1.Mass Spectrometry-based Antibody Sequencing Technologies
Sheng-Mei LIU ; Peng XUE ; Xiao-Jian WANG
Progress in Biochemistry and Biophysics 2026;53(4):840-854
Antibodies play a critical role in adaptive immune responses and serve as key components in disease diagnosis and treatment. These molecules exhibit dynamic post-translational modifications (PTMs), such as glycosylation and phosphorylation, which regulate their effector functions. To date, nearly all of our knowledge about antibody repertoires has come from B cell receptor (BCR) sequencing (BCR-seq), which facilitates the profiling of clonal composition and the tracing of maturation trajectories within B-cell repertoires. However, circulating antibodies found in bodily fluids—such as serum, saliva, milk, mucosal secretions, and cerebrospinal fluid—exhibit diversities and specificities beyond what BCR-seq alone can predict. Therefore, identifying and quantifying antibody clonotypes at the protein level could enhance diagnosis, prognosis, and treatment strategies in personalized medicine. The critical gap between genotype and phenotype necessitates complementary methodologies that enable the direct characterization of antibody proteins in their native functional states. Mass spectrometry (MS)-based antibody repertoire sequencing (Ab-seq) is currently the only feasible approach for this task and primarily includes database-dependent methods—such as bottom-up, middle-down, and top-down approaches—as well as database-independent de novo sequencing technology. These strategies enable multi-level, high-precision characterization ranging from peptides and domains to intact antibody molecules. Unlike the shotgun strategy commonly used in routine proteomics, obtaining full sequences of all antibodies presents unique challenges. It requires specialized methodological adaptations to address issues related to dynamic range, sequence variation, and sample complexity. This review introduces the technical principles, methodological workflows, and recent applications of various mass spectrometry-based antibody repertoire sequencing (Ab-seq) strategies, with a focus on approaches designed to improve sequence coverage and identification accuracy. These include multi-enzyme digestion, hybrid fragmentation methods, and artificial intelligence-assisted de novo sequencing. By systematically comparing database-dependent techniques—such as bottom-up, middle-down, and top-down approaches—with database-independent de novo sequencing, this review outlines their respective advantages and limitations in terms of sample throughput, sequence coverage, post-translational modification characterization, and data analysis complexity. In addition, this review discusses emerging technological trends, including the integration of ion mobility separation, native mass spectrometry, and artificial intelligence-driven data interpretation, which are expected to enhance the depth and accuracy of antibody characterization. Although current methods continue to face challenges related to sample complexity, dynamic range, and unambiguous sequence variant assignment, we emphasize the importance of integrating BCR-seq and Ab-seq data to construct gene-protein association maps. These maps help validate sequence accuracy and facilitate epitope discovery. This dual-platform strategy helps bridge the gap between genotype and phenotype, thereby enhancing both the resolution and scope of antibody repertoire studies. Such an integrative approach also offers a valuable tool for therapeutic antibody development, structure-function analysis, and precise evaluation of vaccine efficacy.
2.Effect of Yang-Reinforcing and Blood-Activating Therapy on the Long-Term Prognosis for Dilated Cardio-myopathy Patients with Yang Deficiency and Blood Stasis Syndrome:A Retrospective Cohort Study
Shiyi TAO ; Jun LI ; Lintong YU ; Ji WU ; Yuqing TAN ; Xiao XIA ; Fuyuan ZHANG ; Tiantian XUE ; Xuanchun HUANG
Journal of Traditional Chinese Medicine 2026;67(1):53-59
