PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis.

Cancer pharmacogenomics studies provide valuable insights into disease progression and associations between genomic features and drug response. PharmacoDB integrates multiple cancer pharmacogenomics datasets profiling approved and investigational drugs across cell lines from diverse tissue types. The web-application enables users to efficiently navigate across datasets, view and compare drug dose-response data for a specific drug-cell line pair. In the new version of PharmacoDB (version 2.0, https://pharmacodb.ca/), we present (i) new datasets such as NCI-60, the Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) dataset, as well as updated data from the Genomics of Drug Sensitivity in Cancer (GDSC) and the Genentech Cell Line Screening Initiative (gCSI); (ii) implementation of FAIR data pipelines using ORCESTRA and PharmacoDI; (iii) enhancements to drug-response analysis such as tissue distribution of dose-response metrics and biomarker analysis; and (iv) improved connectivity to drug and cell line databases in the community. The web interface has been rewritten using a modern technology stack to ensure scalability and standardization to accommodate growing pharmacogenomics datasets. PharmacoDB 2.0 is a valuable tool for mining pharmacogenomics datasets, comparing and assessing drug-response phenotypes of cancer models.

Deciphering Structure-Activity Relationship Towards CO2 Electroreduction over SnO2 by A Standard Research Paradigm.

Authentic surface structures under reaction conditions determine the activity and selectivity of electrocatalysts, therefore, the knowledge of the structure-activity relationship can facilitate the design of efficient catalyst structures for specific reactivity requirements. However, understanding the relationship between a more realistic active surface and its performance is challenging due to the complicated interface microenvironment in electrocatalysis. Herein, we proposed a standard research paradigm to effectively decipher the structure-activity relationship in electrocatalysis, which is exemplified in the CO2 electroreduction over SnO2 . The proposed practice has aided in discovering authentic/resting surface states (Sn layer) of SnO2 accountable for the electrochemical CO2 reduction reaction (CO2 RR) performance under electrocatalytic conditions, which then is corroborated in the subsequent CO2 RR experiments over SnO2 with different morphologies (nanorods, nanoparticles, and nanosheets) in combination with in situ characterizations. This proposed methodology is further extended to the SnO electrocatalysts, providing helpful insights into catalytic structures. It is believed that our proposed standard research paradigm is also applicable to other electrocatalytic systems, in the meantime, decreases the discrepancy between theory and experiments, and accelerates the design of catalyst structures that achieve sustainable performance for energy conversion.

Single-Cell Transcriptional Landscape Reveals the Regulatory Network and Its Heterogeneity of Renal Mitochondrial Damages in Diabetic Kidney Disease.

Diabetic kidney disease (DKD) is one of the common chronic microvascular complications of diabetes in which mitochondrial disorder plays an important role in its pathogenesis. The current study delved into the single-cell level transcriptome heterogeneity of mitochondrial homeostasis in db/db mice, an animal model for study of type 2 diabetes and DKD, with single-cell RNA sequencing (scRNA-Seq) and bulk RNA-seq analyses. From the comprehensive dataset comprising 13 meticulously captured and authenticated renal cell types, an unsupervised cluster analysis of mitochondria-related genes within the descending loop of Henle, collecting duct principal cell, endothelial, B cells and macrophage, showed that they had two types of cell subsets, i.e., health-dominant and DKD-dominant clusters. Pseudotime analysis, cell communication and transcription factors forecast resulted in identification of the hub differentially expressed genes between these two clusters and unveiled that the hierarchical regulatory network of receptor-TF-target genes was triggered by mitochondrial degeneration. Furthermore, the collecting duct principal cells were found to be regulated by the decline of Fzd7, which contributed to the impaired cellular proliferation and development, apoptosis and inactive cell cycle, as well as diminished capacity for material transport. Thereby, both scRNA-Seq and bulk RNA-Seq data from the current study elucidate the heterogeneity of mitochondrial disorders among distinct cell types, particularly in the collecting duct principal cells and B cells during the DKD progression and drug administration, which provide novel insights for better understanding the pathogenesis of DKD.

Evaluation of statistical approaches for association testing in noisy drug screening data.

