1.Clinical Advantages of Traditional Chinese Medicine in Treatment of Childhood Simple Obesity: Insights from Expert Consensus
Qi ZHANG ; Yingke LIU ; Xiaoxiao ZHANG ; Guichen NI ; Heyin XIAO ; Junhong WANG ; Liqun WU ; Zhanfeng YAN ; Kundi WANG ; Jiajia CHEN ; Hong ZHENG ; Xinying GAO ; Liya WEI ; Qiang HE ; Qian ZHAO ; Huimin SU ; Zhaolan LIU ; Dafeng LONG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(6):238-245
Childhood simple obesity has become a significant public health issue in China. Modern medicine primarily relies on lifestyle interventions and often suffers from poor long-term compliance, while pharmacological options are limited and associated with potential adverse effects. Traditional Chinese Medicine (TCM) has a long history in the prevention and management of this condition, demonstrating eight distinct advantages, including systematic theoretical foundation, diversified therapeutic approaches, definite therapeutic efficacy, high safety profile, good patient compliance, comprehensive intervention strategies, emphasis on prevention, and stepwise treatment protocols. Additionally, TCM is characterized by six distinctive features: the use of natural medicinal substances, non-invasive external therapies, integration of medicinal dietetics, simple exercise regimens, precise syndrome differentiation, and diverse dosage forms. By combining internal and external treatments, TCM facilitates individualized regimen adjustment and holistic regulation, demonstrating remarkable effects in improving obesity-related metabolic indicators, regulating constitutional imbalance, and promoting healthy behaviors. However, challenges remain, such as inconsistent operational standards, insufficient high-quality clinical evidence, and a gap between basic research and clinical application. Future efforts should focus on accelerating the standardization of TCM diagnosis and treatment, conducting multicenter randomized controlled trials, and fostering interdisciplinary integration, so as to enhance the scientific validity and international recognition of TCM in the prevention and treatment of childhood obesity.
2.Effect and Mechanism of Xiao Qinglongtang Against Right Ventricular Dysfunction in Rats with Pulmonary Arterial Hypertension Induced by Monocrotaline
Lei QI ; Huifei ZHANG ; Ling GONG ; Jifu HE ; Wenjing CHEN ; Weipin NIU ; Xiao LI ; Yuehua JIANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(4):11-19
ObjectiveThis study aimed to establish a monocrotaline (MCT)-induced pulmonary arterial hypertension (PAH) rat model to systematically evaluate the protective effect of Xiao Qinglongtang (XQLT) on right cardiac function in model rats and further elucidate the underlying regulatory mechanism. MethodsSixty male SD rats were randomly assigned to the normal group, model group, XQLT low-, medium-, and high-dose groups (XQLT-L/M/H), and the beraprost sodium tablet group (BST). Except for the normal group, rats in all other groups were given a single subcutaneous injection of MCT (60 mg·kg-1) to induce PAH. Three weeks after injection, rats in the XQLT-L/M/H groups were administered XQLT intragastrically at 3.07, 6.14, 12.28 g·kg-1·d-1, respectively. Rats in the BST group received beraprost sodium at 12.6 μg·kg-1·d-1, and rats in the model group received an equal volume of saline. All treatments lasted for 3 weeks. Right ventricular systolic pressure (RVSP) was measured by right ventricular catheterization. Cardiac function was assessed by echocardiography. The right ventricle was weighed to calculate the right ventricular hypertrophy index (RVHI). Hematoxylin-eosin (HE) staining, Masson staining, and transmission electron microscopy were used to observe myocardial morphology. Serum metabolomic changes were analyzed using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Data-independent acquisition (DIA) proteomics was used to detect differentially expressed (DE) proteins in the right ventricle, and Western blot was used to measure the expression of uncoupling protein 3 (UCP3), phosphatidylinositol 3-kinase catalytic subunit p110α (PIK3CA), L1 cell adhesion molecule (L1CAM), and quinone oxidoreductase (CRYZ). UPLC-MS/MS was used to analyze the chemical components of XQLT. ResultsCompared with the normal group, the model group showed significantly increased RVSP and RVHI (P<0.05), along with pathological changes in myocardial morphology. Compared with the model group, all XQLT-treated groups exhibited reductions in RVSP and RVHI as well as significant improvements in cardiac function