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.Atelocollagen Improves Bone-to-Tendon Interface Healing in a Rabbit Model of Chronic Rotator Cuff Tear Compared with Polydeoxyribonucleotide
Jian HAN ; Zhan-Feng ZHANG ; Shen-Yun FANG ; Yun-Mei CUI ; Sheng Chen HAN
Clinics in Orthopedic Surgery 2026;18(1):167-175
Background:
Surgeons face challenges in selecting cost-effective and biologically active agents for rotator cuff healing, given the numerous commercial products available, such as polydeoxyribonucleotide (PDRN) and atelocollagen (ATC). However, the precise efficacy of PDRN and ATC in rotator cuff healing remains debatable, and there is currently a lack of studies directly comparing the effects of the 2 agents on repaired cuff tendons. Therefore, the purpose of this study was to compare the efficacy of PDRN and ATC on bone-to-tendon interface (BTI) healing using a chronic rotator cuff tear (RCT) model in rabbits.
Methods:
Forty-eight rabbits were randomly divided into 3 groups. To create chronic RCT models, transected tendons were left untreated for 6 weeks, and then were repaired in a transosseous manner with PDRN and ATC injection into the repair site according to group allocation (group A: saline, group B: PDRN, group C: ATC; n = 16 per group). Genetic and immunofluorescence analyses were performed at 4 weeks after surgery. Furthermore, genetic, histologic, and biomechanical analyses were performed at 12 weeks after surgery.
Results:
At 4 weeks after surgery, ATC-injected shoulders showed the highest mRNA expression levels of collagen type I alpha 1 and aggrecan compared to the other 2 groups (p < 0.001 and p = 0.002, respectively). Meanwhile, there was more preliminary fibrocartilaginous matrix formation in the ATC-injected group. At 12 weeks after surgery, ATC-injected shoulders demonstrated better collagen fiber continuity and orientation, denser collagen fibers, a more mature bone-to-tendon junction, and greater fibrocartilage layer formation compared to the other 2 groups (all p < 0.001). Furthermore, ATC-injected shoulders also demonstrated a significantly higher load-to-failure value (40.4 ± 4.5 N/kg) than the remaining groups (group A, 26.7 ± 3.0 N/kg; group B, 32.8 ± 4.2 N/kg; p < 0.001).
Conclusions
ATC demonstrated superior efficacy in promoting BTI healing following surgical repair in a chronic RCT model of rabbits.
3.Opportunities and challenges in controlling metabolic dysfunction-associated steatotic liver disease: Editorial on “Downregulation of the MARC1 p.A165 risk allele reduces hepatocyte lipid content by increasing beta-oxidation”
Jian XU ; Gang SHI ; Tao SHENG ; Jingdong LI
Clinical and Molecular Hepatology 2026;32(2):919-920
4.Morphological identification of Lispe pumila (Diptera: Muscidae)
Shun-fang HUANG ; Ying SU ; Zi-dong CHENG ; Guo-sheng LIAN ; Ming-jian KE
Acta Parasitologica et Medica Entomologica Sinica 2026;33(2):141-143
In March 2024, three male and two female specimens of the genus Lispe were intercepted on cargo ships inbound for Wan Zai Port under Gongbei Customs. Based on morphological characteristics and molecular analysis, the specimens were identified as Lispe pumila. In this study, we describe the morphological features, diagnostic characteristics, and geographical distribution of L. pumila, with the aim of providing a reference for the identification of this species when intercepted at ports.