ObjectiveTo evaluate the impact of yang-reinforcing and blood-activating therapy on the long-term prognosis for patients with dilated cardiomyopathy (DCM) of yang deficiency and blood stasis syndrome. MethodsA retrospective cohort study was conducted involving 371 DCM patients with yang deficiency and blood stasis syndrome. The yang-reinforcing and blood-activating therapy was defined as the exposure factor. Patients were categorized into exposure group (186 cases) and non-exposure group (185 cases) according to whether they received yang-reinforcing and blood-activating therapy combined with conventional western medicine for 6 months or longer. The follow-up period was set at 48 months, and the Kaplan-Meier survival analysis was used to assess the cumulative incidence of major adverse cardiovascular events (MACE) in both groups. Cox regression analysis was used to explore the impact of yang-reinforcing and blood-activating therapy on the risk of MACE, and subgroup analysis was performed. Changes in traditional Chinese medicine (TCM) syndrome score, left ventricular ejection fraction (LVEF), left ventricular fractional shortening (LVFS), left ventricular end-diastolic diameter (LVEDD), and Minnesota Living with Heart Failure Questionnaire (MLHFQ) score were compared between groups at the time of first combined use of yang-reinforcing and blood-activating therapy (before treatment) and 1 year after receiving the therapy (after treatment). ResultsMACE occurred in 31 cases (16.67%) in the exposure group and 47 cases (25.41%) in the non-exposure group. The cumulative incidence of MACE in the exposure group was significantly lower than that in the non-exposure group [HR=0.559, 95%CI(0.361,0.895), P=0.014]. Cox regression analysis showed that yang-reinforcing and blood-activating therapy was an independent factor for reducing the risk of MACE in DCM patients [HR=0.623, 95%CI(0.396,0.980), P=0.041], and consistent results were observed in different subgroups. Compared with pre-treatment, the exposure group showed decreased TCM syndrome score and MLHFQ score, reduced LVEDD, and increased LVEF and LVFS after treatment (P<0.05); in the non-exposure group, TCM syndrome score decreased, LVEF and LVFS increased, and LVEDD reduced after treatment (P<0.05). After treatment, the exposure group had higher LVEF and LVFS, smaller LVEDD, and lower TCM syndrome score and MLHFQ score compared with the non-exposure group (P<0.05). ConclusionCombining yang-reinforcing and blood-activating therapy with conventional western medicine can reduce the risk of MACE in DCM patients with yang deficiency and blood stasis syndrome, meanwhile improving their clinical symptoms, cardiac function, and quality of life.
3.Application of new antibiotics in the treatment of drug-resistant bacteria infections after solid organ transplantation
Chunrong JU ; Xiao XU ; Wujun XUE
Organ Transplantation 2026;17(2):182-191
Solid organ transplantation (SOT) is an effective treatment method for various end-stage diseases. However, due to the need for long-term use of immunosuppressive drugs to prevent rejection reactions after the surgery, SOT recipients are generally in a state of low immune function, resulting in a significant increase in the risk of infection. Post-transplant infection, especially infections caused by multi-drug resistant bacteria, is one of the common complications for SOT recipients and is also a major cause of graft dysfunction, graft loss and even death of the recipients. As the global situation of bacterial resistance becomes increasingly severe, the burden of infectious diseases continues to increase, seriously threatening the survival prognosis and graft function of SOT recipients. The exploration of new antibiotic research and rational application strategies worldwide has become crucial. The development and launch of various new antibiotics have provided more options for clinical practice. Therefore, systematically reviewing the drug characteristics of new antibiotics and their application status in this special population of SOT recipients is of great significance for guiding clinical practice and improving patients’ prognosis.
4.Mesenchymal stromal cell-derived extracellular vesicles alleviate immune checkpoint inhibitor-related pneumonitis by regulating macrophage inflammasome activation
XIAO Shuyan1,2 ; XUE Fengyuan1 ; JI Yinmin3 ; LYU Yahui1 ; DONG Yi1,2 ; HU Yi2,3
Chinese Journal of Cancer Biotherapy 2026;33(5):521-527