and myocardial morphology. Among the XQLT groups, XQLT-M showed the most pronounced effects (P<0.05), comparable to the BST group. Serum metabolomics revealed 105 differential metabolites in the XQLT groups versus the model group [variable importance in projection (VIP) >1, P<0.05], including 58 upregulated and 47 downregulated metabolites. KEGG enrichment analysis indicated that XQLT intervention downregulated phenylalanine metabolism (P<0.01) and upregulated unsaturated fatty acid biosynthesis (P<0.05). Proteomics analysis showed that 982 DE proteins were identified in the MCT groups versus the normal group, including 455 upregulated and 527 downregulated proteins (|fold change (FC)| >1.3, P<0.05). Compared with the model group, 237 DE proteins were identified in the XQLT groups, including 124 upregulated and 113 downregulated proteins (|FC| >1.3, P<0.05), with 57 overlapping DE proteins. KEGG enrichment suggested that XQLT mainly modulated pathways related to mineral absorption, ribosomal biogenesis, peroxisomes, glycolysis/gluconeogenesis, spliceosomes, and thyroid hormone signaling. Western blot analysis showed that, compared with the model group, XQLT increased the expression of UCP3, PIK3CA, and L1CAM, while decreasing the expression of CRYZ (P<0.05). ConclusionXQLT exerts a protective effect on right heart function in MCT-induced PAH rats, and its mechanism is associated with maintaining myocardial homeostasis and alleviating right ventricular remodeling.
3.Mechanism of action of Qingre huatan huoxue decoction against atherosclerosis based on macrophage polarization
Huaping ZHONG ; Qicheng ZHU ; Zhengwei ZOU ; Zhengyi HE ; Heping XIE ; Xu CHEN ; Zhisheng DUAN ; Tian XIAO
China Pharmacy 2026;37(4):438-443
OBJECTIVE To explore the mechanism of action of Qingre huatan huoxue decoction against atherosclerosis (AS)based on macrophage polarization. METHODS Using atorvastatin served as the positive control, the drug-containing serum of the Qingre huatan huoxue decoction was prepared to treat RAW264.7 macrophages. Macrophage viability, apoptosis rate, and the fluorescence intensities of CD86 and CD206 were measured, along with the levels of tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β). Apolipoprotei n E-deficient (ApoE -/- ) mice (AS model mice) fed with a high-fat diet were randomly assigned to model group, atorvastatin group (2.6 mg/kg), and low-, medium- and high-dose groups of Qingre huatan huoxue decoction (90, 180, 360 mg/kg), respectively. C57BL/6J mice fed with a standard diet served as the normal control group, with 10 mice per group. The treatment group mice were administered the corresponding drugs intragastrically, once daily, for 8 consecutive weeks. Serum levels of TNF-α and IL-1β were measured in all groups. Lipid deposition in the aorta (assessed by the percentage of plaque in the entire aorta and aortic root) and morphological changes in the aortic root were observed. Expression levels of CD86 and CD206 in aortic tissue, as well as the protein expression levels of inducible nitric oxide synthase (iNOS), arginase-1 (Arg-1), AMP-activated protein kinase (AMPK), phosphorylated AMPK (p-AMPK), and peroxisome proliferator-activated receptor γ (PPAR-γ) in aortic tissues were all detected. RESULTS Cell experiment results showed that, at concentrations of 5-100 μg/mL, the drug-containing serum of the Qingre huatan huoxue decoction significantly increased RAW264.7 cell viability ( P <0.05). The drug-containing serum of the Qingre huatan huoxue decoction at concentrations of 10, 50, and 100 μg/mL, along with atorvastatin, significantly reduced apoptosis rates, CD86 fluorescence intensity, and TNF-α and IL-1β levels in RAW264.7 cells, while markedly enhancing CD206 fluorescence intensity ( P <0.05). Animal experiment results showed that, compared with the model group, all dosage groups of Qingre huatan huoxue decoction and the atorvastatin group showed significantly reduced/down-regulated levels of TNF-α and IL-1β in serum, along with decreased aortic total and root plaque percentages, CD86 expression, and iNOS protein expression. CD206 expression and Arg-1, p-AMPK/AMPK, PPAR-γ protein expression were significantly up-regulated ( P <0.05). Pathological morphology of the aorta showed varying degrees of improvement. CONCLUSIONS The formula of Qingre huatan huoxue decoction exerts its anti-AS effects by regulating macrophage polarization, increasing the proportion of M2 macrophages, thereby effectively inhibiting AS plaque formation and reducing inflammatory responses.
