1.ToxBERT:An explainable AI framework for enhancing prediction of adverse drug reactions and structural insights
Yujie HE ; Xiang LV ; Wulin LONG ; Shengqiu ZHAI ; Menglong LI ; Zhining WEN
Journal of Pharmaceutical Analysis 2025;15(8):1926-1936
Accurate prediction of drug-induced adverse drug reactions(ADRs)is crucial for drug safety evaluation,as it directly impacts public health and safety.While various models have shown promising results in predicting ADRs,their accuracy still needs improvement.Additionally,many existing models often lack interpretability when linking molecular structures to specific ADRs and frequently rely on manually selected molecular fingerprints,which can introduce bias.To address these challenges,we propose ToxBERT,an efficient transformer encoder model that leverages attention and masking mechanisms for simplified molecular input line entry system(SMILES)representations.Our results demonstrate that ToxBERT achieved area under the receiver operating characteristic curve(AUROC)scores of 0.839,0.759,and 0.664 for predicting drug-induced QT prolongation(DIQT),rhabdomyolysis,and liver injury,respectively,outperforming previous studies.Furthermore,ToxBERT can identify drug substructures that are closely associated with specific ADRs.These findings indicate that ToxBERT is not only a valuable tool for understanding the mechanisms underlying specific drug-induced ADRs but also for mitigating potential ADRs in the drug discovery pipeline.
2.Habitat radiomics model in predicting the early therapeutic efficacy of hepatic arterial infusion chemotherapy combined with targeted therapy or immunotherapy for advanced hepatocellular carcinoma: a multi-center retrospective study
Mingsong WU ; Zenglong QUE ; Guanhui LI ; Jie LONG ; Yuxin TANG ; Hao ZHONG ; Shujie LAI ; Qixian YAN ; Jun WANG ; Xiang LAN ; Liangzhi WEN
Chinese Journal of Digestion 2025;45(2):89-99
Objective:To develop habitat radiomics models to predict early treatment responses to the hepatic arterial infusion chemotherapy (HAIC) combined with targeted therapy or immunotherapy in advanced hepatocellular carcinoma (HCC) patients, and to guide clinical diagnosis and treatment.Methods:From October 2021 to Decemeber 2023, at Army Characteristic Medical Center of PLA (Chongqing Daping Hospital) and the First Affiliated Hospital of Chongqing Medical University, 94 patients with advanced HCC who received HAIC combined with targeted therapy or immunotherapy were retrospectively enrolled. According to the treatment results, the patients were divided into response group and non-response group. Univariate and multivariate logistic regression were performed to analyze the clinical data of the patients. Based on contrast-enhanced CT images, tumor habitats were delineated and habitat features were extracted with k-means clustering, and the imaging features of arterial and venous phases were also extracted. The least absolute shrinkage and selection operator (LASSO) was used for dimensionality reduction. Feature selection was performed using LASSO to reduce dimensions, and then the selected features were further refined through stepwise logistic regression analysis.Binary logistic regression models were conducted to develop the habitat radiomics model, arterial phase radiomics model (APRM), venous phase radiomics model (VPRM), clinical data model, as well as the combination of radiomics model and clinical data model to predict early treatment (after 2 treatment cycles) response. Receiver operating characteristic curves (ROC) were plotted, and model performance was evaluated by the area under the curve (AUC), calibration curves, and decision curve. The models were validated through Bootstrap methods (1 000 times). DeLong test was used to compare AUC values.Results:The results of cluster analysis identified 3 characteristic habitats in HCC imaging: low-, medium-, and high-enhancement tumor habitats. The proportion of high-enhancement habitats was higher than that in the non-response group. A predictive model was established based on the proportions of these 3 habitats. Based on the proportion of low-, medium-, and high-enhancement habitats within the tumor, a habitat radiomics model was constructed. After