5.Research progress of nano drug delivery system based on metal-polyphenol network for the diagnosis and treatment of inflammatory diseases
Meng-jie ZHAO ; Xia-li ZHU ; Yi-jing LI ; Zi-ang WANG ; Yun-long ZHAO ; Gao-jian WEI ; Yu CHEN ; Sheng-nan HUANG
Acta Pharmaceutica Sinica 2025;60(2):323-336
Inflammatory diseases (IDs) are a general term of diseases characterized by chronic inflammation as the primary pathogenetic mechanism, which seriously affect the quality of patient′s life and cause significant social and medical burden. Current drugs for IDs include nonsteroidal anti-inflammatory drugs, corticosteroids, immunomodulators, biologics, and antioxidants, but these drugs may cause gastrointestinal side effects, induce or worsen infections, and cause non-response or intolerance. Given the outstanding performance of metal polyphenol network (MPN) in the fields of drug delivery, biomedical imaging, and catalytic therapy, its application in the diagnosis and treatment of IDs has attracted much attention and significant progress has been made. In this paper, we first provide an overview of the types of IDs and their generating mechanisms, then sort out and summarize the different forms of MPN in recent years, and finally discuss in detail the characteristics of MPN and their latest research progress in the diagnosis and treatment of IDs. This research may provide useful references for scientific research and clinical practice in the related fields.
6.Translational Research of Electromagnetic Fields on Diseases Related With Bone Remodeling: Review and Prospects
Peng SHANG ; Jun-Yu LIU ; Sheng-Hang WANG ; Jian-Cheng YANG ; Zhe-Yuan ZHANG ; An-Lin LI ; Hao ZHANG ; Yu-Hong ZENG
Progress in Biochemistry and Biophysics 2025;52(2):439-455
Electromagnetic fields can regulate the fundamental biological processes involved in bone remodeling. As a non-invasive physical therapy, electromagnetic fields with specific parameters have demonstrated therapeutic effects on bone remodeling diseases, such as fractures and osteoporosis. Electromagnetic fields can be generated by the movement of charged particles or induced by varying currents. Based on whether the strength and direction of the electric field change over time, electromagnetic fields can be classified into static and time-varying fields. The treatment of bone remodeling diseases with static magnetic fields primarily focuses on fractures, often using magnetic splints to immobilize the fracture site while studying the effects of static magnetic fields on bone healing. However, there has been relatively little research on the prevention and treatment of osteoporosis using static magnetic fields. Pulsed electromagnetic fields, a type of time-varying field, have been widely used in clinical studies for treating fractures, osteoporosis, and non-union. However, current clinical applications are limited to low-frequency, and research on the relationship between frequency and biological effects remains insufficient. We believe that different types of electromagnetic fields acting on bone can induce various “secondary physical quantities”, such as magnetism, force, electricity, acoustics, and thermal energy, which can stimulate bone cells either individually or simultaneously. Bone cells possess specific electromagnetic properties, and in a static magnetic field, the presence of a magnetic field gradient can exert a certain magnetism on the bone tissue, leading to observable effects. In a time-varying magnetic field, the charged particles within the bone experience varying Lorentz forces, causing vibrations and generating acoustic effects. Additionally, as the frequency of the time-varying field increases, induced currents or potentials can be generated within the bone, leading to electrical effects. When the frequency and power exceed a certain threshold, electromagnetic energy can be converted into thermal energy, producing thermal effects. In summary, external electromagnetic fields with different characteristics can generate multiple physical quantities within biological tissues, such as magnetic, electric, mechanical, acoustic, and thermal effects. These physical quantities may also interact and couple with each other, stimulating the biological tissues in a combined or composite manner, thereby producing biological effects. This understanding is key to elucidating the electromagnetic mechanisms of how electromagnetic fields influence biological tissues. In the study of electromagnetic fields for bone remodeling diseases, attention should be paid to the biological effects of bone remodeling under different electromagnetic wave characteristics. This includes exploring innovative electromagnetic source technologies applicable to bone remodeling, identifying safe and effective electromagnetic field parameters, and combining basic research with technological invention to develop scientifically grounded, advanced key technologies for innovative electromagnetic treatment devices targeting bone remodeling diseases. In conclusion, electromagnetic fields and multiple physical factors have the potential to prevent and treat bone remodeling diseases, and have significant application prospects.