[摘 要] 目的:探讨间充质基质细胞来源细胞外囊泡(MSC-EV)对小鼠免疫检查点抑制剂相关肺炎(CIP)模型的改善作用及分子机制。方法:选取Foxp3DTR小鼠,皮下接种MC38小鼠结肠癌细胞,待肿瘤生长至可触及后,随机分为3组(每组n = 6):①对照组;②CIP模型组[接种MC38细胞后腹腔注射白喉毒素(DT)及anti-PD-1抗体,构建Treg细胞耗竭联合anti-PD-1抗体诱导的小鼠CIP模型];③MSC-EV干预组(CIP模型基础上,经鼻滴注MSC-EV干预,剂量109个/只,每3天1次,共2次)。体内实验采用H-E染色观察肺组织病理损伤,测定肺干湿比评估肺水肿程度,ELISA检测支气管肺泡灌洗液(BALF)中IL-1β、IL-6及TNF-α水平,流式细胞术检测BALF中Ly6G⁺粒细胞浸润比例,监测肿瘤体积评价抗肿瘤疗效。体外实验采用DiO荧光标记观察细胞外囊泡(EV)被骨髓来源巨噬细胞摄取的情况,WB法检测NOD样受体家族含Pyrin域蛋白3(NLRP3)炎症小体关键蛋白(剪切型GSDMD、成熟型IL-1β)的表达水平。结合GEO数据库miRNA测序数据(GSE69909)、Dicer敲低及miR-21/miR-125抑制剂干预揭示潜在机制。结果:MSC-EV经鼻滴注可减轻CIP模型小鼠肺部炎症损伤,降低BALF中IL-1β、IL-6、TNF-α水平及Ly6G⁺粒细胞浸润比例(P < 0.05),且不削弱anti-PD-1抗体的抗肿瘤疗效。体外DiO标记示踪显示MSC-EV可被巨噬细胞摄取,WB法检测结果显示,MSC-EV可降低NLRP3炎症小体关键活化蛋白(剪切型GSDMD、成熟型IL-1β)水平(P < 0.05)。体外实验中,Dicer敲低后制备的MSC-EV 对巨噬细胞IL-1β的下调作用减弱(P < 0.05)。miRNA测序显示miR-21、miR-125在MSC-EV中高表达,抑制miR-21或miR-125后,相应MSC-EV对巨噬细胞IL-1β剪切的抑制作用降低(P < 0.05)。结论:MSC-EV通过其携带的miR-21和miR-125等miRNA发挥抗炎效应,其机制可能与抑制巨噬细胞NLRP3炎症小体活化有关,可有效改善CIP且不影响免疫检查点抑制剂的抗肿瘤疗效。
5.Relationship between physical activity and mental health in children with autism spectrum disorder: the mediating role of social response
Guanting DUAN ; Xue XIAO ; Huisheng HOU ; Yunqiao JIANG ; Yuge LIU ; Wenxia SHI
Chinese Journal of Rehabilitation Theory and Practice 2025;31(2):150-157
ObjectiveTo evaluate the levels of physical exercise, mental health and social response in children with autism spectrum disorder (ASD), and explore the mediating effect of social response on physical exercise and mental health. MethodsFrom September, 2019 to April, 2024, 211 children with ASD from three special education schools in Haidian District and Shijingshan District of Beijing were selected. They were assessed with general data questionnaire, Physical Activity Rating Scale (PARS-3), Chinese version of Psycho-Educational Profile (C-PEP) and Social Response Scale-Short Form (SRS-SF). The correlation among physical exercise, mental health and social response was analyzed. The mediating effect of social response on physical exercise and mental health was explored. ResultsThe average physical exercise level was (58.72±3.34), the average mental health level was (14.85±1.67), and the average social response level was (24.98±3.79). Physical exercise was positively correlated with mental health (r = 0.546, P < 0.05) and negatively correlated with social response (r = -0.298, P < 0.05). Mental health was negatively correlated with social response (r = -0.397, P < 0.05). Average monthly family income, parental relationship, repeated transcranial magnetic stimulation therapy, physical exercise, social response were the influencing factors of mental health (P < 0.05). Social response was intermediary between physical exercise and mental health, accounting for 14.56%. ConclusionThe mental health level of children with ASD is poor, and there are many influencing factors. Physical exercise can directly affect the mental health of children with ASD, and can also play an indirect role through social response.
6.Enzyme-directed Immobilization Strategies for Biosensor Applications
Xing-Bao WANG ; Yao-Hong MA ; Yun-Long XUE ; Xiao-Zhen HUANG ; Yue SHAO ; Yi YU ; Bing-Lian WANG ; Qing-Ai LIU ; Li-He ZHANG ; Wei-Li GONG
Progress in Biochemistry and Biophysics 2025;52(2):374-394
Immobilized enzyme-based enzyme electrode biosensors, characterized by high sensitivity and efficiency, strong specificity, and compact size, demonstrate broad application prospects in life science research, disease diagnosis and monitoring, etc. Immobilization of enzyme is a critical step in determining the performance (stability, sensitivity, and reproducibility) of the biosensors. Random immobilization (physical adsorption, covalent cross-linking, etc.) can easily bring about problems, such as decreased enzyme activity and relatively unstable immobilization. Whereas, directional immobilization utilizing amino acid residue mutation, affinity peptide fusion, or nucleotide-specific binding to restrict the orientation of the enzymes provides new possibilities to solve the problems caused by random immobilization. In this paper, the principles, advantages and disadvantages and the application progress of enzyme electrode biosensors of different directional immobilization strategies for enzyme molecular sensing elements by specific amino acids (lysine, histidine, cysteine, unnatural amino acid) with functional groups introduced based on site-specific mutation, affinity peptides (gold binding peptides, carbon binding peptides, carbohydrate binding domains) fused through genetic engineering, and specific binding between nucleotides and target enzymes (proteins) were reviewed, and the application fields, advantages and limitations of various immobilized enzyme interface characterization techniques were discussed, hoping to provide theoretical and technical guidance for the creation of high-performance enzyme sensing elements and the manufacture of enzyme electrode sensors.