4.Clinical significance of establishing a red blood cell alloantibody detection database
Xiao XIAO ; Long CHEN ; Zhenyu ZHAO ; Zhanghan HE ; Mengjun ZHOU ; Jie TANG
Chinese Journal of Blood Transfusion 2025;38(1):54-60
[Objective] To explore the clinical significance and application value of establishing a database for red blood cell alloantibody detection. [Methods] Patients who were scheduled for blood transfusion in our hospital from January 1, 2020 to May 1, 2024 were selected as the research subjects. A red blood cell alloantibody detection database was established using Microsoft Office Excel software to register the detection data of patients' alloantibodies and antibodies of undetermined specificity (AUS). A retrospective analysis was conducted on the clinical characteristics, antibody distribution, antibody decay and repeat positivity of the patients in the database. The LISS-IAT method was routinely used for antibody screening and identification. [Results] Among the alloantibodies, the Rh blood group system had the highest detection rate, followed by antibodies of the MNS blood group system and the Lewis blood group system. The predominant antibody in the Rh blood group system was anti-E. In the univariate analysis, the positivity of antibody was significantly associated with the patient's gender, age, blood transfusion history, pregnancy history and type of disease (all P<0.001). In the database, 48 patients experienced antibody decay, accounting for 15.24%(48/315), with an average time span of antibody decay ranging from 22 to 1 324 days. Six cases showed repeat positivity after decay, which were related to blood transfusions. The shortest interval between blood transfusions that led to antibody repeat positivity was 3 days, and the longest interval was 427 days. Among 58 cases with AUS, 3 converted into alloantibodies, among which 2 were anti-E and 1 was anti-Lea. [Conclusion] Establishing a red blood cell alloantibody detection database is an effective way to guide ambiguous cross-matching in clinical practice and is also an effective measure for the management of transfusion risks.
5.Differential Analysis on Chemical Composition and Pharmacodynamic Effect Between Combined Decoction and Single Decoction of Famous Classical Formula Huaganjian
Yang WANG ; Gaoju ZHANG ; Ling LI ; Liping CHEN ; Li ZHANG ; Xiao LIU ; Yuyu ZHANG ; Yuan CUI ; Minglong LI ; Chaomei FU ; Xin YAN ; Yuxin HE ; Qin DONG
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(16):199-207
ObjectiveThrough qualitatively and quantitatively analysis of the differences in chemical composition between the combined decoction and single decoction of Huaganjian and comparison of their core efficacy, to explore the rationality of the flexible clinical application of Huaganjian compound preparations and single-flavored dispensing granules. MethodsUltra performance liquid chromatography-quadrupole-electrostatic field orbitrap high resolution mass spectrometry(UPLC-Q-Exactive Orbitrap MS) was used to qualitatively analyze the combined decoction and single decoction samples of Huaganjian, and meanwhile, the contents of four index components(geniposide, paeoniflorin, hesperidin and paeonol) were quantitatively analyzed by high performance liquid chromatography(HPLC). Nonalcoholic fatty liver disease(NAFLD) rat model induced by high-fat diet was applied to compare the efficacy of combined decoction and single decoction of Huaganjian. A total of 30 male SD rats were randomly divided into the control group, model group, lovastatin group(1.8 mg·kg-1), combined decoction group(1.26 g·kg-1) and single decoction group(1.18 g·kg-1). After successful modeling, lovastatin group, combined decoction group and single decoction group were given corresponding doses of drugs by intragastric administration every day, and the control group and model group were given equal amounts of normal saline by intragastric administration, after 4 weeks of administration, the serum and liver tissues were collected, and the contents of alanine aminotransferase(ALT), aspartate aminotransferase(AST), total cholesterol(TC), triglyceride(TG), low-density lipoprotein cholesterol(LDL-C) and high-density lipoprotein cholesterol(HDL-C) in serum of rats were detected, and the liver pathological examination was carried out by hematoxylin-eosin(HE) staining and oil red O staining, so as to compare differences of their efficacy. ResultsSeventy chemical components were initially identified and