[Monoterpenoids from Paeoniae Radix Rubra based on UPLC-Q-TOF-MS]

The ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry(UPLC-Q-TOF-MS) was used to conduct the qualitative analysis of the monoterpene chemical components from Paeoniae Radix Rubra. Gradient elution was performed on C_(18) HD(2.1 mm×100 mm, 2.5 μm) column with a mobile phase of 0.1% formic acid(A) and acetonitrile(B). The flow rate was 0.4 mL·min~(-1) and the column temperature was 30 ℃. MS analysis was conducted in both positive and negative ionization modes using electrospray ionization(ESI) source. Qualitative Analysis 10.0 was used for data processing. The identification of chemical components was realized by the combination of standard compounds, fragmentation patterns, and mass spectra data reported in the literature. Forty-one monoterpenoids in Paeoniae Radix Rubra extract were identified. Among them, 8 compounds were reported in Paeoniae Radix Rubra for the first time and 1 was presumed to be the new compound 5″-O-methyl-galloylpaeoniflorin or its positional isomer. The method in this study realizes the rapid identification of monoterpenoids from Paeoniae Radix Rubra and provides a material and scientific basis for quality control and further study on the pharmaceutical effect of Paeoniae Radix Rubra.

Exploration of 68Ga-labelled prostate-specific membrane antigen-11 PET/CT parameters for identifying PBRM1 status in primary clear cell renal cell carcinoma

AIM

To investigate the predictive value of ⁶⁸Ga-labelled prostate-specific membrane antigen-11 (⁶⁸Ga-PSMA-11) integrated positron-emission tomography (PET)/computed tomography (CT) in PBRM1-deficient clear cell renal cell carcinoma (ccRCC).

MATERIALS AND METHODS

A total of 41 patients with ccRCC, were enrolled retrospectively and underwent ⁶⁸Ga-PSMA-11 PET/CT preoperatively. Radiological parameters, including CT attenuation value and maximum standard uptake value (SUVmax), were derived. Immunohistochemical and multiple immunofluorescences staining were performed to evaluate the PBRM1 status and immune response. The predictive value of imaging factors was analysed using a receiver operator characteristic curve analysis. Univariate and multivariate logistic regression analyses were used to investigate the relationship between clinical and radiological variables and PBRM1 status.

RESULTS

A total of 41 patients were included in this study, with 14 patients having PBRM1-deficient status. The tumour diameter on imaging and SUVmax differed significantly in patients with different PBRM1 expression statuses and no difference in CT attenuation was identified. Univariate and multivariate logistic regression analyses showed SUVmax was an obvious predictor for identification of PBRM1-deficient tumours. In addition, PBRM1-deficient tumours tended to be accompanied by greater cytotoxic T-cell infiltration, although most of them were in an exhausted state.

CONCLUSIONS

⁶⁸Ga-PSMA-11 PET/CT could be used to discriminate invasive PBRM1-deficient ccRCC.

Conductive Metal-Organic Framework Microelectrodes Regulated by Conjugated Molecular Wires for Monitoring of Dopamine in the Mouse Brain

Herein, we demonstrated a strategy to regulate the conductive metal-organic framework (MOF) surface, by the conjugated molecule wires for selective and sensitive determination of dopamine (DA) in the live brain. The MOFs were decorated at the carbon fiber electrode deposited by Au nanoleaves as the upper electric transducer to provide rich electrocatalytic sites for electron transfer of neurochemicals at the electrode surface, leading to greatly enhanced sensitivity for detection of neurochemicals. On the other hand, the conjugated molecular wire, 4-(thiophen-3-ylethynyl)-benzaldehyde (RP1), was synthesized and assembled as an underlying bridge to regulate the electrochemical processes at the MOF-based electrode, specifically decreasing the reaction Gibbs free energy of DA oxidation, thus selectively promoting the heterogeneous electron transfer of DA from the MOF layer to the electrode surface. Owing to the electrocatalytic activity for DA oxidation, the present microsensor exhibited high selectivity for real-time tracking of DA in a good linear relationship in the range of 0.004-0.4 μM with a detection limit of 1 nM. Eventually, this functionalized electrode was successfully applied for in vivo monitoring of DA in mouse brains with Parkinson's disease (PD) model. The results indicated that the levels of DA were obviously decreased in both acute and subacute PD models. Moreover, the level of DA strongly depended on the amount of uric acid (UA), a physiological antioxidant, which rose as the UA amount was lower than 200 mg kg^-1 but was downregulated again after treatment by a higher amount of UA.

