1.Structural and epitope characterization of HIV-1 V1V2 highly effective neutralizing antibodies based on AlphaFold 3
Junjie ZHANG ; Qianying WANG ; Ying LIU ; Shuhui WANG ; Li REN ; Shuo WANG ; Yutao SHI ; Yuhua RUAN ; Xiaojing LIU ; Xinran DU ; Yanling HAO ; Dan LI
Chinese Journal of Experimental and Clinical Virology 2025;39(5):548-555
Objective:To screen broadly neutralizing antibodies in human immunodeficiency virus-1(HIV-1)chronically infected individuals and characterize their molecular features and to provide new strategies for rational vaccine development and antibody-based therapeutics.Methods:A total of 34 treatment-na?ve individuals with chronic HIV-1 infection were enrolled. Plasma antibody binding levels were measured against two HIV-1 envelope proteins. Single antigen-specific memory B cells were sorted from high-binding samples,and antibody variable region genes were amplified by PCR for paired expression. The monoclonal antibodies were evaluated for neutralizing activity using pseudovirus assays,and their structural features were analyzed by integrating AlphaFold 3 prediction with Discovery Studio molecular docking.Results:Plasma samples showed strong binding to DU422-GP140 and BG505-GP140. Eight monoclonal antibodies were isolated from two donors. Among them,antibodies 0919-A4,0919-A9 and 0808-A2 could cross-react with GP140 from HIV-1 subtypes AE,BC and B. The monoclonal antibody 0919-A9 demonstrated potent neutralizing activity against SF162(Tier 1)and CH181(Tier 2)pseudoviruses,with somatic hypermutation rates of 13.27%(heavy chain)and 15.58%(light chain). Structural modeling revealed its specific targeting of the V1V2 region on GP120.Conclusion:The isolated antibody 0919-A9 effectively neutralizes Tier 2 pseudoviruses. Its high somatic mutation frequency and V1V2-targeting property underlie its neutralizing activity,providing both a promising candidate and mechanistic insights for HIV vaccine development and antibody-based therapeutic strategies.
2.Revealing potential mechanism of Danggui Buxue decoction in regulating immuno-suppression via PI3K-AKT signaling pathway using network pharmacology and in vivo experiment
Huan HUANG ; Pingrui YANG ; Xifeng LI ; Fuxing GUI ; Yutao LI ; Li ZHANG ; Shuo LIU ; Yufei XIE ; Hongxu DU ; Shicheng BI ; Liting CAO
Chinese Journal of Veterinary Science 2025;45(2):350-361
Danggui Buxue decoction(DBD)is a classic prescription with immunomodulatory and hematopoietic effects.Previous studies have shown the DBD has potential to be used as an oral im-mune booster.However,its immunomodulatory effects and mechanism of action have not been thoroughly studied,especially the protective mechanism of immunomodulatory regulation in the state of immunosuppressive is still unclear.The aim of this study was to explore the protective mechanism of DBD in the immunosuppressive state using network pharmacology combined with animal experiments verification.The active components,core targets and signaling pathways of DBD in treating immunosuppression were obtained using network pharmacology tools.On this ba-sis,the active components of DBD were identified using HPLC-MS,and in vivo studies were con-ducted at the same time.The key active components of DBD obtained using network pharmacology included quercetin,kaempferol and formononetin.The core targets included TP53,RELA,TNF,AKT1,and IL-6.KEGG pathway enrichment analysis showed that phosphoinositide 3-kinase(PI3K)-protein kinase B(AKT)may play an important role in the treatment of immunosuppres-sive diseases using DBD.Molecular docking confirmed that each core target had good binding activ-ity with its corresponding compounds.Animal experiments showed that after DBD intervention,the mRNA gene and protein expression of RELA,TNF,and IL-6 in the serum was significantly down-regulated.The mRNA expression of PI3K and AKT in the ileum and PI3K protein expression were also downregulated.In conclusion,DBD exerts its role in treating immunosuppressive diseases by regulating the PI3K-AKT signaling pathway.
