1.Mechanism of Polygonum cuspidatum in alleviating silicosis based on network pharmacology, molecular docking, and experimental validation
Anning YANG ; Wenyan YANG ; Rui BAO ; Shengpeng WEN ; Huning ZHANG ; Sirong CHANG ; Wenyue ZHANG ; Xiaoyu LUO ; Yue SUN
China Occupational Medicine 2026;53(1):8-16
Objective To explore the potential mechanism of Polygonum cuspidatum in alleviating silicosis using network pharmacology, molecular docking, and experimental validation. Methods i) The targets of active components of Polygonum cuspidatum and silicosis-related targets were retrieved from multiple databases. The overlapping targets were imported into Venny2.1.0 and STRING platforms. "Polygonum cuspidatum-active components-potential therapeutic targets for silicosis" network was constructed and core targets of Polygonum cuspidatum that can alleviate silicosis were identified using the Cytoscape3.10.2 software. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed using the DAVID database, and molecular docking was conducted with AutoDock software. ii) Human embryonic lung fibroblast MRC-5 cells were divided into three groups. Cells in the control group were cultured in high-glucose Dulbecco's modified Eagle's medium containing 10.00% (V/V)fetal bovine serum. Cells in the silica group were treated with silica suspension at a final concentration of 150 μg·cm² (equivalent to 75 mg/L) for 48 hours. Cells in the silica + β-sitosterol group were first treated with silica suspension for 24 hours, then were cultured in medium containing β-sitosterol at a mass concentration of 50 μg/L for another 24 hours. Immunofluorescence assay and Western blotting were used to detect the effects of β-sitosterol, a core component of Polygonum cuspidatum, on the expression of phosphorylated protein kinase B (p-AKT), B-cell lymphoma-2 (BCL-2), and α-smooth muscle actin (α-SMA) in cells. Results i) A total of ten main active components of Polygonum cuspidatum, 840 targets of the active components, and 231 potential therapeutic targets for silicosis were screened through retrieval. A total of 10 core therapeutic targets were further screened, including tumor protein p53, serine/threonine protein kinase B1 (AKT1), heat shock protein 90-α, interleukin (IL)-6 , tumor necrosis factor, Src tyrosine kinase, estrogen receptor 1, epidermal growth factor receptor, BCL-2, and IL-1β. KEGG enrichment analysis yielded 178 related target pathways, among which, the phosphatidylinositol 3-kinase-protein kinase B (PI3K/AKT) signaling pathway was most relevant to silicosis. Molecular docking results showed that the top five compounds of Polygonum cuspidatum with high degree centrality, including quercetin, luteolin, physovenine, rhein, and β-sitosterol, had strong binding affinities with core targets. Among them, β-sitosterol, a key component of Polygonum cuspidatum, ranked high in binding affinity to all core targets. Molecular docking visualization indicated that β-sitosterol ranked high in binding affinitiy with the core target proteins AKT1 and BCL-2. ii) Both immunofluorescence and Western blotting results showed that, the relative expression of p-AKT, BCL-2, and α-SMA proteins increased in MRC-5 cells of the silica group compared with the control group (all P<0.05), except for p-AKT detected by Western blotting. Compared with the silica group, the relative expression levels of p-AKT, BCL-2, and α-SMA proteins in the silica+β-sitosterol group decreased (all P<0.05). Conclusion β-sitosterol, the core component of Polygonum cuspidatum, may alleviate silicosis fibrosis via the PI3K/AKT signaling pathway.