BCAT1, as a prognostic factor for HCC, can promote the development of liver cancer through activation of the AKT signaling pathway and EMT

More and more studies have shown that Branched chain amino acid transaminase 1 (BCAT1) is involved in the occurrence and development of a variety of tumors. However, the mechanism of its occurrence and development in hepatocellular carcinoma (HCC) remains unclear. Here, we demonstrated the relationship between BCAT1 and AKT signaling pathway, as well as EMT, and the clinical significance of BCAT1 by using BCAT1 expression in 5 cell lines and 113 liver cancer and non-liver cancer tissue samples. The results showed that the expression of AKT was positively correlated with BCAT1 in HCC tissues, and BCAT1 could promote the progression of HCC cells through the AKT signaling pathway. Clinical analysis and Bioinformatics technology analysis revealed that BCAT1 was correlated with poor prognosis, and BCAT1 expression in the HCC tissues was evidently correlated with tumor number, vascular invasion, Edmondson grade and TNM stage (P < 0.05). In vitro studies showed that BCAT1 increased the invasion and migration of in MHCC-97H cells a d Huh7 cells. By inhibiting the expression of the BCAT1 gene, we detected the corresponding changes in the expression levels of Twist, E-cadherin and Vimentin, confirming that BCAT1 may promote the invasion and migration of HCC cells through epithelial-mesenchymal transformation (EMT). Overall, BCAT1 can activate AKT signaling pathway and EMT to promote the development and metastasis of HCC cells. this study may provide new ideas and directions for cancer diagnosis and treatment.

D Rhamnose β-hederin Reverses NAP1L5-mediated Adriamycin Resistance in Breast Cancer

Context

The persistent use of anticancer medicines can cause multidrug resistance in many tumors and serious cytotoxicity for healthy cells, including adriamycin (ADR), a treatment for breast cancer (BC). Cell resistance to ADR in patients with recurrent advanced BC can occur. Creating effective treatments that can grapple with multidrug resistance is still challenging. Traditional Chinese medicine (TCM) may offer a solution in D Rhamnose beta-hederin (DRβ-H), an oleanane type of triterpenoid saponin.

Objective

The study intended to assess the ability of DRβ-H to inhibit the ADR resistance of two BC-lineage cell lines, MCF-7 and SUM-1315, and to explore the causal link between DRβ-H and the reversal of chemoresistance.

Design

The research team performed a cell biology study.

Setting

The study took place at laboratory in China.

Outcome Measures

The research team: (1) assessed cell viability and the migration and invasion the cell lines; (2) investigated the molecular mechanism and identified the downstream targets of DRβ-H, and (3) comprehensively examined the expression pattern, underlying functions, and evident prognostic significance of NAP1L5 in BC by gathering the online information available.

Results

DRβ-H can inhibit the viability of the MCF-7/ADR and SUM-1315/ADR cancer cells in a dosage-dependent manner. NAP1L5 might be the main target of DRβ-H in reversing ADR resistance. Its expression decreased in BC cells, and the more advanced the BC was, the lower the NAP1L5 expression was.

Conclusion

DRβ-H at nontoxic concentrations was related to ADR resistance in BC through its downstream target NAP1L5. NAP1L5 is potentially a preferable prognostic marker for BC.

Review on the Diverse Biological Effects of Glabridin

Glabridin is a prenylated isoflavan from the roots of Glycyrrhiza glabra Linne and has posed great impact on the areas of drug development and medicine, due to various biological properties such as anti-inflammation, anti-oxidation, anti-tumor, anti-microorganism, bone protection, cardiovascular protection, neuroprotection, hepatoprotection, anti-obesity, and anti-diabetes. Many signaling pathways, including NF-κB, MAPK, Wnt/β-catenin, ERα/SRC-1, PI3K/AKT, and AMPK, have been implicated in the regulatory activities of glabridin. Interestingly, glabridin has been considered as an inhibitor of tyrosinase, P-glycoprotein (P-gp), and CYP2E1 and an activator of peroxisome proliferator-activated receptor γ (PPARγ), although their molecular regulating mechanisms still need further investigation. However, poor water solubility and low bioavailability have greatly limited the clinical applications of glabridin. Hopefully, several effective strategies, such as nanoemulsions, microneedles, and smartPearls formulation, have been developed for improvement.