LASSO selection and logistic regression analysis, 3 arterial phase and 3 venous phase radiomic features were selected to build the APRM and VPRM, respectively. Logistic regression analysis identified the following factors for the clinical data model: comorbidities ( OR=0.275, P=0.031), maximum tumor diameter ( OR=1.149, P=0.019), red blood cell count ( OR=0.463, P=0.022), alpha fetoprotein >400 μg/L ( OR=3.452, P=0.017), and tyrosine kinase inhibitor therapy ( OR=3.072, P=0.048). Among the single predictive model′s comparison, the AUC of habitat radiomics model was 0.860 (95% confidence interval(95% CI): 0.789 to 0.932), while those of the APRM、VPRM and clinical data model were 0.850 (95% CI: 0.773 to 0.926), 0.855 (95% CI: 0.782 to 0.928), and 0.774 (95% CI: 0.681 to 0.867), respectively, and there were no statistically significant among these models (all P>0.05). Among the combination models, the AUC of the habitat rediomic-clinical data combination model was 0.881 (95% CI: 0.814 to 0.947); the AUC of arterial phase rediomic-clinical data combination model was 0.897 (95% CI: 0.833 to 0.961); and the AUC of venous phase rediomic-clinical data combination model was 0.888 (95% CI: 0.826 to 0.951), but there were no statistically significant among the 3 models (all P>0.05). The calibration curve showed that the habitat rediomic-clinical data combination model had the most accurate predictive probability. Internal validation showed that the AUC of habitat rediomic-clinical data combination model was 0.848 (95% CI: 0.772 to 0.922), and the predictive performance was better than that of the clinical-data model (0.733 (95% CI: 0.670 to 0.863)). Conclusion:The habitat radiomics model based on enhanced CT can effectively predict early treatment responses to the HAIC combined with targeted therapy or immunotherapy in advanced HCC patients, which provides theoretical basis for individualized treatment in advanced HCC.
3.Efficacy and prognosis of preoperative treatment based on arterial infusion chemotherapy in patients with advanced gastric cancer: a real-world study
Xiaosong XIANG ; Feilong GUO ; Yu SU ; Long MA ; Donghong SHI ; Leilei LIU ; Guoli LI
Chinese Journal of Oncology 2025;47(2):183-192
Objective:To explore the efficacy and prognosis of preoperative treatment based on arterial infusion chemotherapy (PTAC) in patients with advanced gastric cancer.Methods:Clinical and follow-up data of 821 patients with advanced gastric cancer who received PTAC treatment at the General Hospital of the Eastern Theater Command of the People's Liberation Army from January 2001 to January 2021 were collected. According to the treatment regimen, patients were divided into the FLEEOX group (89 cases), the XEEOX group (196 cases), the SEEOX group (406 cases), and the SEEOX+PD-1 group (130 cases). The primary endpoint was the 3-year progression-free survival rate. Secondary endpoints included the 3-year overall survival rate, objective response rate, radical resection rate, major pathological response rate, and incidence of treatment associated adverse events.Results:After PTAC treatment, the objective response rate was 74.9% (615/821). A total of 671 patients underwent radical surgery, with a radical resection rate of 81.7% and an R0 resection rate of 70.2% (576/821). The pathological complete response rate was 16.7% (112/671), and the major pathological response rate was 32.2% (216/671). With an average follow-up of 27.7 months, the 3-year progression-free survival rate was 52.2%, and the 3-year overall survival rate was 55.8%. The 3-year progression-free survival rate of patients in the SEEOX+PD-1 group was 66.9%, the objective response rate was 83.8% (109/130), the major pathological response rate was 45.3% (53/117), and the radical resection rate was 90.0% (117/130), all of which were better than those in the XEEOX and SEEOX groups (all P<0.05). However, during the treatment period, three patients in the SEEOX+PD-1 group died from immune-related adverse events. Conclusion:PTAC treatment is an effective preoperative treatment method for advanced gastric cancer, and is expected to further improve the treatment effect when combined with immunotherapy such as PD-1 monoclonal antibodies.