attributed from the lyophilized powder of the combined decoction and single decoction samples of Huaganjian, and there was no obvious difference in composition between the two. Further quantitative analysis showed that the contents of geniposide, paeoniflorin, hesperidin and paeonol in the combined decoction samples were significantly increased when compared with those of the single decoction samples(P<0.01). The pharmacodynamic results showed that compared with the model group, both the combined and single decoction groups of Huaganjian could improve the liver index of NAFLD rats, reduce the serum levels of AST, ALT, TC, TG and LDL-C, increase the serum level of HDL-C, and ameliorate the pathological changes of liver cell steatosis and fat accumulation. However, there was no significant difference in pharmacodynamic effects between the combined decoction group and the single decoction group. ConclusionThere is no significant difference between the combined decoction and single decoction of Huaganjian in terms of chemical composition, but the contents of the four index components show significantly difference. Both of them can significantly improve the fat accumulation and liver function in NAFLD rats. This study provides a reference basis for the rational clinical application and evaluation of famous classical formula compound preparations and single-flavored dispensing granules.
6.Quality changes of volatile oil and chlorogenic acid compounds during extraction process of Artemisiae Argyi Folium: process analysis based on chemical composition, physicochemical properties, and biological activity.
Dan-Dan YANG ; Hao-Zhou HUANG ; Xin-Ming CHEN ; Lin HUANG ; Ya-Nan HE ; Zhen-Feng WU ; Xiao-Ming BAO ; Ding-Kun ZHANG ; Ming YANG
China Journal of Chinese Materia Medica 2025;50(11):3001-3012
To explore the variation laws of volatile oil during the extraction process of Artemisiae Argyi Folium and its impact on the quality of the medicinal solution, as well as to achieve precise control of the extraction process, this study employed headspace solid phase microextraction gas chromatography-mass spectrometry(HS-SPME-GC-MS) in combination with multiple light scattering techniques to conduct a comprehensive analysis, identification, and characterization of the changes in volatile components and the physical properties of the medicinal solution during the extraction process. A total of 82 volatile compounds were identified using the HS-SPME-GC-MS technique, including 21 alcohols, 15 alkenes, 14 ketones, 9 acids, 6 aldehydes, 5 phenols, 3 esters, and 9 other types of compounds. At different extraction time points(15, 30, 45, and 60 min), 71, 72, 64, and 44 compounds were identified in the medicinal solution, respectively. It was observed that the content of volatile components gradually decreased with the extension of extraction time. Through multivariate statistical analysis, four compounds with significant differences during different extraction time intervals were identified, namely 1,8-cineole, terpinen-4-ol, 3-octanone, and camphor. RESULTS:: from multiple light scattering techniques indicated that at 15 minutes of extraction, the transmittance of the medicinal solution was the lowest(25%), the particle size was the largest(0.325-0.350 nm), and the stability index(turbiscan stability index, TSI) was the highest(0-2.5). With the extension of extraction time, the light transmittance of the medicinal solution improved, stability was enhanced, and the particle size decreased. These laws of physicochemical property changes provide important basis for the control of Artemisiae Argyi Folium extraction process. In addition, the changes in the bioactivity of Artemisiae Argyi Folium extracts during the extraction process were investigated through mouse writhing tests and antimicrobial assays. The results indicated that the analgesic and antimicrobial effects of the medicinal solution were strongest at the 15-minute extracting point. In summary, the findings of this study demonstrate that the content of volatile oil in Artemisiae Argyi Folium extracts gradually decreases with the extension of extraction time, and the variation in volatile oil content directly influences the physicochemical properties and pharmacological efficacy of the medicinal solution. This discovery provides important scientific reference for the optimization of Artemisiae Argyi Folium extraction processes and the development and application of process analytical technologies.