Performance of Screened-Exchange Functionals for Band Gaps and Lattice Constants of Crystals

Kohn-Sham density functional theory is the most widely used method for electronic structure calculations of solid-state systems. The screened-exchange functionals developed following the influential work of Scuseria and co-workers in 2003-2006 have significantly improved the accuracy of the predictions of solid-state properties. This work assesses six screened-exchange density functionals for the prediction of 60 band gaps (database BG60) and 68 lattice constants (database LC68). The band gaps are calculated with both consistently calculated lattice constants and experimental lattice constants. Results for the nonlocal screened-exchange functionals are compared with those for six widely used or recently developed local functionals. The results show that all the screened-exchange functionals have smaller mean absolute errors (MAEs) than any of the local functionals. All the functionals except HLE17 overestimate (on average) the lattice constants, and M06-SX gives the best performance among the compared functionals, with a MAE of 0.051 Å. All the functionals underestimate (on average) the band gaps, and M06-SX outperforms all other functionals, with a MAE of 0.47 eV. M06-SX also has the lowest root-mean-squared error for both LC68 and BG60. For the subdatabases of BG60, M06-SX shows better performance for ionic crystals and systems with large band gaps, while HSE12s gives better results for semiconductors and systems with small band gaps. Overall, M06-SX shows the best performance for solid-state systems, followed by N12-SX and HSE12s. The best-performing local functionals are M06-L, revM06-L, and HLE17 for band gaps and M06-L and revM06-L for lattice constants. We found that M06-SX, revM06-L, and N12-SX not only are well optimized for a broad array of chemical properties but also have very good performance for the databases in this paper, making them well-suited for applications involving heterogeneous chemistry.

[Cryptic COL1A1-PDGFB fusion in dermatofibrosarcoma protuberans: a clinicopathological and genetic analysis]

Objective: To investigate the clinicopathological and cytogenetic features of cryptic COL1A1-PDGFB fusion dermatofibrosarcoma protuberans (CC-DFSP). Methods: Three cases of CC-DFSP diagnosed in West China Hospital, Sichuan University, Chengdu, China from January 2021 to September 2021 were studied. Immunohistochemistry for CD34 and other markers, fluorescence in situ hybridization (FISH) for PDGFB, COL1A1-PDGFB and COL1A1, next-generation sequencing (NGS), reverse-transcriptase polymerase chain reaction (RT-PCR) and Sanger sequencing were performed. Results: There were three cases of CC-DFSP, including two females and one male. The patients were 29, 44 and 32 years old, respectively. The sites were abdominal wall, caruncle and scapula. Microscopically, they were poorly circumscribed. The spindle cells of the tumors infiltrated into the whole dermis or subcutaneous tissues, typically arranging in a storiform pattern. Immunohistochemically, the neoplastic cells exhibited diffuse CD34 expression, but were negative for S-100, SMA, and Myogenin. Loss of H3K27me3 was not observed in the tumor cells. The Ki-67 index was 10%-15%. The 3 cases were all negative for PDGFB rearrangement and COL1A1-PDGFB fusion, whereas showing unbalanced rearrangement for COL1A1. Case 1 showed a COL1A1 (exon 31)-PDGFB (exon 2) fusion using NGS, which was further validated through RT-PCR and Sanger sequencing. All patients underwent extended surgical resection. Except for case 3 with recurrence 2 years after surgical resection, the other 2 cases showed no recurrence or metastasis during the follow-up. Conclusions: FISH has shown its validity for detecting PDGFB rearrangement and COL1A1-PDGFB fusion and widely applied in clinical detection. However, for cases with negative routine FISH screening that were highly suspicious for DFSPs, supplementary NGS or at least COL1A1 break-apart FISH screening could be helpful to identify cryptic COL1A1-PDGFB fusions or other variant fusions.

