1.Mechanisms of Shenqi Wenfei Prescription in Intervening in Chronic Obstructive Pulmonary Disease in Rats Based on ROS/TXNIP/NLRP3 Signaling Pathway
Di WU ; Mengyao SHI ; Lu ZHANG ; Tong LIU ; Jiabing TONG ; Cheng YANG ; Zegeng LI
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(3):78-87
ObjectiveTo investigate the effects and underlying mechanisms of Shenqi Wenfei prescription (SQWF) on chronic obstructive pulmonary disease (COPD). MethodsA rat model of COPD with lung Qi deficiency was established using lipopolysaccharide (LPS) combined with cigarette smoke. Forty-eight SD rats were randomly divided into a blank group, a model group, low-, medium-, and high-dose SQWF groups (2.835, 5.67, 11.34 g·kg-1), and a Yupingfeng group (1.35 g·kg-1). Drug administration began on day 29 after modeling and continued for 2 weeks. The general condition of the rats was observed, and the lung function in each group was assessed. Hematoxylin-eosin (HE) staining was used to observe pathological changes in lung tissue. The proportion of inflammatory cells in bronchoalveolar lavage fluid (BALF) was measured. Apoptosis in lung tissue was examined by terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) staining. The release level of lactate dehydrogenase (LDH) in BALF was detected by a microplate assay. Reactive oxygen species (ROS) levels in lung tissue were detected using fluorescent probes. The levels of malondialdehyde (MDA), total superoxide dismutase (SOD), and reduced glutathione (GSH) in BALF were measured by biochemical methods. Ultrastructural changes in lung cells were observed via transmission electron microscopy. Double immunofluorescence staining was performed to detect the expression of thioredoxin-interacting protein (TXNIP) and nucleotide-binding oligomerization domain-like receptor protein 3 (NLRP3) in lung tissue. Western blot analysis was used to detect the protein expression of TXNIP, NLRP3, apoptosis-associated speck-like protein containing a CARD (ASC), cysteinyl aspartate-specific protease-1 (Caspase-1), Caspase-1 p20, gasdermin D (GSDMD), GSDMD N-terminal active fragment (GSDMD-N), interleukin-1β (IL-1β), and IL-18 in lung tissue. Serum IL-1β and IL-18 levels were measured by ELISA. ResultsCompared with the blank group, the model group showed lassitude, fatigue, tachypnea, and audible phlegm sounds, and lung function significantly declined (P0.01). Pulmonary emphysema and inflammatory cell infiltration were obvious. The level of inflammatory cells in BALF increased significantly (P0.05). The number of TUNEL-positive cells increased (P0.01). Levels of LDH, ROS, and MDA in BALF increased significantly (P0.01), while GSH and SOD activities decreased significantly (P0.01). Lung tissue cells showed irregular morphology, swollen mitochondria, disrupted cell membranes, and abundant vesicles, i.e., pyroptotic bodies. Protein levels of TXNIP, NLRP3, ASC, Caspase-1, Caspase-1 p20, GSDMD, GSDMD-N, IL-1β, and IL-18 in lung tissue were significantly elevated (P0.01), and serum IL-1β and IL-18 levels also increased significantly (P0.01). Compared with the model group, each medication group showed alleviation of qi deficiency symptoms and improved lung function (P0.01). Pulmonary emphysema and inflammatory cell infiltration were reduced. Inflammatory cell levels decreased (P0.05). The number of TUNEL-positive cells decreased significantly (P0.01). Levels of LDH, ROS, and MDA decreased significantly (P0.05), while GSH and SOD activities significantly increased (P0.01). Morphological and structural damage in lung tissue was improved to varying degrees. Protein levels of TXNIP, NLRP3, ASC, Caspase-1, Caspase-1 p20, GSDMD, GSDMD-N, IL-1β, and IL-18 in lung tissue significantly decreased (P0.01), and serum IL-1β and IL-18 levels also decreased significantly (P0.05). ConclusionSQWF can improve lung function and alleviate inflammatory responses in COPD rats. Its mechanism may be related to regulating the ROS/TXNIP/NLRP3 pathway and inhibiting pyroptosis.