4.Case report and literature review of myocardial infarction caused by myocardial bridge
Xiao-qing KOU ; Yi-rong GAN ; Yun-long ZHANG ; Ding-xiong XIE ; Rui MAO ; Tian-xiang LIANG ; Xiao-li YANG ; Yan-zhen WANG
Chinese Journal of Interventional Cardiology 2025;33(2):111-116
Medical therapy and surgical intervention are the two primary approaches for treating myocardial bridge.However,there remains controversy regarding the use of coronary artery bypass grafting(CABG)and myocardial bridge unroofing.Here,we report a case of myocardial infarction following CABG in a patient with a myocardial bridge.The patient was admitted to Lanzhou First Peopie's Hospital with persistent chest pain,chest tightness,and shortness of breath lasting 2 hours.Physical examination revealed no significant abnormalities.Electrocardiography(ECG)indicated extensive anterior wall myocardial infarction.Laboratory findings showed myoglobin levels of 140.1 ng/ml and troponin Ⅰ levels of 2.59 ng/ml,with no other significant abnormalities.The initial diagnosis was acute extensive anterior wall myocardial infarction.Emergency coronary angiography revealed a myocardial bridge in the mid-segment of the left anterior descending artery(LAD).Emergency CABG using the left internal mammary artery to the LAD was performed,leading to symptomatic improvement,and the patient was discharged in stable condition.However,the patient experienced a recurrent myocardial infarction seven years post-surgery and received secondary preventive medical therapy.The patient is currently under ongoing follow-up care.CABG is an effective treatment for myocardial bridge.However,based on the case reported in this study,we recommend careful evaluation of whether a patient may benefit from CABG.
5.Evaluation of antimicrobial activity of milk exosomes loaded with rifamycin S derivative
Zhanqun YANG ; Xiang LI ; Chenghua LIU ; Mengzhu ZHENG ; Shiyong FAN ; Yuchao DONG ; Zihao WANG ; Jian LIN ; Guang YANG ; Long CHEN
Chinese Journal of Pharmacology and Toxicology 2025;39(3):208-215
OBJECTIVE To design and synthesize rifamycin S derivatives and load them into milk exosomes to evaluate their in vitro antimicrobial activity.METHODS Rifamycin S derivatives were synthe-sized and characterized by mass spectrometry and NMR.Using the dilution assay method,the inhibitory activity of each rifamycin S derivatives molecule against Staphylococcus aureus and Pseudomonas aerugi-nosa was determined,and the IC50 was calculated.Derivatives molecules with excellent antimicrobial activity were selected and loaded into milk exosomes using the ultrasonication method,resulting in the preparation of milk exosome-loaded rifamycin S derivatives.The antimicrobial activity against Staphylo-coccus aureus was determined using the dilution assay method.The inhibitory effect of the exosome-loaded rifamycin S derivatives on Staphylococcus aureus residing within macrophages was detected using the plate colony counting method.RESULTS Three rifamycin S derivatives were successfully designed and synthesized,which demonstrated superior antimicrobial activity against Staphylococcus aureus(the parent compound's antimicrobial activity is merely from 1/20 to 1/80 of that of the three rifamycin S derivatives)and Pseudomonas aeruginosa(the parent compound's antimicrobial activity is only 1/14 and 1/9 of that of compound 1 and compound 3)compared to the parent compound.The loading of milk exosomes with the rifamycin S derivatives compound 3 was successfully achieved,with a loading efficiency of 10.9%.The antimicrobial activity of the compound after exosome loading was significantly enhanced against Staphylococcus aureus in vitro and against Staphylococcus aureus residing within macrophages(P<0.01).CONCLUSION The designed and synthesized derivatives of rifamycin S possess stronger anti-microbial activity,and their antibacterial efficacy against both extracellular and intracellular bacteria can be further enhanced after loading into exosomes.