3.Revealing potential mechanism of Danggui Buxue decoction in regulating immuno-suppression via PI3K-AKT signaling pathway using network pharmacology and in vivo experiment
Huan HUANG ; Pingrui YANG ; Xifeng LI ; Fuxing GUI ; Yutao LI ; Li ZHANG ; Shuo LIU ; Yufei XIE ; Hongxu DU ; Shicheng BI ; Liting CAO
Chinese Journal of Veterinary Science 2025;45(2):350-361
Danggui Buxue decoction(DBD)is a classic prescription with immunomodulatory and hematopoietic effects.Previous studies have shown the DBD has potential to be used as an oral im-mune booster.However,its immunomodulatory effects and mechanism of action have not been thoroughly studied,especially the protective mechanism of immunomodulatory regulation in the state of immunosuppressive is still unclear.The aim of this study was to explore the protective mechanism of DBD in the immunosuppressive state using network pharmacology combined with animal experiments verification.The active components,core targets and signaling pathways of DBD in treating immunosuppression were obtained using network pharmacology tools.On this ba-sis,the active components of DBD were identified using HPLC-MS,and in vivo studies were con-ducted at the same time.The key active components of DBD obtained using network pharmacology included quercetin,kaempferol and formononetin.The core targets included TP53,RELA,TNF,AKT1,and IL-6.KEGG pathway enrichment analysis showed that phosphoinositide 3-kinase(PI3K)-protein kinase B(AKT)may play an important role in the treatment of immunosuppres-sive diseases using DBD.Molecular docking confirmed that each core target had good binding activ-ity with its corresponding compounds.Animal experiments showed that after DBD intervention,the mRNA gene and protein expression of RELA,TNF,and IL-6 in the serum was significantly down-regulated.The mRNA expression of PI3K and AKT in the ileum and PI3K protein expression were also downregulated.In conclusion,DBD exerts its role in treating immunosuppressive diseases by regulating the PI3K-AKT signaling pathway.
4.Structural and epitope characterization of HIV-1 V1V2 highly effective neutralizing antibodies based on AlphaFold 3
Junjie ZHANG ; Qianying WANG ; Ying LIU ; Shuhui WANG ; Li REN ; Shuo WANG ; Yutao SHI ; Yuhua RUAN ; Xiaojing LIU ; Xinran DU ; Yanling HAO ; Dan LI
Chinese Journal of Experimental and Clinical Virology 2025;39(5):548-555
Objective:To screen broadly neutralizing antibodies in human immunodeficiency virus-1(HIV-1)chronically infected individuals and characterize their molecular features and to provide new strategies for rational vaccine development and antibody-based therapeutics.Methods:A total of 34 treatment-na?ve individuals with chronic HIV-1 infection were enrolled. Plasma antibody binding levels were measured against two HIV-1 envelope proteins. Single antigen-specific memory B cells were sorted from high-binding samples,and antibody variable region genes were amplified by PCR for paired expression. The monoclonal antibodies were evaluated for neutralizing activity using pseudovirus assays,and their structural features were analyzed by integrating AlphaFold 3 prediction with Discovery Studio molecular docking.Results:Plasma samples showed strong binding to DU422-GP140 and BG505-GP140. Eight monoclonal antibodies were isolated from two donors. Among them,antibodies 0919-A4,0919-A9 and 0808-A2 could cross-react with GP140 from HIV-1 subtypes AE,BC and B. The monoclonal antibody 0919-A9 demonstrated potent neutralizing activity against SF162(Tier 1)and CH181(Tier 2)pseudoviruses,with somatic hypermutation rates of 13.27%(heavy chain)and 15.58%(light chain). Structural modeling revealed its specific targeting of the V1V2 region on GP120.Conclusion:The isolated antibody 0919-A9 effectively neutralizes Tier 2 pseudoviruses. Its high somatic mutation frequency and V1V2-targeting property underlie its neutralizing activity,providing both a promising candidate and mechanistic insights for HIV vaccine development and antibody-based therapeutic strategies.
5.Current researches of the role of skull bone marrow in nervous system disease
Fanfan YE ; Yutao DU ; Guodong FENG
Chinese Journal of Neurology 2024;57(11):1274-1280
The skull, surrounding the brain parenchyma, plays a role of protection and support. With the in-depth study of the interface of the central nervous system, ossified vascular channels connecting the dura and the skull bone marrow for cells traffic have been found, and the neuroimmune function of the skull has been gradually paid attention to. Here, this review will introduce the anatomy and immune function of the skull bone marrow, and then explore its changes during health and disease. It will further highlight the role of the skull bone marrow in neurological diseases such as stroke, glioblastoma, and neurodegenerative diseases.
