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.Umbrella decision-making model for diagnosis and treatment of elderly lung cancer patients: Construction and practice
Lunxu LIU ; Jian ZHOU ; Xiang DING ; Nan CHEN ; Jianxin XUE ; Xuelei MA ; Ye WANG ; Weiya WANG ; Liqing PENG ; Xin YOU ; Minggang SU ; Xu CHENG ; Jiao WANG ; Ning GE ; Deying KANG ; Yuchen HUANG ; Jinghan WANG ; Yu TONG ; Yaoxi ZHANG ; Jirong YUE ; Hu LIAO
Chinese Journal of Clinical Thoracic and Cardiovascular Surgery 2026;33(06):833-839
With the accelerating trend of population aging, the number of elderly patients with lung cancer continues to rise, and the disease burden is becoming increasingly heavy. The clinical management of these patients faces severe challenges due to their decreased physiological reserve, complex comorbidities, and significant individual heterogeneity. Consequently, under traditional diagnosis and treatment models, doctors often struggle to identify the individualized risks of elderly patients in a timely and comprehensive manner, which can easily lead to decision biases such as undertreatment or overtreatment. In view of this, this study advocates for the establishment of an umbrella decision-making model specifically tailored for elderly lung cancer patients. Grounded in a multidisciplinary team (MDT) platform, this model deeply integrates oncological indicators with the comprehensive geriatric assessment (CGA) system. By holistically considering multidimensional variables including tumor burden, organ function, frailty index, cognitive status, and social support, the model establishes an operational mechanism characterized by "single entry, precise stratification, and targeted selection". Accordingly, patients can be scientifically triaged into distinct intervention tiers, such as active surveillance, minimally invasive surgery, drug therapy, radiotherapy, and best supportive care, thereby achieving real-time alignment between treatment intensity and patient fitness. This article elaborates on the construction logic and key operational procedures of this novel decision-making framework, aiming to guide clinical practice beyond the limitations of a tumor-centric perspective toward a holistic, dynamic, whole-course management strategy. This transition seeks to ensure optimal quality of life and clinical net benefit for elderly patients alongside survival prolongation.
3.Biparametric MRI-based peritumoral radiomics for preoperative prediction of extracapsular extension in prostate cancer
Honghao XU ; Qicong DU ; Yuanhao MA ; Xueyi NING ; Baichuan LIU ; Xu BAI ; Di CHEN ; Yun ZHANG ; Zhe DONG ; Chuang JIA ; Xiaojing ZHANG ; Xiaohui DING ; Baojun WANG ; Aitao GUO ; Jian XUE ; Xuetao MU ; Huiyi YE ; Haiyi WANG
Chinese Journal of Radiology 2025;59(9):1055-1062
Objective:To investigate the value of biparametric-MRI (bpMRI) based peritumoral radiomics for preoperative prediction of extraprostatic extension (EPE) in prostate cancer (PCa).Methods:In this cross-sectional study, consecutive bpMRI of patients undergoing prostatectomy for PCa were retrospectively collected from the First Medical Center (center 1) and the Third Medical Center (center 2) of Chinese PLA General Hospital. A total of 274 patients were finally enrolled. Patients at center 1 from January 2020 to December 2022 were randomly divided into a training set (149 cases) and an internal validation set (63 cases) by stratified random sampling. Patients at center 2 from January 2023 to March 2024 were assigned to the external test set (62 cases). Patients were categorized into EPE-positive group and EPE-negative group according to pathological assessment postoperatively. In the training set, there were 49 cases in EPE-positive group and 100 cases in EPE-negative group. In the internal validation set, there were 26 cases in EPE-positive group and 37 cases in EPE-negative group. In the external test set, there were 22 cases in EPE-positive group and 40 cases in EPE-negative group. Axial T 2WI and apparent diffusion coefficient (ADC) images were manually annotated to obtain index lesion regions of interest (ROIs), with the peritumoral ROIs subsequently delineated by semi-automatic segmentation technique. Radiomics features were extracted from intra-tumoral, peri-tumoral, and intra-tumoral plus peri-tumoral ROIs. The training set data was employed to select and optimize features to build the radiomics models. The logistic regression analysis was used to develop radiomics, clinical, and integrated models. The predictive performance was assessed by the area under the