6.Locoregional therapeutic strategies for hepatocellular carcinoma
Hua XIANG ; Lin LONG ; Yongjin ZHANG ; Jumei ZHOU ; Yang ZHAO ; Muzi LI ; Rengeng LIU ; Shixiong SHI ; Rongrong WANG
Journal of Clinical Hepatology 2025;41(8):1497-1503
The incidence and mortality rates of hepatocellular carcinoma(HCC)remain high in China,and the application of surgical resection is often limited due to the fact that most patients are in the advanced stage at the time of confirmed diagnosis.This article reviews commonly used advanced locoregional therapies for HCC and the advances in mainstream techniques such as local ablation(radiofrequency ablation,microwave ablation,irreversible electroporation,and cryoablation),intravascular intervention(transcatheter arterial chemoembolization,hepatic arterial infusion chemotherapy,and Y90 hepatic arterial infusion chemotherapy),and radiotherapy(CyberKnife,proton therapy,and heavy-ion therapy),and a multidimensional decision-making framework is constructed for HCC locoregional therapy by comparing treatment principles,indications,limitations,and clinical data of these techniques.This article aims to provide evidence-based support for persistent dilemmas in clinical decision-making,promote the role of locoregional therapies in clinical practice,and propose the directions for future research and clinical application.This article also establishes a comprehensive clinical roadmap for HCC locoregional therapy,which helps to address current challenges regarding technique selection and delineate future directions for innovation,in order to reshape the treatment of HCC through technological integration and paradigm innovation.
7.Effect of multi-mode pre-rehabilitation on patients undergoing Jinling procedure
Li-Yun LI ; Yang YANG ; Xiang-Hong YE ; Ting SUN ; Fei-Long GUO ; Jia-Huan LIU ; Cui-Li WU
Parenteral & Enteral Nutrition 2025;32(3):165-170
Objective:To evaluate the efficacy of multimodal prehabilitation in patients with refractory functional constipation undergoing Jinling procedure(modified Duhamel surgery).Methods:In this prospective randomized controlled trial,80 patients with refractory functional constipation scheduled for Jinling procedure at the Department of General Surgery,the General Hospital of Eastern Theater Command between January 2020 and December 2021 were enrolled.Participants were randomly assigned to either the observation group(n=40,multimodal prehabilitation)or control group(n=40,routine nursing care).Outcome measures included:time to first flatus,time to first ambulation,defecation volume on postoperative day 5,length of hospitalization,nutritional markers(hemoglobin,albumin,total protein at postoperative day 7),anxiety/depression scores(Hospital Anxiety and Depression Scale,HADS),and total complication rates.Results:Compared to controls,the first ventilation time(48.02±6.15)h,first ambulation time(49.92±5.58)h,defecation volume on the fifth day(234.50±51.03)mL,hospital stay(13.15±2.64)d,anxiety score(43.68±3.45)points,depression score(43.81±1.58)points,and the total incidence of postoperative complications(15%)were significantly lower in the observation group(all p values<0.05).By contrast,the serum levels of hemoglobin(115.60±11.60)g/l,albumin(41.19±5.79)g/L and total protein(61.64±4.94)g/L on day 7 post-operatively were significantly higher in the observation group than those in the control group(P<0.05).Conclusions:Multimodal prehabilitation enhances postoperative intestinal recovery,reduces complications,improves nutritional status,and shortens hospital stays in refractory functional constipation patients undergoing Jinling procedure,supporting its clinical adoption.
8.Screening and validation of tsRNAs associated with lung adenocarcinoma
Chunli LU ; Yifan SHAN ; Weijia XIE ; Tingting XIA ; Ying XIANG ; Na WU ; Long WU ; Li BAI ; Yafei LI
Journal of Army Medical University 2025;47(2):122-131
Objective To explore the roles of transfer RNA-derived small RNAs(tsRNAs)in the oncogenesis and progression of lung adenocarcinoma by analyzing the differential expression of tsRNAs in lung adenocarcinoma and the relationship between the expression levels of tsRNAs in lung adenocarcinoma and the prognosis of patients in order to further screen and validate the tsRNAs associated with lung adenocarcinoma.Methods The differential expression of tsRNAs between lung adenocarcinoma tissues and normal tissues was analyzed based on the database of the Computational Medicine Center.The effects of tsRNAs expression levels on the prognosis of lung adenocarcinoma patients were analyzed based on the Cancer Genome Atlas(TCGA)database(TCGA-LUAD).The target genes were predicted based on TRFtarget2.0 and tRFTar databases.Gene ontology(GO)enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis were performed based on DAVID and KOBA KEGG online websites.The expression levels of target genes in lung adenocarcinoma tissues and normal tissues were analyzed based on the University of ALabama at Birmingham CANcer data analysis Portal(UALCAN)database.In vitro cell proliferation,migration,and invasion assays were performed to investigate the biological functions of tRF-19-69M8LOJX in lung adenocarcinoma cells.Results Compared with the normal tissues,tRF-19-69M8LOJX was up-regulated in lung adenocarcinoma tissues(log2FC=4.28,FDR<0.05).High expression level of tRF-19-69M8LOJX was associated with shorter progression-free survival(HR=1.565,95%CI=1.142-2.145,P=0.005).And its overexpression promoted cell proliferation and migration(P<0.001),and invasion(P=0.009)of A549 cells,and up-regulated COL1A1(P=0.002)and VCAN(P=0.022)significantly in the tRF-19-69M8LOJX overexpression cell model.Conclusion tRF-19-69M8LOJX is up-regulated in lung adenocarcinoma tissues.And its high expression is closely associated with poor prognosis.The tsRNA may play an important role in the pathogenesis and development of lung adenocarcinoma.
