Blockade of aryl hydrocarbon receptor restricts omeprazole-induced chronic kidney disease

Chronic kidney disease (CKD) is the 16th leading cause of mortality worldwide. Clinical studies have raised that long-term use of omeprazole (OME) is associated with the morbidity of CKD. OME is commonly used in clinical practice to treat peptic ulcers and gastroesophageal reflux disease. However, the mechanism underlying renal failure following OME treatment remains mostly unknown and the rodent model of OME-induced CKD is yet to be established. We described the process of renal injury after exposure to OME in mice; the early renal injury markers were increased in renal tubular epithelial cells (RTECs). And after long-term OME treatment, the OME-induced CKD mice model was established. Herein, aryl hydrocarbon receptor (AHR) translocation appeared after exposure to OME in HK-2 cells. Then for both in vivo and in vitro, we found that Ahr-knockout (KO) and AHR small interfering RNA (siRNA) substantially alleviated the OME-induced renal function impairment and tubular cell damage. Furthermore, our data demonstrate that antagonists of AHR and CYP1A1 could attenuate OME-induced tubular cell impairment in HK-2 cells. Taken together, these data indicate that OME induces CKD through the activation of the AHR-CYP axis in RTECs. Our findings suggest that blocking the AHR-CYP1A1 pathway acts as a potential strategy for the treatment of CKD caused by OME. KEY MESSAGES: We provide an omeprazole-induced chronic kidney disease (CKD) mice model. AHR activation and translocation process was involved in renal tubular damage and promoted the occurrence of CKD. The process of omeprazole nephrotoxicity can be ameliorated by blockade of the AHR-CYP1A1 axis.

Accurate Characterization of Binding Kinetics and Allosteric Mechanisms for the HSP90 Chaperone Inhibitors Using AI-Augmented Integrative Biophysical Studies

The binding kinetics of drugs to their targets are gradually being recognized as a crucial indicator of the efficacy of drugs in vivo, leading to the development of various computational methods for predicting the binding kinetics in recent years. However, compared with the prediction of binding affinity, the underlying structure and dynamic determinants of binding kinetics are more complicated. Efficient and accurate methods for predicting binding kinetics are still lacking. In this study, quantitative structure-kinetics relationship (QSKR) models were developed using 132 inhibitors targeting the ATP binding domain of heat shock protein 90α (HSP90α) to predict the dissociation rate constant (koff), enabling a direct assessment of the drug-target residence time. These models demonstrated good predictive performance, where hydrophobic and hydrogen bond interactions significantly influence the koff prediction. In subsequent applications, our models were used to assist in the discovery of new inhibitors for the N-terminal domain of HSP90α (N-HSP90α), demonstrating predictive capabilities on an experimental validation set with a new scaffold. In X-ray crystallography experiments, the loop-middle conformation of apo N-HSP90α was observed for the first time (previously, the loop-middle conformation had only been observed in holo-N-HSP90α structures). Interestingly, we observed different conformations of apo N-HSP90α simultaneously in an asymmetric unit, which was also observed in a holo-N-HSP90α structure, suggesting an equilibrium of conformations between different states in solution, which could be one of the determinants affecting the binding kinetics of the ligand. Different ligands can undergo conformational selection or alter the equilibrium of conformations, inducing conformational rearrangements and resulting in different effects on binding kinetics. We then used molecular dynamics simulations to describe conformational changes of apo N-HSP90α in different conformational states. In summary, the study of the binding kinetics and molecular mechanisms of N-HSP90α provides valuable information for the development of more targeted therapeutic approaches.

Novel biomarkers related to oxidative stress and immunity in chronic kidney disease

Introduction

The incidence of chronic kidney disease (CKD) has been increasing in recent years, gradually becoming a global health crisis. Due to limited treatment options, novel molecular pathways are urgently required to advance the treatment and diagnosis of CKD.

Materials and methods

The characteristics of differentially expressed genes (DEGs) in CKD patients were analyzed using Gene Expression Omnibus (GEO) database, and genes related to oxidative stress were retrieved from the Genecard database. Subsequently, a comprehensive approach was applied, including immune infiltration analysis, weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network analysis, to identify hub genes among differentially expressed immune-related oxidative stress genes (DEIOSGs). Validation of hub genes was performed using an external data set, and diagnostic potential capability was evaluated through receiver operating curve (ROC) analysis. In animal experiments, the expression of hub genes in CKD was confirmed by inducing a CKD model through a 5/6 nephrectomy procedure. Finally, the relationship between these hub genes and clinical characteristics were assessed using the Nephroseq v5 database.

Results

29 DEIOSGs were identified by comprehensive bioinformatics analysis. PPI analysis screened the hub genes NCF2, S100A9, and SELL. ROC analysis demonstrated excellent diagnostic efficacy. Further validation from other databases and animal experiments confirmed a substantial upregulation in the expression of hub genes in CKD. Additionally, clinical correlation analysis established a clear link between hub gene expression and renal function deterioration.

Conclusions

Our study confirms NCF2, S100A9, and SELL as diagnostic biomarkers associated with immune response and oxidative stress in CKD, suggesting their potential as novel targets for CKD diagnosis and treatment.

Structure-based design of pan-coronavirus inhibitors targeting host cathepsin L and calpain-1

Respiratory disease caused by coronavirus infection remains a global health crisis. Although several SARS-CoV-2-specific vaccines and direct-acting antivirals are available, their efficacy on emerging coronaviruses in the future, including SARS-CoV-2 variants, might be compromised. Host-targeting antivirals provide preventive and therapeutic strategies to overcome resistance and manage future outbreak of emerging coronaviruses. Cathepsin L (CTSL) and calpain-1 (CAPN1) are host cysteine proteases which play crucial roles in coronaviral entrance into cells and infection-related immune response. Here, two peptidomimetic α-ketoamide compounds, 14a and 14b, were identified as potent dual target inhibitors against CTSL and CAPN1. The X-ray crystal structures of human CTSL and CAPN1 in complex with 14a and 14b revealed the covalent binding of α-ketoamide groups of 14a and 14b to C25 of CTSL and C115 of CAPN1. Both showed potent and broad-spectrum anticoronaviral activities in vitro, and it is worth noting that they exhibited low nanomolar potency against SARS-CoV-2 and its variants of concern (VOCs) with EC50 values ranging from 0.80 to 161.7 nM in various cells. Preliminary mechanistic exploration indicated that they exhibited anticoronaviral activity through blocking viral entrance. Moreover, 14a and 14b exhibited good oral pharmacokinetic properties in mice, rats and dogs, and favorable safety in mice. In addition, both 14a and 14b treatments demonstrated potent antiviral potency against SARS-CoV-2 XBB 1.16 variant infection in a K18-hACE2 transgenic mouse model. And 14b also showed effective antiviral activity against HCoV-OC43 infection in a mouse model with a final survival rate of 60%. Further evaluation showed that 14a and 14b exhibited excellent anti-inflammatory effects in Raw 264.7 mouse macrophages and in mice with acute pneumonia. Taken together, these results suggested that 14a and 14b are promising drug candidates, providing novel insight into developing pan-coronavirus inhibitors with antiviral and anti-inflammatory properties.

Perioperative Insulin Pump Therapy Decreases Readmission Risk and Improves Outcomes in Patients with Diabetes

OBJECTIVE

To evaluate the impact of temporary insulin pump use during hospitalization on glycemia, postoperative complications, and cost/utilization in perioperative patients with diabetes.

METHODS

Patients (n=159) with type 2 diabetes and hospitalized for elective surgery were recruited from three hospitals. Subjects were categorized into the insulin pump group and the multiple daily subcutaneous insulin injection group according to their treatment therapy. Data were collected at admission, discharge, and 3 months post-discharge.

RESULTS

Subjects in the CSII group who were still on insulin therapy transitioned from CSII to MDII; however, their daily insulin dosages were lower than those in the MDII group (15.31±10.98 U/d vs. 23.48±17.02 U/d, P=0.015) after discharge. In terms of medical costs, the CSII group had significantly higher hospitalization costs than the MDII group (112.36±103.43 thousand RMB vs. 82.65±77.98 thousand RMB, P=0.043). After 3 months, the CSII group had significantly lower outpatient costs than the MDII group (3.17±0.94 thousand RMB vs. 3.98±1.76 thousand RMB, P ˂ 0.001). In the MDII group, 10 patients reported severe postoperative complications requiring re-hospitalization; there were no similar reports in the CSII group.

CONCLUSION

Temporary use of insulin pump therapy for perioperative patients with diabetes results in a reduction in blood glucose and blood glucose fluctuation during hospitalization, HbA1c, and the risk of postoperative complication and readmission, thus significantly decreasing costs in this complex patient cohort. Further work is needed to better understand indications for utilizing pump therapy based on diabetes phenotype and the complexity of planned surgical intervention.

Maternal androgen excess inhibits fetal cardiomyocytes proliferation through RB-mediated cell cycle arrest and induces cardiac hypertrophy in adulthood

PURPOSE

Maternal hyperandrogenism during pregnancy is associated with adverse gestational outcomes and chronic non-communicable diseases in offspring. However, few studies are reported to demonstrate the association between maternal androgen excess and cardiac health in offspring. This study aimed to explore the relation between androgen exposure in utero and cardiac health of offspring in fetal and adult period. Its underlying mechanism is also illustrated in this research.

METHODS

Pregnant mice were injected with dihydrotestosterone (DHT) from gestational day (GD) 16.5 to GD18.5. On GD18.5, fetal heart tissue was collected for metabolite and morphological analysis. The hearts from adult offspring were also collected for morphological and qPCR analysis. H9c2 cells were treated with 75 μM androsterone. Immunofluorescence, flow cytometry, qPCR, and western blot were performed to observe cell proliferation and explore the underlying mechanism.

