especially dual-target therapy, has become a hot research field of cancer therapy, which may provide an effective strategy with higher therapeutic efficacy, pharmacokinetic advantages and low toxicity. Many groups have reported that the therapeutic effects could be improved by simultaneously inhibiting VEGFR-2 and other targets, such as EGFR, c-Met, BRAF, HDAC, etc. Therefore, VEGFR-2 inhibitors with multi-targeting capabilities have been considered to be promising and effective anticancer agents for cancer therapy. In this work, we reviewed the structure and biological functions of VEGFR-2, and summarized the drug discovery strategies, and inhibitory activities of VEGFR-2 inhibitors with multi-targeting capabilities reported in recent years. This work might provide the reference for the development of VEGFR-2 inhibitors with multi-targeting capabilities as novel anticancer agents.

Nuclear Condensation of CDYL Links Histone Crotonylation and Cystogenesis in Autosomal Dominant Polycystic Kidney Disease.

BACKGROUND: Emerging evidence indicates that epigenetic modulation of gene expression plays a key role in the progression of autosomal dominant polycystic kidney disease (ADPKD). However, the molecular basis for how the altered epigenome modulates transcriptional responses, and thereby disease progression in ADPKD, remains largely unknown. METHODS: Kidneys from control and ADPKD mice were examined for the expression of CDYL and histone acylations. CDYL expression and its correlation with disease severity were analyzed in a cohort of patients with ADPKD. Cdyl transgenic mice were crossed with Pkd1 knockout mice to explore CDYL's role in ADPKD progression. Integrated cistromic and transcriptomic analyses were performed to identify direct CDYL target genes. High-sensitivity mass spectrometry analyses were undertaken to characterize CDYL-regulated histone lysine crotonylations (Kcr). Biochemical analysis and zebrafish models were used for investigating CDYL phase separation. RESULTS: CDYL was downregulated in ADPKD kidneys, accompanied by an increase of histone Kcr. Genetic overexpression of Cdyl reduced histone Kcr and slowed cyst growth. We identified CDYL-regulated cyst-associated genes, whose downregulation depended on CDYL-mediated suppression of histone Kcr. CDYL assembled nuclear condensates through liquid-liquid phase separation in cultured kidney epithelial cells and in normal kidney tissues. The phase-separating capacity of CDYL was required for efficient suppression of locus-specific histone Kcr, of expression of its target genes, and of cyst growth. CONCLUSIONS: These results elucidate a mechanism by which CDYL nuclear condensation links histone Kcr to transcriptional responses and cystogenesis in ADPKD.

First Report of Penicillium cellarum Causing Rot Disease on Dioscorea polystachya in China.

Dioscorea polystachya (Chinese yam) is a kind of medicine and food homologous crop, the tubers as its main production organ, with high potassium, low fiber, high protein and rich nutrition characteristics. In 2022, at the Chinese herbal medicine planting experimental site in Anguo, Baoding City, Hebei Province, China, we found the symptoms of Chinese yam decay during the storage, with an incidence of 15%~25%. The diseased part of Chinese yam tuber rots expands from the outside to the inside and sags, with a brown or dark brown discoloration, and the surface covered with a thick grayish green mold. The diseased tissue was first rinsed with clean water to remove dirts from the surface. Thereafter, 3 to 4 mm Chinese yam pieces were picked from rotting edge with a sterilized forceps, sterilized with 75% alcohol for 30 s followed by 0.1% mercuric chloride solution for 1min, and then rinsed three times with sterile water. The sterilized pieces were cultured on potato dextrose agar (PDA). One isolated fungus was obtained, and conidia were observed after incubation for 5 days at 26°C. Pure cultures were isolated by single-spore isolation. Conidia were single spore, round or oval, colorless. Conidiophores produce several rounds of symmetric or asymmetric small stems after multiple branches, which were shaped like brooms. The length and width of 100 conidia were measured, and size ranged from 3 to 4×3 to 4 µm. On the basis of morphological characteristics, the isolate was identified as Penicillium spp. (Uy et al. 2022). To further assess the identity of isolated species, the genomic DNA of the fungal isolate (SYRF1) was extracted by CTAB protocol. The ribosomal DNA internal transcribed spacer (ITS) region and the ribosomal large subunit (LSU) were amplified and sequenced with primers ITS1/4, LR5/LROR respectively (White et al. 1990, Xu et al. 2010). The obtained ITS-rDNA region and LSU sequences (GenBank accession OQ707937 and OQ704185) of the isolate were more than 99% identity to the corresponding sequences of Penicillium cellarum in GenBank (KM249068 and MG714818). Phylogenetic results based on a maximum-likelihood analysis revealed that SYRF1 was grouped with P. cellarum. To determine the pathogenicity of the isolated fungi, tests were carried out by aseptic inoculation of fresh and healthy tubers. Before the experiment, the healthy tubers were washed, surface disinfected and dried. The tubers were then wounded with sterile inoculation needles, and the conidium-bearing hyphal discs (5 mm) were inoculated on the surface of the wounded tubers and covered with wet sterile cotton. Three tubers were inoculated repeatedly each time as the experimental group. Inoculate sterile PDA with three tubers as the control group. Each tuber was inoculated with four mycelium disks, and the pathogenicity test was repeated four times. The inoculated tubers were incubated at 26°C for 14 days with sterile PDA as control. After ten days, the inoculated points showed symptoms similar to those of the initial infection, whereas controls remained symptomless. The reisolated fungus matched SYRF1 based on morphological and sequence analyses, thereby fulfilling Koch's postulates. To the best of our knowledge, this is the first report of Penicillium cellarum as causative agent of postharvest rot of Chinese yam tubers in China. This finding will help inform the prevention and management of postharvest diseases of Chinese yam tubers.