6.Evaluation of the Criterion Validity of the Patient-reported Outcome Measure for Chronic Heart Failure
Na YUAN ; Qing ZHANG ; Yutao DU
Chinese Journal of Health Statistics 2024;41(6):857-861
Objective To evaluate the concurrent validity and predictive validity of the patient-reported outcome measure for chronic heart failure(CHF-PROM).Methods A prospective cohort of 1128 patients with chronic heart failure who met the inclusion and exclusion criteria was followed.To analyze the correlation between the concurrent validity criterion and the CHF-PROM each field score and total score using Pearson and Spearman.As a predictive validity criterion,readmission and death from heart failure were used.Analyze the effects of CHF-PROM each field score and total score on the risk of readmission and death using univariate and multivariate two-level Cox regression models.Results The results of concurrent validity analysis showed that the physiological field score,psychological field score and total score were negatively correlated with the New York Heart Association(NYHA)class.Physiological field scores were inversely correlated with N-terminal pro-B type natriuretic peptide(NT-proBNP)levels.The results of predictive validity analysis showed that the physiological field score was a predictor of readmission and death in patients with heart failure,and the psychological field score was only related to patient readmission.Conclusion CHF-PROM is a valid tool to evaluate in patients with chronic heart failure.The scale has good concurrent validity and predictive power.
7.Evaluation of the Criterion Validity of the Patient-reported Outcome Measure for Chronic Heart Failure
Na YUAN ; Qing ZHANG ; Yutao DU
Chinese Journal of Health Statistics 2024;41(6):857-861
Objective To evaluate the concurrent validity and predictive validity of the patient-reported outcome measure for chronic heart failure(CHF-PROM).Methods A prospective cohort of 1128 patients with chronic heart failure who met the inclusion and exclusion criteria was followed.To analyze the correlation between the concurrent validity criterion and the CHF-PROM each field score and total score using Pearson and Spearman.As a predictive validity criterion,readmission and death from heart failure were used.Analyze the effects of CHF-PROM each field score and total score on the risk of readmission and death using univariate and multivariate two-level Cox regression models.Results The results of concurrent validity analysis showed that the physiological field score,psychological field score and total score were negatively correlated with the New York Heart Association(NYHA)class.Physiological field scores were inversely correlated with N-terminal pro-B type natriuretic peptide(NT-proBNP)levels.The results of predictive validity analysis showed that the physiological field score was a predictor of readmission and death in patients with heart failure,and the psychological field score was only related to patient readmission.Conclusion CHF-PROM is a valid tool to evaluate in patients with chronic heart failure.The scale has good concurrent validity and predictive power.
8.Current researches of the role of dural immunity in neuroinfectious and neuroimmune diseases
Hanxiao CAI ; Wenmian HUANG ; Tao LIU ; Yutao DU ; Guodong FENG
Chinese Journal of Neurology 2023;56(5):572-577
Dura mater, rich in vasculature and immune cells, is the outermost layer of the central nervous system, and thus acts as the first barrier to protect brain. Meningeal lymphatic vessels and immune cells are main components of dural immunity, which respond to a variety of central nervous system diseases. Meanwhile, compared with brain parenchyma, dura mater communicates more with peripheral tissues and is more susceptible to medical interventions. Therefore, dura mater is a promising target to prevent, diagnose and treat intracranial diseases. Here dural immunity is clarified based on meningeal lymphatic vessels and dural immune cells, and current researches inquiring the role of dural immunity in infectious and immune diseases of central nervous system are summarized.
9.KLF7 in epicardial adipose tissue of coronary heart disease promotes inflammation and adipose differentiation
Yajun Xue ; Wenhua Huang ; Yayan Du ; Yijun Zhou ; Xingxing Dong ; Yutao Wei
Acta Universitatis Medicinalis Anhui 2022;57(2):197-202
Objective :
To explore the epicardial adipose tissue ( EAT) of patients with coronary heart disease , KLF7 stimulates macrophages to secrete inflammatory factors and promotes the differentiation and maturation of adipocytes through the NF⁃κB signaling pathway , and to clarify the mechanism of KLF7 in the occurrence and development of CAD.
