1.Screening key genes of PANoptosis in hepatic ischemia-reperfusion injury based on bioinformatics
Lirong ZHU ; Qian GUO ; Jie YANG ; Qiuwen ZHANG ; Guining HE ; Yanqing YU ; Ning WEN ; Jianhui DONG ; Haibin LI ; Xuyong SUN
Organ Transplantation 2025;16(1):106-113
Objective To explore the relationship between PANoptosis and hepatic ischemia-reperfusion injury (HIRI), and to screen the key genes of PANoptosis in HIRI. Methods PANoptosis-related differentially expressed genes (PDG) were obtained through the Gene Expression Omnibus database and GeneCards database. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were used to explore the biological pathways related to PDG. A protein-protein interaction network was constructed. Key genes were selected, and their diagnostic value was assessed and validated in the HIRI mice. Immune cell infiltration analysis was performed based on the cell-type identification by estimating relative subsets of RNA transcripts. Results A total of 16 PDG were identified. GO analysis showed that PDG were closely related to cellular metabolism. KEGG analysis indicated that PDG were mainly enriched in cellular death pathways such as apoptosis and immune-related signaling pathways such as the tumor necrosis factor signaling pathway. GSEA results showed that key genes were mainly enriched in immune-related signaling pathways such as the mitogen-activated protein kinase (MAPK) signaling pathway. Two key genes, DFFB and TNFSF10, were identified with high accuracy in diagnosing HIRI, with areas under the curve of 0.964 and 1.000, respectively. Immune infiltration analysis showed that the control group had more infiltration of resting natural killer cells, M2 macrophages, etc., while the HIRI group had more infiltration of M0 macrophages, neutrophils, and naive B cells. Real-time quantitative polymerase chain reaction results showed that compared with the Sham group, the relative expression of DFFB messenger RNA in liver tissue of HIRI group mice increased, and the relative expression of TNFSF10 messenger RNA decreased. Cibersort analysis showed that the infiltration abundance of naive B cells was positively correlated with DFFB expression (r=0.70, P=0.035), and the infiltration abundance of M2 macrophages was positively correlated with TNFSF10 expression (r=0.68, P=0.045). Conclusions PANoptosis-related genes DFFB and TNFSF10 may be potential biomarkers and therapeutic targets for HIRI.
2.Artificial intelligence in traditional Chinese medicine: from systems biological mechanism discovery, real-world clinical evidence inference to personalized clinical decision support.
Dengying YAN ; Qiguang ZHENG ; Kai CHANG ; Rui HUA ; Yiming LIU ; Jingyan XUE ; Zixin SHU ; Yunhui HU ; Pengcheng YANG ; Yu WEI ; Jidong LANG ; Haibin YU ; Xiaodong LI ; Runshun ZHANG ; Wenjia WANG ; Baoyan LIU ; Xuezhong ZHOU
Chinese Journal of Natural Medicines (English Ed.) 2025;23(11):1310-1328
Traditional Chinese medicine (TCM) represents a paradigmatic approach to personalized medicine, developed through the systematic accumulation and refinement of clinical empirical data over more than 2000 years, and now encompasses large-scale electronic medical records (EMR) and experimental molecular data. Artificial intelligence (AI) has demonstrated its utility in medicine through the development of various expert systems (e.g., MYCIN) since the 1970s. With the emergence of deep learning and large language models (LLMs), AI's potential in medicine shows considerable promise. Consequently, the integration of AI and TCM from both clinical and scientific perspectives presents a fundamental and promising research direction. This survey provides an insightful overview of TCM AI research, summarizing related research tasks from three perspectives: systems-level biological mechanism elucidation, real-world clinical evidence inference, and personalized clinical decision support. The review highlights representative AI methodologies alongside their applications in both TCM scientific inquiry and clinical practice. To critically assess the current state of the field, this work identifies major challenges and opportunities that constrain the development of robust research capabilities-particularly in the mechanistic understanding of TCM syndromes and herbal formulations, novel drug discovery, and the delivery of high-quality, patient-centered clinical care. The findings underscore that future advancements in AI-driven TCM research will rely on the development of high-quality, large-scale data repositories; the construction of comprehensive and domain-specific knowledge graphs (KGs); deeper insights into the biological mechanisms underpinning clinical efficacy; rigorous causal inference frameworks; and intelligent, personalized decision support systems.