9.Transcriptomic and Metabolomic Investigations on the Effects of High Salt Stress on Hydroxyectoine Biosynthesis in Virgibacillus Salexigens
Meng-Yao DONG ; Qi-Fu LONG ; Jiang-Wa XING ; Xiang GAO ; Yong-Zhen LI
Chinese Journal of Biochemistry and Molecular Biology 2025;41(4):586-596
To investigate the impact of high salt stress on the metabolic pathways and regulatory mecha-nisms involved in synthesizing hydroxyectoine(5-HE)in Virgibacillus salexigens,cultures were supple-mented with 1.5 and 2.5 mol/L NaCl as control and experimental groups,respectively.High-perform-ance liquid chromatography(HPLC)was used to detect the difference in the amount of 5-HE synthesis.Transcriptomic and metabolomic analyses identified differential genes and metabolites under varying salt concentrations.Key differential gene expressions related to 5-HE synthesis were validated using qRT-PCR.Results showed that 5-HE synthesis reached 121.9 mg/L at 2.5 mol/L NaCl.Transcriptomic anal-ysis identified 652 differentially expressed genes across 348 KEGG pathways,with 210 upregulated and 442 downregulated,primarily enriched in pathways such as purine metabolism,amino acid biosynthesis,sulfur metabolism,and biotin metabolism.Validation of 13 genes,including lysC,asd,ectA,ectB,ectC,ectD,thrB,thrC,ilvA,ilvE,AGXT,YckA and GlnQ,showed expression trends consistent with transcriptome data.Metabolomic analysis identified 1153 metabolites predominantly enriched in histidine metabolism,lysine degradation,and arginine and proline metabolism.This study preliminarily elucidated the effect of high salt on the 5-HE synthesis pathway,and provided a basis for the subsequent construc-tion of 5-HE high-yielding strains.
10.Metallic nanomedicine in cancer immunotherapy.
Shixuan LI ; Xiaohu WANG ; Huiyun HAN ; Shuting XIANG ; Mingxi LI ; Guangyu LONG ; Yanming XIA ; Qiang ZHANG ; Suxin LI
Acta Pharmaceutica Sinica B 2025;15(9):4614-4643
Immunotherapy has become a pivotal modality in clinical cancer treatment. However, its effectiveness is limited to a small subset of patients due to the low antigenicity, impaired innate response, and various adaptive immune resistance mechanisms of the tumor microenvironment (TME). Accumulating evidence reveals the critical roles of metal elements in shaping immunity against tumor progression and metastasis. The marriage of metalloimmunotherapy and nanotechnology further presents new opportunities to optimize the physicochemical and pharmacokinetic properties of metal ions in a precise spatiotemporal control manner. Several metallodrugs have demonstrated encouraging immunotherapeutic potential in preliminary studies and are currently undergoing clinical trials at different stages, yet challenges persist in scaling up production and addressing long-term biosafety concerns. This review delineates how metal materials modulate biological activities across diverse cell types to orchestrate antitumor immunity. Moreover, it summarizes recent progress in smart drug delivery-release systems integrating metal elements, either as cargo or vehicles, to enhance antitumor immune responses. Finally, the review introduces current clinical applications of nanomedicines in metalloimmunotherapy and discusses potential challenges that impede its widespread translation into clinical practice.

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