1.Single-cell Protein Localization Method Based on Class Perception Graph Convolutional Network
Hao-Yang TANG ; Xin-Yue YAO ; Meng-Meng WANG ; Si-Cong YANG
Progress in Biochemistry and Biophysics 2025;52(9):2417-2427
ObjectiveThis study proposes a novel single-cell protein localization method based on a class perception graph convolutional network (CP-GCN) to overcome several critical challenges in protein microscopic image analysis, including the scarcity of cell-level annotations, inadequate feature extraction, and the difficulty in achieving precise protein localization within individual cells. The methodology involves multiple innovative components designed to enhance both feature extraction and localization accuracy. MethodsFirst, a class perception module (CPM) is developed to effectively capture and distinguish semantic features across different subcellular categories, enabling more discriminative feature representation. Building upon this, the CP-GCN network is designed to explore global features of subcellular proteins in multicellular environments. This network incorporates a category feature-aware module to extract protein semantic features aligned with label dimensions and establishes a subcellular relationship mining module to model correlations between different subcellular structures. By doing so, it generates co-occurrence embedding features that encode spatial and contextual relationships among subcellular locations, thereby improving feature representation. To further refine localization, a multi-scale feature analysis approach is employed using the K-means clustering algorithm, which classifies multi-scale features within each subcellular category and generates multi-cell class activation maps (CAMs). These CAMs highlight discriminative regions associated with specific subcellular locations, facilitating more accurate protein localization. Additionally, a pseudo-label generation strategy is introduced to address the lack of annotated single-cell data. This strategy segments multicellular images into single-cell images and assigns reliable pseudo-labels based on the CAM-predicted regions, ensuring high-quality training data for single-cell analysis. Under a transfer learning framework, the model is trained to achieve precise single-cell-level protein localization, leveraging both the extracted features and pseudo-labels for robust performance. ResultsExperimental validation on multiple single-cell test datasets demonstrates that the proposed method significantly outperforms existing approaches in terms of robustness and localization accuracy. Specifically, on the Kaggle 2021 dataset, the method achieves superior mean average precision (mAP) metrics across 18 subcellular categories, highlighting its effectiveness in diverse protein localization tasks. Visualization of the generated CAM results further confirms the model’s capability to accurately localize subcellular proteins within individual cells, even in complex multicellular environments. ConclusionThe integration of the CP-GCN network with a pseudo-labeling strategy enables the proposed method to effectively capture heterogeneous cellular features in protein images and achieve precise single-cell protein localization. This advancement not only addresses key limitations in current protein image analysis but also provides a scalable and accurate solution for subcellular protein studies, with potential applications in biomedical research and diagnostic imaging. The success of this method underscores the importance of combining advanced deep learning architectures with innovative training strategies to overcome data scarcity and improve localization performance in biological image analysis. Future work could explore the extension of this framework to other types of microscopic imaging and its application in large-scale protein interaction studies.
2.Mechanism of quercetin inhibiting neutrophil extracellular trap formation based on LOX-1/NOX2 signaling pathway
Si LIU ; Gang LUO ; Jun-Chang WANG ; Lin-Yao YING ; Yan WANG ; Lin XIAO
Chinese Pharmacological Bulletin 2024;40(11):2047-2054
Aim To investigate the molecular mecha-nism of lysophosphatidylcholine(LPC)-induced neu-trophil extracellular trap formation and the intervening role of quercetin.Methods An in vitro model of NETs formation was constructed using LPC-induced primary rat neutrophils,and quercetin intervention was performed.The formation of NETs and the expression level of related pathway proteins were detected.Results 100 mg·L-1 LPC induced the formation of NETs in vitro,and NETs formation was associated with the up-regulation of LOX-1/NOX2 pathway protein expres-sion.Quercetin intervention effectively decreased LOX-1 and NOX2 protein expression,then inhibiting NETs formation.Conclusions Quercetin inhibits the forma-tion of NETs by regulating the LOX-1/NOX2 signaling pathway and exerting a protective effect against related inflammatory diseases.