Medicine, Chinese Traditional/methods*
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Artificial Intelligence
;
Humans
;
Precision Medicine
;
Decision Support Systems, Clinical
3.High expression of ELFN1 is a prognostic biomarker and promotes proliferation and metastasis of colorectal cancer cells.
Kang WANG ; Haibin LI ; Jing YU ; Yuan MENG ; Hongli ZHANG
Journal of Southern Medical University 2025;45(7):1543-1553
OBJECTIVES:
To explore the correlation of ELFN1 expression level with prognosis of colorectal cancer and its regulatory role in colorectal cancer cell proliferation and metastasis.
METHODS:
We analyzed the expression levels of ELFN1 across 33 cancer types using publicly available databases and identified differential genes related to ELFN1 in colorectal cancer. Gene function annotation and enrichment analysis were used to identify the involved signaling pathways. Logistic analysis, Kaplan-Meier analysis and Cox regression analysis were performed to evaluate the correlation between ELFN1 expression and clinicopathological parameters and survival of colorectal cancer patients. qPCR and Western blotting were used to validate the expression levels of ELFN1 in different colorectal cancer cell lines and tissues, and Transwell and EDU experiments were carried out to assess the effect of ELFN1 knockdown on biological behaviors of SW480 cells.
RESULTS:
ELFN1 was highly expressed in 14 cancers, and its expression was significantly higher in colon cancer tissues than in adjacent tissues. A high expression of ELFN1 mRNA was associated with a poorer overall survival of colorectal cancer patients. Cox regression analysis indicated that ELFN1 expression was an independent prognostic factor for overall survival of the patients. ELFN1 was significantly enriched in tumor metastasis and proliferation and participated in several tumor signaling pathways. The colon cancer cell lines showed significantly higher expression levels of ELFN1 than normal cells, ELFN1 knockdown obviously inhibited proliferation and migration of SW480 cells in vitro.
CONCLUSIONS
ELFN1 is overexpressed in colorectal cancer and is associated with poor clinical prognosis of the patients. A high ELFN1 expression is associated with malignant phenotypes of colorectal cancer and promotes cancer cell proliferation and metastasis, suggesting its potential as a prognostic biomarker for colorectal cancer.
Humans
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Colorectal Neoplasms/diagnosis*
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Cell Proliferation
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Prognosis
;
Cell Line, Tumor
;
Biomarkers, Tumor/metabolism*
;
Neoplasm Metastasis
;
Gene Expression Regulation, Neoplastic
;
Nerve Tissue Proteins/metabolism*
;
Female
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Male
4.Genetic Variations and Nonalcoholic Fatty Liver Disease:Field Synopsis,Systematic Meta-Analysis,and Epidemiological Evidence
Li YAMEI ; Xiao XIANG ; Wang JIE ; Liu YIXU ; Pan XIONGFENG ; Yu HAIBIN ; Luo JIAYOU ; Luo MIYANG
Biomedical and Environmental Sciences 2024;37(7):762-773
Objective To systematically summarize the published literature on the genetic variants associated with nonalcoholic fatty liver disease(NAFLD). Methods Literature from Web of Science,PubMed,and Embase between January 1980 and September 2022 was systematically searched.Meta-analyses of the genetic variants were conducted using at least five data sources.The epidemiologic credibility of the significant associations was graded using the Venice criteria. Results Based on literature screening,399 eligible studies were included,comprising 381 candidate gene association,16 genome-wide association,and 2 whole-exome sequencing studies.We identified 465 genetic variants in 173 genes in candidate gene association studies,and 25 genetic variants in 17 genes were included in the meta-analysis.The meta-analysis identified 11 variants in 10 genes that were significantly associated with NAFLD,with cumulative epidemiological evidence of an association graded as strong for two variants in two genes(HFE,TNF),moderate for four variants in three genes(TM6SF2,GCKR,and ADIPOQ),and weak for five variants in five genes(MBOAT7,PEMT,PNPLA3,LEPR,and MTHFR). Conclusion This study identified six variants in five genes that had moderate to strong evidence of an association with NAFLD,which may help understand the genetic architecture of NAFLD risk.