7.Dispersion effect of bone cement after vertebroplasty using individualized unilateral external pedicle approach and bilateral pedicle approach
Lichuang ZHANG ; Wen YANG ; Guangjiang DING ; Peikun LI ; Zhongyu XIAO ; Ying CHEN ; Xue FANG ; Teng ZHANG
Chinese Journal of Tissue Engineering Research 2025;29(4):800-808
BACKGROUND:According to existing clinical studies,vertebroplasty treatment with both the external pedicle approach and the pedicle approach can improve the pain and quality of life of patients with spinal compression fractures.Compared with the pedicle approach,the external pedicle approach has a freer puncture angle,and good bone cement dispersion effect can be obtained by adjusting the puncture angle. OBJECTIVE:To compare the impact of vertebroplasty through individualized unilateral external pedicle approach and bilateral pedicle approach on the treatment of spinal compression fractures by quantifying the dispersion effect of bone cement. METHODS:A total of 80 patients with thoracolumbar compression fracture were divided into two groups by random number table method.The bilateral pedicle group(n=40)underwent vertebroplasty through a bilateral pedicle approach,while the unilateral external pedicle group(n=40)underwent individualized vertebroplasty through a unilateral external pedicle approach.Anteroposterior and lateral X-rays of the affected vertebrae from two groups of patients were photographed to assess effect and type of bone cement dispersion within 3 days after surgery.Visual analog scale score,tenderness threshold around fracture,and Oswestry dysfunction index were assessed before,1,7 days,and 1 month after surgery. RESULTS AND CONCLUSION:(1)Dispersion effect of bone cement in unilateral external pedicle group was better than that in bilateral pedicle group(P<0.001),and the amount of bone cement perfusion was higher than that in bilateral pedicle group(P<0.001).In the bilateral pedicle group,the bone cement dispersion types were mainly concentrated in type Ⅰ and type Ⅲ,while in the unilateral external pedicle group,the bone cement dispersion types were mainly concentrated in type I and type Ⅱ,and there was a significant difference in bone cement dispersion types between the two groups(P<0.001).(2)Postoperative visual analog scale scores and Oswestry disability index of both groups were lower than those before surgery(P<0.001),and postoperative tenderness threshold around fracture showed a trend of decreasing first and then increasing.At the same time point after treatment,there were no significant differences in visual analog scale score,Oswestry disability index,and tenderness threshold around fracture between the two groups(P>0.05).(3)The results indicate that individualized vertebroplasty via unilateral external pedicle approach can achieve better bone cement dispersion,and the treatment effect is consistent with the vertebroplasty via classical bilateral pedicle approach.
8.Value of Mimics 3D reconstruction technology combined with Hookwire localization in pulmonary nodules
Xiao RAO ; Jianbo XUE ; Zhiyou ZHOU
China Modern Doctor 2025;63(17):34-37
Objective To explore the application value of Mimics 3D reconstruction technology combined with Hookwire localization in video-assisted thoracoscopic surgery(VATS)for pulmonary nodules.Methods A total of 100 patients with pulmonary nodules who underwent VATS at Jinhua Hospital Affiliated to Zhejiang University School of Medicine(Jinhua City Central Hospital)from June 2022 to June 2023 were selected as research subjects.The patients were divided into control group(n=51)and observation group(n=49)based on different localization methods.The observation group used Mimics 3D reconstruction technology combined with Hookwire intervention,while control group used methylene blue localization intervention.The surgical outcomes of both groups were compared.Results The operation time,nodule resection start time and hospital stay of patients in observation group were shorter than those in control group,and the intraoperative bleeding volume and hospitalization cost were less than those in control group(P<0.05).The incidence of postoperative complications of patients in observation group was lower than that in control group(P<0.05).Conclusion The combination of Mimics 3D reconstruction and Hookwire localization in patients with pulmonary nodules VATS can shorten the operation time,reduce the damage to lung function and improve the safety of surgery.