RESULTS

Intrauterine exposure to excessive androgen led to thinner ventricular wall, decreased number of cardiomyocytes in fetal offspring and caused cardiac hypertrophy, compromised cardiac function in adult offspring. The analysis of steroid hormone metabolites in fetal heart tissue by ultra performance liquid chromatography and tandem mass spectrometry showed that the content of androgen metabolite androsterone was significantly increased. Mechanistically, H9c2 cells treated with androsterone led to a significant decrease in phosphorylated retinoblastoma protein (pRB) and cell cycle-related protein including cyclin-dependent kinase 2 (CDK2), cyclin-dependent kinase 4 (CDK4), and cyclin D1 (CCND1) in cardiomyocytes. This resulted in cell cycle arrest at G1-S phase, which in turn inhibited cardiomyocyte proliferation.

CONCLUSION

Taken together, our results indicate that in utero exposure to DHT, its metabolite androsterone could directly decrease cardiomyocytes proliferation through cell cycle arrest, which has a life-long-lasting effect on cardiac health. Our study highlights the importance of monitoring sex hormones in women during pregnancy and the follow-up of cardiac function in offspring with high risk of intrauterine androgen exposure.

Salvianolic acid B attenuates liver fibrosis by targeting Ecm1 and inhibiting hepatocyte ferroptosis

Hepatocyte ferroptosis promotes the pathogenesis and progression of liver fibrosis. Salvianolic acid B (Sal B) exerts antifibrotic effects. However, the pharmacological mechanism and target has not yet been fully elucidated. In this study, liver fibrosis was induced by CCl4 in wild-type mice and hepatocyte-specific extracellular matrix protein 1 (Ecm1)-deficient mice, which were separately treated with Sal B, ferrostatin-1, sorafenib or cilengitide. Erastin- or CCl4-induced hepatocyte ferroptosis models with or without Ecm1 gene knockdown were evaluated in vitro. Subsequently, the interaction between Ecm1 and xCT and the binding kinetics of Sal B and Ecm1 were determined. We found that Sal B significantly attenuated liver fibrosis in CCl4-induced mice. Ecm1 deletion in hepatocytes abolished the antifibrotic effect of Sal B. Mechanistically, Sal B protected against hepatocyte ferroptosis by upregulating Ecm1. Further research revealed that Ecm1 as a direct target for treating liver fibrosis with Sal B. Interestingly, Ecm1 interacted with xCT to regulate hepatocyte ferroptosis. Hepatocyte ferroptosis in vitro was significantly attenuated by Sal B treatment, which was abrogated after knockdown of Ecm1 in LO2 cells. Therefore, Sal B alleviates liver fibrosis in mice by targeting up-regulation of Ecm1 and inhibiting hepatocyte ferroptosis. The interaction between Ecm1 and xCT regulates hepatocyte ferroptosis.

TEFDTA: a transformer encoder and fingerprint representation combined prediction method for bonded and non-bonded drug-target affinities

MOTIVATION

The prediction of binding affinity between drug and target is crucial in drug discovery. However, the accuracy of current methods still needs to be improved. On the other hand, most deep learning methods focus only on the prediction of non-covalent (non-bonded) binding molecular systems, but neglect the cases of covalent binding, which has gained increasing attention in the field of drug development.

RESULTS

In this work, a new attention-based model, A Transformer Encoder and Fingerprint combined Prediction method for Drug-Target Affinity (TEFDTA) is proposed to predict the binding affinity for bonded and non-bonded drug-target interactions. To deal with such complicated problems, we used different representations for protein and drug molecules, respectively. In detail, an initial framework was built by training our model using the datasets of non-bonded protein-ligand interactions. For the widely used dataset Davis, an additional contribution of this study is that we provide a manually corrected Davis database. The model was subsequently fine-tuned on a smaller dataset of covalent interactions from the CovalentInDB database to optimize performance. The results demonstrate a significant improvement over existing approaches, with an average improvement of 7.6% in predicting non-covalent binding affinity and a remarkable average improvement of 62.9% in predicting covalent binding affinity compared to using BindingDB data alone. At the end, the potential ability of our model to identify activity cliffs was investigated through a case study. The prediction results indicate that our model is sensitive to discriminate the difference of binding affinities arising from small variances in the structures of compounds.

AVAILABILITY AND IMPLEMENTATION

The codes and datasets of TEFDTA are available at https://github.com/lizongquan01/TEFDTA.

The association of normal-range serum phosphorus with immunoglobulin A nephropathy progression: a retrospective cohort study

PURPOSE

The relationship between serum phosphorus and immunoglobulin A (IgA) nephropathy progression remains uncertain, especially normal-range serum phosphorus. Therefore, we herein examined the relationship between the normal-range serum phosphorus and the progression of IgA nephropathy.

METHODS

One hundred sixty-two patients with primary IgA nephropathy were divided into three groups according to tertiles of baseline serum phosphorus (first tertile: 0.73-1.04 mmol/L; second tertile: 1.04-1.21 mmol/L; third tertile: 1.21-1.60 mmol/L). Estimated glomerular filtration rate (eGFR) was calculated using the chronic kidney disease epidemiology collaboration. The composite outcome was defined as a decrease of at least 50% in eGFR from baseline or end-stage kidney disease (ESKD). The association of serum phosphorus with IgA nephropathy progression was estimated using Cox proportional hazards models, adjusting for potential confounders.

RESULTS

During a median 16 month follow-up period, 15 patients reached a composite outcome. In the crude Cox proportional hazard model, baseline serum phosphorus as a continuous variable was associated with increased risk for adverse renal outcomes [hazard ratio (HR) = 63.510, 95% confidence interval (CI) = 3.953-1020.284, P = 0.003], and the high tertile of serum phosphorus group had an increased risk of the composite outcome by using the low tertile group as the reference (HR = 11.895, 95% CI = 1.522-92.993, P = 0.018). After adjustment for traditional risk factors, the high tertile of serum phosphorus group was significantly related to IgA nephropathy progression compared with the low tertile group (HR = 9.424, 95% CI = 1.019-87.165, P = 0.048).

CONCLUSIONS

Relatively higher serum phosphorus levels within the normal range were significantly associated with the progression of IgA nephropathy.

THEMIS is a substrate and allosteric activator of SHP1, playing dual roles during T cell development

THEMIS plays an indispensable role in T cells, but its mechanism of action has remained highly controversial. Using the systematic proximity labeling methodology PEPSI, we identify THEMIS as an uncharacterized substrate for the phosphatase SHP1. Saturated mutagenesis assays and mass spectrometry analysis reveal that phosphorylation of THEMIS at the evolutionally conserved Tyr34 residue is oppositely regulated by SHP1 and the kinase LCK. Similar to THEMIS-/- mice, THEMISY34F/Y34F knock-in mice show a significant decrease in CD4 thymocytes and mature CD4 T cells, but display normal thymic development and peripheral homeostasis of CD8 T cells. Mechanistically, the Tyr34 motif in THEMIS, when phosphorylated upon T cell antigen receptor activation, appears to act as an allosteric regulator, binding and stabilizing SHP1 in its active conformation, thus ensuring appropriate negative regulation of T cell antigen receptor signaling. However, cytokine signaling in CD8 T cells fails to elicit THEMIS Tyr34 phosphorylation, indicating both Tyr34 phosphorylation-dependent and phosphorylation-independent roles of THEMIS in controlling T cell maturation and expansion.

Computer-Aided Prediction of the Interactions of Viral Proteases with Antiviral Drugs: Antiviral Potential of Broad-Spectrum Drugs

Human society is facing the threat of various viruses. Proteases are promising targets for the treatment of viral infections. In this study, we collected and profiled 170 protease sequences from 125 viruses that infect humans. Approximately 73 of them are viral 3-chymotrypsin-like proteases (3CLpro), and 11 are pepsin-like aspartic proteases (PAPs). Their sequences, structures, and substrate characteristics were carefully analyzed to identify their conserved nature for proposing a pan-3CLpro or pan-PAPs inhibitor design strategy. To achieve this, we used computational prediction and modeling methods to predict the binding complex structures for those 73 3CLpro with 4 protease inhibitors of SARS-CoV-2 and 11 protease inhibitors of HCV. Similarly, the complex structures for the 11 viral PAPs with 9 protease inhibitors of HIV were also obtained. The binding affinities between these compounds and proteins were also evaluated to assess their pan-protease inhibition via MM-GBSA. Based on the drugs targeting viral 3CLpro and PAPs, repositioning of the active compounds identified several potential uses for these drug molecules. As a result, Compounds 1-2, modified based on the structures of Ray1216 and Asunaprevir, indicate potential inhibition of DENV protease according to our computational simulation results. These studies offer ideas and insights for future research in the design of broad-spectrum antiviral drugs.

A new variant of the colistin resistance gene MCR-1 with co-resistance to β-lactam antibiotics reveals a potential novel antimicrobial peptide

The emerging and global spread of a novel plasmid-mediated colistin resistance gene, mcr-1, threatens human health. Expression of the MCR-1 protein affects bacterial fitness and this cost correlates with lipid A perturbation. However, the exact molecular mechanism remains unclear. Here, we identified the MCR-1 M6 variant carrying two-point mutations that conferred co-resistance to β-lactam antibiotics. Compared to wild-type (WT) MCR-1, this variant caused severe disturbance in lipid A, resulting in up-regulation of L, D-transpeptidases (LDTs) pathway, which explains co-resistance to β-lactams. Moreover, we show that a lipid A loading pocket is localized at the linker domain of MCR-1 where these 2 mutations are located. This pocket governs colistin resistance and bacterial membrane permeability, and the mutated pocket in M6 enhances the binding affinity towards lipid A. Based on this new information, we also designed synthetic peptides derived from M6 that exhibit broad-spectrum antimicrobial activity, exposing a potential vulnerability that could be exploited for future antimicrobial drug design.