BACKGROUND: Identifying associations among biological variables is a major challenge in modern quantitative biological research, particularly given the systemic and statistical noise endemic to biological systems. Drug sensitivity data has proven to be a particularly challenging field for identifying associations to inform patient treatment. RESULTS: To address this, we introduce two semi-parametric variations on the commonly used concordance index: the robust concordance index and the kernelized concordance index (rCI, kCI), which incorporate measurements about the noise distribution from the data. We demonstrate that common statistical tests applied to the concordance index and its variations fail to control for false positives, and introduce efficient implementations to compute p-values using adaptive permutation testing. We then evaluate the statistical power of these coefficients under simulation and compare with Pearson and Spearman correlation coefficients. Finally, we evaluate the various statistics in matching drugs across pharmacogenomic datasets. CONCLUSIONS: We observe that the rCI and kCI are better powered than the concordance index in simulation and show some improvement on real data. Surprisingly, we observe that the Pearson correlation was the most robust to measurement noise among the different metrics.

Reproducible pharmacogenomic profiling of cancer cell line panels.

The use of large-scale genomic and drug response screening of cancer cell lines depends crucially on the reproducibility of results. Here we consider two previously published screens, plus a later critique of these studies. Using independent data, we show that consistency is achievable, and provide a systematic description of the best laboratory and analysis practices for future studies.

The tonoplast-localized transporter OsNRAMP2 is involved in iron homeostasis and affects seed germination in rice.

Vacuolar storage of iron (Fe) is important for Fe homeostasis in plants. When sufficient, excess Fe could be stored in vacuoles for remobilization in the case of Fe deficiency. Although the mechanism of Fe remobilization from vacuoles is critical for crop development under low Fe stress, the transporters that mediate vacuolar Fe translocation into the cytosol in rice remains unknown. Here, we showed that under high Fe2+ concentrations, the Δccc1 yeast mutant transformed with the rice natural resistance-associated macrophage protein 2 gene (OsNRAMP2) became more sensitive to Fe toxicity. In rice protoplasts and transgenic plants expressing Pro35S:OsNRAMP2-GFP, OsNRAMP2 was localized to the tonoplast. Vacuolar Fe content in osnramp2 knockdown lines was higher than in the wild type, while the growth of osnramp2 knockdown plants was significantly influenced by Fe deficiency. Furthermore, the germination of osnramp2 knockdown plants was arrested. Conversely, the vacuolar Fe content of Pro35S:OsNRAMP2-GFP lines was significantly lower than in the wild type, and overexpression of OsNRAMP2 increased shoot biomass under Fe deficiency. Taken together, we propose that OsNRAMP2 transports Fe from the vacuole to the cytosol and plays a pivotal role in seed germination.

High and Tunable Proton Conduction in Six 3D-Substituted Imidazole Dicarboxylate-Based Lanthanide-Organic Frameworks.

Six isostructural three-dimensional (3D) Ln(III)-organic frameworks, {[Ln2(HMIDC)2(µ4-C2O4)(H2O)3]·4H2O}n [LnIII = GdIII (1), EuIII (2), SmIII (3), NdIII (4), PrIII (5), and CeIII (6)], have been fabricated by using a multifunctional ligand of 2-methyl-1H-imidazole-4,5-dicarboxylic acid (H3MIDC). Ln-metal-organic frameworks (MOFs) 1-6 present 3D structures and possess abundant H-bonded networks between imidazole-N atoms and coordinated and free water molecules. All the six Ln-MOFs demonstrate humidity- and temperature-dependent proton conductivity (σ) having the optimal values of 2.01 × 10-3, 1.40 × 10-3, 0.93 × 10-3, 2.25 × 10-4, 1.11 × 10-4, and 0.96 × 10-4 S·cm-1 for 1-6, respectively, at 100 °C/98% relative humidity, in the order of CeIII (6) < PrIII (5) < NdIII (4) < SmIII (3) < EuIII (2) < GdIII (1). In particular, the σ for 1 is 1 order of magnitude higher than that for 6, and it enhances systematically according to the decreasing order of the ionic radius, indicating that the lanthanide-contraction tactics can effectively regulate the proton conductivity while retaining the proton conduction routes. This will offer valuable guidance for the acquisition of new proton-conducting materials. In addition, the outstanding water stability and electrochemical stability of such Ln-MOFs will afford a solid material basis for future applications.