2.Mechanisms of Shenqi Wenfei Prescription in Intervening in Chronic Obstructive Pulmonary Disease in Rats Based on ROS/TXNIP/NLRP3 Signaling Pathway
Di WU ; Mengyao SHI ; Lu ZHANG ; Tong LIU ; Jiabing TONG ; Cheng YANG ; Zegeng LI
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(3):78-87
ObjectiveTo investigate the effects and underlying mechanisms of Shenqi Wenfei prescription (SQWF) on chronic obstructive pulmonary disease (COPD). MethodsA rat model of COPD with lung Qi deficiency was established using lipopolysaccharide (LPS) combined with cigarette smoke. Forty-eight SD rats were randomly divided into a blank group, a model group, low-, medium-, and high-dose SQWF groups (2.835, 5.67, 11.34 g·kg-1), and a Yupingfeng group (1.35 g·kg-1). Drug administration began on day 29 after modeling and continued for 2 weeks. The general condition of the rats was observed, and the lung function in each group was assessed. Hematoxylin-eosin (HE) staining was used to observe pathological changes in lung tissue. The proportion of inflammatory cells in bronchoalveolar lavage fluid (BALF) was measured. Apoptosis in lung tissue was examined by terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) staining. The release level of lactate dehydrogenase (LDH) in BALF was detected by a microplate assay. Reactive oxygen species (ROS) levels in lung tissue were detected using fluorescent probes. The levels of malondialdehyde (MDA), total superoxide dismutase (SOD), and reduced glutathione (GSH) in BALF were measured by biochemical methods. Ultrastructural changes in lung cells were observed via transmission electron microscopy. Double immunofluorescence staining was performed to detect the expression of thioredoxin-interacting protein (TXNIP) and nucleotide-binding oligomerization domain-like receptor protein 3 (NLRP3) in lung tissue. Western blot analysis was used to detect the protein expression of TXNIP, NLRP3, apoptosis-associated speck-like protein containing a CARD (ASC), cysteinyl aspartate-specific protease-1 (Caspase-1), Caspase-1 p20, gasdermin D (GSDMD), GSDMD N-terminal active fragment (GSDMD-N), interleukin-1β (IL-1β), and IL-18 in lung tissue. Serum IL-1β and IL-18 levels were measured by ELISA. ResultsCompared with the blank group, the model group showed lassitude, fatigue, tachypnea, and audible phlegm sounds, and lung function significantly declined (P0.01). Pulmonary emphysema and inflammatory cell infiltration were obvious. The level of inflammatory cells in BALF increased significantly (P0.05). The number of TUNEL-positive cells increased (P0.01). Levels of LDH, ROS, and MDA in BALF increased significantly (P0.01), while GSH and SOD activities decreased significantly (P0.01). Lung tissue cells showed irregular morphology, swollen mitochondria, disrupted cell membranes, and abundant vesicles, i.e., pyroptotic bodies. Protein levels of TXNIP, NLRP3, ASC, Caspase-1, Caspase-1 p20, GSDMD, GSDMD-N, IL-1β, and IL-18 in lung tissue were significantly elevated (P0.01), and serum IL-1β and IL-18 levels also increased significantly (P0.01). Compared with the model group, each medication group showed alleviation of qi deficiency symptoms and improved lung function (P0.01). Pulmonary emphysema and inflammatory cell infiltration were reduced. Inflammatory cell levels decreased (P0.05). The number of TUNEL-positive cells decreased significantly (P0.01). Levels of LDH, ROS, and MDA decreased significantly (P0.05), while GSH and SOD activities significantly increased (P0.01). Morphological and structural damage in lung tissue was improved to varying degrees. Protein levels of TXNIP, NLRP3, ASC, Caspase-1, Caspase-1 p20, GSDMD, GSDMD-N, IL-1β, and IL-18 in lung tissue significantly decreased (P0.01), and serum IL-1β and IL-18 levels also decreased significantly (P0.05). ConclusionSQWF can improve lung function and alleviate inflammatory responses in COPD rats. Its mechanism may be related to regulating the ROS/TXNIP/NLRP3 pathway and inhibiting pyroptosis.