MvaT binds to the PexsC promoter to repress the type III secretion system in Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic human pathogen capable of causing a variety of acute and chronic infections. Its type III secretion system (T3SS) plays a critical role in pathogenesis during acute infection. ExsA is a master regulator that activates the expression of all T3SS genes. Transcription of exsA is driven by two distinct promoters, its own promoter PexsA and its operon promoter PexsC. Here, in combination with a DNA pull-down assay and mass spectrometric analysis, we found that a histone-like nucleoid-structuring (H-NS) family protein MvaT can bind to the PexsC promoter. Using EMSA and reporter assays, we further found that MvaT directly binds to the PexsC promoter to repress the expression of T3SS genes. The repression of MvaT on PexsC is independent of ExsA, with MvaT binding to the -429 to -380 bp region relative to the transcription start site of the exsC gene. The presented work further reveals the complex regulatory network of the T3SS in P. aeruginosa.

DeepSA: a deep-learning driven predictor of compound synthesis accessibility

With the continuous development of artificial intelligence technology, more and more computational models for generating new molecules are being developed. However, we are often confronted with the question of whether these compounds are easy or difficult to synthesize, which refers to synthetic accessibility of compounds. In this study, a deep learning based computational model called DeepSA, was proposed to predict the synthesis accessibility of compounds, which provides a useful tool to choose molecules. DeepSA is a chemical language model that was developed by training on a dataset of 3,593,053 molecules using various natural language processing (NLP) algorithms, offering advantages over state-of-the-art methods and having a much higher area under the receiver operating characteristic curve (AUROC), i.e., 89.6%, in discriminating those molecules that are difficult to synthesize. This helps users select less expensive molecules for synthesis, reducing the time and cost required for drug discovery and development. Interestingly, a comparison of DeepSA with a Graph Attention-based method shows that using SMILES alone can also efficiently visualize and extract compound's informative features. DeepSA is available online on the below web server ( https://bailab.siais.shanghaitech.edu.cn/services/deepsa/ ) of our group, and the code is available at https://github.com/Shihang-Wang-58/DeepSA .

DnaJ-induced miRNA-146a negatively regulates the expression of IL-8 in macrophages

As a member of the damage-associated molecular patterns, heat shock proteins (HSPs) are widely recognized for their role in initiating innate immune responses. These highly conserved proteins are expressed ubiquitously in both prokaryotes and eukaryotes. In this study, our aim was to investigate how DnaJ, a HSP40 homolog derived from Pseudomonas aeruginosa (P. aeruginosa), influences the regulation of IL-8 expression in macrophages. Treatment with DnaJ served as a stimulus, inducing a more robust expression of IL-8 compared to other HSP homologs, including DnaK, GroEL, and HtpG. This effect was achieved through the activation of the NF-κB signaling pathway. Interestingly, DnaJ treatment also significantly increased the expression of microRNA-146a (miR-146a), which appears to play a role in modulating the expression of innate defense genes. As a consequence, pre-treatment with DnaJ led to a reduction in the extent of IL-8 induction in response to P. aeruginosa treatment. Notably, this reduction was counteracted by transfection of a miR-146a inhibitor, highlighting the involvement of miR-146a in P. aeruginosa-mediated induction of IL-8 expression. Therefore, this study uncovers the role of DnaJ in triggering the expression of miR-146a, which, in turn, modulates the excessive expression of IL-8 induced by P. aeruginosa infection.

A Comparative Study of Measuring Bladder Volume in Patients with Pelvic Tumor Receiving Radiotherapy Using a Portable Bladder Scanner Made in China and CT Analog Positioning Machine

PURPOSE/OBJECTIVE(S)

The purpose of this study was to investigate whether the bladder volume of patients with pelvic tumor treated with radiotherapy (RT) can be accurately measured using the Meike Palm Bladder Scanner PBSV3.2 manufactured in China and the accuracy of its measurement under different influencing factors.

MATERIALS/METHODS

One hundred and sixty-five patients with pelvic tumor radiotherapy who were positioned in our department from January 12, 2022, to July 7, 2022, were selected. All patients voided their bowels and urine one hour before positioning, had a gynecological examination, were instructed to drink 500-800 ml of water, urine volume was measured using PBSV3.2 when they felt the urge to urinate, and urine volume reached 150-350 ml given for positioning (20 minutes expected from making the film appliance to the end of positioning), and the data were measured and recorded using a cystometric device immediately after positioning. The CT bladder volume outlined by the treating physician is viewed in the planning system. The accuracy of PBSV3.2 was evaluated by comparing the bladder volume measured by the bladder scanner and CT. To investigate the accuracy of PBSV3.2 in different sex, ages, treatment purpose, and bladder volume.

RESULTS

There was a significant positive correlation with bladder volume on CT and PBSV (r = 0.874; p<0.001). The mean difference between CT measured values and PBSV was (-0.14±50.17) ml. The results of the different variables showed that the overall mean of PBSV and CT measurements were statistically different in the age ≥65 years, bladder volumes >400ml and ≤400ml groups (p = 0.028, 0.002, 0.001). There was no statistical significance between the remaining variables. The volume difference between PBSV measurement and CT was 12.87ml in male patients, which was larger than that in female patients 3.27ml. Pearson correlation analysis showed that the correlation coefficient was 0.473 for bladder volume greater than 400ml and 0.868 for bladder volume less than 400ml; the correlation coefficient of the other variables ranged from 0.802 to 0.893.

CONCLUSION

This is the first large-sample study to evaluate the accuracy of PBSV in a pelvic tumor RT population using the convenient bladder scanner PBSV3.2 made in China. PBSV provides an acceptable indicator for monitoring bladder volume in patients with pelvic RT. It is recommended to monitor bladder volume with PBSV when the planned bladder volume is 200-400ml. For male and patients ≥65 years old, at least two repeat measurements are required when using a bladder scanner and the volume should be corrected by using a modified feature to improve bladder volume consistency.

Optimizing the Imaging Scheme of Small-Dose Contrast Agent in 4D-CT Localization Enhancement Scan for Radiotherapy of Liver Cancer

PURPOSE/OBJECTIVE(S)

The primary liver cancer radiation therapy 4D-CT-enhanced (CE-4DCT) scan can accurately reflect the state of the liver as it moves with respiration, and enables clear visualization of the tumor, providing a precise range for target area outlining. However, the CE-4DCT scan localization time of primary liver cancer is long, and the fixed delay time of diagnostic CT cannot obtain high-quality 4DCT images. To this end, we designed a randomized controlled study to investigate the ideal localization scan delay time parameters for primary liver cancer CE-4DCT.

MATERIALS/METHODS

Patients with primary hepatocellular carcinoma who presented to our department for radiotherapy CT localization from January to December 2022 participated in this study. All subjects were randomly divided into two groups in a 1:1 ratio. CE-4DCT scans were performed using a high concentration of iodomepril (400 mg/ml) contrast agent with a contrast volume equal to the patient's body weight. The scanning parameters were set according to scheme A (flow rate 2.0 ml/s, delay time 30s) and B (2.0 ml/s, 35s) respectively. Before the CE-4D CT scan, CT plain scan was routinely performed, physicians measured the CT value (HU) of abdominal aorta, portal vein, left hepatic vein, middle hepatic vein, right hepatic vein, liver parenchyma and tumor lesion on CT40 time item and plain scan images respectively. The image quality was subjectively and qualitatively assessed. The image enhancement effect is divided into excellent, good, relatively poor and poor.

RESULTS

A total of 18 patients were included in this study. Patient characteristics were well-balanced in both groups. There were statistical differences between the two groups (A vs B) in the abdominal aorta (226.66 ± 45.59 vs. 176.66 ± 32.84, p = 0.017), left hepatic vein (142.77 ± 24.41 vs. 164.88 ± 19.02, p = 0.048); in the portal vein, middle hepatic vein, right hepatic vein, liver parenchyma, and tumor lesions CT values were not statistically different. The comparison of all flat-scan images between the two groups was statistically significant. The comparison of all flat-scan images in both groups was statistically significant. The subjective qualitative assessment of the developing effect was excellent in 44.4% (33.3% vs. 11.1%), good in 16.7% (5.6% vs. 11.1%), and poor in 38.9% (16.7% vs. 22.2%) in both groups. image quality was slightly higher in group A than in group B, but did not reach statistical significance (χ2 = 1.088, p = 0.698). In patients with primary hepatocellular carcinoma with portal vein carcinoma thrombosis 83.33% subjectively evaluated poor results.

CONCLUSION

Qualitatively acceptable enhanced images were obtained for primary hepatocellular carcinoma (CE-4DCT) localization scans with a delay time controlled at 30s when using the least amount of contrast agent and the same flow rate.

Pseudo CT Synthesis Using Cone-Beam CT of Cervical Cancer with GAN-Based Neural Network Model

PURPOSE/OBJECTIVE(S)

Cervical cancer (CC) is a tumor disease that threatens the health of women. As an important treatment of CC, radiotherapy has been widely used in clinic. With the rapid development of radiotherapy technology, adaptive radiotherapy has received much attention. Adaptive radiotherapy means more accurate radiation dose and more accurate radiation area, which can effectively protect normal tissue. It is significant to improve the local control rate of tumor and the quality of life of patients. However, the Cone-Beam CT (CBCT) images collected during radiotherapy are of poor quality and cannot provide real-time radiation effect information, resulting in timely and effective adjustment of radiation dose and radiation area in the process of radiotherapy for cervical cancer. To alleviate this issue, this study will establish a model to leverage CC CBCT images to synthetize pseudo computed tomography (CT) images with high quality, so as to achieve the purpose of quality improvement.

MATERIALS/METHODS

This study included the data of 20 patients with CC in ** hospital. The planning CT and CBCT scan data of each patient before radiotherapy were collected, and the interval between the two kinds of image data was required to be less than one week. After data preprocessing, a total of 1206 pairs of images were trained and tested. The generative adversarial network (GAN) is constructed. In order to ensure the similarity between the input image and the output image, the L1 loss function is leveraged. And the full supervision method is used to train the model to achieve a better effect of image synthesis and improve the quality of CBCT image. Peak signal-to-noise ratio (PSNR) and structural similarity (SSIM) were used as evaluation indexes.

