1.Screening of biomarkers for fibromyalgia syndrome and analysis of immune infiltration
Yani LIU ; Jinghuan YANG ; Huihui LU ; Yufang YI ; Zhixiang LI ; Yangfu OU ; Jingli WU ; Bing WEI
Chinese Journal of Tissue Engineering Research 2025;29(5):1091-1100
BACKGROUND:Fibromyalgia syndrome,as a common rheumatic disease,is related to central sensitization and immune abnormalities.However,the specific mechanism has not been elucidated,and there is a lack of specific diagnostic markers.Exploring the possible pathogenesis of this disease has important clinical significance. OBJECTIVE:To screen the potential diagnostic marker genes of fibromyalgia syndrome and analyze the possible immune infiltration characteristics based on bioinformatics methods,such as weighted gene co-expression network analysis(WGCNA),and machine learning. METHODS:Gene expression profiles in peripheral serum of fibromyalgia syndrome patients and healthy controls were obtained from the gene expression omnibus(GEO)database.The differentially co-expressed genes were screened in the expression profile by differential analysis and WGCNA analysis.Least absolute shrinkage and selection operator(LASSO)and support vector machine-recursive feature elimination(SVM-RFE)machine learning algorithm were further used to identify hub biomarkers,and draw receiver operating characteristic curve(ROC)to evaluate the accuracy of diagnosing fibromyalgia syndrome.Finally,single sample gene set enrichment analysis(ssGSEA)and gene set enrichment analysis(GSEA)were used to evaluate the immune cell infiltration and pathway enrichment in patients with fibromyalgia syndrome. RESULTS AND CONCLUSION:Eight down-regulated differentially expressed genes(DEGs)were obtained after differential analysis of the GSE67311 dataset according to the conditions of log2|(FC)|>0 and P<0.05.After WGCNA analysis,497 genes were included in the module(MEdarkviolet)with the highest positive correlation(r=0.22,P=0.04),and 19 genes were included in the module(MEsalmon2)with the highest negative correlation(r=-0.41,P=6×10-5).After intersecting DEGs and the module genes of WGCNA,seven genes were obtained.Four genes were screened out by LASSO regression algorithm and five genes were screened out by SVM-RFE machine learning algorithm.After the intersection of the two,three core genes were identified,which were germinal center associated signaling and motility like,integrin beta-8,and carboxypeptidase A3.The areas under the ROC curve of the three core genes were 0.744,0.739,and 0.734,respectively,indicating that they have good diagnostic value and can be used as biomarkers for fibromyalgia syndrome.The results of immune infiltration analysis showed that memory B cells,CD56 bright NK cells,and mast cells were significantly down-regulated in patients with fibromyalgia syndrome compared with the control group(P<0.05),and were significantly positively correlated with the above three biomarkers(P<0.05).The enrichment analysis suggested that there were nine fibromyalgia syndrome enrichment pathways,mainly related to olfactory transduction pathway,neuroactive ligand-receptor interaction,and infection pathway.The above results showed that the occurrence and development of fibromyalgia syndrome are related to the involvement of multiple genes,abnormal immune regulation,and multiple pathways imbalance.However,the interactions between these genes and immune cells,as well as their relationships with various pathways need to be further investigated.
2.Bupleuri Radix Associated Prescriptions Against Depression: A Review
Congwei LI ; Mingliang QIAO ; Peiyuan ZHAO ; Bing LI ; Yi MENG
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(10):295-304
In today's society, depression is a kind of highly prevalent chronic mental illness. It leads to a high disability rate and a heavy economic burden. Depression is defined by fundamental symptoms of low mood and diminished pleasure. Its causes and mechanisms remain unclear, and it presents a broad spectrum of symptoms and a persistent nature that significantly impacts both physical and mental well-being. Treatment in Western medicine primarily focuses on alleviating symptoms, yet it entails numerous adverse effects and contraindications. Traditional Chinese medicine (TCM) treatment is based on resolving depression, which is often accompanied by soothing liver, and the key medicine is Bupleuri Radix. Bupleuri Radix associated prescriptions refer to a class of prescriptions using Bupleuri Radix as the sovereign medicinal or having a high dose of Bupleuri Radix, which are widely used in the field of anti-depression. Previous studies from animal experiments, clinical research, and modern pharmacological research have confirmed that Bupleuri Radix associated prescriptions have precise anti-depression efficacy in multiple ways and at multiple levels, but lack a comprehensive and systematic summarization. This paper summarized and analyzed the literature related to the clinical application and mechanism of action of Bupleuri Radix associated prescriptions in anti-depression treatment. The results showed that the anti-depression mechanism of the Bupleuri Radix associated prescriptions (such as Xiaochaihu Tang, Xiaoyao San, Sini San, Chaihu Shugan San, and Chaihu jia Longgu Muli San) was associated with the effects of regulating monoamine neurotransmitters, the brain-derived neurotrophic factor (BDNF), intestinal flora, and the hypothalamic-pituitary-adrenal (HPA) axis, inhibiting inflammatory responses, and modulating related signaling pathways. Applying them in clinical practice can effectively alleviate patient symptoms, lower the TCM syndrome score and the severity of depression, and also reduce adverse reactions. This underscores advantages of TCM in depression treatment, which offers patients a secure, effective, and more individualized alternative treatment regimen. On this basis, the shortcomings of current studies and the future trend were analyzed. This study aimed to provide an evidence-based medicine basis for the research and development of novel antidepressant medications.