High Proton Conduction in Two Highly Water-Stable Lanthanide Coordination Polymers from a Triazole Multicarboxylate Ligand.

Two lanthanide coordination polymers (CPs) {[Er(Hmtbd)(H2mtbd)(H2O)3]·2H2O}n (1) and [Yb(Hmtbd)(H2mtbd)(H2O)3]n (2) carrying an N-heterocyclic carboxylate ligand 5-(3-methylformate-1H-1,2,4-triazole-1-methyl)benzen-1,3-dicarboxylate (H3mtbd) were prepared under solvothermal conditions. The single-crystal X-ray diffraction data demonstrate that 1 and 2 are isostructural and display 1D chain structure. Alternating current (AC) impedance measurements illustrate that the highest proton conductivities of 1 and 2 can attain 5.09 × 10-3 and 3.09 × 10-3 S·cm-1 at 100 °C and 98% relative humidity (RH), respectively. The value of 1 exceeds those of most reported lanthanide-based crystalline materials and ranks second among the described Er-CPs under similar conditions, whereas the value for 2 is the highest proton conductivity among the previous Yb-CPs. Coupled with the structural analyses of the two CPs and H2O vapor adsorption, the calculated Ea values help to deduce their proton conductive mechanisms. Notably, the N-heterocyclic units (triazole), carboxyl, and hydrogen-bonding network all play key roles in the proton-transfer process. The prominent proton conductive abilities of both CPs show great promise as efficient proton conductors.

SFRP2 suppresses trophoblast cell migration by inhibiting the Wnt/ß­catenin pathway.

The present study investigates the role of Secreted Frizzled­Related Protein 2 (SFRP2) in trophoblast cells, a key factor in preeclampsia (PE) progression. Elevated levels of Secreted Frizzled­Related Protein 1/3/4/5 (SFRP1/3/4/5) are associated with PE, but the role of SFRP2 is unclear. We analyzed SFRP2 expression in PE placental tissue using the GSE10588 dataset and overexpressed SFRP2 in JEG­3 cells via lentiviral transfection. The viability, migration, apoptosis, and proliferation of SFRP2­overexpressing JEG­3 cells were assessed using Cell Counting Kit­8, Transwell assays, flow cytometry, and EdU staining. Additionally, we evaluated the impact of SFRP2 overexpression on key proteins in the Wnt/ß­catenin pathway and apoptosis markers (Bax, cleaved­caspase 3, BCL­2, MMP9, E­cadherin, Wnt3a, Axin2, CyclinD1, c­Myc, p­ß­catenin, ß­catenin, phosphorylated Glycogen Synthase Kinase 3 beta (p­GSK3ß), and GSK3ß) through western blotting. Results showed high SFRP2 mRNA and protein expression in PE placenta and JEG­3 cells post­transfection. SFRP2 overexpression significantly reduced JEG­3 cell viability, proliferation, and migration, while increasing apoptosis. It also altered expression levels of Wnt pathway proteins, suggesting SFRP2's potential as a therapeutic target for PE by inhibiting trophoblast cell migration through the Wnt/ß­catenin signaling cascade.

Bulk-immiscible CuAg alloy nanorods prepared by phase transition from oxides for electrochemical CO2 reduction.

Combining Cu and Ag in an alloy state holds promise to serve as a tandem catalyst for electrocatalytic CO2 reduction, but is restricted by immiscibility in the bulk. Here, a far-from-equilibrium method is developed to synthesize CuAg alloy by electroreduction of Cu2Ag2O3 under a large cathodic overpotential. The alloy state of CuAg is conducive to the formation of C2+ molecules. A high formation rate of C2H4 of 159.8 µmol cm-2 h-1 is reached on the CuAg alloy nanorods, 2.3 times higher than that on pure Cu.

Acrylamide formation and aroma evaluation of fried pepper sauce under different exogenous Maillard reaction conditions.