7.Expert Consensus on Clinical Application of Qinbaohong Zhike Oral Liquid in Treatment of Acute Bronchitis and Acute Attack of Chronic Bronchitis
Jian LIU ; Hongchun ZHANG ; Chengxiang WANG ; Hongsheng CUI ; Xia CUI ; Shunan ZHANG ; Daowen YANG ; Cuiling FENG ; Yubo GUO ; Zengtao SUN ; Huiyong ZHANG ; Guangxi LI ; Qing MIAO ; Sumei WANG ; Liqing SHI ; Hongjun YANG ; Ting LIU ; Fangbo ZHANG ; Sheng CHEN ; Wei CHEN ; Hai WANG ; Lin LIN ; Nini QU ; Lei WU ; Dengshan WU ; Yafeng LIU ; Wenyan ZHANG ; Yueying ZHANG ; Yongfen FAN
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(4):182-188
The Expert Consensus on Clinical Application of Qinbaohong Zhike Oral Liquid in Treatment of Acute Bronchitis and Acute Attack of Chronic Bronchitis (GS/CACM 337-2023) was released by the China Association of Chinese Medicine on December 13th, 2023. This expert consensus was developed by experts in methodology, pharmacy, and Chinese medicine in strict accordance with the development requirements of the China Association of Chinese Medicine (CACM) and based on the latest medical evidence and the clinical medication experience of well-known experts in the fields of respiratory medicine (pulmonary diseases) and pediatrics. This expert consensus defines the application of Qinbaohong Zhike oral liquid in the treatment of cough and excessive sputum caused by phlegm-heat obstructing lung, acute bronchitis, and acute attack of chronic bronchitis from the aspects of applicable populations, efficacy evaluation, usage, dosage, drug combination, and safety. It is expected to guide the rational drug use in medical and health institutions, give full play to the unique value of Qinbaohong Zhike oral liquid, and vigorously promote the inheritance and innovation of Chinese patent medicines.
8.Impact of auricular acupressure combined with repetitive transcranial magnetic stimulation on swallowing and neurological function in stroke patients
Wandan WEI ; Liuhua LAN ; Jian LIANG ; Xiaoxia CHEN ; Sheng LIANG ; Ying JIANG
Chongqing Medicine 2025;54(8):1811-1815
Objective To investigate the influence of auricular acupressure combined with repetitive transcranial magnetic stimulation(rTMS)on swallowing function and neurological function in stroke pa-tients.Methods A total of 120 patients with dysphagia after stroke admitted to the hospital from January 2022 to June 2023 were selected as the research objects and divided into the control group,the auricular acu-pressure group,the rTMS group and the combined group according to the random number table method,with 30 cases in each group.The control group received routine care,the auricular acupressure group received auric-ular acupressure treatment on the basis of the control group,while the rTMS group received rTMS treatment,and the combined group received both auricular acupressure and rTMS treatment.All interventions lasted 4 weeks.Swallowing function was assessed before and after treatment using Functional Oral Intake Scale(FOIS),modified Mann Assessment of Swallowing Ability(MASA),and Water Swallow Test.Swallowing-related quality of life was evaluated before and after treatment by the Swallowing Quality of Life(SWAL-QOL)questionnaire.Neurological impairment was assessed before and after treatment using National Institu-tes of Health Stroke Scale(NIHSS).Results After treatment,FOIS and MASA scores in the four groups were higher than those before treatment,with the auricular acupressure group and the rTMS group showing higher scores than the control group,and the combination group significantly higher than the other three groups(P<0.05).The overall effectiveness rate for swallowing function in the combination group was 93.33%,significantly higher than 60.00%in the control group,63.33%in the auricular acupressure group,and 73.33%in the rTMS group(P<0.05),while there was no significant difference among the other three groups(P>0.05).After treatment,SWAL-QOL scores in the four groups were higher than that before treat-ment,with the auricular acupressure group and the rTMS group showing higher scores than the control group,and the combination group significantly higher than the other three groups(P<0.05).After treat-ment,NIHSS scores in the four groups were lower than that before treatment,and the combination group had significantly lower scores compared to the other three groups(P<0.05).Conclusion Auricular acupressure combined with rTMS could improve swallowing function and quality of life,and promote neurological function recovery in stroke patients.
