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.Mechanism of Aerobic Exercise in Delaying Brain Aging in Aging Mice by Regulating Tryptophan Metabolism
De-Man ZHANG ; Chang-Ling WEI ; Yuan-Ting ZHANG ; Yu JIN ; Xiao-Han HUANG ; Min-Yan ZHENG ; Xue LI
Progress in Biochemistry and Biophysics 2025;52(6):1362-1372
ObjectiveTo explore the molecular mechanism of aerobic exercise to improve hippocampal neuronal degeneration by regulating tryptophan metabolic pathway. Methods60 SPF-grade C57BL/6J male mice were divided into a young group (2 months old, n=30) and a senile group (12 months old, n=30), and each group was further divided into a control group (C/A group, n=15) and an exercise group (CE/AE group, n=15). An aerobic exercise program was used for 8 weeks. Learning memory ability was assessed by Y-maze, and anxiety-depression-like behavior was detected by absent field experiment. Hippocampal Trp levels were measured by GC-MS. Nissl staining was used to observe the number and morphology of hippocampal neurons, and electron microscopy was used to detect synaptic ultrastructure. ELISA was used to detect the levels of hippocampal Trp,5-HT, Kyn, KATs, KYNA, KMO, and QUIN; Western blot was used to analyze the activities of TPH2, IDO1, and TDO enzymes. ResultsGroup A mice showed significant decrease in learning and memory ability (P<0.05) and increase in anxiety and depressive behaviors (P<0.05); all of AE group showed significant improvement (P<0.05). Hippocampal Trp levels decreased in group A (P<0.05) and increased in AE group (P<0.05). Nidus vesicles were reduced and synaptic structures were degraded in group A (P<0.05), and both were significantly improved in group AE (P<0.05). The levels of Trp, 5-HT, KATs, and KYNA were decreased (P<0.05) and the levels of Kyn, KMO, and QUIN were increased (P<0.05) in group A. The activity of TPH2 was decreased (P<0.05), and the activities of IDO1 and TDO were increased (P<0.05). The AE group showed the opposite trend. ConclusionThe aging process significantly reduces the learning memory ability and increases the anxiety-depression-like behavior of mice, and leads to the reduction of the number of nidus vesicles and degenerative changes of synaptic structure in the hippocampus, whereas aerobic exercise not only effectively enhances the spatial learning memory ability and alleviates the anxiety-depression-like behavior of aging mice, but also improves the morphology and structure of neurons in hippocampal area, which may be achieved by the mechanism of regulating the tryptophan metabolic pathway.
5.Effects of Exercise Training on The Behaviors and HPA Axis in Autism Spectrum Disorder Rats Through The Gut Microbiota
Xue-Mei CHEN ; Yin-Hua LI ; Jiu-Gen ZHONG ; Zhao-Ming YANG ; Xiao-Hui HOU
Progress in Biochemistry and Biophysics 2025;52(6):1511-1528
ObjectiveThe study explores the influence of voluntary wheel running on the behavioral abnormalities and the activation state of the hypothalamic-pituitary-adrenal (HPA) axis in autism spectrum disorder (ASD) rats through gut microbiota. MethodsSD female rats were selected and administered either400 mg/kg of valproic acid (VPA) solution or an equivalent volume of saline via intraperitoneal injection on day 12.5 of pregnancy. The resulting offspring were divided into 2 groups: the ASD model group (PASD, n=35) and the normal control group (PCON, n=16). Behavioral assessments, including the three-chamber social test, open field test, and Morris water maze, were conducted on postnatal day 23. After behavioral testing, 8 rats from each group (PCON, PASD) were randomly selected for serum analysis using enzyme-linked immunosorbent assay (ELISA) to measure corticotropin-releasing hormone (CRH), adrenocorticotropic hormone (ACTH), and corticosterone (CORT) concentration, to evaluate the functional state of the HPA axis in rats. On postnatal day 28, the remaining 8 rats in the PCON group were designated as the control group (CON, n=8), and the remaining 27 rats in the PASD group were randomly divided into 4 groups: ASD non-intervention group (ASD, n=6), ASD exercise group (ASDE, n=8), ASD fecal microbiota transplantation group (FMT, n=8), and ASD sham fecal microbiota transplantation group (sFMT, n=5). The rats in the ASD group and the CON group were kept under standard conditions, while the rats in the ASDE group performed 6 weeks of voluntary wheel running intervention starting on postnatal day 28. The rats in the FMT group were gavaged daily from postnatal day 42 with 1 ml/100 g fresh fecal suspension from ASDE rats which had undergone exercise for 2 weeks, 5 d per week, continuing for 4 weeks. The sFMT group received an equivalent volume of saline. After the interventions were completed, behavioral assessments and HPA axis markers were measured for all groups. ResultsBefore the intervention, the ASD model group exhibited significantly reduced social ability, social novelty preference, spontaneous activity, and exploratory interest, as well as impaired spatial learning, memory, and navigation abilities compared to the normal control group (P<0.05). Serum concentration of corticotropin-releasing hormone (CRH), adrenocorticotropic hormone (ACTH), and corticosterone (CORT) in the PASD group were significantly higher than those in the PCON group (P<0.05). Following 6 weeks of voluntary wheel running, the ASDE group showed significant improvements in social ability, social novelty preference, spontaneous activity, exploratory interest, spatial learning, memory, and navigation skills compared to the ASD group (P<0.05), with a significant decrease in serum CORT concentration (P<0.05), and a downward trend in CRH and ACTH concentration. After 4 weeks of fecal microbiota transplantation in the exercise group, the FMT group showed marked improvements in social ability, social novelty preference, spontaneous activity, exploratory interest, as well as spatial learning, memory, and navigation abilities compared to both the ASD and sFMT groups (P<0.05). In addition, serum ACTH and CORT concentration were significantly reduced (P<0.05), and CRH concentration also showed a decreasing trend. ConclusionExercise may improve ASD-related behaviors by suppressing the activation of the HPA axis, with the gut microbiota likely playing a crucial role in this process.