RESULTS

Using five-fold cross-validation, the values of PSNR between the pseudo-CT (sCT) and the planning CT (pCT) image and between the CBCT and the pCT image are calculated. The results are 26.9 and 22.6, respectively. The sCT obtained from the GAN model increases the peak signal-to-noise ratio by 19% compared with the original CBCT, which means that the proposed model built in this study can improve the useful information of the CBCT image. The SSIM values between sCT and pCT and between CBCT and pCT are also calculated, and the average values of them are 0.89 and 0.63, respectively. Therefore, in this experiment, the structure of the sCT obtained by the proposed model is closer to pCT. And the SSIM increases by 41.2% compared with the original CBCT, which means that the sCT by the proposed model is more similar to the pCT in structure. These results could make a more accurate judgment on the effect of radiotherapy.

CONCLUSION

In this study, the pseudo-CT synthesis method based on GAN can improve the quality of CC CBCT image. The results show this method makes the structure clearer and could assist doctors to adjust the radiation dose and radiation area in time. This study is able to facilitate the development of adaptive radiotherapy for CC.

Preheating Thermoplastic Membrane Reduce Setup Error in Patients with Thoracic Cancer Undergoing Radiation Therapy: A Prospective Randomized Controlled Study

PURPOSE/OBJECTIVE(S)

Thermoplasticfilm routinely placed in the treatment room always led to uncomfortable feeling in patients receiving thorax radiation therapy because of significant temperature difference between thermoplastic film and body surface. Therefore, it may result in setup error and further affect accuracy of radiation therapy. Here, we designed a randomized controlled study to investigate the efficacy of preheat thermoplastic film to reduce setup error in patients receiving thorax radiotherapy.

MATERIALS/METHODS

Patients with thoracic cancer receiving radiotherapy once daily with five fraction per week were enrolled in this study from October 2022 to January 2023. All participants were randomly assigned into room-temperature group and preheating group in a 1:1 ratio. For the preheating group, the thermoplastic film was preheated for 10 minutes in a 37°C thermostat before it was used for patients' setup. For controlled group, the thermoplastic film with room-temperature was used for patients' setup. The cone beam computed tomography (CBCT) was used to evaluate setup errors once a week. The setup errors in translational directions X, Y and Z were recorded based on CBCT image. to measure the left-right as well as anterior-posterior diameter of the thorax in cross-section to observe whether there was any difference in thorax size from that at positioning. A modified Likert questionnaire was conducted to investigate the setup comfort level between two groups before radiotherapy and Day 5 of radiotherapy.

RESULTS

A total of 34 patients were enrolled in this study. Patient characteristics were well balanced in both arms. The setup errors in the X, Y, and Z axes in group A were 1(-1,1) mm, 0(-1,2.75) mm and 0(-1,1) mm, respectively, while those in group B were 0(-2,2) mm, 1(-1.25,3) mm, and -1(-2,1) mm in the X, Y, and Z axes, respectively. Setup error in preheating group was smaller than room-temperature group in the X-axis direction (Z = 2.04, P = 0.042), but no significant differences were detected in Y and Z axes. Comparison of changes in anteroposterior thoracic diameter between the two groups. The preheated group was smaller than the normothermic group (-0.19 ± 0.48 vs -0.38 ± 0.36, P < 0.01). The total comfort scale scores of the two groups were 30.88 ± 3.39 vs 30.59 ± 3.34 (p = 0.42) before treatment and 32.125 ± 4.31 vs 31.06 ± 3.15 (p = 0.80) after treatment. Among the eight sub-items, only the fourth dimension of temperature was statistically different (pre 3.12 ± 0.48 vs 2.88 ± 0.60, P = 0.218; post 4.12 ± 0.78 vs 2.94 ± 0.43, P < 0.01).

CONCLUSION

Ourcenter proposed the first method of heating the mold for postural fixation during patient radiotherapy. Compared with room-temperature thermoplastic film, our study found preheating thermoplastic film with 37°C could significantly reduce setup error in the X direction with less effect on the anterior-posterior diameter change of the thorax and higher patient temperature comfort satisfaction.

Discovery and Mechanism Study of SARS-CoV-2 3C-like Protease Inhibitors with a New Reactive Group

3CLpro is an attractive target for the treatment of COVID-19. Using the scaffold hopping strategy, we identified a potent inhibitor of 3CLpro (3a) that contains a thiocyanate moiety as a novel warhead that can form a covalent bond with Cys145 of the protein. Tandem mass spectrometry (MS/MS) and X-ray crystallography confirmed the mechanism of covalent formation between 3a and the protein in its catalytic pocket. Moreover, several analogues of compound 3a were designed and synthesized. Among them, compound 3h shows the best inhibition of 3CLpro with an IC50 of 0.322 μM and a kinact/Ki value of 1669.34 M-1 s-1, and it exhibits good target selectivity for 3CLpro against host proteases. Compound 3c inhibits SARS-CoV-2 in Vero E6 cells (EC50 = 2.499 μM) with low cytotoxicity (CC50 > 200 μM). These studies provide ideas and insights to explore and develop new 3CLpro inhibitors in the future.

Correlation Between the Variability of Different Obesity Indices and Diabetic Kidney Disease: A Retrospective Cohort Study Based on Populations in Taiwan

Purpose

To investigate the association of five obesity indices and the variability of these indices with diabetic kidney disease (DKD) in patients with type 2 diabetes and compare the predictive validity of these markers for the risk of DKD in this large longitudinal cohort study.

Patients and Methods

A total of 2659 patients with type 2 diabetes who did not have DKD were enrolled between 2006 and 2019 at Lee's United Clinic in Taiwan. Data were collected for each subject, including demographic data, personal medical history, clinical parameters and calculated Body mass index (BMI), visceral adiposity index (VAI), lipid accumulation product (LAP), body roundness index (BRI) and variability of five obesity indices. Cox regression analysis was performed to determine the relationship between different obesity indicators and DKD risk. Cox's proportional hazards model was evaluated the predictive effect of obesity indices on DKD.

Results

The risk of developing DKD increased with an increase in the BRI, LAP, VAI, WC and BMI (all P trend<0.05), and the variability of VAI was significantly associated with DKD [HR=1.132, 95% CI (1.001, 1.281)] after adjusting for corresponding variables. BRI had the strongest predictive effect on DKD. BRI had the best predictive performance, with AUC of 0.807, 0.663 and 0.673 at 1, 3 and 5 years, respectively. Cox regression analysis of risk factors for DKD in patients stratified by BRI quartiles showed that patients in the Q4 group had the highest risk of developing DKD [HR=1.356, 95% CI (1.131, 1.626)].

Conclusion

BMI, WC, VAI, LAP, BRI and VAI variability were associated with a significant increase in the risk of DKD events, and BRI was superior and alternative obesity index for predicting DKD.

Murepavadin induces envelope stress response and enhances the killing efficacies of β-lactam antibiotics by impairing the outer membrane integrity of Pseudomonas aeruginosa

Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen that can cause a variety of acute and chronic infections. The bacterium is highly resistant to numerous antibiotics. Murepavadin is a peptidomimetic antibiotic that blocks the function of P. aeruginosa lipopolysaccharide (LPS) transport protein D (LptD), thus inhibiting the insertion of LPS into the outer membrane. In this study, we demonstrated that sublethal concentrations of murepavadin enhance the bacterial outer membrane permeability. Proteomic analyses revealed the alteration of protein composition in bacterial inner and outer membranes following murepavadin treatment. The antisigma factor MucA was upregulated by murepavadin. In addition, the expression of the sigma E factor gene algU and the alginate synthesis gene algD was induced by murepavadin. Deletion of the algU gene reduces bacterial survival following murepavadin treatment, indicating a role of the envelope stress response in bacterial tolerance. We further demonstrated that murepavadin enhances the bactericidal activities of β-lactam antibiotics by promoting drug influx across the outer membrane. In a mouse model of acute pneumonia, the murepavadin-ceftazidime/avibactam combination showed synergistic therapeutic effect against P. aeruginosa infection. In addition, the combination of murepavadin with ceftazidime/avibactam slowed down the resistance development. In conclusion, our results reveal the response mechanism of P. aeruginosa to murepavadin and provide a promising antibiotic combination for the treatment of P. aeruginosa infections.IMPORTANCEThe ever increasing resistance of bacteria to antibiotics poses a serious threat to global public health. Novel antibiotics and treatment strategies are urgently needed. Murepavadin is a novel antibiotic that blocks the assembly of lipopolysaccharide (LPS) into the Pseudomonas aeruginosa outer membrane by inhibiting LPS transport protein D (LptD). Here, we demonstrated that murepavadin impairs bacterial outer membrane integrity, which induces the envelope stress response. We further found that the impaired outer membrane integrity increases the influx of β-lactam antibiotics, resulting in enhanced bactericidal effects. In addition, the combination of murepavadin and a β-lactam/β-lactamase inhibitor mixture (ceftazidime/avibactam) slowed down the resistance development of P. aeruginosa. Overall, this study demonstrates the bacterial response to murepavadin and provides a new combination strategy for effective treatment.

Ultrasound-Guided Human Islet Transplantation: Safety, Feasibility, and Efficacy Analysis

RATIONALE AND OBJECTIVES

We aimed to analyze the safety, feasibility, and efficacy of human islet transplantation (IT) using ultrasound (US) throughout the entire procedure.

MATERIALS AND METHODS

A total of 22 recipients (18 males; mean age 42.6 ± 17.5years) with 35 procedures were retrospective included. Under US guidance, percutaneous transhepatic portal catheterization was successfully performed through a right-sided transhepatic approach, and islets were infused into the main portal vein. Color Doppler and contrast-enhanced ultrasound were used to guide the procedure and monitor the complications. After infusion of the islet mass, the access track was embolized by embolic material. If hemorrhage persisted, US-guided radiofrequency ablation (RFA) was performed to stop bleeding. Factors that could affect the complication were analyzed. After transplantation, primary graft function was evaluated with a β-score 1month after the last islet infusion.