Methods :
30 patients with coronary heart disease ( CAD group) and 30 patients without coronary heart disease (non⁃CAD group) were collected , and general data and biochemical indicators were collected. qRT⁃PCR was used to detect the expression levels of KLF7 , APN , IL⁃6 , and TNF⁃α mRNA in EAT. Human THP⁃1 cells were cultured in vitro and induced into M1 type macrophages and 3T3 ⁃L1 preadipocytes. The cells were divied into 3 groups : KLF7 up⁃regulated group ( transfected with KLF7 mimic) , KLF7 down⁃regulated group ( transfected with siRNA knockdown KLF7 ) , NC group ( transfected oligopeptide sequence) , transfected two kinds of cells. qRT⁃PCR was used to detect the expression of APN , MCP⁃1 , IL⁃6 and TNF⁃α mRNA in M1 type macrophages , and the protein expression levels of key factors in the NF⁃κB signaling pathway were detected by Westren blot.
The qRT⁃PCR method was used to detect APN , KLF4 , IL⁃6 , MCP⁃1 mRNA and adipocyte differentiation marker peroxisome proliferator⁃activated receptor⁃γ (PPARγ) in 3T3 ⁃L1 preadipocytes 24 h after transfection. CCAAT/enhancer binding protein α (C/EBPα ) , fatty acid binding protein 4 (FABP4) mRNA relative expression levels , and Westren blot was used to detect protein expression levels.
Results :
Compared with the non⁃CAD group , the expression of CAD group decreased , APN decreased , IL⁃6 and TNF⁃α increased significantly , and the difference was statistically significant (P < 0. 01) . KLF7 was highly expressed in human THP⁃1 derived M1 macrophages induced by inflammatory stimuli (LPS) . In M1 macrophages derived from human THP⁃1 , knocking down KLF7 could inhibit the release of inflammatory factors. Transfection with KLF7 ⁃siRNA could significantly inhibit LPS⁃induced phosphorylation of JNK⁃MAPKs , the level of p⁃p65 and the activation of p ⁃IκBa (P < 0. 05) . In 3T3 ⁃L1 preadipocytes , upregulation of KLF7 increased the expression of adipocyte differentiation markers PPARγ , C/EBPa , FABP4 mRNA , and promoted the differentiation of 3T3 ⁃L1 preadipocytes into adipocytes (P < 0. 05) .
Conclusion
The expression of KLF7 in EAT in CAD patients increases. KLF7 activates the activation of macrophages mediated by the JNK⁃NF⁃KB signaling pathway in EAT , promotes inflammation in EAT in CAD patients , and promotes the differentiation and maturation of adipocytes , thereby promoting the development of CAD. It indicates that KLF7 may be a potential therapeutic target for cardiovascular diseases (such as CAD) .
10.Molecular biological characteristics of the 2019 novel Coronavirus in Shijiazhuang
Huixia GAO ; Lin YANG ; Yun GUO ; Yicong WANG ; Yuzhen LIU ; Yue TANG ; Zhang HE ; Xinming LIANG ; Shunkai HUANG ; Peng GAO ; Ying HUANG ; Muwei DAI ; Zhi ZHANG ; Qian HU ; Yuling WANG ; Fang CHEN ; Erhei DAI ; Ping JIANG ; Yutao DU
Chinese Journal of Laboratory Medicine 2022;45(6):637-641
Objective:To analyze the molecular epidemiological characteristics of the Corona virus disease 2019 (COVID-19) cases in Shijiazhuang, which can reveal the origin of the outbreak and provide a scientific basis for COVID-19 prevention and control.Methods:From January 2 to January 8, 2021, a total of 404 samples from 170 COVID-19 cases were collected from the Shijiazhuang Fifth Hospital. The consensus sequence of 2019 novel Coronavirus(2019-nCoV) was obtained through multiplex polymerase chain reaction-based sequencing. The sequences of 170 COVID-19 cases were analyzed by the PANGOLIN, and the data were statistically analyzed by T-test.Results:Among the 404 COVID-19 samples, a total of 356 samples obtained high quality genome sequences (>95%,100×sequencing depth). The whole genome sequences of 170 COVID-19 cases were obtained by eliminating repeated samples. All 170 sequences were recognized as lineage B1.1 using PANGOLIN. The number of single nucleotide polymorphism arrange from 18-22 and most of the single nucleotide polymorphism were synonymous variants. All of 170 genomes could be classified into 48 sub-groups and most of the genomes were classified into 2 sub-groups (66 and 31, respectively).Conclusions:All cases in this study are likely originated from one imported case. The viruses have spread in the community for a long time and have mutated during the community transmission.


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