2.Predictive value of dose surface histogram for acute radiation proctitis induced by image guided radiotherapy for cervical cancer
Qing-xiao LIU ; Yue-xiang ZHU ; Wei WEI ; Long TIAN ; Song-lin YANG ; Zheng WANG ; Yu-sen ZHAO ; Su-li WANG ; Mao-ye CHANG
Chinese Medical Equipment Journal 2025;46(3):48-53
Objective To explore the predictive value of dose surface histogram(DSH)in image guided radiotherapy(IGRT)for radiotherapy-induced acute radiation proctitis(ARP)in cervical cancer(CCA).Methods Totally 380 patients with CCA IGRT admitted to some hospital from May 2019 to May 2023 were selected prospectively and randomly divided into a control group(n=1 80)and an experimental group(n=200).The patients in the 2 groups were followed up and the incidence rates of ARP were counted,and rectal dose distribution was evaluated using dose volume histogram(DVH)in the control group and DSH in the experimental group.The predictive values of DVH and DSH for ARP were evaluated and compared using ROC curves.Statistical analysis was performed using SPSS 21.0 software.Results The two groups did not have statistically significant difference in the incidence rate of ARP(P>0.05),while there were significant differences in the evaluation indicators of the rectal dose distribution(P<0.05).V40,V50,S40 and S50 proved to have low predictive values for grade Ⅰ-Ⅳ ARP with AUC 0.700(P<0.05);V60 and S60 had moderate predictive values for grade Ⅰ-Ⅳ ARP with AUC greater than 0.700 and less than or equal to 0.900(P<0.05);V70,V78,S70 and S7s showed high predictive values for grade Ⅰ-Ⅳ ARP with AUC higher than 0.900(P<0.05).Delong's test results indicated that DVH and DSH had no significant differences in AUC when used to predict gradeⅠ-Ⅳ ARP(allP>0.05).Conclusion DSH is essentially the same as DVH when used for the prediction of grade Ⅰ-Ⅳ ARP due to CCA IGRT,and thus can be used for the supplementation and optimization of radiotherapy planning systems.[Chinese Medical Equipment Journal,2025,46(3):48-53]
3.Screening and Identification of Nanobodies Against β-Conglycinin
Jia-Shu CHANG ; Hua-Bo SUN ; Yu-Ting WANG ; Xiao-Hui WANG ; Bo YANG ; Hong-Rui LIU ; Yue-Xin LI ; Yuan-Zhao SUN ; Shao-Peng GU ; Jin-Xin HE
Chinese Journal of Biochemistry and Molecular Biology 2025;41(5):764-770
Soy is a vital source of plant carbohydrates.However,it poses significant allergenic risks,particularly to young children and animals.Among the various proteins in soy,β-conglycinin,which con-stitutes approximately 30%of total soy carbohydrates,is a primary allergen.Undigested β-conglycinin can lead to intestinal damage by inhibiting cell growth,disrupting the cytoskeleton,and inducing apopto-sis.It can also enter the lymphatic and circulatory systems,triggering allergic reactions.Conventional ELISA methods for detecting β-conglycinin rely on polyclonal or monoclonal antibodies,which are limited by their large molecular weight,difficulty in accessing the protein core,and sensitivity to acidic and bas-ic conditions.To address these limitations,this study aimed to develop nanobodies(Nbs)against β-con-glycinin.Nbs,derived from the variable regions of heavy-chain antibodies found in camelids,have a mo-lecular weight approximately one-tenth that of conventional antibodies.They offer advantages such as small size,stable structure,high specificity,and strong affinity.A female alpacas was immunized five times using β-conglycinin,which showed a heavy chain antibody potency of 1∶16 000 by ELISA.Pe-ripheral blood lymphocytes were subsequently isolated and total RNA was extracted.The variable region of the heavy-chain antibody was amplified via PCR,and recombinant plasmids were constructed and transformed into the E.coli competency strain ER2738.The resulting library contained about 3.5×108 CFU/mL,which increased to 1.15×1012 PFU/mL after phage rescue,with a 100%Nbs gene insertion rate,indicating high diversity.Its Nbs phage output was significantly enriched by four rounds of solid-phase elution with an enrichment rate of 155.9.Four rounds of solid-phase panning yielded 35 positive clones,all of which shared the same amino acid sequence upon sequencing.The selected Nb was ex-pressed in a prokaryotic system,and its binding ability to β-conglycinin was confirmed using Western blotting and ELISA.The results demonstrated excellent specificity and affinity.This research lays the groundwork for developing a rapid and efficient detection method for β-conglycinin using Nbs,potentially enhancing food safety and allergen management.