3.Operation guide for the visual electrophysiology data collection in small animals(2025)
Yi SHAO ; Shiying LI ; Biao YAN ; Biao YAN ; Biao YAN ; Biao YAN ; Biao YAN ; Biao YAN
International Eye Science 2025;25(5):689-697
Visual electrophysiology measurements have become a routine method of functional examination in ophthalmology. Small animal visual electrophysiology is an important tool for exploring the functionality of the visual system in small animals, finding widespread applications in neuroscience and drug research and development. This guide aims to offer a standardized operational guide for the operation of visual electrophysiological norms in small animals to ensure the accuracy and repeatability of the test. The study emphasizes different types of visual electrophysiological tests, such as electroretinogram(ERG)and visual evoked potential(VEP), evoked in small animals, and their application in different disease models. Detailed descriptions are provided regarding the selection and preparation of experimental animals, including the requirements of animal species, anesthesia methods and test environment. In terms of operational procedures, this guide highlights the correct electrode placement, the selection of stimulus parameters, and the key steps for signal acquisition and processing. According to different animal models, the corresponding operation suggestions were provided, and the troubleshooting methods of common problems were introduced. Beyond fundamental operations, this guide also focuses on the interpretation and reporting of test results. It explains various types of electrophysiological waveforms. In summary, this operational specification for small animal visual electrophysiology provides a comprehensive and detailed framework for researchers to ensure the standardization and reliability of tests. By following these guidelines, researchers can effectively utilize small animal visual electrophysiology techniques to gain insight into the function and abnormalities of the visual system.
4.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.
5.Inhibition of HDAC3 Promotes Psoriasis Development in Mice Through Regulating Th17
Fan XU ; Xin-Rui ZHANG ; Yang-Chen XIA ; Wen-Ting LI ; Hao CHEN ; An-Qi QIN ; Ai-Hong ZHANG ; Yi-Ran ZHU ; Feng TIAN ; Quan-Hui ZHENG
Progress in Biochemistry and Biophysics 2025;52(4):1008-1017
ObjectiveTo investigate the influence of histone deacetylase 3 (HDAC3) on the occurrence, development of psoriasis-like inflammation in mice, and the relative immune mechanisms. MethodsHealthy C57BL/6 mice aged 6-8 weeks were selected and randomly divided into 3 groups: control group (Control), psoriasis model group (IMQ), and HDAC3 inhibitor RGFP966-treated psoriasis model group (IMQ+RGFP966). One day prior to the experiment, the back hair of the mice was shaved. After a one-day stabilization period, the mice in Control group was treated with an equal amount of vaseline, while the mice in IMQ group was treated with imiquimod (62.5 mg/d) applied topically on the back to establish a psoriasis-like inflammation model. The mice in IMQ+RGFP966 group received intervention with a high dose of the HDAC3-selective inhibitor RGFP966 (30 mg/kg) based on the psoriasis-like model. All groups were treated continuously for 5 d, during which psoriasis-like inflammation symptoms (scaling, erythema, skin thickness), body weight, and mental status were observed and recorded, with photographs taken for documentation. After euthanasia, hematoxylin-eosin (HE) staining was used to assess the effect of RGFP966 on the skin tissue structure of the mice, and skin thickness was measured. The mRNA and protein expression levels of HDAC3 in skin tissues were detected using reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) and Western blot (WB), respectively. Flow cytometry was employed to analyze neutrophils in peripheral blood and lymph nodes, CD4+ T lymphocytes, CD8+ T lymphocytes in peripheral blood, and IL-17A secretion by peripheral blood CD4+ T lymphocytes. Additionally, spleen CD4+ T lymphocyte expression of HDAC3, CCR6, CCR8, and IL-17A secretion levels were analyzed. Immunohistochemistry was used to detect the localization and expression levels of HDAC3, IL-17A, and IL-10 in skin tissues. ResultsCompared with the Control group, the IMQ group exhibited significant psoriasis-like inflammation, characterized