receiver operating characteristic curve (AUC) in the external test set, and compared by the DeLong test. The sensitivity and specificity were compared by the exact McNemar test. Results:In the external test set, the peri-tumoral radiomics model based on bpMRI showed the highest performance in evaluating EPE, with an AUC of 0.739 (95% CI 0.611-0.842), which was identified as the optimal radiomics model. EPE grade ( OR=6.151, 95% CI 3.371-11.226, P<0.001) was incorporated into the clinical model, with an AUC of 0.780 (95% CI 0.657-0.875) in the external test set. The integrated model had an AUC of 0.817 (95% CI 0.698-0.904) in the external test set. There was no statistically significant difference in comparisons of AUCs among the three models (all P>0.05). The sensitivity of the integrated model (68.2%) showed no significant difference from those of the clinical model and the optimal radiomics model (77.3% and 86.4%, respectively; P=0.500 and P=0.289). However, the specificity of the integrated model (85.0%) was significantly higher than those of the clinical model (67.5%, P=0.016) and the optimal radiomics model (50.0%, P<0.001). Conclusion:A bpMRI-based peritumoral radiomics integrating clinical model demonstrates high performance for preoperative prediction of EPE in PCa.
4.Craniocerebral penetrating injury caused by nail shooting:one case report
Jiang-hao LI ; Zi-xuan WANG ; Xue-lin CHEN ; Xiang-lu LIU ; Jian DING
Fudan University Journal of Medical Sciences 2025;52(5):759-764
We reported the clinical,imaging,and treatment process of a patient with severe cranial penetrating injury caused by a nail from a nail gun that accidentally shot into the eye and penetrated into the skull while working.The patient was admitted to the Qingpu Branch of Zhongshan Hospital,Fudan University after being injured by the nail gun.The patient was admitted to the hospital 1 hour after injury with coma.After admission,the foreign body was completely removed and part of the hematoma was cleared through emergency surgery.After surgery,there were high-risk complications such as cerebral edema peak,intracranial hypertension,intracranial infection,cerebrospinal fluid leakage,and intracranial pseudoaneurysm.The patient eventually regained consciousness and was transferred to rehabilitation treatment.
5.The Effect of Electric Acupuncture Combined with Tianding Acupoint Treatment on the Efficacy,Syndrome Score,and Quality of Life of Post-stroke Intractable Hiccup
Yu-yang LI ; Yan-guan LIU ; Hui-hui HU ; Jian-tang XUE ; Cheng-qin YANG
Progress in Modern Biomedicine 2025;25(15):2445-2450
Objective:To explore the effect of electric acupuncture combined with Tianding acupoint on the efficacy,syndrome score,and quality of life of post-stroke intractable hiccup(IH).Methods:A total of 102 post-stroke IH patients admitted to our hospital from October 2022 to October 2023 were retrospectively included,and were divided into control group and observation group,with 51 cases in each group.The matched group patients were given conventional acupuncture treatment,while the observation group patients were given conventional electric acupuncture combined with Tianding acupoint treatment.The clinical efficacy,effectiveness,hiccup symptom scores before and Post-treatment,and quality of life score between two groups of patients.Results:The proportion of patients in the observation group who took immediate effect(27.45%vs.5.88%)and the proportion of patients who took effect within 24 hours of the first treatment(60.78%vs.17.65%)were higher than matched group.The average onset time[(32.14±9.72)h vs.(70.34±23.51)h]was significantly shorter than matched group(P<0.05).The treatment recovery rate of observation group was higher than matched group(80.39%vs.50.98%,P<0.05),and the total effective rate of treatment was not different from matched group(96.08%vs.86.27%,P>0.05).Post-treatment,both groups of patients showed a significant decrease in hiccup symptom scores,and there were significant differences at different time points(P<0.05).The hiccup symptom scores of the observation group patients at 1 d,3 d,and 5 d post-treatment were lower than matched group(P<0.05).Post-treatment,the overall scores of appetite,mental state,sleep,and quality of life in both groups increased,and the scores in the observation group were higher than matched group(P<0.05).Conclusion:The combination of electric acupuncture and Tianding acupoint has a significant therapeutic effect on post-stroke IH,which can quickly take effect,improve patients'clinical symptoms,and enhance their quality of life.