9.Mortality Trends and Age-Period-Cohort Model of Pan-creatic Cancer in Shanghai Pudong New Area,2002-2022
Caixia HU ; Jiayi SHENG ; Lianghong SUN ; Hua CHEN ; Xiaobin QU ; Sen WANG ; Siyue HAN ; Yichen CHEN ; Caoyi XUE ; Shaotan XIAO ; Lipeng HAO
China Cancer 2025;34(7):522-529
[Purpose]To analyze the trends in pancreatic cancer mortality and disease burden among residents in Shanghai Pudong New Area from 2002 to 2022,and to investigate the effects of age,period,and birth cohort on mortality risk.[Methods]Data on pancreatic cancer deaths among residents of Pudong New Area from 2002 to 2022 were collected through the Shanghai Population Cause of Death Registration System.The crude mortality rate,age-standardized mortality rate by Chinese standard population(ASMRC),potential years of life lost(PYLL),potential years of life lost rate(PYLLR),and average years of life lost(AYLL)were calculated.Joinpoint regression was applied to calculate the average annual percentage change(AAPC)for analyzing the changing trend of the mortality rate of pancreatic cancer.The age-period-cohort model was applied with R 4.4.1 to analyze the age,period,and cohort effects on the mortality risk of pancreatic cancer.[Results]The crude mortality rate of pancreatic cancer among residents in Pudong New Area increased from 10.42/105 in 2002 to 18.73/105 in 2022,showing a significant upward trend(AAPC=2.90%,P<0.001);the ASMRC was generally stable(AAPC=-0.05%,P=0.775).The crude mortality rate of males(17.09/105)was higher than that of females(13.75/105),and both showed an upward trend(AAPC=3.05%and 2.75%respectively,both P<0.001).After the age of 40,the mortality rate of pancreatic cancer increased significantly with the growth of age in both sexes.The PYLL was 31 347 person-years,showing an upward trend(AAPC=1.83%,P<0.001),and the AYLL was 3.59 years,showing a downward trend(AAPC=-2.45%,P<0.001).The age effect showed that the mortality risk of pan-creatic cancer was increased with age;the period effect showed that the mortality risk decreased from 2002 to 2016 and then increased;the cohort effect showed that the mortality risk increased with the advancement of the birth cohort.[Conclusion]From 2002 to 2022,the crude mortality rate of pancreatic cancer in Pudong New Area showed an upward trend,and the mortality rate of males was higher than that of females.The mortality risk of pancreatic cancer increases with age,and the later the birth year of the residents,the higher the mortality risk.Early screening should be strengthened for men and the elderly,environmental and lifestyle risk factors should be paid attention to in combination with the characteristics of cohort effect,and the prevention and control strategy for the whole population should be optimized.
10.Exploring the Path of Ideological and Political Construction in Biology Major Courses Empowered by Digital Intelligence
Wei-Ye SHI ; Xue-Ling GUO ; Yu FU ; Xiao-Lei ZHOU ; Ying-Ze WANG
Chinese Journal of Biochemistry and Molecular Biology 2025;41(6):914-923
The aim of this study is to explore a new path of empowering ideological and political educa-tion in courses with digital intelligence technology,therefore to improve the teaching quality of biology courses in universities,promote the comprehensive implementation of the fundamental task of cultivating morality and talents,and continuously improve the level of"three pronged education".By using the biol-ogy course"Immunology"as a practical carrier,we have constructed a dual-driven framework of"ideo-logical and political guidance+digital intelligence empowerment"utilizing digital tools to further highlight pedagogical feature enhancement,curricular optimization,innovative teaching models,multidimensional assessment,and enhanced teaching refinement.The empowerment of digital intelligence in the ideological and political construction of the course"Immunology"has achieved notable progress.Students' profes-sional abilities and ideological and political literacy have significantly improved,and the proportion of students with excellent grades has been increasing year by year(81.93%of students with good grades or above in 2024),demonstrating outstanding performance in various social practice activities;The course exhibits excellent demonstration and radiation effects on campus,and the teaching results have been sup-ported by the Ministry of Education and provincial-level education reform projects.This study serves as a practical example for the digital transformation of ideological and political education in higher education courses,providing reference and innovative insights for implementing ideological and political elements in other courses of biology majors.

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