by erythema, scaling, and skin wrinkling. Compared with the IMQ group, RGFP966 exacerbated psoriasis-like inflammatory symptoms, leading to increased hyperkeratosis. The psoriasis area and severity index (PASI) skin symptom scores were higher in the IMQ group than those in the Control group, and the scores were further elevated in the IMQ+RGFP966 group compared to the IMQ group. Skin thickness measurements showed a trend of IMQ+RGFP966>IMQ>Control. The numbers of neutrophils in the blood and lymph nodes increased sequentially in the Control, IMQ, and IMQ+RGFP966 groups, with a similar trend observed for CD4+ and CD8+ T lymphocytes in the blood. In skin tissues, compared with the Control group, the mRNA and protein levels of HDAC3 decreased in the IMQ group, but RGFP966 did not further reduce these expressions. HDAC3 was primarily located in the nucleus. Compared with the Control group, the nuclear HDAC3 content decreased in the skin tissues of the IMQ group, and RGFP966 further reduced nuclear HDAC3. Compared with the Control and IMQ groups, RGFP966 treatment decreased HDAC3 expression in splenic CD4+ and CD8+ T cells. RGFP966 treatment increased the expression of CCR6 and CCR8 in splenic CD4+ T cells and enhanced IL-17A secretion by peripheral blood and splenic CD4+ T lymphocytes. Additionally, compared with the IMQ group, RGFP966 reduced IL-10 protein levels and upregulated IL-17A expression in skin tissues. ConclusionRGFP966 exacerbates psoriatic-like inflammatory responses by inhibiting HDAC3, increasing the secretion of the cytokine IL-17A, and upregulating the expression of chemokines CCR8 and CCR6.
6.Terms Related to The Study of Biomacromolecular Condensates
Ke RUAN ; Xiao-Feng FANG ; Dan LI ; Pi-Long LI ; Yi LIN ; Zheng WANG ; Yun-Yu SHI ; Ming-Jie ZHANG ; Hong ZHANG ; Cong LIU
Progress in Biochemistry and Biophysics 2025;52(4):1027-1035
Biomolecular condensates are formed through phase separation of biomacromolecules such as proteins and RNAs. These condensates exhibit liquid-like properties that can futher transition into more stable material states. They form complex internal structures via multivalent weak interactions, enabling precise spatiotemporal regulations. However, the use of inconsistent and non-standardized terminology has become increasingly problematic, hindering academic exchange and the dissemination of scientific knowledge. Therefore, it is necessary to discuss the terminology related to biomolecular condensates in order to clarify concepts, promote interdisciplinary cooperation, enhance research efficiency, and support the healthy development of this field.
7.Impacts of ambient air pollutants on childhood asthma from 2019 to 2023: An analysis based on asthma outpatient visits of Nanjing Children's Hospital
Li WEI ; Xing GONG ; Lilin XIONG ; Yi ZHANG ; Fengxia SUN ; Wei PAN ; Changdi XU
Journal of Environmental and Occupational Medicine 2025;42(4):408-414
Background Asthma poses a serious threat to children's growth, development, and mental health, thus there has been an increasing focus on the control of asthma morbidity in children and the assessment of its risk factors. A growing body of research has found that exposure to ambient air pollutants an significatly increase the risk of childhood asthma. Objective To understand the changes of ambient air pollutant concentrations in Nanjing and asthma outpatient visits to Nanjing Children's Hospital, and to quantitatively analyze the effects of exposure to different ambient air pollutants on children's asthma outpatient visits. Methods Daily data of ambient air pollutants fine particulate matter (PM2.5), inhalable particle (PM10), sulfur dioxide (SO2), nitrogen dioxide (NO2), carbon monoxide (CO), ozone (O3), meteorological factors (air temperature & relative humidity), and outpatient visits due to asthma in the hospital from January 1, 2019 to December 31, 2023 were collected, and a generalized additive model based on quasi poisson distributions was used to quantitatively analyze the short-term effects of ambient air pollutant exposure on outpatient visits due to asthma in the hospital. Results The annual average concentrations of PM2.5, PM10, SO2, and NO2 in Nanjing from 2019 to 2023 did not exceed the national limits. For single-day lagged effects, the single-pollutant model showed that the effects of PM2.5, PM10, NO2, and CO on