3.Study on inhibitory effect of alisol B on non-small cell lung cancer based on network pharmacology and its mechanism
Liu-Yan XIANG ; Wen-Xuan WANG ; Si-Meng GU ; Xiao-Qian ZHANG ; Lu-Yao LI ; Yu-Qian LI ; Yuan-Ru WANG ; Qi-Qi LEI ; Xue YANG ; Ya-Jun CAO ; Xue-Jun LI
Chinese Pharmacological Bulletin 2024;40(12):2375-2384
Aim To explore the potential genes and mechanism of alisol B in the treatment of non-small cell lung cancer(NSCLC).Methods The proliferation and migration of NSCLC cells were detected by CCK-8 and Transwell.Genes of NSCLC and alisol B were col-lected through TCGA and compound gene prediction database,and their intersection genes were obtained.The network of protein-protein interaction(PPI)was constructed by using String database,and the top 20 key nodes were screened out,and the prognosis-related proteins related to the prognosis of NSCLC were screened out by using R language,and the intersection of them was obtained.The potential mechanism of ali-sol B on NSCLC was explored by KEGG and GO en-richment analysis and the relationship between related genes and immune cells,which was verified by cell-lev-el experiments.Results Alisol B inhibited the cell activity and migration ability of NSCLC cells.Five im-portant genes were identified by network pharmacologi-cal analysis:CCNE1,CDK1,COL1A1,COL1A2 and COL3A1.The results of cell experiment showed that al-isol B down-regulated the expression of Cyclin E1,CDK1 and COL1A2 in NSCLC cells.In addition,alisol B could inhibit the expression of COL1A2 and M2 macrophage marker CD206 in macrophages.Conclu-sions Alisol B may inhibit the proliferation of tumor cells by down-regulating CDK1 and Cyclin E1,and may affect the function of macrophages by inhibiting COL1A2,thus regulating the tumor immune microenvi-ronment and inhibiting NSCLC.
4.Clinical analysis of indocyanine green fluorescence laparo-scopic lateral lymph node dissection in middle and low rec-tal cancer
Yang YANG ; Xin-Chen WANG ; Yuan-Yao ZHANG ; Zhi-Wei LIU ; Si-Yuan WANG ; Dong WEI
Chinese Journal of Current Advances in General Surgery 2024;27(5):377-381
Objective:To investigate the application value of indocyanine green fluorescence laparoscopic lateral lymph node dissection(LLND)in the treatment of middle and low rectal can-cer.Methods:Clinical data of 76 patients with middle and low rectal cancer who underwent surgi-cal treatment from February 2018 to June 2020 were retrospectively analyzed,including 42 patients in the TME group who underwent laparoscopic total mesorectal resection and 34 patients in the TME+LLND group who underwent laparoscopic TME combined with indocyanine green fluores-cence LLND.Results:The operation time of TME+LLND group was longer than that of TME group(P<0.001).Compared with TME group,the total number of lymph nodes dissected in TME+LLND group was higher(P<0.05).In the TME+LLND group,7 cases(20.59%)reported lateral lymph node metastasis.After 3 years of follow-up,the local recurrence rate was 2.94%in TME+LLND group and 19.05%in TME group(P<0.05).The distant metastasis rate was 14.71%in the TME+LLND group and 9.52%in the TME group(P>0.05).Conclusion:Indocyanine green fluorescence laparoscopic LLND can reduce the local recurrence rate and does not increase postoperative com-plications,so it is safe,effective and feasible in the treatment of middle and low rectal cancer.
5.Constructing A Knowledge-driven and Data-driven Hybrid Decision Model for Etiological Diagnosis of Ventricular Tachycardia
Min WANG ; Zhao HU ; Xiaowei XU ; Si ZHENG ; Jiao LI ; Yan YAO
Medical Journal of Peking Union Medical College Hospital 2024;16(2):454-461
To construct a hybrid decision-making model that integrates knowledge-driven and data-driven approaches, and to apply it to the etiological diagnosis of ventricular tachycardia (VT). Clinical practice guidelines, expert consensus documents, and medical literature in the field of arrhythmia diseases from 2018 to 2023 were retrieved as knowledge sources. Retrospective electronic medical record data of VT patients from Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, from 2013 to 2023 were collected as the dataset. A knowledge-driven model was constructed using a knowledge-rule-based approach to establish clinical pathways. A three-class machine learning model for VT etiology diagnosis was developed based on real-world data, and the best-performing model was selected as the representative of the data-driven approach. The machine learning model was embedded into the decision nodes of the clinical pathway in the form of custom operators, forming the hybrid model. The precision, recall, and F1 score of the three models were evaluated. Three clinical practice guidelines were included as knowledge sources for the knowledge-driven model. A total of 1305 patient records were collected as the dataset, and five machine learning models were constructed, with the XGBoost model performing the best. The hybrid model adopted a knowledge-driven decision-making framework, embedding the XGBoost model into the decision nodes of a two-level classification. The precision, recall, and F1 scores of the three models were as follows: the knowledge-driven model achieved 80.4%, 79.1%, and 79.7%; the data-driven model achieved 88.4%, 88.5%, and 88.4%; and the hybrid model achieved 90.4%, 90.2%, and 90.3%. The hybrid model integrating knowledge-driven and data-driven approaches demonstrated higher accuracy, and all its decision outcomes were based on evidence-based practices, aligning more closely with the actual diagnostic reasoning of clinicians. Further rigorous validation is needed to assess the feasibility of widely applying the hybrid model in the medical field.