RESULTS

The technical success rates were 100% with a single puncture attempt. Six (17.1%) abdominal bleeding episodes were immediately stopped by US-guided RFA. No portal vein thrombosis were encountered. Dialysis (OR (Odd Ratio): 32.0; 95% CI: 1.561-656.054; and P = .025) was identified as a significant factor associated with bleeding. Primary graft function was optimal in eight patients (36.4%), suboptimal in 13 patients (59.1%), and poor in one patient (4.5%).

CONCLUSION

In conclusion, whole-procedure US-guided IT is a safe, feasible, and effective method for diabetes. Complications are either self-limiting or manageable with noninvasive treatment.

PitA Controls the H2- and H3-T6SSs through PhoB in Pseudomonas aeruginosa

Pseudomonas aeruginosa possesses three type VI secretion systems (T6SSs) that are involved in interspecies competition, internalization into epithelial cells, and virulence. Host-derived mucin glycans regulate the T6SSs through RetS, and attacks from other species activate the H1-T6SS. However, other environmental signals that control the T6SSs remain to be explored. Previously, we determined PitA to be a constitutive phosphate transporter, whose mutation reduces the intracellular phosphate concentration. Here, we demonstrate that mutation in the pitA gene increases the expression of the H2- and H3-T6SS genes and enhances bacterial uptake by A549 cells. We further found that mutation of pitA results in activation of the quorum sensing (QS) systems, which contributes to the upregulation of the H2- and H3-T6SS genes. Overexpression of the phosphate transporter complex genes pstSCAB or knockdown of the phosphate starvation response regulator gene phoB in the ΔpitA mutant reduces the expression of the QS genes and subsequently the H2- and H3-T6SS genes and bacterial internalization. Furthermore, growth of wild-type PA14 in a low-phosphate medium results in upregulation of the QS and H2- and H3-T6SS genes and bacterial internalization compared to those in cells grown in a high-phosphate medium. Deletion of the phoB gene abolished the differences in the expression of the QS and T6SS genes as well as bacterial internalization in the low- and high- phosphate media. Overall, our results elucidate the mechanism of PitA-mediated regulation on the QS system and H2- and H3-T6SSs and reveal a novel pathway that regulates the T6SSs in response to phosphate starvation. IMPORTANCE Pseudomonas aeruginosa is an opportunistic pathogenic bacterium that causes acute and chronic infections in humans. The type VI secretion systems (T6SSs) have been shown to associate with chronic infections. Understanding the mechanism used by the bacteria to sense environmental signals and regulate virulence factors will provide clues for developing novel effective treatment strategies. Here, we demonstrate a relationship between a phosphate transporter and the T6SSs and reveal a novel regulatory pathway that senses phosphate limitation and controls bacterial virulence factors in P. aeruginosa.

MvfR Controls Tolerance to Polymyxin B by Regulating rfaD in Pseudomonas aeruginosa

Polymyxins are currently the last-resort antibiotics for the treatment of multidrug-resistant Gram-negative bacterial infections. To expand the understanding of the intrinsic resistance mechanism against polymyxins, a laboratory strain of Pseudomonas aeruginosa PAO1 was subjected to serial passage in the presence of sublethal doses of polymyxin B over a period of 30 days. By whole-genome sequencing of successively isolated polymyxin B-resistant isolates, we identified a frameshift mutation (L183fs) in the mvfR gene that further increased polymyxin resistance in the pmrB mutant background. A ΔmvfR mutation alone showed higher tolerance to polymyxin B due to altered lipopolysaccharide (LPS) on the surface of bacterial cells, which decreases its outer membrane permeability. In the ΔmvfR mutant, polymyxin B treatment caused the upregulation of rfaD, the gene involved in LPS core oligosaccharide synthesis, which is responsible for polymyxin tolerance. To the best of our knowledge, this is the first report of mvfR mutation conferring polymyxin resistance in P. aeruginosa via increased integrity of bacterial outer membrane. IMPORTANCE Antibiotic resistance imposes a considerable challenge for the treatment of P. aeruginosa infections. Polymyxins are the last-resort antibiotics for the treatment of multidrug-resistant P. aeruginosa infections. Understanding the development and mechanisms of bacterial resistance to polymyxins may provide clues for the development of new or improved therapeutic strategies effective against P. aeruginosa. In this study, using an in vitro evolution assay in combination with whole-genome sequencing, we demonstrated that MvfR controls tolerance to polymyxin B by regulating the rfaD gene in P. aeruginosa. Our results reveal a novel mechanism employed by P. aeruginosa in the defense against polymyxin antibiotics.

Integrated physiological and metabolomic analysis reveals new insights into toxicity pathways of paraquat to Microcystis aeruginosa

Chemical pollutants, such as herbicides, released into the aquatic environment adversely affect the phytoplankton community structure. While majority of herbicides are specifically designed to target photosynthetic processes, they also can be toxic to phytoplankton; however, despite the photosynthetic toxicity, some herbicides can target multiple physiological processes. Therefore, a full picture of toxicity pathway of herbicide to phytoplankton is necessary. In the present study, the cyanobacterium Microcystis aeruginosa was exposed to two levels (17 μg L^-1 (EC₁₀) and 65 μg L^-1 (EC₅₀)) of paraquat for 72 h. The physiological and metabolic responses were analyzed to elucidate the toxicity pathway and establish the adverse outcome pathway of paraquat to M. aeruginosa. The results revealed that enhanced glycolysis (upregulation of pyruvic acid level) and tricarboxylic acid cycle (upregulation of the levels of malic acid, isocitric acid and citric acid) exposed to EC₁₀ level of paraquat, which probably acted as a temporary strategy to maintain a healthy energy status in M. aeruginosa cells. Meanwhile, the expressions of glutathione and benzoic acid were enhanced to scavenge the excessive reactive oxygen species (ROS). Additionally, the accumulation of pigments (chlorophyll a and carotenoid) might play a supplementary role in the acclimation to EC₁₀ level paraquat treatment. In cells exposed to paraquat by EC₅₀ level, the levels of SOD, CAT, glutathione and benzoic acid increased significantly; however, the ROS exceeded the tolerance level of antioxidant system in M. aeruginosa. The adverse effects were revealed by inhibition of chlorophyll a fluorescence, the decreases in several carbohydrates (e.g., glucose 1-phosphate, fructose and galactose) and total protein content. Consequently, paraquat-induced oxidative stress caused the growth inhibition of M. aeruginosa. These findings provide new insights into the mode of action of paraquat in M. aeruginosa.

Maximum Emission Peak Over 1500 nm of Organic Assembly for Blood-Brain Barrier-Crossing NIR-IIb Phototheranostics of Orthotopic Glioblastoma

The development of blood-brain barrier (BBB)-crossing phototheranostic agents in second near-infrared window (NIR-II), especially in the range of 1500-1700 nm (NIR-IIb), affords great opportunities for glioblastoma (GBM) management. Herein, an organic assembly (denoted as LET-12) with the maximum absorption peak at 1400 nm and emission peak at 1512 nm with trailing over 1700 nm through the self-assembly of organic small molecule IR-1064 is designed and subsequently decorated with choline and acetylcholine analogs. The LET-12 can effectively cross BBB through the brain's choline-like receptors-mediated transcytosis and accumulated in tumor tissues, thus achieving fluorescence/photoacoustic (FL/PA) duplex imaging of orthotopic GBM with ≈3.0 mm depth and a superior tumor-to-normal tissue signal ratio (20.93 ± 0.59 for FL imaging and 32.63 ± 1.16 for PA imaging, respectively). Owing to its good photothermal conversion ability, the LET-12 also can serve as a photothermal conversion agent, achieving obvious tumor repression of orthotopic murine GBM model after once treatment. The findings indicate that the LET-12 holds great potential for BBB-crossing NIR-IIb phototheranostics of orthotopic GBM. This self-assembly strategy of organic small molecules opens a new avenue for the construction of NIR-IIb phototheranostics.

Adipocyte Na, K-ATPase Signaling Attenuates Experimental Uremic Cardiomyopathy

Oxidative stress has been shown to cause an alteration of intracellular signaling in adipocytes that may lead to various comorbidities of obesity and cardiovascular complications. Evidence suggests that dysregulation of Na, K-ATPase signaling can contribute to systemic inflammation and redox signaling that leads to various metabolic disturbances. Hence the present study aims to explore the specific role of adipocyte Na, K-ATPase signaling in the amelioration of pathophysiological alterations of experimental uremic cardiomyopathy. Experimental uremic cardiomyopathy was induced by partial nephrectomy (PNx), and adipocyte-specific expression of NaKtide, a peptide that inhibits Na, K-ATPase signaling, was achieved using a lentivirus construct with NaKtide expression driven by an adiponectin promoter. Cardiomyopathy and anemia induced in partial nephrectomy mice were accompanied by an altered molecular phenotype of adipocytes, increased systemic inflammatory cytokines and oxidant stress within 4 weeks. These changes were significantly worsened by the addition of a Western diet (enriched in fat and fructose contents) but were prevented with specific expression of NaKtide in adipocytes. The skeletal muscle-specific expression of NaKtide did not ameliorate the disease phenotype. Adipocyte dysfunction and uremic cardiomyopathy developed in PNx mice, both were significantly ameliorated by the adipocyte-specific expression of NaKtide. These findings suggest that oxidative milieu in the adipocyte has a pivotal role in the development and progression of uremic cardiomyopathy in mice subjected to partial nephrectomy. If confirmed in humans, this may be a lead for future research to explore novel therapeutic targets in chronic renal failure.