To explore the impact of the Maillard reaction on fried pepper sauce (FPS) flavor and safety quality, acrylamide and volatile organic compounds (VOCs) were measured in FPS. Acrylamide was detected in 10 Maillard treated groups and a total of 110 VOCs were identified, mainly aldehydes, ketones, alcohols, acids, etc., but the content of each group differed. Partial least squares discriminant analysis showed that acrylamide in white sugar-sodium glutamate group and xylose-soy peptide group processing accumulated most acrylamide and least VOCs; Lactose-glycine, lactose-cysteine, lactose-soy peptide, and white sugar-glycine groups were positively correlated with typical Maillard reaction product (2,3-Dihydro-3,5-dihydroxy-6-methyl-4(H)-pyran-4-One); Xylose-glycine, xylose-cysteine, and white sugar-cysteine groups were weakly correlated with typical products, but positively correlated with most VOCs, whereas white sugar-cysteine group lipids showed high oxidation levels. Although white sugar-soy peptide group is not harmful on acrylamide, it has little correlation with VOCs with large responses. Conventional excipient group aroma is relatively simple with a fresh fatty taste, whereas xylose-glycine, xylose-cysteine, xylose-soy peptide, lactose-glycine, and white sugar-cysteine groups all present basic fresh and fatty tastes; lactose-cysteine group has a fruity base note; and lactose-soybean peptide, white sugar-glycine, and white sugar-soybean peptide groups have a fruity base note on an unpleasant fatty aroma. Therefore, processing different exogenous Maillard reaction substrates can achieve FPS aroma regulation and reduce acrylamide harm.

Anxiolytic effect of YangshenDingzhi granules: Integrated network pharmacology and hippocampal metabolomics.

Anxiety disorder is one of the most common mental diseases. It is mainly characterized by a sudden, recurring but indescribable panic, fear, tension and/or anxiety. Yangshendingzhi granules (YSDZ) are widely used in the treatment of anxiety disorders, but its active ingredients and underlying mechanisms are not yet clear. This study integrates network pharmacology and metabolomics to investigate the potential mechanism of action of YSDZ in a rat model of anxiety. First, potential active ingredients and targets were screened by network pharmacology. Then, predictions were verified by molecular docking, molecular dynamics and western blotting. Metabolomics was used to identify differential metabolites and metabolic pathways. All results were integrated for a comprehensive analysis. Network pharmacology analysis found that Carotene, ß-sitosterol, quercetin, Stigmasterol, and kaempferol in YSDZ exert anxiolytic effects mainly by acting on IL1ß, GABRA1, PTGS1, ESR1, and TNF targets. Molecular docking results showed that all the affinities were lower than -5 kcal/mol, and the average affinities were -7.7764 kcal/mol. Molecular dynamics simulation results showed that RMSD was lower than 2.5 A, and the overall conformational changes of proteins were small, indicating that the small molecules formed stable complexes with proteins. The results of animal experiments showed that YSDZ exerts anxiolytic effects by regulating GABRA1 and TNF-α, ameliorating pathological damage in hippocampal CA1, and regulating metabolic pathways such as thiamine, cysteine and methionine metabolism, lysine biosynthesis and degradation. Altogether, we reveal multiple mechanisms through which YSDZ exerts its anti-anxiety effects, which may provide a reference for its clinical application and drug development.

Antidepressant Active Components of Bupleurum chinense DC-Paeonia lactiflora Pall Herb Pair: Pharmacological Mechanisms.

Depression is a serious psychological disorder with a rapidly increasing incidence in recent years. Clinically, selective serotonin reuptake inhibitors are the main therapy. These drugs, have serious adverse reactions, however. Traditional Chinese medicine has the characteristics of multiple components, targets, and pathways, which has huge potential advantages for the treatment of depression. The antidepressant potential of the herbal combination of Bupleurum chinense DC (Chaihu) and Paeonia lactiflora Pall (Baishao) has been extensively studied previously. In this review, we summarized the antidepressant active components and mechanism of Chaihu-Baishao herb pair. We found that it works mainly through relieving oxidative stress, regulating HPA axis, and protecting neurons. Nevertheless, current research of this combined preparation still faces many challenges. On one hand, most of the current studies only stay at the level of animal models, lacking of sufficient clinical double-blind controlled trials for further verification. In addition, studies on the synergistic effect between different targets and signaling pathways are scarce. On the other hand, this preparation has numerous defects such as poor stability, low solubility, and difficulty in crossing the blood-brain barrier.