children's asthma outpatient visits were greatest for every 10 units increase at lag0, with excess risk (ER) of 1.39% (95%CI: 0.65%, 2.14%), 1.46% (95%CI: 0.97%, 1.95%), 5.46% (95%CI: 4.36%, 6.57%), and 0.18% (95%CI: 0.11%, 0.26%), respectively, and SO2 reached the maximum effect at lag1, with an ER of 23.15% (95%CI: 13.57%, 33.53%) for each 10 units increase in concentration. Different pollutants reached their maximum cumulative lag effects at different time. The PM10, PM2.5, SO2, NO2, and CO showed the largest cumulative lag effects at lag01, lag01, lag02, lag02, and lag03, respectively, with ERs of 1.35% (95%CI: 0.77%, 1.92%), 0.96% (95%CI: 0.10%, 1.83%), 28.50% (95%CI: 15.49%, 42.98%), 6.92% (95%CI: 5.53%, 8.33%), and 0.31% (95%CI: 0.20%, 0.42%), respectively. The influences of PM2.5 and PM10 on outpatient visits due to asthma in the hospital became more pronounced with advancing age, while the associations with NO₂, SO₂, and CO were weakened as children grew older. Conclusion Ambient air pollutants (PM2.5, PM10, SO2, NO2, CO) can increase childhood asthma visits, and different pollutants have varied effects on the number of asthmatic children's visits at different ages.
8.Inhibition of Angiogenesis by Sanguisorbae Radix and Sophorae Flos in Ulcerative Colitis Mice by Regulating PI3K/Akt Signaling Pathway
Yuzhuo WEI ; Li LIU ; Shu BU ; Yongqi WANG ; Zhiwei MIAO ; Yi XU
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(11):40-50
ObjectiveTo explore the potential mechanism of action of the combination of Sanguisorbae Radix-Sophorae Flos (DH) in the treatment of ulcerative colitis (UC) using network pharmacology methods and molecular docking technology. MethodsNetwork pharmacology analysis was utilized to predict the potential targets of DH for the treatment of UC. The therapeutic effects were experimentally validated by inducing a UC model in mice with 3% dextran sulfate sodium (DSS). The experimental groups were the normal group, the model group, the salazosulfapyridine group (100 mg·kg-1), and the low, medium, and high dose groups of DH (1.2, 2.4, and 4.8 g·kg-1). The efficacy of the treatment was assessed through the general condition of the mice, histopathological examination, and the expression levels of inflammatory markers in the colon. The effect of DH on angiogenesis was explored by messenger RNA (mRNA) detection of colonic angiogenesis-related mediators, vascular endothelial growth factor (VEGF) immunohistochemistry, microvessel density (MVD) detection, and transmission electron microscopy. The phosphatidylinositol-3-kinase (PI3K)-protein kinase B (Akt) signaling pathway proteins were quantitatively analyzed through Western blot to assess whether the suppression of pathological angiogenesis by DH is associated with this pathway. ResultsNetwork pharmacological analysis yielded 112 potential core therapeutic targets for the treatment of UC with DH, of which the core targets were tumor protein 53 (TP53), JUN, interleukin (IL)-6, Akt1, and tumor necrosis factor (TNF). Compared with the normal group, mice in the model group showed significant weight loss, colon shortening, and high DAI score, increased expression of inflammatory factors IL-6, IL-1β, and TNF-α, as well as increased mRNA expression levels of angiogenesis-related mediators VEGF, vascular cell adhesion molecule 1 (VCAM1), angiotensin 1 (Ang1), matrix metalloproteinase (MMP)-1, MMP-2, and MMP-9. The positive expression of CD31 and VEGF in colonic tissue increased, and the protein expression of the PI3K/Akt pathway was increased (P<0.05). The endothelial cells of the colonic mucosa and the colonic vasculature were severely damaged. Compared with the model group, mice in the DH groups had significantly reduced weight loss and colon shortening, lower DAI scores, and a significant decrease in mRNA expression of inflammatory factors and angiogenesis-related mediators. In addition, there was decreased positive expression of CD31 and VEGF in colonic tissue and decreased protein expression of the PI3K/Akt pathway (P<0.05). ConclusionNetwork pharmacology, molecular docking, and experimental validation are applied to explore the mechanism of action of DH in the treatment of UC, and it is found that DH is able to improve the symptoms of colitis and inhibit the pathological angiogenesis in UC mice. Its action might be related to affecting the PI3K/Akt pathway.