APOC1 exacerbates renal fibrosis through the activation of the NF-κB signaling pathway in IgAN

Introduction: IgA nephropathy (IgAN) is the most common disease leading to end-stage renal disease, and tubular fibrosis represents an important risk factor for disease progression. However, research on early molecular diagnostic indicators of tubular fibrosis and the mechanisms underlying disease progression is still lacking. Methods: The GSE93798 dataset was downloaded from the GEO database. DEGs were screened and analyzed for GO and KEGG enrichment in IgAN. The least absolute shrinkage and selection operator (LASSO) and support vector machine recursive feature elimination (SVM-RFE) algorithms were applied to screen for hub secretory genes. The expression and diagnostic efficacy of hub genes were confirmed by the GSE35487 dataset. ELISA was applied to detect the expression of APOC1 in serum. The expression and localization of hub genes in IgAN were verified by the expression of IHC and IF in human kidney tissues, and the correlation of expression with clinical data was verified in the Nephroseq database. Finally, cellular experiments clarified the role of hub genes in the signaling pathway. Results: A total of 339 DEGs were identified in IgAN, of which 237 were upregulated and 102 downregulated. The KEGG signaling pathway is enriched in the ECM-receptor interaction and AGE-RAGE signaling pathway. APOC1, ALB, CCL8, CXCL2, SRPX2, and TGFBI identified six hub secretory genes using the LASSO and SVM-RFE algorithms. In vivo and in vitro experiments demonstrated that APOC1 expression was elevated in IgAN. The serum concentration of APOC1 was 1.232 ± 0.1812 μg/ml in IgAN patients, whereas it was 0.3956 ± 0.1233 μg/ml in healthy individuals. APOC1 exhibited high diagnostic efficacy for IgAN (AUC of 99.091%, specificity of 95.455%, and sensitivity of 99.141%) in the GSE93798 dataset. APOC1 expression negatively correlated with eGFR (R ² = 0.2285, p = 0.0385) and positively correlated with serum creatinine (R ² = 0.41, p = 0.000567) in IgAN. APOC1 exacerbated renal fibrosis, possibly in part by activating the NF-κB pathway in IgAN. Conclusion: APOC1 was identified as the core secretory gene of IgAN, which was closely associated with blood creatinine and eGFR and had significant efficacy in the diagnosis of IgAN. Mechanistic studies revealed that the knockdown of APOC1 could improve IgAN renal fibrosis by inhibiting the NF pathway, which may be a potential therapeutic target for improving renal fibrosis in IgAN.

Discovery, structural optimization, and anti-tumor bioactivity evaluations of betulinic acid derivatives as a new type of RORγ antagonists

Betulinic acid (BA) is a natural pentacyclic triterpenoid that has a wide range of biological and pharmacological effects. Here, computational methods such as pharmacophore screening and reverse docking were used to predict the potential target for BA. Retinoic acid receptor-related orphan receptor gamma (RORγ) was confirmed as its target by several molecular assays as well as crystal complex structure determination. RORγ has been the focus of metabolic regulation, but its potential role in cancer treatment has only recently come to the fore. In this study, rationale optimization of BA was performed and several new derivatives were generated. Among them, the compound 22 showed stronger binding affinity with RORγ (K_D = 180 nM), good anti-proliferative activity against cancer cell lines, and potent anti-tumor efficacy with a TGI value of 71.6% (at a dose of 15 mg/kg) in the HPAF-II pancreatic cancer xenograft model. Further RNA-seq analysis and cellular validation experiments supported that RORγ antagonism was closely related to the antitumor activity of BA and 22, resulting in suppression of the RAS/MAPK and AKT/mTORC1 pathway and inducing caspase-dependent apoptosis in pancreatic cancer cells. RORγ was highly expressed in cancer cells and tissues and positively correlated with the poor prognosis of cancer patients. These results suggest that BA derivatives are potential RORγ antagonists worthy of further exploration.

The Proxy Step-Size Technique for Regularized Optimization on the Sphere Manifold

We give an effective solution to the regularized optimization problem g (x) + h (x), where x is constrained on the unit sphere ||x ||₂ = 1. Here g (·) is a smooth cost with Lipschitz continuous gradient within the unit ball {x : ||x ||₂ ≤ 1 } whereas h (·) is typically non-smooth but convex and absolutely homogeneous, e.g., norm regularizers and their combinations. Our solution is based on the Riemannian proximal gradient, using an idea we call proxy step-size - a scalar variable which we prove is monotone with respect to the actual step-size within an interval. The proxy step-size exists ubiquitously for convex and absolutely homogeneous h(·), and decides the actual step-size and the tangent update in closed-form, thus the complete proximal gradient iteration. Based on these insights, we design a Riemannian proximal gradient method using the proxy step-size. We prove that our method converges to a critical point, guided by a line-search technique based on the g(·) cost only. The proposed method can be implemented in a couple of lines of code. We show its usefulness by applying nuclear norm, l₁ norm, and nuclear-spectral norm regularization to three classical computer vision problems. The improvements are consistent and backed by numerical experiments. available at https://bitbucket.org/FangBai/proxystepsize-pgs.

Primary lacrimal sac lymphoma: a case-based retrospective study in a Chinese population

AIM: To determine the clinical characteristics, pathological types, tumor markers, treatments, and outcomes of Chinese patients with primary lacrimal sac lymphoma. METHODS: This case-based retrospective study analyzed 15 Chinese patients with primary lacrimal sac lymphoma. The clinical data collected included gender, age at diagnosis, symptoms, imaging examination results, pathologic diagnosis, pathogen identification, tumor markers, treatments, follow-up, and prognosis. Descriptive statistics were used to characterize the patients. Progression-free survival (PFS) was defined as the time from surgery to the last follow-up, first record of tumor recurrence, or death. RESULTS: There were 7 males and 8 females with unilateral primary lacrimal sac lymphoma in the left eye (n=6) or right eye (n=9). The initial symptom in 13 patients was epiphora, and 2 patients had redness and swelling in the lacrimal sac area. All patients ultimately developed epiphora, and 12 had masses in the lacrimal sac area. Analysis of preoperative plasma tumor markers indicated 14 patients had elevated homocysteine, 9 had elevated β2-microglobulin, and 2 had elevated lactate dehydrogenase (LDH); 2 patients had elevations of all three markers, and 1 patient had no elevation of any marker. All patients underwent surgical resection and 12 patients received postoperative chemotherapy. The pathological types were DLBCL (n=8), MALT lymphoma (n=5), and NK/T-cell lymphoma, nasal type (n=2). The mean follow-up time was 25.8mo (range: 4-41) and 2 patients died. Seven patients who underwent mass excision combined with dacryocystorhinostomy (DCR) had no postoperative epiphora. Eight patients who only underwent mass excision had varying degrees of postoperative epiphora. Preoperative LDH elevation and NK/T-cell lymphoma, nasal type were associated with poor prognoses. CONCLUSION: Early diagnosis and treatment can lead to a good prognosis for most patients with primary lacrimal sac lymphoma. Mass resection combined with DCR can reduce the occurrence of post-surgical epiphora. The pathology type and tumor marker status are associated with prognosis.

Identification of a novel mutation in the FGF10 gene in a Chinese family with obvious congenital lacrimal duct dysplasia in lacrimo-auriculo-dento-digital syndrome

AIM: To identify the pathogenic gene variant in a family with lacrimo-auriculo-dento-digital syndrome [LADD (MIM 149730)] showing congenital lacrimal duct dysplasia as the main clinical manifestation and lay the foundation for future research on the pathogenic gene. METHODS: Ophthalmological examinations, including slit-lamp biomicroscopy and lacrimal duct probing, and computed tomography dacryocystography (CT-DCG) were performed for all participants. The family pedigree was drawn, genetic features were analyzed, and the genomic DNA of the subjects was extracted. Pathogenic genes were screened via whole exome sequencing (WES) and confirmed using Sanger sequencing. RESULTS: Six patients belonged to this three-generation family, and their clinical manifestations included congenital nasolacrimal duct obstruction, congenital absence of lacrimal puncta and canaliculi, lacrimal fistulae, and limb deformities. This pattern indicates autosomal dominant inheritance. Diagnosis was based on the clinical characteristics of LADD syndrome, which presented in all the patients in this family. A novel frameshift mutation in the FGF10 gene (NM_004465.1), c.234dupC (p.Trp79Leus*15), was identified in all patients via WES. The variant was confirmed by Sanger sequencing and classified as a “pathogenic mutation” according to the American College of Medical Genetics and Genomics (ACMG) variant interpretation guidelines. CONCLUSION: A novel frameshift mutation in the FGF10 gene is found in all patients. This finding helps this family with LADD syndrome receiving a more accurate clinical diagnosis and genetic counseling by extending the mutation range of the FGF10 gene.

Discovery, evaluation and mechanism study of WDR5-targeted small molecular inhibitors for neuroblastoma

Neuroblastoma is the most common and deadliest tumor in infancy. WDR5 (WD Repeat Domain 5), a critical factor supporting an N-myc transcriptional complex via its WBM site and interacting with chromosome via its WIN site, promotes the progression of neuroblastoma, thus making it a potential anti-neuroblastoma drug target. So far, a few WIN site inhibitors have been reported, and the WBM site disruptors are rare to see. In this study we conducted virtual screening to identify candidate hit compounds targeting the WBM site of WDR5. As a result, 60 compounds were selected as candidate WBM site inhibitors. Cell proliferation assay demonstrated 6 structurally distinct WBM site inhibitors, numbering as compounds 4, 7, 11, 13, 19 and 22, which potently suppressed 3 neuroblastoma cell lines (MYCN-amplified IMR32 and LAN5 cell lines, and MYCN-unamplified SK-N-AS cell line). Among them, compound 19 suppressed the proliferation of IMR32 and LAN5 cells with EC50 values of 12.34 and 14.89 μM, respectively, and exerted a moderate inhibition on SK-N-AS cells, without affecting HEK293T cells at 20 μM. Analysis of high-resolution crystal complex structure of compound 19 against WDR5 revealed that it competitively occupied the hydrophobic pocket where V264 was located, which might disrupt the interaction of MYC with WDR5 and further MYC-medicated gene transcription. By performing RNA-seq analysis we demonstrated the differences in molecular action mechanisms of the compound 19 and a WIN site inhibitor OICR-9429. Most interestingly, we established the particularly high synergy rate by combining WBM site inhibitor 19 and the WIN site inhibitor OICR-9429, providing a novel therapeutic avenue for neuroblastoma.

Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches

Allosteric mechanisms are commonly employed regulatory tools used by proteins to orchestrate complex biochemical processes and control communications in cells. The quantitative understanding and characterization of allosteric molecular events are among major challenges in modern biology and require integration of innovative computational experimental approaches to obtain atomistic-level knowledge of the allosteric states, interactions, and dynamic conformational landscapes. The growing body of computational and experimental studies empowered by emerging artificial intelligence (AI) technologies has opened up new paradigms for exploring and learning the universe of protein allostery from first principles. In this review we analyze recent developments in high-throughput deep mutational scanning of allosteric protein functions; applications and latest adaptations of Alpha-fold structural prediction methods for studies of protein dynamics and allostery; new frontiers in integrating machine learning and enhanced sampling techniques for characterization of allostery; and recent advances in structural biology approaches for studies of allosteric systems. We also highlight recent computational and experimental studies of the SARS-CoV-2 spike (S) proteins revealing an important and often hidden role of allosteric regulation driving functional conformational changes, binding interactions with the host receptor, and mutational escape mechanisms of S proteins which are critical for viral infection. We conclude with a summary and outlook of future directions suggesting that AI-augmented biophysical and computer simulation approaches are beginning to transform studies of protein allostery toward systematic characterization of allosteric landscapes, hidden allosteric states, and mechanisms which may bring about a new revolution in molecular biology and drug discovery.

Discovery, synthesis and mechanism study of 2,3,5-substituted [1,2,4]-thiadiazoles as covalent inhibitors targeting 3C-Like protease of SARS-CoV-2

The 3C-like protease (3CL^pro) is essential for the replication and transcription of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), making it a promising target for the treatment of corona virus disease 2019 (COVID-19). In this study, a series of 2,3,5-substituted [1,2,4]-thiadiazole analogs were discovered to be able to inhibit 3CL^pro as non-peptidomimetic covalent binders at submicromolar levels, with IC₅₀ values ranging from 0.118 to 0.582 μM. Interestingly, these compounds were also shown to inhibit PL^pro with the same level of IC₅₀ values, but had negligible effect on proteases such as chymotrypsin, cathepsin B, and cathepsin L. Subsequently, the antiviral abilities of these compounds were evaluated in cell-based assays, and compound 6g showed potent antiviral activity with an EC₅₀ value of 7.249 μM. It was proposed that these compounds covalently bind to the catalytic cysteine 145 via a ring-opening metathesis reaction mechanism. To understand this covalent-binding reaction, we chose compound 6a, one of the identified hit compounds, as a representative to investigate the reaction mechanism in detail by combing several computational predictions and experimental validation. The process of ring-opening metathesis was theoretically studied using quantum chemistry calculations according to the transition state theory. Our study revealed that the 2,3,5-substituted [1,2,4]-thiadiazole group could covalently modify the catalytic cysteine in the binding pocket of 3CL^pro as a potential warhead. Moreover, 6a was a known GPCR modulator, and our study is also a successful computational method-based drug-repurposing study.

Programmably Controllable Delivery of Metastable Ferrous Ions for Multiscale Dynamic Imaging Guided Photothermal Primed Chemodynamic Therapy

Metallomodulation cell death strategies are extensively investigated for antitumor therapy, such as cuproptosis, ferroptosis, and chemodynamic therapy (CDT). Undoubtedly, the accurate and specific elevation of metal ions levels in cancer cells is key to boosting their therapeutic index. Herein, a programmably controllable delivery system based on croconium dye (Croc)-ferrous ion (Fe²⁺ ) nanoprobes (CFNPs) is developed for multiscale dynamic imaging guided photothermal primed CDT. The Croc, with kinds of electron-rich iron-chelating groups, can form the Croc-Fe²⁺ complex with a precise stoichiometry of 1:1 to steadily maintain the valence state of Fe²⁺ . The CFNPs can achieve pH-responsive visualization and accurate Fe²⁺ release in cancerous tissues under the coactivation of "dual-key" stimulation of "acidity and near-infrared (NIR) light". The acidic tumor microenvironment actuates NIR fluorescence/photoacoustic imaging and photothermal properties of CFNPs. Sequentially, under exogenous NIR light, the CFNPs enable in vivo accurate visualization of Croc-Fe²⁺ complex delivery for photothermal primed Fe²⁺ release, thus achieving CDT of tumors. By leveraging multiscale dynamic imaging technologies, the complicated spatiotemporal release of Fe²⁺ is sketched in a programmably controllable manner, and the domino effect of tumor pH level, photothermal effect, and CDT is also revealed, endowing customized feedback of the therapeutic panorama within the disease microenvironment.

NHPI-Mediated Electrochemical α-Oxygenation of Amides to Benzimides

This report describes a mild electrochemical α-oxygenation of a wide range of linear and cyclic benzamides mediated by N-hydroxyphthalimide (NHPI) in an undivided cell using O₂ as the oxygen source and 2,4,6-trimethylpyridine perchlorate as an electrolyte. The radical scavenger experiment and the ¹⁸O labeling experiment were carried out, which indicated the involvement of a radical pathway and suggested O₂ as an oxygen source in the imides, respectively.

Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis in Pseudomonas aeruginosa

Pseudomonas aeruginosa is capable of causing acute and chronic infections in various host tissues, which depends on its abilities to effectively utilize host-derived nutrients and produce protein virulence factors and toxic compounds. However, the regulatory mechanisms that direct metabolic intermediates towards production of toxic compounds are poorly understood. We previously identified a regulatory protein PvrA that controls genes involved in fatty acid catabolism by binding to palmitoyl-coenzyme A (CoA). In this study, transcriptomic analyses revealed that PvrA activates the Pseudomonas quinolone signal (PQS) synthesis genes, while suppressing genes for production of polyhydroxyalkanoates (PHAs). When palmitic acid was the sole carbon source, mutation of pvrA reduced production of pyocyanin and rhamnolipids due to defective PQS synthesis, but increased PHA production. We further solved the co-crystal structure of PvrA with palmitoyl-CoA and identified palmitoyl-CoA-binding residues. By using pvrA mutants, we verified the roles of the key palmitoyl-CoA-binding residues in gene regulation in response to palmitic acid. Since the PQS signal molecules, rhamnolipids and PHA synthesis pathways are interconnected by common metabolic intermediates, our results revealed a regulatory mechanism that directs carbon flux from carbon/energy storage to virulence factor production, which might be crucial for the pathogenesis.

BAP1 is a novel regulator of HIF-1α

BAP1 is a powerful tumor suppressor gene characterized by haplo insufficiency. Individuals carrying germline BAP1 mutations often develop mesothelioma, an aggressive malignancy of the serosal layers covering the lungs, pericardium, and abdominal cavity. Intriguingly, mesotheliomas developing in carriers of germline BAP1 mutations are less aggressive, and these patients have significantly improved survival. We investigated the apparent paradox of a tumor suppressor gene that, when mutated, causes less aggressive mesotheliomas. We discovered that mesothelioma biopsies with biallelic BAP1 mutations showed loss of nuclear HIF-1α staining. We demonstrated that during hypoxia, BAP1 binds, deubiquitylates, and stabilizes HIF-1α, the master regulator of the hypoxia response and tumor cell invasion. Moreover, primary cells from individuals carrying germline BAP1 mutations and primary cells in which BAP1 was silenced using siRNA had reduced HIF-1α protein levels in hypoxia. Computational modeling and co-immunoprecipitation experiments revealed that mutations of BAP1 residues I675, F678, I679, and L691 -encompassing the C-terminal domain-nuclear localization signal- to A, abolished the interaction with HIF-1α. We found that BAP1 binds to the N-terminal region of HIF-1α, where HIF-1α binds DNA and dimerizes with HIF-1β forming the heterodimeric transactivating complex HIF. Our data identify BAP1 as a key positive regulator of HIF-1α in hypoxia. We propose that the significant reduction of HIF-1α activity in mesothelioma cells carrying biallelic BAP1 mutations, accompanied by the significant reduction of HIF-1α activity in hypoxic tissues containing germline BAP1 mutations, contributes to the reduced aggressiveness and improved survival of mesotheliomas developing in carriers of germline BAP1 mutations.

Synthesis of maleimide-braced peptide macrocycles and their potential anti-SARS-CoV-2 mechanisms

Macrocycles often exhibit good biological properties and potential druggability, which lead to versatile applications in the pharmaceutical industry. Herein, we report a highly efficient and practical methodology for the functionalization and macrocyclization of Trp and Trp-containing peptides via Pd(II)-catalyzed C-H alkenylation at the Trp C4 position. This method provides direct access to C4 maleimide-decorated Trp-containing peptidomimetics and maleimide-braced 17- to 30-membered peptide macrocycles. In particular, these unique macrocycles revealed low micro- to sub-micromolar EC₅₀ values with promising anti-SARS-CoV-2 activities. Further explorations with computational methodologies and experimental validations indicated that these macrocycles exert antiviral effects through binding with the N protein of SARS-CoV-2.