4.Research progress on exosomes in bovine nutritional metabolic diseases
Qingnian HUANG ; Renxu CHANG ; Jingyi WANG ; Huijing ZHANG ; Yue YANG ; Shihao SONG ; Ming LI ; Chuang XU
Chinese Journal of Veterinary Science 2025;45(9):2086-2094
In recent years,the intensification of dairy farming has significantly improved production efficiency but has also led to a rise in the incidence of metabolic diseases.Conditions such as keto-sis,fatty liver,and hypocalcemia pose serious threats to dairy cattle health and productivity.These diseases not only profoundly affect individual physiological function but also impose considerable economic pressures and challenges on farm management.As research advances,exosomes have e-merged as a novel intercellular signaling molecule,showing unique potential in regulating dairy cattle's nutritional metabolism.Studies suggest that exosomes hold promise as biomarkers for dis-ease and can even serve as carriers for disease detection and prevention.Acting as a crucial mediator of intercellular communication,exosomes play an important role in modulating the metabolic processes of dairy cattle.This review aims to systematically explore the role of exosomes in bovine nutritional metabolism and to provide new perspectives and theoretical support for their potential as tools for diagnosing,treating,and preventing metabolic diseases in dairy cattle,thus advancing research and practice in this field.
5.Construction of Agtpbp1 gene knockout mouse model and preliminary phenotypic analysis
Yue CHANG ; Jingyuan SONG ; Chenxi YANG ; Huder SONG ; Houke LU ; Chuanling ZHANG ; Jianjun REN ; Rui XIAO
Chinese Journal of Pathophysiology 2025;41(7):1449-1456
AIM:To construct and breed infertility model mice with ATP/GTP binding carboxypeptidase 1(Agtpbp1)gene knockout homozygote(Agtpbp1-/-)by CRISPR/Cas9 technology,so as to provide an animal model for the subsequent exploration of the pathogenesis of Agtpbp1 gene in male sterility.METHODS:The CRISPR/Cas9 technology was used to obtain Agtpbp1 gene knockout heterozygote(Agtpbp1+/-)mice according to the data of the main protein functional region of Agtpbp1 gene and combined with Cas9 nuclease.The obtained Agtpbp1+/-mice were mated,and their offspring were genotyped by PCR and agarose gel electrophoresis.The expression of Agtpbp1 at different levels was detected by RT-PCR,Western blot and immunohistochemical staining to support the identification results.The HE staining was used to observe the mouse cerebellum and eyeball structure to analyze the effect of Agtpbp1 gene knockout on Purkinje cells and photoreceptor cells.The symptoms of ataxia in mice were observed in combination with behavioral tests.The growth of mice was observed,and the changes of testicular tissue volume and weight of male mice were analyzed.The HE staining was used to observe the changes of testicular structure,and PAS staining was used to observe the changes of testicular germ cell cycle.Finally,sperm analyzer was used to analyze the sperm motility,so as to analyze the growth and develop-ment of the mice.RESULTS:The male and female Agtpbp1+/-mice could continue to mate,and three genotypes,Agtpbp1 wild-type(Agtpbp1+/+),Agtpbp1+/-and Agtpbp1-/-,were obtained.The genotypes of the offspring mice were successfully identified by PCR.The results of RT-PCR,Western blot and immunohistochemical staining verified the successful con-struction of Agtpbp1-/-mouse model at different levels(P<0.05).The results of HE staining showed that Purkinje cells were lost in the cerebellum of Agtpbp1-/-mice and the number of photoreceptor cells in the eyeball was reduced.Behavioral tests confirmed that Agtpbp1-/-mice had ataxia symptoms such as motor dysfunction and uncoordinated movements.Com-pared with control group,the testicular volume and weight of Agtpbp1-/-mice were significantly reduced.The results of HE staining showed a very small amount of sperm in the testis of Agtpbp1-/-mice.Combined with the sperm analyzer,it was ob-served that the sperm motility,vitality and movement rate of Agtpbp1-/-mice were significantly lower than those of the con-trol mice.Testicular sections with PAS staining showed cell cycle arrest of the sperm from Agtpbp1-/-mice.CONCLU-SION:In this study,Agtpbp1 knockout mice were successfully bred.The deletion of Agtpbp1 caused the arrest of sper-matogenic cell differentiation and the decrease in sperm motility in adult male mice,resulting in infertility.At the same time,it provides a new experimental tool for further exploring the molecular mechanism of Agtpbp1-induced male sterility.