Fluorescence spectroscopy and molecular docking analysis of the binding of Lactobacillus acidophilus GIM1.208 ß-glucosidase with quercetin glycosides.

Lactobacillus acidophilus is an important probiotic. The ß-glucosidase produced by L. acidophilus GIM1.208 can transform quercetin glycosides of Rosa roxburghii Tratt to release quercetin and improve the functional activity of raw materials. Understanding the interaction and the characteristics of the two will lay a theoretical foundation for the site-directed transformation and functional application of the catalytic active site of enzymes. In our study, using the heterologously expressed and highly stable, purified L. acidophilus GIM1.208 BGL as the strain, the representative quercetin in ß-glucosidase and Rosa roxburghii Tratt was preliminarily predicted and explored using ultraviolet-visible absorption spectroscopy. Fluorescence spectroscopy combined with molecular docking was used to determine the interaction characteristics of the glycoside substrates, rutin (Rut) and isoquercitrin (Iso). Results from molecular docking showed that Asp159, Arg56, Iso294, Phe292, and Gly25 were the main residues of ß-glucosidase and Rut. Arg56 was found to be the most crucial residue of ß-glucosidase and isoquercitrin; the interaction between Rut and Iso and ß-glucosidase was mainly driven by hydrogen bonding. The combined free energy of ß-glucosidase and Iso was found to be -182.10 kcal/mol, while that of ß-glucosidase and Rut was -32.37 kcal/mol. The results of fluorescence spectroscopy showed that the fluorescence intensity of ß-glucosidase decreased with an increase in Rut and Iso concentrations. This interaction made ß-glucosidase quench endogenous fluorescence, which was static quenching. The binding constants of Rut and Iso with ß-glucosidase were determined to be 0.50×107 and 0.31×107 L/mol, respectively, indicating that rutin had a stronger affinity when interacting with ß-glucosidase. These findings were consistent with our prediction results determined using molecular docking studies.

Expression of a Brassica napus metal transport protein (BnMTP3) in Arabidopsis thaliana confers tolerance to Zn and Mn.

The essential micronutrient elements zinc (Zn) and manganese (Mn) are crucial for plant growth and development. As an important oil crop, the yield and quality of rapeseed are affected by Zn and Mn toxicity. The cation diffusion facilitator (CDF) family of proteins play significant roles in maintaining intracellular ionic homeostasis and tolerance in plants. However, research on CDF proteins in rapeseed is lacking. In this study, the function of a Brassica napus cation diffusion facilitator/ metal tolerance protein (CDF/MTP) was investigated. The protein, abbreviated BnMTP3 is homologous to the Arabidopsis thaliana MTP3 (AtMTP3). Heterologous expression of BnMTP3 in yeast enhanced tolerance and intracellular sequestration of Zn and Mn. Expression of BnMTP3 in A. thaliana increased Zn and Mn tolerance and markedly increased Zn accumulation in roots. Quantitative RT-PCR analysis showed that BnMTP3 is primarily expressed in roots, and subcellular localization suggested that BnMTP3 is localized in the trans-Golgi network (TGN) and the prevacuolar compartment (PVC) in Arabidopsis and rape protoplast. After treatment with Zn and Mn, BnMTP3 was observed on the vacuolar membrane in transgenic Arabidopsis lines. These findings suggest that BnMTP3 confers Zn and Mn tolerance by sequestering Zn and/or Mn into the vacuole.

Orchestrating and sharing large multimodal data for transparent and reproducible research.

Reproducibility is essential to open science, as there is limited relevance for findings that can not be reproduced by independent research groups, regardless of its validity. It is therefore crucial for scientists to describe their experiments in sufficient detail so they can be reproduced, scrutinized, challenged, and built upon. However, the intrinsic complexity and continuous growth of biomedical data makes it increasingly difficult to process, analyze, and share with the community in a FAIR (findable, accessible, interoperable, and reusable) manner. To overcome these issues, we created a cloud-based platform called ORCESTRA ( orcestra.ca ), which provides a flexible framework for the reproducible processing of multimodal biomedical data. It enables processing of clinical, genomic and perturbation profiles of cancer samples through automated processing pipelines that are user-customizable. ORCESTRA creates integrated and fully documented data objects with persistent identifiers (DOI) and manages multiple dataset versions, which can be shared for future studies.