6.Value of serum P-selectin,IL-18,and Hcy levels in predicting poor out-come of interventional therapy for elderly patients with lower extremity deep venous thrombosis
Hong-jian CHI ; Yan-bing JI ; Min LIU ; Qi-xue LIU
Chinese Journal of Current Advances in General Surgery 2025;28(3):185-190
Objective:To explore the value of serum P-selectin,Interleukin-18(IL-18),and Homocysteine(Hcy)levels in predicting the adverse outcomes of interventional therapy in elderly patients with deep vein thrombosis(DVT)in the lower extremities.Methods:A total of 165 elderly patients with DVT from January 2020 to August 2023 were se-lected.All patients underwent transcatheter intervention thrombolysis therapy.Patients were divided into good outcome group and poor outcome group according to the clinical treatment outcome.Serum P-selectin,IL-18,and Hcy levels were compared between the two groups.The correlation between serum P-selectin,IL-18,and Hcy levels and disease indicators,as well as the outcomes of interventional therapy was analyzed.The predictive value of serum P-selectin,IL-18,and Hcy levels for the outcomes of interventional therapy was evaluated.Results:The total effective rate of catheter-based interventional thrombolysis in 165 patients was 81.82%(135/165).The patients with good outcomes were included in the good outcome group,and the patients with poor outcomes were included in the poor outcome group.The difference in circumference between the affected side and the healthy side of the thigh and the difference in circumference between the affected side and the healthy side of the calf in the poor outcome group were greater than those in the good outcome group(P<0.05).The levels of serum P-selectin,IL-18,and Hcy in the poor outcome group were higher than those in the good outcome group(P<0.05).The levels of serum P-selectin,IL-18,and Hcy were posi-tively correlated with the difference in circumference between the affected and healthy thighs and the difference in cir-cumference between the affected and healthy calves,and negatively correlated with the outcome of interventional therapy(P<0.05).Before and after correcting other factors,serum P-selectin,IL-18,and Hcy were all independent risk factors for the outcome of interventional therapy in elderly patients with DVT(P<0.05).The area under the curve(AUC)of serum P-selectin,IL-18,and Hcy for predicting the outcome of interventional therapy for elderly DVT was 0.789(95%CI:0.718-0.848),0.812(95%CI:0.744-0.868),and 0.792(95%CI:0.722-0.851),respectively.The cutoff values were 44.21 ng/mL,185.73 ng/L,and 23.60 μmol/L,with sensitivities of 70.00%,70.00%,and 80.00%,and specificities of 82.22%,82.96%,and 68.15%,respectively.The AUC of the combined prediction of the outcomes of interventional therapy for elderly DVT was 0.935(95%CI:0.886-0.967),with a cutoff value of 44.08 ng/mL,185.16 ng/L,and 23.37 μmol/L for the three variables,with a sensitivity of 86.67%and a specificity of 88.15%.This was significantly better than the individual prediction values of the three variables(Z=5.817,4.753,5.206,all P<0.001).Conclusion:Serum P-selectin,IL-18,and Hcy are significantly correlated with disease indicators and interventional treatment outcomes in el-derly patients with DVT,and can effectively predict the outcome of interventional treatment,with a high combined pre-dictive value.