3.STAR Guideline Terminology(Ⅱ): Clinical Question Formulation, Evidence Retrieval and Appraisal, and Recommendation Development
Di ZHU ; Haodong LI ; Zijun WANG ; Qianling SHI ; Hui LIU ; Yishan QIN ; Yuanyuan YAO ; Zhewei LI ; Hongfeng HE ; Jinhui TIAN ; Long GE ; Yaolong CHEN ;
Medical Journal of Peking Union Medical College Hospital 2025;16(3):756-764
To introduce and analyze guideline terminology related to clinical question formulation, evidence retrieval and appraisal, and recommendation development. A systematic search was conducted in guideline development manuals and relevant methodological literature, covering publications up to October 25, 2024. Terminology related to the three aforementioned stages of related to guideline development was extracted from the included literature, standardized, and refined through consensus meetings to finalize a comprehensive terminology list and definitions. A total of 30 guideline development manuals and 15 methodological articles were included, and 23 core terms were identified. It is recommended to develop a standardized and scientifically sound guideline terminology system with unified naming, clear definitions, and alignment with the linguistic environment and usage habits in China. At the same time, it is essential to strengthen terminology training for both guideline developers and users based on this system, in order to deepen their correct understanding and proper application of guideline terminology.
4.Secular trend and projection of overweight and obesity among Chinese children and adolescents aged 7-18 years from 1985 to 2019: Rural areas are becoming the focus of investment.
Jiajia DANG ; Yunfei LIU ; Shan CAI ; Panliang ZHONG ; Di SHI ; Ziyue CHEN ; Yihang ZHANG ; Yanhui DONG ; Jun MA ; Yi SONG
Chinese Medical Journal 2025;138(3):311-317
BACKGROUND:
The urban-rural disparities in overweight and obesity among children and adolescents are narrowing, and there is a need for long-term and updated data to explain this inequality, understand the underlying mechanisms, and identify priority groups for interventions.
METHODS:
We analyzed data from seven rounds of the Chinese National Survey on Students Constitution and Health (CNSSCH) conducted from 1985 to 2019, focusing on school-age children and adolescents aged 7-18 years. Joinpoint regression was used to identify inflection points (indicating a change in the trend) in the prevalence of overweight and obesity during the study period, stratified by urban/rural areas and sex. Annual percent change (APC), average annual percent change (AAPC), and 95% confidence interval (CI) were used to describe changes in the prevalence of overweight and obesity. Polynomial regression models were used to predict the prevalence of overweight and obesity among children and adolescents in 2025 and 2030, considering urban/rural areas, sex, and age groups.
RESULTS:
The prevalence of overweight and obesity in urban boys and girls showed an inflection point of 2000, with AAPC values of 10.09% (95% CI: 7.33-12.92%, t = 7.414, P <0.001) and 8.67% (95% CI: 6.10-11.30%, t = 6.809, P <0.001), respectively. The APC for urban boys decreased from 18.31% (95% CI: 4.72-33.67%, t = 5.926, P = 0.027) to 4.01% (95% CI: 1.33-6.75%, t = 6.486, P = 0.023), while the APC for urban girls decreased from 13.88% (95% CI: 1.82-27.38%, t = 4.994, P = 0.038) to 4.72% (95% CI: 1.43-8.12%, t = 6.215, P = 0.025). However, no inflection points were observed in the best-fit models for rural boys and girls during the period 1985-2019. The prevalence of overweight and obesity for both urban and rural boys is expected to converge at 35.76% by approximately 2027. A similar pattern is observed for urban and rural girls, with a prevalence of overweight and obesity reaching 20.86% in 2025.
CONCLUSIONS
The prevalence of overweight and obesity among Chinese children and adolescents has been steadily increasing from 1985 to 2019. A complete reversal in urban-rural prevalence is expected by 2027, with a higher prevalence of overweight and obesity in rural areas. Urgent action is needed to address health inequities and increase investments, particularly policies targeting rural children and adolescents.
Humans
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Child
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Adolescent
;
Female
;
Male
;
Rural Population/statistics & numerical data*
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Overweight/epidemiology*
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Prevalence
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China/epidemiology*
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Pediatric Obesity/epidemiology*
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Obesity/epidemiology*
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Urban Population
5.Mechanism related to bile acids metabolism of liver injury induced by long-term administration of emodin.