9.Effects of parenteral nutrition containing ω-3 fish oil fat emulsion on the inflammatory status of patients with intestinal fistula at the early stage
Zheng ZHOU ; Kun-Jian WEI ; Qun XU ; Kai GUO ; Ting GONG ; Guo-Sheng GU
Parenteral & Enteral Nutrition 2025;32(1):15-22
Objective:To study the effects of parenteral nutrition containing ω-3 fish oil fat emulsion on the inflammatory status of patients with intestinal fistula at the early stage.Methods:A retrospective analysis was conducted on 28 patients with intestinal fistula who were admitted to the Sixth Department of General Surgery of Anhui Provincial Second People's Hospital from November 2023 to May 2024.The patients were either divided into control group(n=15,parenteral nutrition alone group)or study group(n=13,parenteral nutrition plus ω-3 fish oil fat emulsion)according to whether ω-3 fish oil fat emulsion was added to parenteral nutrition.Both groups of patients received parenteral nutrition support treatment,and the study group was given ω-3 fish oil fat emulsion during treatment.The general information,inflammatory factors in the blood,nutrition,and immune status of two groups of patients were collected and compared.The feces samples on the first and 14th day of admission were collected and analyzed by 16S rRNA high-throughput sequencing of gut microbiota.Results:There was no statistically significant difference in the general information,inflammation,nutrition,immune status,and gut microbiota between the two groups of patients on the first day of admission(P>0.05),indicating comparability between the two groups.After two weeks of parenteral nutrition support,the counts of red blood cells,white blood cells,platelets,lymphocytes,and levels of C-reactive protein,glutamate-pyruvate transaminase,aspartate aminotransferase,total bilirubin,direct bilirubin,total protein,albumin,and creatinine in the research group were similar to those in the control group without statistically significant differences(P>0.05).However,the counts of neutrophils and levels of blood urea nitrogen in the study group were significantly lower than those in the control group(P=0.03 and P=0.01).In addition,the abundance of intestinal flora in the study group was significantly higher than that in the control group(P<0.05).At the genus level,the abundance of Bacteroides_uniformis,Parabacteroides_merdae,Alistipes_finegoldii,Streptococcus_constellatus,Christensenella_minuta were different between the two groups after two weeks of treatment(P<0.05).Conclusion:Parenteral nutrition containing ω-3 fish oil fat emulsion can reduce the counts of neutrophils,which may alleviate inflammatory responses for patients with intestinal fistula at the early stage.
10.Research Advances of Deep Learning-based Raman Spectroscopy and Their Application in Detection of Microplastics
Yong-Hui HAN ; Chun-Bo SHI ; Wang LIANG ; Xiao-Yue ZHANG ; Jian-Sheng CUI ; Bo YAO
Chinese Journal of Analytical Chemistry 2025;53(2):153-163
Microplastics are widely present in various environments such as water bodies,land,and atmosphere,which pose threats to the ecological environment and human health through transmission and accumulation in the food chain.The existing detection techniques for microplastics face challenges such as complex preparation procedure of samples,low efficiency in processing large batches of samples,and difficulties in handling complex samples.Therefore,there is an urgent need for rapid and efficient detection techniques suitable for complex microplastics samples in the field of environmental monitoring.Raman spectroscopy,known for its advantages such as rapidity,accuracy,high sensitivity,non-destructiveness,and non-contact,demonstrates great application potential in detection of microplastics.Deep learning,an artificial intelligence method known for its large-scale data processing,nonlinear modeling and automatic feature extraction capabilities,is receiving increasing attention in the analysis of Raman spectroscopy signals.The application of deep learning-based Raman spectroscopy has significantly improved performance indicators such as detection efficiency and accuracy.This article introduced the existing Raman enhancement techniques,summarized the deep learning methods applied in Raman spectroscopy signal analysis,reviewed the recent research and application progress of deep learning-based Raman spectroscopy in detection of microplastics,and finally discussed the challenges and future prospects of deep learning-based Raman spectroscopy in detection of microplastics.


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