7.Moxibustion combined with low-dose tadalafil for diabetes mellitus-induced erectile dysfunction:A prospective,single-center,three-arm randomized controlled trial
Tao LIU ; Zhao-xu YANG ; Yan XU ; Qi ZHAO ; Xue LIU ; Xin-fei HUANG ; Zhi-xing SUN ; Yun CHEN ; Jian-huai CHEN
National Journal of Andrology 2025;31(1):55-60
Objective:To investigate the clinical efficacy of moxibustion(Mox)combined with low-dose tadalafil(TAD)in the treatment of diabetes mellitus-induced erectile dysfunction(DMED)with the syndrome of Qi deficiency and blood stasis.Meth-ods:According to the inclusion and exclusion criteria,we selected 90 patients with DMED for this trial and equally randomized them into a Mox,a TAD,and a Mox combined with TAD(Mox+TAD)group to be treated by mild Mox applied to the acupoints Zusanli,Sanyinjiao and Yinlingquan qd alt,oral medication with low-dose TAD at 5 mg per dose qd,and combination of the above two thera-pies,respectively,all for 4 weeks.We obtained from the patients their IIEF-5 scores,traditional Chinese medicine(TCM)symptoms scores,Erectile Hardness Scale(EHS)scores,corpus cavernosal hemodynamic indexes,and the peak systolic velocity(PSV),end diastolic velocity(EDV)and resistance index(RI)of the corpus cavernosal arteries before and after treatment,and compared them among the three groups.Results:The total effectiveness rate was significantly higher in the Mox+TAD(90.0%)than in the Mox(46.7%)and TAD groups(60.0%)(P<0.05).Compared with the baseline,the IIEF-5 and EHS scores were increased,while the TCM symptoms scores decreased in all the three groups after treatment,more significantly in the Mox+TAD group than in the other two(P<0.05).And the PSV and RI were remarkably increased,while the EDV decreased(P<0.05)in all the three groups(P<0.05)after treatment,with PSV even higher in the Mox+TAD than in the Mox and TAD groups(P<0.05).Conclusion:Moxi-bustion combined with tadalafil has a definite efficacy and safety for the treatment of DMED,which can effectively improve the erectile function of the patients by increasing penile blood supply,benefiting qi and activating blood circulation.
8.Research of Achyranthoside Ⅰ inhibiting pyroptosis in chondrocytes based on the NF-κB/NLRP3/caspase-1 signaling axis
Ze-xuan LIU ; Yi-yan HAN ; Xue-feng GUAN ; Yu ZHANG ; Jian-yu DAI
The Chinese Journal of Clinical Pharmacology 2025;41(2):198-202
Objective To investigate the mechanism of Achyranthoside Ⅰ inhibits pyroptosis in chondrocytes through the nuclear factor-κB(NF-κB)/NOD receptor protein structure domain related proteins 3(NLRP3)/cystine containing aspartate specific proteins-1(caspase-1)signaling pathway.Methods Primary mouse chondrocytes were divided into blank group(phosphate buffered solution with the same volume),model group[10 ng·mL-1 interleukin-1β(IL-1 β)],control group(10 ng·mL-1 IL-1β+20 μmol·L-1 celecoxib)and experimental group(10 ng·mL-1 IL-1β+3 μg·mL-1 Achyranthoside Ⅰ).After 24 hours of intervention,the cell proliferation was measured by cell counting kit 8,the levels of superoxide dismutase(SOD),malondialdehyde(MDA),IL-1 and IL-6 were detected by enzyme-linked immunosorbent assay,the protein expression levels of NF-κB p65,NLRP3 and caspase-1 were detected by Western Blot.Results The apoptosis rates in experimental,control,model and blank groups were(13.34±0.61)%,(15.64±1.01)%,(21.81±1.10)%and 0;the SOD levels were(147.03±16.49),(130.09±7.33),(122.03±10.71)and(164.40±22.74)nU·mL-1;the MDA levels were(6.43±0.71),(7.63±1.01),(8.89±1.84)and(5.69±0.81)nmol·L-1;the IL-1 levels were(338.69±40.95),(361.78±32.15),(391.44±30.59)and(289.23±25.19)pg·mL-1;the IL-6 levels were(89.96±8.81),(101.10±11.59),(120.39±14.71)and(60.29±6.03)pg·mL-1;the relative expression levels of NF-κB p65 were 0.68±0.05,0.97±0.05,1.26±0.05 and 0.57±0.05;the relative expression levels of NLRP3 were 0.71±0.08,1.02±0.10,1.50±0.06 and 0.31±0.05;the relative expression levels of caspase-1 were 0.70±0.07,1.29±0.08,1.66±0.07 and 0.51±0.07,respectively.Compared with the model group,the differences of above indexes were statistically significant in the experimental group(all P<0.05).Conclusion Achyranthoside Ⅰ can improve the oxidative stress status induced by IL-1 β in chondrocytes,reduce the expression of proteins related to the NF-κB signaling pathway,and thereby decrease the occurrence of caspase-1 dependent pyroptosis,providing a protective effect on chondrocytes.