Jing-Zhuo TIAN ; Lian-Mei WANG ; Yan YI ; Zhong XIAN ; Nuo DENG ; Yong ZHAO ; Chun-Ying LI ; Yu-Shi ZHANG ; Su-Yan LIU ; Jia-Yin HAN ; Chen PAN ; Chen-Yue LIU ; Jing MENG ; Ai-Hua LIANG
China Journal of Chinese Materia Medica 2025;50(11):3079-3087
Emodin is a hydroxyanthraquinone compound that is widely distributed and has multiple pharmacological activities, including anti-diarrheal, anti-inflammatory, and liver-protective effects. Research indicates that emodin may be one of the main components responsible for inducing hepatotoxicity. However, studies on the mechanisms of liver injury are relatively limited, particularly those related to bile acids(BAs) metabolism. This study aims to systematically investigate the effects of different dosages of emodin on BAs metabolism, providing a basis for the safe clinical use of traditional Chinese medicine(TCM)containing emodin. First, this study evaluated the safety of repeated administration of different dosages of emodin over a 5-week period, with a particular focus on its impact on the liver. Next, the composition and content of BAs in serum and liver were analyzed. Subsequently, qRT-PCR was used to detect the mRNA expression of nuclear receptors and transporters related to BAs metabolism. The results showed that 1 g·kg~(-1) emodin induced hepatic damage, with bile duct hyperplasia as the primary pathological manifestation. It significantly increased the levels of various BAs in the serum and primary BAs(including taurine-conjugated and free BAs) in the liver. Additionally, it downregulated the mRNA expression of farnesoid X receptor(FXR), retinoid X receptor(RXR), and sodium taurocholate cotransporting polypeptide(NTCP), and upregulated the mRNA expression of cholesterol 7α-hydroxylase(CYP7A1) in the liver. Although 0.01 g·kg~(-1) and 0.03 g·kg~(-1) emodin did not induce obvious liver injury, they significantly increased the level of taurine-conjugated BAs in the liver, suggesting a potential interference with BAs homeostasis. In conclusion, 1 g·kg~(-1) emodin may promote the production of primary BAs in the liver by affecting the FXR-RXR-CYP7A1 pathway, inhibit NTCP expression, and reduce BA reabsorption in the liver, resulting in BA accumulation in the peripheral blood. This disruption of BA homeostasis leads to liver injury. Even doses of emodin close to the clinical dose can also have a certain effect on the homeostasis of BAs. Therefore, when using traditional Chinese medicine or formulas containing emodin in clinical practice, it is necessary to regularly monitor liver function indicators and closely monitor the risk of drug-induced liver injury.
Emodin/administration & dosage*
;
Bile Acids and Salts/metabolism*
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Animals
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Male
;
Liver/injuries*
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Chemical and Drug Induced Liver Injury/genetics*
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Drugs, Chinese Herbal/adverse effects*
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Humans
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Rats, Sprague-Dawley
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Mice
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Rats
6.Effect and mechanism of Bufei Decoction on improving Klebsiella pneumoniae pneumonia in rats by regulating IL-17 signaling pathway.
Li-Na HUANG ; Zheng-Ying QIU ; Xiang-Yi PAN ; Chen LIU ; Si-Fan LI ; Shao-Guang GE ; Xiong-Wei SHI ; Hao CAO ; Rui-Hua XIN ; Fang-di HU
China Journal of Chinese Materia Medica 2025;50(11):3097-3107
Based on the interleukin-17(IL-17) signaling pathway, this study explores the effect and mechanism of Bufei Decoction on Klebsiella pneumoniae pneumonia in rats. SD rats were randomly divided into the control group, model group, Bufei Decoction low-dose group(6.68 g·kg~(-1)·d~(-1)), Bufei Decoction high-dose group(13.36 g·kg~(-1)·d~(-1)), and dexamethasone group(1.04 mg·kg~(-1)·d~(-1)), with 10 rats in each group. A pneumonia model was established by tracheal drip injection of K. pneumoniae. After successful model establishment, the improvement in lung tissue damage was observed following drug administration. Core targets and signaling pathways were screened using transcriptomics techniques. Real-time fluorescence quantitative polymerase chain reaction was used to detect the mRNA expression of core targets interleukin-6(IL-6), interleukin-1β(IL-1β), tumor necrosis factor-α(TNF-α), and chemokine CXC ligand 6(CXCL6). Western blot was used to assess key proteins in the IL-17 signaling pathway, including interleukin-17A(IL-17A), nuclear transcription factor-κB activator 1(Act1), tumor necrosis factor receptor-associated factor 6(TRAF6), and downstream phosphorylated p38 mitogen-activated protein kinase(p-p38 MAPK), and phosphorylated nuclear factor-κB p65(p-NF-κB p65). Apoptosis of lung tissue cells was detected by terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling(TUNEL). The results showed that, compared with the control group, the model group exhibited significant pathological damage in lung tissue. The mRNA expression of IL-6, IL-1β, TNF-α, and CXCL6, as well as the protein levels of IL-17A, Act1, TRAF6, p-p38 MAPK/p38 MAPK, and p-NF-κB p65/NF-κB p65, were significantly increased, and the number of apoptotic cells was notably higher, indicating successful model establishment. Compared with the model group, both low-and high-dose groups of Bufei Decoction showed reduced pathological damage in lung tissue. The mRNA expression levels of IL-6, IL-1β, TNF-α, and CXCL6, and the protein levels of IL-17A, Act1, TRAF6, p-p38 MAPK/p38 MAPK, and p-NF-κB p65/NF-κB p65, were significantly decreased, with a significant reduction in apoptotic cells in the high-dose group. In conclusion, Bufei Decoction can effectively improve lung tissue damage and reduce inflammation in rats with K. pneumoniae. The mechanism may involve the regulation of the IL-17 signaling pathway and the reduction of apoptosis.