Oils, Volatile/pharmacology*
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Artemisia/chemistry*
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Gas Chromatography-Mass Spectrometry
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Drugs, Chinese Herbal/pharmacology*
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Chlorogenic Acid/pharmacology*
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Solid Phase Microextraction
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Quality Control
7.Comparison on chemical components of Angelicae Sinensis Radix before and after wine processing by HS-GC-IMS, HS-SPME-GC-MS, and UPLC-Q-Orbitrap-MS combined with chemometrics.
Xue-Hao SUN ; Jia-Xuan CHEN ; Jia-Xin YIN ; Xiao HAN ; Zhi-Ying DOU ; Zheng LI ; Li-Ping KANG ; He-Shui YU
China Journal of Chinese Materia Medica 2025;50(14):3909-3917
The study investigated the intrinsic changes in material basis of Angelicae Sinensis Radix during wine processing by headspace-gas chromatography-ion mobility spectrometry(HS-GC-IMS), headspace-solid phase microextraction-gas chromatography-mass spectrometry(HS-SPME-GC-MS), and ultra-high performance liquid chromatography-quadrupole-orbitrap mass spectrometry(UPLC-Q-Orbitrap-MS) combined with chemometrics. HS-GC-IMS fingerprints of Angelicae Sinensis Radix before and after wine processing were established to analyze the variation trends of volatile components and characterize volatile small-molecule substances before and after processing. Principal component analysis(PCA) and orthogonal partial least squares-discriminant analysis(OPLS-DA) were employed for differentiation and difference analysis. A total of 89 volatile components in Angelicae Sinensis Radix were identified by HS-GC-IMS, including 14 unsaturated hydrocarbons, 16 aldehydes, 13 ketones, 9 alcohols, 16 esters, 6 organic acids, and 15 other compounds. HS-SPME-GC-MS detected 118 volatile components, comprising 42 unsaturated hydrocarbons, 11 aromatic compounds, 30 alcohols, 8 alkanes, 6 organic acids, 4 ketones, 7 aldehydes, 5 esters, and 5 other volatile compounds. UPLC-Q-Orbitrap-MS identified 76 non-volatile compounds. PCA revealed distinct clusters of raw and wine-processed Angelicae Sinensis Radix samples across the three detection methods. Both PCA and OPLS-DA effectively discriminated between the two groups, and 145 compounds(VIP>1) were identified as critical markers for evaluating processing quality, including 4-methyl-3-penten-2-one, ethyl 2-methylpentanoate, and 2,4-dimethyl-1,3-dioxolane detected by HS-GC-IMS, angelic acid, β-pinene, and germacrene B detected by HS-SPME-GC-MS, and L-tryptophan, licoricone, and angenomalin detected by UPLC-Q-Orbitrap-MS. In conclusion, the integration of the three detection methods with chemometrics elucidates the differences in the chemical material basis between raw and wine-processed Angelicae Sinensis Radix, providing a scientific foundation for understanding the processing mechanisms and clinical applications of wine-processed Angelicae Sinensis Radix.