A Recyclable Magnetic Aminated Lignin Supported Zr-La Dual-Metal Hydroxide for Rapid Separation and Highly Efficient Sequestration of Phosphate.

The application of lignin-based adsorbents in the efficient removal of phosphate from wastewater has attracted much attention and been intensively studied in recent years. However, most currently reported lignin-based adsorbents are difficult to recover and recycle. Herein, we have developed a recyclable, nanostructured bio-adsorbent, poly(ethyleneimine) (PEI)-modified lignin (LG) integrated with Fe3O4 and Zr-La dual-metal hydroxide (LG-NH2@Fe3O4@Zr-La), by the Mannich reaction followed by the chemical coprecipitation method. Multilayer adsorption existed on the surface of LG-NH2@Fe3O4@Zr-La based on the isotherm fitting curve, and its adsorption capacity reached 57.8 mg P g-1, exhibiting a higher phosphate uptake than most reported metallic oxide-based composites. The adsorption process was dominated by inner-sphere complexation of ligand-exchange and electrostatic interactions. Moreover, LG-NH2@Fe3O4@Zr-La exhibited excellent selectivity against coexisting anions, and the adsorption was more efficient under acidic conditions. When the phosphate concentration was 2.0 mg P L-1, the removal efficiency of phosphate reached 99.5% and the residual concentration was only 10 µg P L-1, which meets the United States Environmental Protection Agency (USEPA) standard for eutrophication prevention. In addition, the LG-NH2@Fe3O4@Zr-La displayed excellent reusability, maintaining 91.8% of removal efficiency after five cycles. Importantly, owing to the magnetic properties of the loaded Fe3O4, the resulting composite could be separated within 30 s under an external magnetic field. Thus, the separable and recyclable biobased magnetic adsorbent developed in this work exhibited promising application in phosphate capture from real sewage. This research study provides a new perspective for lignin valorization in lignocellulose biorefineries and establishes an approach for developing an economical and efficient bio-adsorbent for phosphate removal from wastewater.

Unique Fluorescence Turn-On and Turn-Off-On Responses to Acids by a Carbazole-Based Metal-Organic Framework and Theoretical Studies.

Distinct from predominately known fluorescence quenching (turn-off) detection, turn-on response to hazardous substances by luminescent metal-organic frameworks (LMOFs) could greatly avoid signal loss and susceptibility to environmental stimulus. However, such detection rarely occurs and lacks theoretical elucidations. Here, we present the first example of unique turn-on and unprecedented turn-off-on responses to a variety of acids by a stable 12-connected hexanuclear Y(III)-cluster-based LMOF material─JLU-MOF111, featuring the nondefault pcu topology. Benefiting from the "pocket" structures formed by the carbazole-containing ligands, JLU-MOF111 can sense multiple inorganic and organic acids via different degrees of fluorescence turn-on behaviors. Particularly, turn-on sensing of HNO3, HCl, HBr, and TFA is hypersensitive with LODs as low as the ppb level. Theoretical calculations confirm weak interactions in acid-ligand complexes, which lead to constrained rotations of benzene moieties of the ligands when the complexes decay from excited states. These account for the turn-on response through reduced nonradiative energy consumption that competes with emissive decay. The turn-off-on response to 4-NBA and 3,5-DNBA involves an excited-state electron transfer process that dominates the turn-off stage and prohibited nonradiative decay that competes with the intrinsic emission of the ligand and dominates the turn-on stage. This work has a guiding significance for the full-scale understanding of turn-on and turn-off-on sensing performance in LMOF materials and beyond.

Bone marrow mesenchymal stem cell-derived extracellular vesicles facilitate endometrial injury repair by carrying the E3 ubiquitin ligase WWP1.

Bone marrow mesenchymal stem cells-derived extracellular vesicles (BMSC-EVs) relieve endometrial injury. This study aimed to elucidate the BMSC-EV mechanism in alleviating endometrial injury. Endometrial injury model in vivo was induced using 95% ethanol, and endometrial epithelial cells (EECs) treated with mifepristone were applied as an endometrial injury model in vitro. After BMSCs and BMSC-EVs were isolated and identified, the BMSC-EV function was evaluated by hematoxylin-eosin and Masson staining, immunohistochemistry, quantitative real-time PCR, Cell Counting Kit-8 assay, flow cytometry, enzyme-linked immunosorbent assay, and Transwell and tubule formation assays. The BMSC-EV mechanism was assessed using Western blot, ubiquitination, and cycloheximide-chase assays. After isolation and identification, BMSC-EVs were effective in endometrial injury repair in vivo and facilitated EEC proliferation and repressed cell apoptosis in vitro; the EEC supernatants accelerated human umbilical vein endothelial cell proliferation, migration, and invasion and facilitated angiogenesis after endometrial injury in vitro. For the BMSC-EV mechanism, E3 ubiquitin ligase WWP1 in BMSC-EVs mediated the ubiquitination of peroxisome proliferator-activated receptor gamma (PPARγ), thus relieving the PPARγ inhibition on vascular endothelial growth factor expression. Furthermore, the WWP1 in BMSC-EVs alleviated endometrial injury in vitro and in vivo. BMSC-EVs facilitated endometrial injury repair by carrying WWP1.