9.Inhibition of Angiogenesis by Sanguisorbae Radix and Sophorae Flos in Ulcerative Colitis Mice by Regulating PI3K/Akt Signaling Pathway
Yuzhuo WEI ; Li LIU ; Shu BU ; Yongqi WANG ; Zhiwei MIAO ; Yi XU
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(11):40-50
ObjectiveTo explore the potential mechanism of action of the combination of Sanguisorbae Radix-Sophorae Flos (DH) in the treatment of ulcerative colitis (UC) using network pharmacology methods and molecular docking technology. MethodsNetwork pharmacology analysis was utilized to predict the potential targets of DH for the treatment of UC. The therapeutic effects were experimentally validated by inducing a UC model in mice with 3% dextran sulfate sodium (DSS). The experimental groups were the normal group, the model group, the salazosulfapyridine group (100 mg·kg-1), and the low, medium, and high dose groups of DH (1.2, 2.4, and 4.8 g·kg-1). The efficacy of the treatment was assessed through the general condition of the mice, histopathological examination, and the expression levels of inflammatory markers in the colon. The effect of DH on angiogenesis was explored by messenger RNA (mRNA) detection of colonic angiogenesis-related mediators, vascular endothelial growth factor (VEGF) immunohistochemistry, microvessel density (MVD) detection, and transmission electron microscopy. The phosphatidylinositol-3-kinase (PI3K)-protein kinase B (Akt) signaling pathway proteins were quantitatively analyzed through Western blot to assess whether the suppression of pathological angiogenesis by DH is associated with this pathway. ResultsNetwork pharmacological analysis yielded 112 potential core therapeutic targets for the treatment of UC with DH, of which the core targets were tumor protein 53 (TP53), JUN, interleukin (IL)-6, Akt1, and tumor necrosis factor (TNF). Compared with the normal group, mice in the model group showed significant weight loss, colon shortening, and high DAI score, increased expression of inflammatory factors IL-6, IL-1β, and TNF-α, as well as increased mRNA expression levels of angiogenesis-related mediators VEGF, vascular cell adhesion molecule 1 (VCAM1), angiotensin 1 (Ang1), matrix metalloproteinase (MMP)-1, MMP-2, and MMP-9. The positive expression of CD31 and VEGF in colonic tissue increased, and the protein expression of the PI3K/Akt pathway was increased (P<0.05). The endothelial cells of the colonic mucosa and the colonic vasculature were severely damaged. Compared with the model group, mice in the DH groups had significantly reduced weight loss and colon shortening, lower DAI scores, and a significant decrease in mRNA expression of inflammatory factors and angiogenesis-related mediators. In addition, there was decreased positive expression of CD31 and VEGF in colonic tissue and decreased protein expression of the PI3K/Akt pathway (P<0.05). ConclusionNetwork pharmacology, molecular docking, and experimental validation are applied to explore the mechanism of action of DH in the treatment of UC, and it is found that DH is able to improve the symptoms of colitis and inhibit the pathological angiogenesis in UC mice. Its action might be related to affecting the PI3K/Akt pathway.
10.Novel outpatient infusion model of blinatumomab: case studies of two patients
Guijun LI ; Xuemei JIANG ; Xin WANG ; Qiuxia XU ; Jianhui LI ; Susi DAI ; Ying HE ; Hai YI ; Dan CHEN
Chinese Journal of Blood Transfusion 2025;38(4):557-561
[Objective] To evaluate the feasibility of a novel outpatient infusion model for blinatumomab in two acute lymphoblastic leukemia (ALL) patients, aiming to address challenges of poor treatment tolerance, high healthcare costs, and compromised quality of life, thereby providing clinical insights for broader adoption of this approach. [Methods] Two post-allogeneic hematopoietic stem cell transplantation (allo-HSCT) patients undergoing blinatumomab maintenance therapy were selected to evaluate the efficacy of the outpatient infusion model. Patient selection criteria, nursing protocols, standardized workflows, and advancements in infusion practices were systematically analyzed combined with a review of global developments in this field. [Results] Both patients completed outpatient blinatumomab infusion without severe adverse events, demonstrating preliminary feasibility and safety of this model. The novel approach enhanced treatment convenience, reduced hospitalization costs, and improved quality of life. [Conclusion] Despite the limited sample size, this pilot study highlights the potential of outpatient blinatumomab administration as a viable alternative to traditional inpatient regimens.

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