Phonon-assisted upconversion in twisted two-dimensional semiconductors

Phonon-assisted photon upconversion (UPC) is an anti-Stokes process in which incident photons achieve higher energy emission by absorbing phonons. This letter studies phonon-assisted UPC in twisted 2D semiconductors, in which an inverted contrast between UPC and conventional photoluminescence (PL) of WSe₂ twisted bilayer is emergent. A 4-fold UPC enhancement is achieved in 5.5° twisted bilayer while PL weakens by half. Reduced interlayer exciton conversion efficiency driven by lattice relaxation, along with enhanced pump efficiency resulting from spectral redshift, lead to the rotation-angle-dependent UPC enhancement. The counterintuitive phenomenon provides a novel insight into a unique way that twisted angle affects UPC and light-matter interactions in 2D semiconductors. Furthermore, the UPC enhancement platform with various superimposable means offers an effective method for lighting bilayers and expanding the application prospect of 2D stacked van der Waals devices.

Supervised learning of a chemistry functional with damped dispersion

Kohn-Sham density functional theory is widely used in chemistry, but no functional can accurately predict the whole range of chemical properties, although recent progress by some doubly hybrid functionals comes close. Here, we optimized a singly hybrid functional called CF22D with higher across-the-board accuracy for chemistry than most of the existing non-doubly hybrid functionals by using a flexible functional form that combines a global hybrid meta-nonseparable gradient approximation that depends on density and occupied orbitals with a damped dispersion term that depends on geometry. We optimized this energy functional by using a large database and performance-triggered iterative supervised training. We combined several databases to create a very large, combined database whose use demonstrated the good performance of CF22D on barrier heights, isomerization energies, thermochemistry, noncovalent interactions, radical and nonradical chemistry, small and large systems, simple and complex systems and transition-metal chemistry.

Discovery of Mcl-1 inhibitors through virtual screening, molecular dynamics simulations and in vitro experiments

As a member of the B-cell lymphoma 2 (Bcl-2) protein family, the myeloid leukemia cell differentiation protein (Mcl-1) can inhibit apoptosis and plays an active role in the process of tumor escape from apoptosis. Therefore, inhibition of Mcl-1 protein can effectively promote the apoptosis of tumor cells and may also reduce tumor cell resistance to drugs targeting other anti-apoptotic proteins. This research is dedicated to the development of Mcl-1 inhibitors, aiming to provide more references for lead compounds with different scaffolds for the development of targeted anticancer drugs. We obtained a series of small molecules with a common core skeleton through molecular docking from Specs database and searched the core structure in ZINC database for more similar small molecules. Collecting these small molecules for preliminary experimental screening, we found a batch of active compounds, and selected two small molecules with the strongest inhibitory activity on B16F10 cells: compound 7 and compound 1. Their IC₅₀s are 7.86 ± 1.25 and 24.72 ± 1.94 μM, respectively. These two compounds were also put into cell scratch test for B16F10 cells and cell viability assay of other cell lines. Furthermore, through molecular dynamics (MD) simulation analysis, we found that compound 7 formed strong binding with the key P2, P3 pocket and ARG 263 of Mcl-1. Finally, ADME results showed that compound 7 performs well in terms of drug similarity. In conclusion, this study provides hits with co-scaffolds that may aid in the design of effective clinical drugs targeting Mcl-1 and the future drug development.

ATF3 Modulates the Proliferation, Migration, and Apoptosis of Synovial Fibroblasts after Arthroscopy by Promoting RGS1 Transcription

BACKGROUND

Osteoarthritis (OA) is a degenerative joint disease involving both cartilage and synovium. Activating transcription factor 3 (ATF3) and regulator of G protein signaling 1 (RGS1) have been reported to be up-regulated in OA. However, little is known regarding the relationship between these two genes and the mechanism of this relationship in OA development. Therefore, the present study explores the mechanism of ATF3-mediated RGS1 in the proliferation, migration, and apoptosis of synovial fibroblasts.

METHODS

After the OA cell model was constructed with TGF-β1 induction, human fibroblast-like synoviocytes (HFLSs) were transfected with ATF3 shRNA or RGS1 shRNA alone or co-transfected with ATF3 shRNA and pcDNA3.1-RGS1. Then, proliferation, migration, apoptosis, and the expression of ATF3, RGS1, α-SMA, BCL-2, caspase3, and cleaved-caspase3 were measured. Meanwhile, the potential relationship between ATF3 and RGS1 was predicted and validated.