6.Design of wireless transmission system of ECG signal in dynamic ECG monitor
Chinese Medical Equipment Journal 2024;45(6):28-32
Objective To design an ECG signal wireless transmission system for the dynamic ECG monitor.Methods The ECG signal wireless transmission system developed was composed of an ECG signal acquisition module,a wireless transceiver module,a wireless communication protocol module and a digital filtering module.The ECG signal acquisition module consisted of a digital interface circuit,an A/D converter microprocessor and an ECG amplification circuit.The wireless transceiver module was made up of a wireless RF unit,a crystal oscillator circuit,an RF circuit,a debug serial port,a register,a power supply module and a reset circuit.The wireless communication protocol module involved in a data link layer and a physical layer,of which the data link layer had two mechanisms of automatic response and frequency modulation.The digital filtering module mainly included a digital filter,a signal input module,a delay unit and a coefficient registers,and the digital filter was designed using the equiripple method and realized signal denoising by converting ECG signals into output sequences.The performance of this system for wireless transmission of ECG signals at different proximity remote transmission distances was validated with the ECG signal wireless transmission methods based on ZigBee networking and general packet radio service(GPRS)and based on wireless networking module used as comparative methods.Results The system developed gained advan-tages over the other two methods in average rate,sucess rate,average time consumption and average frequency for re-transmission of ECG signal wireless transmission.Conclusion The system developed can be used for efficient,stable and clear ECG signal wireless transmission for the dynamic ECG monitor.[Chinese Medical Equipment Journal,2024,45(6):28-32]
7.Targeting the chromatin structural changes of antitumor immunity
Li NIAN-NIAN ; Lun DENG-XING ; Gong NINGNING ; Meng GANG ; Du XIN-YING ; Wang HE ; Bao XIANGXIANG ; Li XIN-YANG ; Song JI-WU ; Hu KEWEI ; Li LALA ; Li SI-YING ; Liu WENBO ; Zhu WANPING ; Zhang YUNLONG ; Li JIKAI ; Yao TING ; Mou LEMING ; Han XIAOQING ; Hao FURONG ; Hu YONGCHENG ; Liu LIN ; Zhu HONGGUANG ; Wu YUYUN ; Liu BIN
Journal of Pharmaceutical Analysis 2024;14(4):460-482
Epigenomic imbalance drives abnormal transcriptional processes,promoting the onset and progression of cancer.Although defective gene regulation generally affects carcinogenesis and tumor suppression networks,tumor immunogenicity and immune cells involved in antitumor responses may also be affected by epigenomic changes,which may have significant implications for the development and application of epigenetic therapy,cancer immunotherapy,and their combinations.Herein,we focus on the impact of epigenetic regulation on tumor immune cell function and the role of key abnormal epigenetic processes,DNA methylation,histone post-translational modification,and chromatin structure in tumor immunogenicity,and introduce these epigenetic research methods.We emphasize the value of small-molecule inhibitors of epigenetic modulators in enhancing antitumor immune responses and discuss the challenges of developing treatment plans that combine epigenetic therapy and immuno-therapy through the complex interaction between cancer epigenetics and cancer immunology.
8.GLUT1-targeted Nano-delivery System for Active Ingredients of Traditional Chinese Medicine:A Review
Hua ZHU ; Huimin LUO ; Si LIN ; Bingbing WANG ; Jinwei LI ; Liba XU ; Miao ZHANG ; Fengfeng XIE ; Long CHEN ; Meilin LI ; Lu LU
Chinese Journal of Experimental Traditional Medical Formulae 2024;30(12):270-280
Tumor cells use glycolysis to provide material and energy under hypoxic conditions to meet the energy requirements for rapid growth and proliferation, namely the Warburg effect. Even under aerobic conditions, tumor cells mainly rely on glycolysis to provide energy. Therefore, glucose transporter protein 1(GLUT1), which is involved in the process of glucose metabolism, plays an important role in tumorigenesis, development and drug resistance, and is considered to be one of the important targets in the treatment of malignant tumors. In recent years, research on tumor glucose metabolism has gradually become a hot spot. It has been shown that various factors are involved in the regulation of tumor energy metabolism, among which the role of GLUT1 is the most critical. In this paper, the authors reviewed the latest research progress of GLUT1-targeted traditional Chinese medicine(TCM) active ingredient nano-delivery system in tumor therapy, aiming to reveal the feasibility and effectiveness of this system in the delivery of chemotherapeutic drugs. The GLUT1-targeted TCM active ingredient nano-delivery system can overcome the bottleneck of the traditional targeting strategy as well as the high-permeability long retention(EPR) effect. In summary, the authors believe that the GLUT1-targeted TCM active ingredient nano-delivery system provides a new strategy for targeted treatment of tumors and has a broad application prospect in tumor prevention and treatment.