Animals
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Interleukin-17/metabolism*
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Drugs, Chinese Herbal/administration & dosage*
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Rats, Sprague-Dawley
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Signal Transduction/drug effects*
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Rats
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Male
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Klebsiella pneumoniae/physiology*
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Klebsiella Infections/immunology*
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Humans
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Lung/drug effects*
7.Establishment of different pneumonia mouse models suitable for traditional Chinese medicine screening.
Xing-Nan YUE ; Jia-Yin HAN ; Chen PAN ; Yu-Shi ZHANG ; Su-Yan LIU ; Yong ZHAO ; Xiao-Meng ZHANG ; Jing-Wen WU ; Xuan TANG ; Ai-Hua LIANG
China Journal of Chinese Materia Medica 2025;50(15):4089-4099
In this study, lipopolysaccharide(LPS), ovalbumin(OVA), and compound 48/80(C48/80) were administered to establish non-infectious pneumonia models under simulated clinical conditions, and the correlation between their pathological characteristics and traditional Chinese medicine(TCM) syndromes was compared, providing the basis for the selection of appropriate animal models for TCM efficacy evaluation. An acute pneumonia model was established by nasal instillation of LPS combined with intraperitoneal injection for intensive stimulation. Three doses of OVA mixed with aluminum hydroxide adjuvant were injected intraperitoneally on days one, three, and five and OVA was administered via endotracheal drip for excitation on days 14-18 to establish an OVA-induced allergic pneumonia model. A single intravenous injection of three doses of C48/80 was adopted to establish a C48/80-induced pneumonia model. By detecting the changes in peripheral blood leukocyte classification, lung tissue and plasma cytokines, immunoglobulins(Ig), histamine levels, and arachidonic acid metabolites, the multi-dimensional analysis was carried out based on pathological evaluation. The results showed that the three models could cause pulmonary edema, increased wet weight in the lung, and obvious exudative inflammation in lung tissue pathology, especially for LPS. A number of pyrogenic cytokines, inclading interleukin(IL)-6, interferon(IFN)-γ, IL-1β, and IL-4 were significantly elevated in the LPS pneumonia model. Significantly increased levels of prostacyclin analogs such as prostaglandin E2(PGE2) and PGD2, which cause increased vascular permeability, and neutrophils in peripheral blood were significantly elevated. The model could partly reflect the clinical characteristics of phlegm heat accumulating in the lung or dampness toxin obstructing the lung. The OVA model showed that the sensitization mediators IgE and leukotriene E4(LTE4) were increased, and the anti-inflammatory prostacyclin 6-keto-PGF2α was decreased. Immune cells(lymphocytes and monocytes) were decreased, and inflammatory cells(neutrophils and basophils) were increased, reflecting the characteristics of "deficiency", "phlegm", or "dampness". Lymphocytes, monocytes, and basophils were significantly increased in the C48/80 model. The phenotype of the model was that the content of histamine, a large number of prostacyclins(6-keto-PGE1, PGF2α, 15-keto-PGF2α, 6-keto-PGF1α, 13,14-D-15-keto-PGE2, PGD2, PGE2, and PGH2), LTE4, and 5-hydroxyeicosatetraenoic acid(5S-HETE) was significantly increased, and these indicators were associated with vascular expansion and increased vascular permeability. The pyrogenic inflammatory cytokines were not increased. The C48/80 model reflected the characteristics of cold and damp accumulation. In the study, three non-infectious pneumonia models were constructed. The LPS model exhibited neutrophil infiltration and elevated inflammatory factors, which was suitable for the efficacy study of TCM for clearing heat, detoxifying, removing dampness, and eliminating phlegm. The OVA model, which took allergic inflammation as an index, was suitable for the efficacy study of Yiqi Gubiao formulas. The C48/80 model exhibited increased vasoactive substances(histamine, PGs, and LTE4), which was suitable for the efficacy study and evaluation of TCM for warming the lung, dispersing cold, drying dampness, and resolving phlegm. The study provides a theoretical basis for model selection for the efficacy evaluation of TCM in the treatment of pneumonia.