5.Screening and bioinformatics analysis of SNP in PPARGC1B gene of Sichuan Yak
Xuanxu CHEN ; Xinyi JIANG ; Jinghao PENG ; Jing LI ; Fengshuai MIAO ; Zhihui ZHAO ; Haibin YU ; Weizhong LAI ; Ping JIANG ; Ziwei LIN
Chinese Journal of Veterinary Science 2024;44(10):2179-2189
The peroxisome proliferator-activated receptor gamma(peroxisome proliferator-activated receptor gamma,coactivator 1 beta,PPARGC1B)gene is an intranuclear receptor transcription fac-tor responsible for regulating the expression of target genes.To comprehend the characteristics and mutations of the PPARGC1B gene within the Sichuan yak population,the SNP loci of the PPARGC1B gene were identified through direct sequencing of PCR products.Additionally,the cod-ing region of the PPARGC1B gene was obtained via PCR amplification and sequencing.Bioinforma-tics analyses were conducted to predict protein-coding and mRNA secondary structure.This study identified four exon SNP mutation sites(E9-189A→C,E9-387G→A,E9-542C→T,and E9-554T→C)based on the single nucleotide polymorphism analysis of the PPARGC1B gene in Sichuan yaks.Notably,the E9-387G→A and E9-554T→C loci exhibited significant correlations with shear force and backfat thickness in Sichuan yaks.Subsequently,bioinformatics analysis of the four mutation sites revealed that the PPARGC1B protein is an acidic,unstable,non-transmembrane,and non-secretory hydrophilic protein with a coiled helix structure.It lacks a signal peptide and transmembrane region,predominantly functions in the nucleus,and features 106 phosphorylation sites,one glycosylation site,and one conserved RRM structure.The secondary structure comprises mainly α-helix and random coils.Although the protein structure of the PPARGC1B gene remained unchanged post-mutation,there were significant differences in mRNA secondary structure.These findings suggest that the polymorphic loci of the PPARGC1B gene in Sichuan yaks could serve as a theoretical basis for enhancing meat quality traits through molecular biological methods,presen-ting practical applications in breeding.
6.Genetic polymorphism of ACOX1 gene and its correlation with milk quality traits in China Holstein dairy cows
Yurong HAO ; Zhihui ZHAO ; Tao YOU ; Haibin YU ; Guanghui LI ; Ping JIANG ; Ziwei LIN
Chinese Journal of Veterinary Science 2024;44(10):2260-2265
The SNP loci of ACOX1 gene in 83 China Holstein cows were detected by PCR amplifica-tion and direct sequencing,and the association between the genetic polymorphism loci of ACOX 1 gene and milk quality traits of China Holstein cows was analyzed by SPSS 25.0 software.The re-sults showed that a SNP locus I3-2 267 G→C was found in the third intron of ACOX1 gene,it was moderately polymorphic and in Hardy Weinberg equilibrium in the population.By correlation anal-ysis,it was found that the SNP locus was significantly related to the somatic cell content and cor-rected milk quantity of dairy cows.The I3-2 267 G→C locus of ACOX1 gene can be used as a mo-lecular marker of quality traits of Holstein cows in China,and provide reference for the study of quality traits of Holstein cows in China.