6.Analysis of risk factors for MRI invisible prostate cancer
Yushi HOU ; Mingyu CHANG ; Ruiyu YUE ; Jian SONG ; Xuanhao LI ; Jingcheng LYU ; Yichen ZHU ; Boyu YANG
International Journal of Surgery 2025;52(2):98-108
Objective:To investigate the risk factors for detecting clinically significant prostate cancer (CSPCa) in patients with Prostate Imaging Reporting and Data System (PI-RADS) score≤3 on multi-parameter magnetic resonance imaging (mpMRI).Methods:Retrospective analysis was performed on the case data of 335 patients with suspected prostate cancer and PI-RADS score ≤3 who were admitted to Beijing Friendship Hospital, Capital Medical University from January 2013 to October 2022. All patients underwent 24-needle prostate biopsy. Clinical data such as age, body mass index, past medical history, serological laboratory indicators, and mpMRI imaging data were collected. The patients were grouped according to whether the puncture pathology was CSPCa or not, and the differences in clinical data between the two groups were analyzed by t-test, rank sum test and Chi-test. Multivariate Logistic regression analysis was further used to determine independent risk factors for MRI invisible prostate cancer, and receiver operating characteristics (ROC) curves were drawn. At the same time, further subgroup analysis was conducted based on whether prostate-specific antigen (PSA) was positive before puncture and PI-RADS score, respectively, and the same statistical method was used to further determine the influence of different serological indicators and PI-RADS score on the analysis results of risk factors. Results:Among all patients, 81 were CSPCa patients and 254 were non-CSPCa patients. Multivariate Logistic regression analysis showed that prostate-specific antigen density (PSAD) and PI-RADS score of 3 were independent risk factors for MRI invisible prostate cancer. At the same time, compared with suspected lesions located only in the transitional zone, the incidence of CSPCa in patients with suspected lesions located in the peripheral zone would increase, and the incidence of CSPCa would further increase when suspected lesions were found in both the transitional zone and the peripheral zone. In PSA-negative patients, only suspected lesion location was an independent risk factor for MRI invisible prostate cancer, while in PSA-positive patients, prostate volume, PSAD, and PI-RADS scores were independent risk factors. In subgroup analysis with different PI-RADS scores, suspicious lesions in both the transitional zone and peripheral zone indicate a higher likelihood of CSPCa. For patients with PI-RADS scores of 1 to 2, suspicious lesions in the peripheral zone alone may also indicated CSPCa, while for patients with PI-RADS scores of 3, the lower free prostate-specific antigen/total prostate-specific anti-principle was more accurate in predicting CSPCa.Conclusions:For patients who are clinically suspected of prostate cancer but whose PI-RADS score is less than or equal to 3 points indicated by mpMRI, it is necessary to further focus on the results of different serological indicators according to whether their PSA is positive and PI-RADS score respectively to judge whether patients should receive systemic prostate puncture, instead of using PSA level as a single indication for puncture. At the same time, clinicians should also pay full attention to the location of suspected lesions, when they are located in the peripheral zone, or there are suspected lesions in both the peripheral zone and the transitional zone, the possibility of CSPCa should be fully considered.