6.Influencing factors of bladder management practices in patients with spinal cord injury
Zhirong LUO ; Xuyan GUO ; Qi XUE ; Xiao TAN ; Yunhua JI ; Fuxun ZHANG ; Yong JIAO ; Bo ZHANG
Journal of Modern Urology 2025;30(4):284-289
Objective: To explore the key factors affecting the selection and effectiveness of bladder management modalities in patients with spinal cord injury,so as to provide reference for the optimization of individualized bladder management strategies. Methods: The clinical and follow-up data of 78 patients with spinal cord injury treated in our hospital during Jan.1,2013 and Dec.31,2022 were retrospectively analyzed.The distribution of bladder management modalities among different grades of injuries was analyzed. Bowker symmetry test was used to evaluate the difference between bladder management modalities at discharge and at the end of follow-up. Multiple linear regression was used to explore the influencing factors of bladder management effects. Plotting Kaplan-Meier survival curves were adopted to calculate the median time of changes in bladder management. Results: At discharge,there were 9 cases of self-catheterization,19 cases of intermittent catheterization,22 cases of reflexive voiding,26 cases of long-term catheterization,and 2 cases using urinary collector.At the end of follow-up,there were 15 cases of self-catheterization,8 cases of intermittent catheterization,34 cases of reflexive voiding,14 cases of long-term catheterization,and 7 cases using urinary collector.There was a significant difference between the modalities of bladder management at discharge and at the end of follow-up (χ
=21.43,P=0.018).Multiple linear regression showed a significant decrease of 8.60 in the total neurogenic bladder symptom score (NBSS) for grade D injuries compared with grade A injuries (P=0.026). The median time to bladder management change was 7.93 months (95%CI:5.44-9.44), with approximately 50% of patients experiencing a change in bladder management within 8 months after discharge. Conclusion: The modalities of bladder management changed significantly after discharge.The grade of injury was a key factor affecting the effectiveness of bladder management.Higher grade was associated with worse effectiveness of bladder management.
7.Analysis of the causal relationship between gut microbiota and bladder cancer with Mendelian randomization
Xuyan GUO ; Zhirong LUO ; Qi XUE ; Yunhua JI ; Xiao TAN ; Yong JIAO
Journal of Modern Urology 2025;30(5):400-407
Objective: Previous observational studies have confirmed the correlation between gut microbiota and bladder cancer,but the causal relationship is still unclear.This study aimed to explore the causal relationship between them with Mendelian randomization. Methods: Genetic variation summary data of 211 gut microbiota and bladder cancer genome-wide association studies (GWAS) were obtained from the MiBioGen Consortium and Finngen database.Single nucleotide polymorphisms (SNPs) closely related to these studies were screened as instrumental variables.The causal relationship between gut microbiota and bladder cancer were analyzed with inverse variance weighting (IVW),MR-Egger,weighted median,maximum likelihood,robust adjustment feature score and MR-PRESSO,with IVW as the primary analysis method.Additionally,sensitivity analysis was used to test the heterogeneity (Cochran Q) and horizontal pleiotropy (MR-Egger intercept term and global test from MR-PRESSO estimator) to ensure the robustness of the results. Results: The IVW results indicated that Lachnospiraceae UCG004 (OR:1.42),Desulfovibrionales (Order) (OR:1.48),Eubacterium ruminantium group (OR:1.33),Olsenella (OR:1.24),Ruminococcaceae UCG002 (OR:1.39),Ruminococcaceae UCG005 (OR:1.42) and Ruminococcaceae UCG013 (OR:1.64) significantly increased the risk of bladder cancer.Conversely,Bacteroidetes (Phylum) (OR:0.61),Eubacterium brachy group (OR:0.80),Ruminococcaceae UCG004 (OR:0.73),Rikenellaceae (Family) (OR:0.67),Lachnospiraceae ND3007 group (OR:0.47), Adlercreutzia (OR:0.73) and an unknow genus (OR:0.75) were associated with a reduced risk of bladder cancer.Sensitivity analyses did not reveal any heterogeneity or horizontal pleiotropy. Conclusion: This study reveals the causal role of 14 gut microbiota in the pathogenesis of bladder cancer,among which Lachnospiraceae UCG004,Desulfovibrionales (Order),Eubacterium ruminantium group,Olsenella,Ruminococcaceae UCG002,Ruminococcaceae UCG005 and Ruminococcaceae UCG013 are risk factors for bladder cancer,while Bacteroidetes (Phylum),Eubacterium brachy group,Ruminococcaceae UCG004,Rikenellaceae (Family),Lachnospiraceae ND3007 group,Adlercreutzia and an unknown genus are the protective factors.