7.Polymorphism analysis of PPP1R15A gene in Chinese Holstein cattle and its asso-ciation with milk production traits
Qiwen LU ; Quanheng GUO ; Panpan XU ; Yisan HUANG ; Haibin YU ; Ziwei LIN ; Zhihui ZHAO ; Ping JIANG
Chinese Journal of Veterinary Science 2024;44(11):2458-2462
The gene encoding regulatory subunit 15 A of protein phosphatase 1 produces a protein that is a universally present protein phosphatase in eukaryotic cells.In this study,genomic DNAs were extracted from the blood of 89 Chinese Holstein cows and were used as templates for PCR amplification of the target fragment of the PPP1R15A gene.The product was tested and a polymor-phic site,E3-250T>A was found.The polymorphism of this side and its correlation with milk pro-duction traits in Chinese Holstein cattle were statistically analyzed using SPSS 23.0 software.The findings revealed three genotypes at this site:AA,AT and TT.Cows possessing the AT and TT genotypes exhibited significant differences(P<0.01)in milk fat and solid non-fat content com-pared to those with the AA genotype.While no significant differences were noted for other milk production traits,including milk yield,protein,lactose,somatic cell count,blood urea nitrogen,and corrected milk.The identification of functional SNPs in the PPP1R15A gene provides a theoretical basis for further research and identification of causal variations in the cow PPP1R15A gene.
8.Analysis of the timing of TEVAR intervention for Stanford type B aortic dissection
Xueliang YUAN ; Haibin YU ; Ximing WANG
Journal of Interventional Radiology 2024;33(5):523-528
Objective To explore the efficacy of thoracic endovascular aortic repair(TEVAR)for the treatment of Stanford type B aortic dissection at different intervention timing.Methods The clinical data of 126 patients with Stanford B type aortic dissection,who were admitted to authors'hospital between January 2018 and April 2023,were retrospectively analyzed.Based on the time interval from the onset of disease to receiving surgery,the patients were divided into group A(<24 h),group B(2-7 d)and group C(8-14 d).The incidences of perioperative adverse events,including endoleak,cerebral infarction,death,aortic rupture and total complications,were compared between each other among the three groups,and survival analysis was performed according to the follow-up findings.Results A total of 126 patients with Stanford type B aortic dissection were included in this study,including 50 patients of group A,43 patients of group B,and 33 patients of group C.No statistically significant differences in the general clinical data existed between each other among the three groups(P>0.05).The differences in the incidences of perioperative acute cerebral infarction,endoleak,infection and death between each other among the three groups were not statistically significant(P>0.05).The difference in the overall complication rate between each other among the three groups was statistically significant(P<0.05).Log-rank testing was used to compare the survival curves of the three groups,which showed that the cumulative 5-year recurrence rate and survival rate in group A were lower than those in group B and in group C,and the differences were statistically significant(P<0.05).Conclusion The results of this study indicate that the patients may have high incidence of adverse events and poor short-to-middle-term curative efficacy when TEVAR is performed within 24 hours after the onset of symptoms,while the patients may have better perioperative and short-to-middle-term curative efficacy if TEVAR is carried out in 2-14 days after the onset of symptoms(J Intervent Radiol,2024,33:523-528)
9.Treatment of Chronic Urticaria with Traditional Chinese Medicine by Regulating PI3K/Akt Molecular Pathway: A Review
Kaifeng JI ; Haibin CAI ; Zhouwei WU ; Yuting ZHENG ; Xiaoqian XU ; Yu SONG
Chinese Journal of Experimental Traditional Medical Formulae 2024;30(17):292-298
Chronic urticaria (CU) is a common skin disease worldwide, and its incidence is increasing year by year in various regions. Clinical manifestations such as severe itching can affect normal work, sleep, and daily life and increase the negative psychological burden caused by stress, anxiety, and depression. Mast cell activation and degranulation induced by immunoglobulin(Ig)E hypersensitivity is one of the core pathogenic mechanisms of CU, and there is no cure. Antihistamines such as cetirizine and loratadine are preferred for the clinical treatment of CU. Although they can effectively improve clinical manifestations such as itchiness, long-term application can increase the risk of adverse reactions and drug resistance. The phosphatidylinositol kinase/serine-threonine protein kinase B(PI3K/Akt) signaling pathway, as a classical signaling pathway regulated by phosphatidylinositol and tyrosine kinase receptor (RTK), is a key target regulating the production and release of cytokines in macrophages and affecting the migration of leukocytes and the activation of mast cells and inflammation, and it can be involved in a variety of metabolic processes, such as mast cell activation and degranulation induced by IgE hypersensitivity and abnormal activation of the complement system so that the PI3K/Akt molecular pathway could be an important target for the future eradication of CU. However, the mechanism and potential role of the PI3K/Akt signaling pathway in the treatment of CU are less reported in China. Now, this paper reviewed the molecular mechanism of PI3K/Akt signaling pathway regulation in the treatment of CU and provided corroborative evidence and therapeutic strategy choices for the treatment of CU with traditional Chinese medicine (TCM) from the perspectives of molecular regulation and network pharmacology analysis.