7.Clinical characteristics of juvenile dermatomyositis in anti-nuclear matrix protein 2 antibody-positive patients and risk factors for severity: a national multicenter retrospective study
Huiyuan YANG ; Wanzhen GUAN ; Ling2 YANG ; Haimei LIU ; Xiaoqing3 LI ; Haiguo YU ; Meiping LU ; Jun YANG ; Xiaohui LIU ; Hongxia ZHANG ; Wei ZHANG ; Jihong XIAO ; Xiaozhong LI ; Guomin LI ; Hong CHANG ; Sheng HAO ; Yue DU ; Daliang XU ; Ling WU ; Wenjie ZHENG ; Li LIU ; Xinhui JIANG ; Shaohui ZHU ; Dongmei ZHAO ; Xuemei TANG ; Li SUN
Chinese Journal of Pediatrics 2025;63(12):1299-1305
Objective:To investigate the clinical characteristics and independent risk factors of severe disease in patients with anti-nuclear matrix protein (NXP) 2 antibody-positive juvenile dermatomyositis (JDM).Methods:A retrospective cohort study was conducted, including 219 anti-NXP2 antibody-positive JDM patients admitted to 23 children′s hospitals across China from July 2011 to July 2023. Patients were classified into severe and non-severe groups based on classification criteria for severe dermatomyositis. Demographic characteristics, clinical manifestations, and laboratory parameters were compared between the 2 groups using independent sample t-test, Mann-Whitney U test, or χ2 test. Univariate and multivariate Logistic regression analyses were performed to identify risk factors for severe disease. The receiver operating characteristic curve was employed to calculate optimal cut-off values. Results:Among the 219 patients, 108 were male and 111 were female, with an age at onset of 6.3 (3.5, 9.4) years. The severe group comprised 69 patients, and the non-severe group 150 patients. The severe group had significantly higher rates of fever, heliotrope rash, subcutaneous edema, periorbital edema, anti-Ro52 antibody positivity, as well as elevated levels of ferritin-to-albumin ratio (FAR), creatine kinase (CK), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH) (all P<0.05). Multivariate analysis identified anti-Ro52 antibody positivity ( OR=13.26, 95% CI 1.37-128.29) and elevated FAR ( OR=1.90, 95% CI 1.09-2.31) as independent risk factors for severe anti-NXP2 antibody-positive JDM (both P<0.05). Receiver operating characteristic curve analysis revealed that a FAR cutoff value of 6.82 predicted severe disease with an area under the curve of 0.87 (95% CI 0.81-0.94, P<0.001), sensitivity of 0.85, and specificity of 0.70. All patients received glucocorticoid therapy, and the severe group received higher proportions of steroid pulse therapy, cyclophosphamide, mycophenolate mofetil, intravenous immunoglobulin, biologics, and adjuvant treatments compared to the non-severe group (all P<0.05). In terms of outcomes, 2 patients (2.9%) in the severe group died (due to neurological involvement and intestinal perforation, respectively), while the remaining patients achieved complete clinical response or remission. All patients in the non-severe group achieved remission. Conclusions:The primary clinical features of anti-NXP2 antibody-positive JDM included fever, heliotrope rash, subcutaneous edema, periorbital edema, anti-Ro52 antibody positivity, and elevated levels of CK, AST, LDH, and FAR. Furthermore, anti-Ro52 antibody positivity and a FAR>6.82 were identified as independent risk factors.