8.Mechanism of Kaixuan Jiedu Core Prescription in Regulating PTGS2 to Improve Skin Lesions in Psoriasis Mouse Models
Xue XIAO ; Liping KANG ; Dan DAI ; Yidi MA ; Bin YANG ; Ping SONG
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(17):49-59
ObjectiveTo identify the active constituents of Kaixuan Jiedu core prescription (KXJD) and investigate its effective components and therapeutic targets in the treatment of common psoriasis
9.Exploration of Kaixuan Jiedu Core Prescription's Efficacy in Alleviating Psoriasis Through Modulation of Ferroptosis Pathways: An Integrative Approach Involving Bioinformatics and Experimental Validation
Haoruo YANG ; Xue XIAO ; Jiaqi LI ; Ningxin ZHANG ; Bin YANG ; Ping SONG
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(17):69-78
ObjectiveTo use bioinformatics technology to screen the molecular patterns and diagnostic biomarkers of ferroptosis closely related to psoriasis, observe the therapeutic effect of Kaixuan Jiedu core prescription on psoriasis and explore its potential mechanism through animal experiments. MethodsPsoriasis microarray data from GEO were analyzed to identify differentially expressed genes (DEGs). Intersection with a ferroptosis gene set yielded psoriasis ferroptosis-related genes (FRGs), which underwent correlation, consensus clustering, enrichment, and immune infiltration analyses. Core diagnostic FRGs (Hub-FRGs) were identified using random forest (RF), support vector machine (SVM), LASSO regression, Nomogram, and ROC analyses. In vivo, imiquimod (5% cream) induced psoriasis in mice (except controls). Drug treatment groups received respective doses, while control and model groups received saline via daily gavage for 7 days. Back skin changes were recorded and PASI scored. Hematoxylin-eosin (HE) staining assessed histopathology. The levels of ferrous ion (Fe2+), malondialdehyde (MDA), 4-hydroxynonenal (4-HNE) and free fatty acid (FFA) in skin tissue were detected. The level of reactive oxygen species (ROS) in skin tissue was detected by immunofluorescence. Immunohistochemistry was used to detect the expression of ChaC glutathione-specific γ-glutamyl transferase 1 (CHAC1), arachidonic acid 12-lipoxygenase β (ALOX12B), trimotif protein 21 (TRIM21), proliferation marker (Ki67) and nuclear transcription factor-κB (NF-κB) protein. ResultsAnalysis of GSE30999 identified 2 100 DEGs and 24 FRGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed 1 000 biological functions and 75 pathways. After cluster analysis, combined with three machine learning algorithms, Nomogram and ROC curve analysis, the core Hub-FRGs (CHAC1, ALOX12 B, TRIM21) were obtained. Immunoinfiltration showed inactive memory CD4+T cells and activated dendritic cells abundance significantly correlated with Hub-FRGs. In vivo, model group vs. control showed significantly increased PASI/Baker scores (P<0.05), epidermal hyperkeratosis, inflammatory infiltration, and elevated levels of Fe2+, MDA, 4-HNE, FFA, ROS, CHAC1, ALOX12B, TRIM21, Ki67, and NF-κB (P<0.05). Drug groups vs. model group exhibited significantly reduced scores (P<0.05), alleviated skin lesions, and decreased levels of Fe2+, MDA, 4-HNE, FFA, ROS, Hub-FRGs, Ki67, and NF-κB (P<0.05). ConclusionKaixuan Jiedu core prescription can significantly improve the skin pathological injury of psoriasis mice, showing good therapeutic and repair effects, and its mechanism may be related to regulating the expression of ferroptosis genes CHAC1, ALOX12B and TRIM21, which are closely related to the pathogenesis of psoriasis.
10.Mechanism of Kaixuan Jiedu Core Prescription in Regulating PTGS2 to Improve Skin Lesions in Psoriasis Mouse Models
Xue XIAO ; Liping KANG ; Dan DAI ; Yidi MA ; Bin YANG ; Ping SONG
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(17):49-59
ObjectiveTo identify the active constituents of Kaixuan Jiedu core prescription (KXJD) and investigate its effective components and therapeutic targets in the treatment of common psoriasis

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