Hemin protects UVB-induced skin damage through inhibiting keratinocytes apoptosis and reducing neutrophil infiltration

Ultraviolet-B (UVB) exposure on the skin triggers apoptosis, oxidative stress and acute inflammatory responses, which eventually increases the risk of various skin disorders. Hemin, an iron-binding porphyrin, has been clinically used for porphyria treatment. However, whether hemin contributes to the skin protection against UVB injury remains to be elucidated. Here, we found that hemin treatment (10 and 20 mg/kg) by intraperitoneal administration could dramatically relieve UVB irradiation-induced skin damage featured by erythema, edema, epidermal hyperplasia and collagen loss in C57BL/6 J mice. Importantly, hemin treatment attenuated UVB irradiation-triggered cell apoptosis in skin epidermis. Consistently, hemin (10, 20 μM) treatment decreased Caspase-3 activation and protected against UVB-induced apoptosis in HaCaT cells. Besides, hemin treatment reduced the infiltration of neutrophils in skin under UVB irradiation, thus restrained neutrophil extracellular traps (NET) formation and myeloperoxidase (MPO) release. We further revealed that hemin inhibited the expression of inflammation associated cytokines and chemokines in UVB-induced HaCaT cells and blocked the chemotaxis of dHL-60 cells to preconditioned media from HaCaT culture upon UVB irradiation. Furthermore, hemin inhibited the excessive maturation and mobilization of bone marrow neutrophils and rectified the proportion of abnormally elevated neutrophils in the blood under UVB irradiation. In conclusion, our study showed that hemin treatment protects against UVB-induced skin damage through inhibiting keratinocytes apoptosis, and suppressing neutrophils infiltration in the skin via externally restraining the keratinocyte attraction and internally regulating bone marrow neutrophil maturation and mobilization, suggesting that hemin is an effective drug candidate for the therapy of UVB damage.

Paraquat induces different programmed cell death patterns in Microcystis aeruginosa and Chlorella luteoviridis

Although programmed cell death (PCD) has been reported in phytoplankton, knowledge of the characterization of the PCD pathway and cascade process in different phytoplankton species is still limited. In this study, PCD progression in cyanobacterium Microcystis aeruginosa and green algae Chlorella luteoviridis by paraquat-induced oxidative stress was monitored. The results showed that paraquat-induced PCD in the two species belonged to the caspase-dependent pathway. Dose- and time-dependent PCD characteristics in the two strains under paraquat included the increase in caspase-like activity, DNA fragmentation, and chromatin condensation. However, the signaling pathway and cascade events of PCD in M. aeruginosa and C. luteoviridis differed. In M. aeruginosa, the free Ca²⁺ concentration was rapidly increased at 8 h, followed by a significant elevation of the reactive oxygen species (ROS) level at 24 h, and eventual cell death. In C. luteoviridis, the mitochondrial apoptosis pathway, revealed by the depolarization of the mitochondrial membrane potential at 1 h and increase in the ROS level and caspase-like activity at 8 h, might contribute to cell death. In addition, the dynamics of ROS levels and metacaspase activity were synchronized, suggesting that paraquat-triggered PCD was ROS-mediated in both M. aeruginosa and C. luteoviridis. These results provide insights into PCD patterns in prokaryotic cyanobacteria and eukaryotic green algae under similar stress.

Delivery of spike-RBD by bacterial type three secretion system for SARS-CoV-2 vaccine development

COVID-19 pandemic continues to spread throughout the world with an urgent demand for a safe and protective vaccine to effectuate herd protection and control the spread of SARS-CoV-2. Here, we report the development of a bacterial vector COVID-19 vaccine (aPA-RBD) that carries the gene for the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Live-attenuated strains of Pseudomonas aeruginosa (aPA) were constructed which express the recombinant RBD and effectively deliver RBD protein into various antigen presenting cells through bacterial type 3 secretion system (T3SS) in vitro. In mice, two-dose of intranasal aPA-RBD vaccinations elicited the development of RBD-specific serum IgG and IgM. Importantly, the sera from the immunized mice were able to neutralize host cell infections by SARS-CoV-2 pseudovirus as well as the authentic virus variants potently. T-cell responses of immunized mice were assessed by enzyme-linked immunospot (ELISPOT) and intracellular cytokine staining (ICS) assays. aPA-RBD vaccinations can elicit RBD-specific CD4⁺and CD8⁺T cell responses. T3SS-based RBD intracellular delivery heightens the efficiency of antigen presentation and enables the aPA-RBD vaccine to elicit CD8⁺T cell response. Thus, aPA vector has the potential as an inexpensive, readily manufactured, and respiratory tract vaccination route vaccine platform for other pathogens.

Genetic polymorphisms in MIR1208 and MIR5708 are associated with susceptibility to COPD in the Chinese population

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by limited airflow and is influenced by genetic and environmental factors. The purpose of this study was to investigate the effects of gene polymorphisms in MIR5708 and MIR1208 on COPD risk.

METHODS

Four single nucleotide polymorphisms (SNPs) in MIR5708 (rs6473227 and rs16907751) and MIR1208 (rs2608029 and rs13280095) were selected and genotyped among 315 COPD patients and 314 healthy controls using the Agena MassARRAY platform. SPSS 18.0 was used for statistical analysis and data processing. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the association between genetic variants of MIR1208 and MIR5708 and COPD risk.

RESULTS

The results suggested that rs16907751 variants in MIR5708 contributed to an increased susceptibility to COPD in the allelic (P = 0.001), co-dominant (homozygous) (P = 0.001), dominant (P = 0.017), recessive (P = 0.002), and additive (P = 0.002) models. The effects of MIR5708 and MIR1208 gene polymorphisms on the risk of COPD were age-, sex-, smoking status-, and BMI-related. Furthermore, the C-A and G-A haplotypes of rs2608029 and rs13280095 in MIR1208 were identified as risk factors for COPD in the population over 70 years (P = 0.029) and in women (P = 0.049), respectively. Finally, significant associations between rs16907751genotypes with pulse rate and forced expiratory volume in 1 s were found among COPD patients.

CONCLUSION

Genetic polymorphisms in MIR5708 and MIR1208 are associated with increased risk of COPD in China.

PPI-Miner: A Structure and Sequence Motif Co-Driven Protein-Protein Interaction Mining and Modeling Computational Method

Protein-protein interactions (PPIs) play important roles in biological processes of life, and predicting PPIs becomes a critical scientific issue of concern. Most PPIs occur through small domains or motifs (fragments), which are challenging and laborious to map by standard biochemical approaches because they generally require the cloning of several truncation mutants. Here, we present a computational method, named as PPI-Miner, to fish potential protein interacting partners utilizing protein motifs as queries. In brief, this work first developed a motif-matching algorithm designed to identify the proteins that contain sequential or structural similar motifs with the given query motif. Being aligned to the query motif, the binding mode of the discovered motif and its receptor protein will be initially determined to be used to build PPI complexes accordingly. Eventually, a PPI complex structure could be built and optimized with a designed automatic protocol. Besides discovering PPIs, PPI-Miner can also be applied to other areas, i.e., the rational design of molecular glues and protein vaccines. In this work, PPI-Miner was employed to mine the potential cereblon (CRBN) substrates from human proteome. As a result, 1,739 candidates were predicted, and 16 of them have been experimentally validated in previous studies. The source code of PPI-Miner can be obtained from the GitHub repository (https://github.com/Wang-Lin-boop/PPI-Miner), the webserver is freely available for users (https://bailab.siais.shanghaitech.edu.cn/services/ppi-miner), and the database of predicted CRBN substrates is accessible at https://bailab.siais.shanghaitech.edu.cn/services/crbn-subslib.

CtrA activates the expression of glutathione S-transferase conferring oxidative stress resistance to Ehrlichia chaffeensis

Ehrlichia chaffeensis, the causative agent of human monocytic ehrlichiosis (HME), is a Gram-negative obligatory intracellular bacterium, which infects and multiplies in human monocytes and macrophages. Host immune cells produce reactive oxygen species (ROS) to eliminate E. chaffeensis upon infection. E. chaffeensis global transcriptional regulator CtrA activates the expression of GshA and GshB to synthesize glutathione (GSH), the most potent natural antioxidant, upon oxidative stress to combat ROS damage. However, the mechanisms exploited by E. chaffeensis to utilize GSH are still unknown. Here, we found that in E. chaffeensis CtrA activated the expression of glutathione S-transferase (GST) upon oxidative stress, and E. chaffeensis GST utilizes GSH to eliminate ROS and confers the oxidative stress resistance to E. chaffeensis. We found that CtrA bound to the promoter regions of 211 genes, including gst, in E. chaffeensis using chromatin immunoprecipitation coupled to deep sequencing (ChIP-seq). Recombinant E. chaffeensis CtrA directly bound to the gst promoter region determined with electrophoretic mobility shift assay (EMSA), and activated the gst expression determined with reporter assay. Recombinant GST showed GSH conjugation activity towards its typical substrate 2,4-dinitrochlorobenzene (CDNB) in vitro and peptide nucleic acid (PNA) transfection of E. chaffeensis, which can knock down the gst transcription level, reduced bacterial survival upon oxidative stress. Our results demonstrate that E. chaffeensis CtrA regulates GSH utilization, which plays a critical role in resistance to oxidative stress, and aid in the development of new therapeutics for HME.

Reversion of Ceftazidime Resistance in Pseudomonas aeruginosa under Clinical Setting

Pseudomonas aeruginosa is an important nosocomial pathogen which frequently becomes resistant to most antibiotics used in chemotherapy, resulting in treatment failure among infected individuals. Although the evolutionary trajectory and molecular mechanisms for becoming β-lactam resistant have been well established for P. aeruginosa, the molecular basis of reversion from β-lactam resistant to susceptible is largely unexplored. In this study, we investigated the molecular mechanisms by which a ceftazidime-resistant clinical strain is converted to a ceftazidime-susceptible isolate under the clinical setting. RNA sequencing and genomic DNA reference mapping were conducted to compare the transcriptional profiles and chromosomal mutations between these two isolates. Our results demonstrate that a gain-of-function mutation in ampD, via deletion of a 53 bp duplicated nucleotide sequence, is the contributory factor for the conversion. Furthermore, we show for the first time that AmpD is involved in intraspecies competitiveness in P. aeruginosa. We also found that AmpD is not responsible for phenotypic changes between R1 and S2, including growth rate, motilities, pyocyanin, rhamnolipid, and biofilm production. This finding provides novel insights into the alteration of β-lactam sensitivity in P. aeruginosa under the clinical setting.