8.Risk factors and predictive model for GC regimen chemoresistance post-radical cystectomy
Ruiyu YUE ; Meijuan CUI ; Mingyu CHANG ; Boyu YANG ; Jingcheng LYU ; Yichen ZHU ; Xinyi HU
Chinese Journal of Urology 2025;46(3):173-179
Objective:To explore the independent risk factors for chemoresistance during gemcitabine plus cisplatin (GC) adjuvant chemotherapy in patients with locally advanced bladder cancer after radical cystectomy and to construct a related predictive model.Methods:The clinical data of 228 patients with locally advanced bladder cancer who received GC chemotherapy after radical cystectomy at Beijing Friendship Hospital, Capital Medical University, from January 2013 to June 2024 were retrospectively analyzed. Among them, 184 were males, and 44 were females, with an average age of (68.8±10.6)years and an average body mass index (BMI) of (24.2±3.6)kg/m 2. According to tumor progression during chemotherapy, patients were divided into a chemotherapy-resistant(CR) group ( n=59) and a non-chemotherapy-resistant(NCR) group ( n=169). Independent sample t-test, chi-square test, and non-parametric test were used to compare general clinical characteristics and relevant examination results during chemotherapy between the two groups. Multivariate linear regression analysis was used to identify independent risk factors for GC chemoresistance. Propensity score matching (PSM) was used to match the TNM stage data between the two groups, and Kaplan-Meier and log-rank tests were used to compare overall survival(OS)after matching. Results:The median number of chemotherapy cycles was 3 in the CR group and 4 in the NCR group. Compared with the NCR group, CR patients were younger [(66.3±9.4) years vs.(69.7±10.9)years], had a higher proportion of kidney transplantation history[6.8%(4/59) vs. 0.6%(1/169)], hypertension [50.8%(30/59) vs. 36.1%(61/169)], coronary heart disease[23.7%(14/59) vs.9.5% (16/169)], and hydronephrosis [13.6%(8/59) vs. 4.1%(7/169)](all P<0.05). CR patients had a higher proportion of T 4 stage [20.3% (12/59) vs. 5.9% (10/169)], N 2 stage [42.4% (25/59) vs. 8.3% (14/169)], multifocal tumors at initial diagnosis [59.3% (35/59) vs. 26.6% (45/169)], and larger maximum tumor diameter [2.5 (1.5, 3.4) cm vs. 1.6 (1.2, 2.5) cm] (all P < 0.05). The CR group showed higher proportions of long-term urinary tract infection (UTI) [90.1% (53/59) vs. 7.7% (15/169)], higher systemic immune-inflammation index (SII) [991.6 (451.0, 1577.9) vs. 462.8 (309.0, 766.7)], absolute neutrophil count [6.5(4.1, 7.8)× 10 9/L vs. 3.9 (2.9, 5.1)× 10 9/L], and platelet count [(220.0 ± 96.2)× 10 9/L vs. (191.0 ± 64.8)× 10 9/L], but lower albumin levels [(34.3 ± 4.2) g/L vs. (39.9 ± 3.8) g/L] and albumin-to-globulin ratio (A/G) [(1.2 ± 0.3) vs. (1.3 ± 0.2)] (all P < 0.05). Multivariate linear regression analysis identified only T stage and long-term UTI as independent risk factors for GC chemoresistance( P<0.05).The probability of GC chemoresistance in bladder cancer patients was calculated as: P(Chemoresistance)=[0.155×T stage+ 0.624×(long-term UTI)]×100%(long-term UTI = 1 if present during chemotherapy, otherwise=0). After PSM, survival analysis showed that the median OS was significantly higher in the NCR group (55 months) than that in the CR group (30 months) ( P=0.020). Conclusions:This study demonstrates that advanced T stage and persistent UTI are independent risk factors for GC chemotherapy resistance in locally advanced bladder cancer patients. Based on these findings, a predictive model for chemotherapy resistance probability was constructed using multivariate linear regression analysis.