Wine/analysis*
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Gas Chromatography-Mass Spectrometry/methods*
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Chromatography, High Pressure Liquid/methods*
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Angelica sinensis/chemistry*
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Solid Phase Microextraction/methods*
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Drugs, Chinese Herbal/isolation & purification*
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Chemometrics
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Volatile Organic Compounds/chemistry*
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Principal Component Analysis
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Ion Mobility Spectrometry/methods*
8.Effect of Modified Yiyi Fuzi Baijiang Powder on intestinal mucosal permeability and expression of AQP3, AQP4 in ulcerative colitis rats.
Wen-Xiao LI ; Jiang CHEN ; Zhi-Cheng HE ; Lu-Rong ZHANG ; Guo-Qiang LIANG ; Xing-Xing JIANG ; Yong-Na WEI ; Qin ZHOU
China Journal of Chinese Materia Medica 2025;50(14):3962-3968
This study investigated the therapeutic effects and mechanisms of Modified Yiyi Fuzi Baijiang Powder on ulcerative colitis(UC) in rats from the perspective of dampness. SD rats were randomly allocated into six groups(n=10): control, model, mesalazine, and Modified Yiyi Fuzi Baijiang Powder at low(3.96 g·kg~(-1)·d~(-1)), medium(7.92 g·kg~(-1)·d~(-1)), and high(15.84 g·kg~(-1)·d~(-1)) doses. UC was induced in all groups except the control by administration with 3% dextran sulfate sodium(DSS) solution for 7 days. The disease activity index(DAI) was recorded, and the colon tissue was collected for analysis. Histopathological changes were assessed by hematoxylin-eosin staining. Serum levels of D-lactic acid(D-LA) and diamine oxidase(DAO) were measured by ELISA. Immunohistochemistry and PCR were employed to evaluate the expression of aquaporins(AQP3, AQP4) and tight junction proteins [zonula occludens-1(ZO-1) and occludin] at both protein and mRNA levels. Compared with the control group, the model group showed an increased DAI scores(P<0.05), intestinal mucosal damage, elevated serum levels of DAO and D-LA(P<0.05), and decreased expression of AQP3, AQP4, ZO-1, and occludin(P<0.05). Treatment with Modified Yiyi Fuzi Baijiang Powder reduced the DAI scores(P<0.05), lowered the serum levels of D-LA and DAO(P<0.05), and upregulated the expression of AQP3, AQP4, ZO-1, and occludin at both protein and mRNA levels compared with the model group. These findings suggest that Modified Yiyi Fuzi Baijiang Powder exerts therapeutic effects on UC by reducing the intestinal mucosal permeability, promoting colonic mucosal repair, and regulating abnormal intestinal water metabolism, which may involve the upregulation of AQP3 and AQP4 expression.
Animals
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Colitis, Ulcerative/genetics*
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Drugs, Chinese Herbal/administration & dosage*
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Rats, Sprague-Dawley
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Rats
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Intestinal Mucosa/metabolism*
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Male
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Aquaporin 3/metabolism*
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Aquaporin 4/metabolism*
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Permeability/drug effects*
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Humans
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Powders
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Intestinal Barrier Function
9.Single-cell transcriptomics identifies PDGFRA+ progenitors orchestrating angiogenesis and periodontal tissue regeneration.