10.Trunk pressure biofeedback and its correlation with diaphragmatic functional parameters in young adults
Junfeng KONG ; Haibin XIAO ; Tian MA ; Yu LUO
Chinese Journal of Tissue Engineering Research 2024;28(32):5196-5202
BACKGROUND:Trunk pressure biofeedback is considered a reliable indicator for assessing core muscle strength.It not only reflects the status of an individual's trunk strength but also has a close relationship with the function of respiratory muscles. OBJECTIVE:To explore the correlation between trunk pressure biofeedback and diaphragmatic function in young adults. METHODS:A total of 80 young adults from Shangrao Normal University,China were enrolled,including 34 males and 46 females,with an average age of(19.83±1.45)years.Diaphragmatic thickness and mobility were measured using a bedside musculoskeletal ultrasound system.Maximum inspiratory pressure was determined using a portable pulmonary function tester.Lumbar and abdominal pressures in prone and supine positions were assessed using a pressure biofeedback device.The degree of correlation between trunk pressure biofeedback and diaphragmatic function was determined using Pearson or Spearman correlation coefficients.A multivariate linear regression analysis was used to determine predictive models for diaphragmatic function. RESULTS AND CONCLUSION:Grouped by sex,age,height,body mass,trunk pressure biofeedback values,diaphragm thickness during quiet inspiration and expiration,diaphragmatic thickening ratio during quiet breathing,diaphragmatic thickness during deep inspiration and expiration,diaphragmatic thickening ratio during deep breathing,diaphragmatic mobility during deep inspiration,and maximum inspiratory pressure were higher in the male group than the female group(all P<0.05).Grouped by physical activity level,trunk pressure biofeedback values and maximum inspiratory pressure were lower in the sedentary group than in the exercise group(both P<0.05).Both anterior and posterior trunk pressure biofeedback were significantly correlated with diaphragmatic thickness during quiet inspiration and expiration,diaphragmatic thickening ratio during quiet breathing,diaphragmatic thickness during deep inspiration and expiration,diaphragmatic thickening ratio during deep breathing,diaphragmatic mobility during deep inspiration,and maximum inspiratory pressure(all P<0.01).Anterior trunk pressure biofeedback entered the predictive model for diaphragmatic thickness during quiet inspiration(F=27.228,P<0.001),during deep inspiration(F=38.615,P<0.001),and along with age for diaphragmatic mobility during deep inspiration(F=15.408,P<0.001).Anterior trunk pressure biofeedback,body mass,and age entered the predictive model for maximum inspiratory pressure(F=22.314,P<0.001).To conclude,there is a strong correlation between trunk pressure biofeedback and diaphragmatic thickness,diaphragmatic mobility,and maximum inspiratory pressure.The rapid and simple measurement of trunk pressure biofeedback can serve as a method for screening the diaphragmatic function in healthy young adults.

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