9.The Role of Mechanical Sensitive Ion Channel Piezo in Digestive System Diseases
Si-Qi WANG ; Xiang-Yun YAN ; Yan-Qiu LI ; Fang-Li LUO ; Jun-Peng YAO ; Pei-Tao MA ; Yu-Jun HOU ; Hai-Yan QIN ; Yun-Zhou SHI ; Ying LI
Progress in Biochemistry and Biophysics 2024;51(8):1883-1894
The Piezo protein is a non-selective mechanosensitive cation channel that exhibits sensitivity to mechanical stimuli such as pressure and shear stress. It converts mechanical signals into bioelectric activity within cells, thus triggering specific biological responses. In the digestive system, Piezo protein plays a crucial role in maintaining normal physiological activities, including digestion, absorption, metabolic regulation, and immune modulation. However, dysregulation in Piezo protein expression may lead to the occurrence of several pathological conditions, including visceral hypersensitivity, impairment of intestinal mucosal barrier function, and immune inflammation.Therefore, conducting a comprehensive review of the physiological functions and pathological roles of Piezo protein in the digestive system is of paramount importance. In this review, we systematically summarize the structural and dynamic characteristics of Piezo protein, its expression patterns, and physiological functions in the digestive system. We particularly focus on elucidating the mechanisms of action of Piezo protein in digestive system tumor diseases, inflammatory diseases, fibrotic diseases, and functional disorders. Through the integration of the latest research findings, we have observed that Piezo protein plays a crucial role in the pathogenesis of various digestive system diseases. There exist intricate interactions between Piezo protein and multiple phenotypes of digestive system tumors such as proliferation, apoptosis, and metastasis. In inflammatory diseases, Piezo protein promotes intestinal immune responses and pancreatic trypsinogen activation, contributing to the development of ulcerative colitis, Crohn’s disease, and pancreatitis. Additionally, Piezo1, through pathways involving co-action with the TRPV4 ion channel, facilitates neutrophil recruitment and suppresses HIF-1α ubiquitination, thereby mediating organ fibrosis in organs like the liver and pancreas. Moreover, Piezo protein regulation by gut microbiota or factors like age and gender can result in increased or decreased visceral sensitivity, and alterations in intestinal mucosal barrier structure and permeability, which are closely associated with functional disorders like irritable bowel sydrome (IBS) and functional consitipaction (FC). A thorough exploration of Piezo protein as a potential therapeutic target in digestive system diseases can provide a scientific basis and theoretical support for future clinical diagnosis and treatment strategies.
10.Association between ELL2 polymorphism and susceptibility to pleomorphic adenoma of salivary gland
Si-Yao YANG ; Yuan-Yuan WANG ; Jian-Bing LIU ; Zhi-Rong LIU
Medical Journal of Chinese People's Liberation Army 2024;49(2):171-176
Objective To analyze the correlation between the ELL2 gene 1119 T>C polymorphism and the susceptibility to pleomorphic adenoma of the salivary gland.Methods The pedigree of the pleomorphic adenoma family of salivary gland was drawn.The exons of ELL2 gene in 5 members of salivary pleomorphic adenoma family were sequenced.A case-control study was conducted.One hundred and twelve patients with pleomorphic adenoma of the salivary gland who visited the Department of Oral and Maxillofacial Surgery of Shanxi Bethune Hospital from January 2016 to July 2020 were taken as case group,and 176 healthy examinees from January 2019 to January 2020 were taken as control group with age and sex as matching conditions.The 1119 T>C polymorphism of ELL2 genes in the two groups were detected with high resolution melting(HRM)curve.Chi-square test was adopted to analyze the correlation between gene polymorphism and the occurrence of pleomorphic adenoma of the salivary gland,stratified analysis was performed to evaluate the synergistic effect of smoking and genotype,and real time quantitative reverse transcription polymerase chain reaction(RT-PCR)was used to detect the expression level of ELL2 in individuals with different genotypes.Results The 1119 T>C polymorphism site existed in the exon 8 of ELL2 gene in a family with pleomorphic adenoma of salivary gland.The results of case-control study showed that the genotype frequency of homozygous CC was significantly higher in patients with pleomorphic adenoma of salivary gland than that in the controls(24.1%vs.11.9%,P=0.002).Homozygous CC was associated with increased risk for developing pleomorphic adenoma of salivary gland(OR=3.059,95%CI 1.494-6.263)in this cohort.Stratification analysis showed that smoking and 1119C allele cooperated to increase the risk of pleomorphic adenoma of salivary gland(OR=3.200,95%CI 1.460-7.014).The expression level of ELL2 mRNA in CC genotype was significantly higher than that in individuals with CT or TT genotype(P<0.05).Conclusion The genetic variation of ELL2 may play an important role in the occurrence of pleomorphic adenoma of salivary gland,and smoking combined with the 1119C allele increased the risk of this disease.

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