Animals
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Disease Models, Animal
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Mice
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Pneumonia/genetics*
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Medicine, Chinese Traditional
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Male
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Humans
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Cytokines/immunology*
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Female
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Lipopolysaccharides/adverse effects*
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Lung/drug effects*
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Drugs, Chinese Herbal
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Ovalbumin
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Mice, Inbred BALB C
8.USP20 as a super-enhancer-regulated gene drives T-ALL progression via HIF1A deubiquitination.
Ling XU ; Zimu ZHANG ; Juanjuan YU ; Tongting JI ; Jia CHENG ; Xiaodong FEI ; Xinran CHU ; Yanfang TAO ; Yan XU ; Pengju YANG ; Wenyuan LIU ; Gen LI ; Yongping ZHANG ; Yan LI ; Fenli ZHANG ; Ying YANG ; Bi ZHOU ; Yumeng WU ; Zhongling WEI ; Yanling CHEN ; Jianwei WANG ; Di WU ; Xiaolu LI ; Yang YANG ; Guanghui QIAN ; Hongli YIN ; Shuiyan WU ; Shuqi ZHANG ; Dan LIU ; Jun-Jie FAN ; Lei SHI ; Xiaodong WANG ; Shaoyan HU ; Jun LU ; Jian PAN
Acta Pharmaceutica Sinica B 2025;15(9):4751-4771
T-cell acute lymphoblastic leukemia (T-ALL) is a highly aggressive hematologic malignancy with a poor prognosis, despite advancements in treatment. Many patients struggle with relapse or refractory disease. Investigating the role of the super-enhancer (SE) regulated gene ubiquitin-specific protease 20 (USP20) in T-ALL could enhance targeted therapies and improve clinical outcomes. Analysis of histone H3 lysine 27 acetylation (H3K27ac) chromatin immunoprecipitation sequencing (ChIP-seq) data from six T-ALL cell lines and seven pediatric samples identified USP20 as an SE-regulated driver gene. Utilizing the Cancer Cell Line Encyclopedia (CCLE) and BloodSpot databases, it was found that USP20 is specifically highly expressed in T-ALL. Knocking down USP20 with short hairpin RNA (shRNA) increased apoptosis and inhibited proliferation in T-ALL cells. In vivo studies showed that USP20 knockdown reduced tumor growth and improved survival. The USP20 inhibitor GSK2643943A demonstrated similar anti-tumor effects. Mass spectrometry, RNA-Seq, and immunoprecipitation revealed that USP20 interacted with hypoxia-inducible factor 1 subunit alpha (HIF1A) and stabilized it by deubiquitination. Cleavage under targets and tagmentation (CUT&Tag) results indicated that USP20 co-localized with HIF1A, jointly modulating target genes in T-ALL. This study identifies USP20 as a therapeutic target in T-ALL and suggests GSK2643943A as a potential treatment strategy.
9.Differential Resting-State Brain Activity Following Early- and Late-Night Sleep Loss.
Tianqi DI ; Libo ZHANG ; Shiqiu MENG ; Yang GUO ; Wangyue LIU ; Enyu ZHENG ; Zhoulong YU ; Yan SUN ; Jie SHI
Neuroscience Bulletin 2025;41(9):1696-1700
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
;
DNA Footprinting/methods*

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