9.Novel Structural Features of Isoflavone Synthase from Medicago truncatula Shed Light on Its Unique Enzymatic Mechanism
Chao SHI ; Zhao-Yang YE ; Fei XU ; Xiang-Ning DU ; Zhang-Xin CHEN ; Ming-Yue GU ; Jie DENG ; Wei WANG ; Liang-Yu LIU ; Mei-Ying WANG ; Xiao-Dong SU ; He-Li LIU ; Ming-Ying SHANG ; Li-Xin HUANG ; Zhen-Zhan CHANG
Chinese Journal of Biochemistry and Molecular Biology 2025;41(8):1204-1213,中插1-中插6
Isoflavones which mainly distributed in leguminous plants have plenty of health benefits.Isoflavone synthase(IFS)is a membrane-associated cytochrome P450 enzyme(CYP450)which carries out the unique aryl-ring migration and hydroxylation.So far,few crystal structures of plant P450s have been obtained.We determined the crystal structure of IFS from Medicago truncatula at 1.9 ? by MAD method using a selenomethionine substituted crystal and conducted molecular docking and mutagenesis study.The structure of IFS complexed with imidazole exhibits the helix Ⅰa-loop-helix Ⅰβ motif which cor-responds to helix Ⅰ of other P450s.Compared with structures of common P450s,IFS/imidazole structure contains an extra domain,i.e.,the γ-domain.The structure reveals a homodimer in which the γ-domain of one molecule interacts with the β-domain of another.The plane of heme group makes an angle of ap-proximately 40° with the helix Ⅰa-loop-helix Ⅰβ motif.Molecular docking combined with mutagenesis study suggested that Trp-128 and Asp-300 might play important roles in substrate binding and recogni-tion.Phe-301,Ser-303 and Gly-305 from the helix Ⅰa-loop-helix Ⅰβ motif may play important roles in the aryl-ring migration.These novel structural features reveal insights into the unique reaction mechanism of IFS and provide a basis for engineering IFS in leguminous crops for health purpose.
10.Structural and Spatial Analysis of The Recognition Relationship Between Influenza A Virus Neuraminidase Antigenic Epitopes and Antibodies
Zheng ZHU ; Zheng-Shan CHEN ; Guan-Ying ZHANG ; Ting FANG ; Pu FAN ; Lei BI ; Yue CUI ; Ze-Ya LI ; Chun-Yi SU ; Xiang-Yang CHI ; Chang-Ming YU
Progress in Biochemistry and Biophysics 2025;52(4):957-969
ObjectiveThis study leverages structural data from antigen-antibody complexes of the influenza A virus neuraminidase (NA) protein to investigate the spatial recognition relationship between the antigenic epitopes and antibody paratopes. MethodsStructural data on NA protein antigen-antibody complexes were comprehensively collected from the SAbDab database, and processed to obtain the amino acid sequences and spatial distribution information on antigenic epitopes and corresponding antibody paratopes. Statistical analysis was conducted on the antibody sequences, frequency of use of genes, amino acid preferences, and the lengths of complementarity determining regions (CDR). Epitope hotspots for antibody binding were analyzed, and the spatial structural similarity of antibody paratopes was calculated and subjected to clustering, which allowed for a comprehensively exploration of the spatial recognition relationship between antigenic epitopes and antibodies. The specificity of antibodies targeting different antigenic epitope clusters was further validated through bio-layer interferometry (BLI) experiments. ResultsThe collected data revealed that the antigen-antibody complex structure data of influenza A virus NA protein in SAbDab database were mainly from H3N2, H7N9 and H1N1 subtypes. The hotspot regions of antigen epitopes were primarily located around the catalytic active site. The antibodies used for structural analysis were primarily derived from human and murine sources. Among murine antibodies, the most frequently used V-J gene combination was IGHV1-12*01/IGHJ2*01, while for human antibodies, the most common combination was IGHV1-69*01/IGHJ6*01. There were significant differences in the lengths and usage preferences of heavy chain CDR amino acids between antibodies that bind within the catalytic active site and those that bind to regions outside the catalytic active site. The results revealed that structurally similar antibodies could recognize the same epitopes, indicating a specific spatial recognition between antibody and antigen epitopes. Structural overlap in the binding regions was observed for antibodies with similar paratope structures, and the competitive binding of these antibodies to the epitope was confirmed through BLI experiments. ConclusionThe antigen epitopes of NA protein mainly ditributed around the catalytic active site and its surrounding loops. Spatial complementarity and electrostatic interactions play crucial roles in the recognition and binding of antibodies to antigenic epitopes in the catalytic region. There existed a spatial recognition relationship between antigens and antibodies that was independent of the uniqueness of antibody sequences, which means that antibodies with different sequences could potentially form similar local spatial structures and recognize the same epitopes.

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