Jianing LIU ; Junxi HE ; Ziqi ZHANG ; Lu LIU ; Yuan CAO ; Xiaohui ZHANG ; Xinyue CAI ; Xinyan LUO ; Xiao LEI ; Nan ZHANG ; Hao WANG ; Ji CHEN ; Peisheng LIU ; Jiongyi TIAN ; Jiexi LIU ; Yuru GAO ; Haokun XU ; Chao MA ; Shengfeng BAI ; Yubohan ZHANG ; Yan JIN ; Chenxi ZHENG ; Bingdong SUI ; Fang JIN
International Journal of Oral Science 2025;17(1):56-56
Periodontal bone defects, primarily caused by periodontitis, are highly prevalent in clinical settings and manifest as bone fenestration, dehiscence, or attachment loss, presenting a significant challenge to oral health. In regenerative medicine, harnessing developmental principles for tissue repair offers promising therapeutic potential. Of particular interest is the condensation of progenitor cells, an essential event in organogenesis that has inspired clinically effective cell aggregation approaches in dental regeneration. However, the precise cellular coordination mechanisms during condensation and regeneration remain elusive. Here, taking the tooth as a model organ, we employed single-cell RNA sequencing to dissect the cellular composition and heterogeneity of human dental follicle and dental papilla, revealing a distinct Platelet-derived growth factor receptor alpha (PDGFRA) mesenchymal stem/stromal cell (MSC) population with remarkable odontogenic potential. Interestingly, a reciprocal paracrine interaction between PDGFRA+ dental follicle stem cells (DFSCs) and CD31+ Endomucin+ endothelial cells (ECs) was mediated by Vascular endothelial growth factor A (VEGFA) and Platelet-derived growth factor subunit BB (PDGFBB). This crosstalk not only maintains the functionality of PDGFRA+ DFSCs but also drives specialized angiogenesis. In vivo periodontal bone regeneration experiments further reveal that communication between PDGFRA+ DFSC aggregates and recipient ECs is essential for effective angiogenic-osteogenic coupling and rapid tissue repair. Collectively, our results unravel the importance of MSC-EC crosstalk mediated by the VEGFA and PDGFBB-PDGFRA reciprocal signaling in orchestrating angiogenesis and osteogenesis. These findings not only establish a framework for deciphering and promoting periodontal bone regeneration in potential clinical applications but also offer insights for future therapeutic strategies in dental or broader regenerative medicine.
Receptor, Platelet-Derived Growth Factor alpha/metabolism*
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Humans
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Neovascularization, Physiologic/physiology*
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Dental Sac/cytology*
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Single-Cell Analysis
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Transcriptome
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Mesenchymal Stem Cells/metabolism*
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Bone Regeneration
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Animals
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Dental Papilla/cytology*
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Periodontium/physiology*
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Stem Cells/metabolism*
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Regeneration
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Angiogenesis
10.Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq.
Heng WANG ; Ang WU ; Meng-Chen YANG ; Di ZHOU ; Xiyang CHEN ; Zhifei SHI ; Yiqun ZHANG ; Yu-Xin LIU ; Kai CHEN ; Xiaosong WANG ; Xiao-Fang CHENG ; Baodan HE ; Yutao FU ; Lan KANG ; Yujun HOU ; Kun CHEN ; Shan BIAN ; Juan TANG ; Jianhuang XUE ; Chenfei WANG ; Xiaoyu LIU ; Jiejun SHI ; Shaorong GAO ; Jia-Min ZHANG
Protein & Cell 2025;16(11):932-952
Gene regulation relies on the precise binding of transcription factors (TFs) at regulatory elements, but simultaneously detecting hundreds of TFs on chromatin is challenging. We developed cFOOT-seq, a cytosine deaminase-based TF footprinting assay, for high-resolution, quantitative genome-wide assessment of TF binding in both open and closed chromatin regions, even with small cell numbers. By utilizing the dsDNA deaminase SsdAtox, cFOOT-seq converts accessible cytosines to uracil while preserving genomic integrity, making it compatible with techniques like ATAC-seq for sensitive and cost-effective detection of TF occupancy at the single-molecule and single-cell level. Our approach enables the delineation of TF footprints, quantification of occupancy, and examination of chromatin influences on TF binding. Notably, cFOOT-seq, combined with FootTrack analysis, enables de novo prediction of TF binding sites and tracking of TF occupancy dynamics. We demonstrate its application in capturing cell type-specific TFs, analyzing TF dynamics during reprogramming, and revealing TF dependencies on chromatin remodelers. Overall, cFOOT-seq represents a robust approach for investigating the genome-wide dynamics of TF occupancy and elucidating the cis-regulatory architecture underlying gene regulation.
Transcription Factors/genetics*
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Humans
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Chromatin/genetics*
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Animals
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Binding Sites
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Mice
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DNA Footprinting/methods*

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