RESULTS AND DISCUSSION

Analysis of the GSE185059 dataset suggested that RGS1 was up-regulated in OA synovial fluid exosomes. Moreover, ATF3 and RGS1 were both highly expressed in TGF-β1-induced HFLSs. Transfection of ATF3 shRNA or RGS1 shRNA significantly reduced proliferation and migration and promoted apoptosis of TGF- β1-induced HFLSs. Mechanistically, ATF3 bound to the RGS1 promoter and elevated RGS1 expression. Silencing ATF3 repressed proliferation and migration and enhanced apoptosis of TGF-β1-induced HFLSs by down-regulating RGS1.

CONCLUSION

ATF3 binds to the RGS1 promoter and enhances RGS1 expression to accelerate cell proliferation and block cell apoptosis in TGF-β1-induced synovial fibroblasts.

Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications

The application of single-cell RNA sequencing (scRNA-seq) in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic strategies. With the expansion of capacity for high-throughput scRNA-seq, including clinical samples, the analysis of these huge volumes of data has become a daunting prospect for researchers entering this field. Here, we review the workflow for typical scRNA-seq data analysis, covering raw data processing and quality control, basic data analysis applicable for almost all scRNA-seq data sets, and advanced data analysis that should be tailored to specific scientific questions. While summarizing the current methods for each analysis step, we also provide an online repository of software and wrapped-up scripts to support the implementation. Recommendations and caveats are pointed out for some specific analysis tasks and approaches. We hope this resource will be helpful to researchers engaging with scRNA-seq, in particular for emerging clinical applications.

Cross talk between glucose metabolism and immunosuppression in IFN-γ–primed mesenchymal stem cells

This study reveals a novel relationship between mesenchymal stem cell immunomodulation and metabolism and provides a new strategy to improve their therapeutic efficacy in inflammatory diseases.

The immunosuppressive function “licensed” by IFN-γ is a vital attribute of mesenchymal stem cells (MSCs) widely used in the treatment of inflammatory diseases. However, the mechanism and impact of metabolic reprogramming on MSC immunomodulatory plasticity remain unclear. Here, we explored the mechanism by which glucose metabolism affects the immunomodulatory reprogramming of MSCs “licensed” by IFN-γ. Our data showed that glucose metabolism regulates the immunosuppressive function of human umbilical cord MSCs (hUC-MSCs) challenged by IFN-γ through the Janus kinase–signal transducer and activator of transcription (JAK-STAT) pathway. Furthermore, ATP facilitated the cross talk between glucose metabolism and the JAK-STAT system, which stimulates the phosphorylation of JAK2 and STATs, as well as the expression of indoleamine 2, 3-dioxygenase and programmed cell death-1 ligand. Moreover, ATP synergistically enhanced the therapeutic efficacy of IFN-γ–primed hUC-MSCs against acute pneumonia in mice. These results indicate a novel cross talk between the immunosuppressive function, glucose metabolism, and mitochondrial oxidation and provide a novel targeting strategy to enhance the therapeutic efficacies of hUC-MSCs.

Carbonate Minerals and Dissimilatory Iron-Reducing Organisms Trigger Synergistic Abiotic and Biotic Chain Reactions under Elevated CO2 Concentration

Increasing CO₂ emission has resulted in pressing climate and environmental issues. While abiotic and biotic processes mediating the fate of CO₂ have been studied separately, their interactions and combined effects have been poorly understood. To explore this knowledge gap, an iron-reducing organism, Orenia metallireducens, was cultured under 18 conditions that systematically varied in headspace CO₂ concentrations, ferric oxide loading, and dolomite (CaMg(CO₃)₂) availability. The results showed that abiotic and biotic processes interactively mediate CO₂ acidification and sequestration through "chain reactions", with pH being the dominant variable. Specifically, dolomite alleviated CO₂ stress on microbial activity, possibly via pH control that transforms the inhibitory CO₂ to the more benign bicarbonate species. The microbial iron reduction further impacted pH via the competition between proton (H⁺) consumption during iron reduction and H⁺ generation from oxidization of the organic substrate. Under Fe(III)-rich conditions, microbial iron reduction increased pH, driving dissolved CO₂ to form bicarbonate. Spectroscopic and microscopic analyses showed enhanced formation of siderite (FeCO₃) under elevated CO₂, supporting its incorporation into solids. The results of these CO₂-microbe-mineral experiments provide insights into the synergistic abiotic and biotic processes that alleviate CO₂ acidification and favor its sequestration, which can be instructive for practical applications (e.g., acidification remediation, CO₂ sequestration, and modeling of carbon flux).