9.Diagnostic value of ultrasonic shear wave elastography for clinically significant prostate cancer
Fang-rui YANG ; Yong-hao JI ; Li-tao RUAN ; Jian-xue LIU ; Yao-ren ZHANG ; Xiao ZHANG ; Qin-yun WAN ; Si-fan REN
National Journal of Andrology 2025;31(6):505-511
Objective:To explore the diagnostic value of shear wave elastography(SWE)for clinically significant prostate cancer(csPCa).Methods:We retrospectively analyzed the clinical data of 359 cases with suspected prostate cancer(PCa)in Baoji Central Hospital from June 2017 to July 2023.All the patients underwent the following examinations in the order of serum prostate-spe-cific antigen(PSA)testing,transrectal ultrasonography(TRUS),measurement of the stiffness of the entire prostate gland by SWE,and TRUS-guided prostate puncture biopsy.The stiffness of the entire prostate gland was defined as the average of Young's modulus at both sides of the base,middle,and apex of the prostate,including the maximum Young's modulus(Emax),mean Young's modulus(Emean),and minimum Young's modulus(Emin).We analyzed the correlation of the parameters of the stiffness of the entire prostate gland with the pathological results,focusing on their diagnostic performance for csPCa.Results:Of the 359 cases,189 were diag-nosed by pathological puncture biopsy as BPH,26 as non-csPCa,and 144 as csPCa.The PSA level,Emax,Emean and Emin were significantly higher in the csPCa than those in the BPH and non-csPCa groups(all P<0.01),but showed no statistically significant difference between the BPH and non-csPCa groups(all P>0.05).The area under the receiver operating characteristic curve(AUC),optimal cut-off value,sensitivity,specificity,positive predictive value(PPV),negative predictive value(NPV)and accura-cy of Emax in the diagnosis of csPCa were 0.852,143.92 kPa,72.22%,84.65%,75.91%,81.98%and 79.67%;those of Emean were 0.868,82.42 kPa,67.36%,91.16%,83.62%,80.66%and 81.62%;and those of Emin were 0.682,32.73 kPa,47.22%,89.30%,73.91%,71.54%and 72.14%,respectively.In the non-csPCa group,Emax,Emean and Emin were found be-low the optimal cut-off value in 73.08%(19/26),92.31%(24/26)and 88.46%(23/26),respectively.Conclusion:The stiff-ness of the entire prostate gland measured by SWE contributes to the diagnosis of csPCa,reduces unnecessary detection of non-csPCa,and provides some reference for its active surveillance.
10.Craniocerebral penetrating injury caused by nail shooting:one case report
Jiang-hao LI ; Zi-xuan WANG ; Xue-lin CHEN ; Xiang-lu LIU ; Jian DING
Fudan University Journal of Medical Sciences 2025;52(5):759-764
We reported the clinical,imaging,and treatment process of a patient with severe cranial penetrating injury caused by a nail from a nail gun that accidentally shot into the eye and penetrated into the skull while working.The patient was admitted to the Qingpu Branch of Zhongshan Hospital,Fudan University after being injured by the nail gun.The patient was admitted to the hospital 1 hour after injury with coma.After admission,the foreign body was completely removed and part of the hematoma was cleared through emergency surgery.After surgery,there were high-risk complications such as cerebral edema peak,intracranial hypertension,intracranial infection,cerebrospinal fluid leakage,and intracranial pseudoaneurysm.The patient eventually regained consciousness and was transferred to rehabilitation treatment.

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