Identification of response signatures for tankyrase inhibitor treatment in tumor cell lines.

Small-molecule tankyrase 1 and tankyrase 2 (TNKS1/2) inhibitors are effective antitumor agents in selected tumor cell lines and mouse models. Here, we characterized the response signatures and the in-depth mechanisms for the antiproliferative effect of tankyrase inhibition (TNKSi). The TNKS1/2-specific inhibitor G007-LK was used to screen 537 human tumor cell lines and a panel of particularly TNKSi-sensitive tumor cell lines was identified. Transcriptome, proteome, and bioinformatic analyses revealed the overall TNKSi-induced response signatures in the selected panel. TNKSi-mediated inhibition of wingless-type mammary tumor virus integration site/ß-catenin, yes-associated protein 1 (YAP), and phosphatidylinositol-4,5-bisphosphate 3-kinase/AKT signaling was validated and correlated with lost expression of the key oncogene MYC and impaired cell growth. Moreover, we show that TNKSi induces accumulation of TNKS1/2-containing ß-catenin degradasomes functioning as core complexes interacting with YAP and angiomotin proteins during attenuation of YAP signaling. These findings provide a contextual and mechanistic framework for using TNKSi in anticancer treatment that warrants further comprehensive preclinical and clinical evaluations.

Pharmacological Induction of RAS-GTP Confers RAF Inhibitor Sensitivity in KRAS Mutant Tumors.

Targeting KRAS mutant tumors through inhibition of individual downstream pathways has had limited clinical success. Here we report that RAF inhibitors exhibit little efficacy in KRAS mutant tumors. In combination drug screens, MEK and PI3K inhibitors synergized with pan-RAF inhibitors through an RAS-GTP-dependent mechanism. Broad cell line profiling with RAF/MEK inhibitor combinations revealed synergistic efficacy in KRAS mutant and wild-type tumors, with KRASG13D mutants exhibiting greater synergy versus KRASG12 mutant tumors. Mechanistic studies demonstrate that MEK inhibition induced RAS-GTP levels, RAF dimerization and RAF kinase activity resulting in MEK phosphorylation in synergistic tumor lines regardless of KRAS status. Taken together, our studies uncover a strategy to rewire KRAS mutant tumors to confer sensitivity to RAF kinase inhibition.

Dual regulation of AP-2alpha transcriptional activation by poly(ADP-ribose) polymerase-1.

Poly(ADP-ribose) polymerase-1 (PARP-1) is a co-activator for AP-2alpha (activator protein 2alpha)-mediated transcriptional activation. In the present study, we find that the role of PARP-1 in AP-2alpha transcription is distinctly dualistic with opposing effects. Separate regions of PARP-1 interact with AP-2alpha and independently control its transcriptional activation. The C-terminus containing the catalytic domain strongly interacts with AP-2alpha, whereas low-affinity binding is seen in the middle region, which includes the breast-cancer susceptibility gene 1 C-terminal domain and automodification region. The middle region enhances AP-2alpha transcription. Even portions of this region independently interact and have partial effects on transcription. The catalytic domain strongly poly-(ADP-ribosyl)ates AP-2alpha. This modification, on the other hand, affects its DNA binding. 3-Aminobenzamide and 6(5H)-phenanthridinone that inhibit the enzymic activity significantly enhance the binding of AP-2alpha to its target sequence and increase its transcriptional activity. The enzymic activity of PARP-1 is known to be induced by stress conditions that damage cellular DNA, and the poly(ADP-ribosyl)ation of target proteins is transient in nature with a half-life of less than a minute. We hypothesize that PARP-1 enhances the transcriptional activity of AP-2alpha in normal circumstances, whereas its enzymic activity is used as a temporary shut-off mechanism during unfavourable conditions.