1.Identification of telomere-related diagnostic markers in osteoarthritis based on bioinformatics analysis and machine learning
Sheng XU ; Jia YE ; Xiaochong CAI
The Korean Journal of Physiology and Pharmacology 2025;29(3):359-372
Osteoarthritis (OA) is one of the most prevalent joint disorders, with aging considered a primary, irreversible factor contributing to its progression. Telomere-related cellular senescence may be a crucial factor influencing the OA process, yet biomarkers for OA based on telomere-related genes have not been clearly identified. The datasets GSE51588, GSE12021, and GSE55457 were retrieved from the Gene Expression Omnibus database. Initially, R software was utilized to identify differentially expressed genes between OA and normal samples. Subsequently, differentially expressed telomere-related genes (DETMRGs) were obtained, and their functional enrichment was analyzed. Feature genes for OA diagnosis were selected from DETMRGs using a combination of least absolute shrinkage and selection operator, support vector machine-recursive feature elimination, and Random Forest algorithms. The diagnostic value of these feature genes was then validated through receiver operating characteristic (ROC) curves and decision curve analysis. Additionally, CIBERSORT and xCell were employed to assess the infiltration of immune cells in OA tissues.Finally, potential drugs targeting candidate genes were predicted. Three telomererelated genes, PGD, SLC7A5, and TKT, have been identified as biomarkers for OA diagnosis and were confirmed through ROC diagnostic tests. The immune infiltration of mast cells, neutrophils, common lymphoid precursors, and eosinophils associated with PGD, SLC7A5, and TKT was reduced. Recognizing telomere-related genes PGD, SLC7A5, and TKT as potential diagnostic biomarkers for OA is significant, as it offers valuable insights into the role of telomere-related genes in OA. This discovery also provides valuable information for the diagnosis and treatment of OA.
2.Identification of telomere-related diagnostic markers in osteoarthritis based on bioinformatics analysis and machine learning
Sheng XU ; Jia YE ; Xiaochong CAI
The Korean Journal of Physiology and Pharmacology 2025;29(3):359-372
Osteoarthritis (OA) is one of the most prevalent joint disorders, with aging considered a primary, irreversible factor contributing to its progression. Telomere-related cellular senescence may be a crucial factor influencing the OA process, yet biomarkers for OA based on telomere-related genes have not been clearly identified. The datasets GSE51588, GSE12021, and GSE55457 were retrieved from the Gene Expression Omnibus database. Initially, R software was utilized to identify differentially expressed genes between OA and normal samples. Subsequently, differentially expressed telomere-related genes (DETMRGs) were obtained, and their functional enrichment was analyzed. Feature genes for OA diagnosis were selected from DETMRGs using a combination of least absolute shrinkage and selection operator, support vector machine-recursive feature elimination, and Random Forest algorithms. The diagnostic value of these feature genes was then validated through receiver operating characteristic (ROC) curves and decision curve analysis. Additionally, CIBERSORT and xCell were employed to assess the infiltration of immune cells in OA tissues.Finally, potential drugs targeting candidate genes were predicted. Three telomererelated genes, PGD, SLC7A5, and TKT, have been identified as biomarkers for OA diagnosis and were confirmed through ROC diagnostic tests. The immune infiltration of mast cells, neutrophils, common lymphoid precursors, and eosinophils associated with PGD, SLC7A5, and TKT was reduced. Recognizing telomere-related genes PGD, SLC7A5, and TKT as potential diagnostic biomarkers for OA is significant, as it offers valuable insights into the role of telomere-related genes in OA. This discovery also provides valuable information for the diagnosis and treatment of OA.
3.Identification of telomere-related diagnostic markers in osteoarthritis based on bioinformatics analysis and machine learning
Sheng XU ; Jia YE ; Xiaochong CAI
The Korean Journal of Physiology and Pharmacology 2025;29(3):359-372
Osteoarthritis (OA) is one of the most prevalent joint disorders, with aging considered a primary, irreversible factor contributing to its progression. Telomere-related cellular senescence may be a crucial factor influencing the OA process, yet biomarkers for OA based on telomere-related genes have not been clearly identified. The datasets GSE51588, GSE12021, and GSE55457 were retrieved from the Gene Expression Omnibus database. Initially, R software was utilized to identify differentially expressed genes between OA and normal samples. Subsequently, differentially expressed telomere-related genes (DETMRGs) were obtained, and their functional enrichment was analyzed. Feature genes for OA diagnosis were selected from DETMRGs using a combination of least absolute shrinkage and selection operator, support vector machine-recursive feature elimination, and Random Forest algorithms. The diagnostic value of these feature genes was then validated through receiver operating characteristic (ROC) curves and decision curve analysis. Additionally, CIBERSORT and xCell were employed to assess the infiltration of immune cells in OA tissues.Finally, potential drugs targeting candidate genes were predicted. Three telomererelated genes, PGD, SLC7A5, and TKT, have been identified as biomarkers for OA diagnosis and were confirmed through ROC diagnostic tests. The immune infiltration of mast cells, neutrophils, common lymphoid precursors, and eosinophils associated with PGD, SLC7A5, and TKT was reduced. Recognizing telomere-related genes PGD, SLC7A5, and TKT as potential diagnostic biomarkers for OA is significant, as it offers valuable insights into the role of telomere-related genes in OA. This discovery also provides valuable information for the diagnosis and treatment of OA.
4.Identification of telomere-related diagnostic markers in osteoarthritis based on bioinformatics analysis and machine learning
Sheng XU ; Jia YE ; Xiaochong CAI
The Korean Journal of Physiology and Pharmacology 2025;29(3):359-372
Osteoarthritis (OA) is one of the most prevalent joint disorders, with aging considered a primary, irreversible factor contributing to its progression. Telomere-related cellular senescence may be a crucial factor influencing the OA process, yet biomarkers for OA based on telomere-related genes have not been clearly identified. The datasets GSE51588, GSE12021, and GSE55457 were retrieved from the Gene Expression Omnibus database. Initially, R software was utilized to identify differentially expressed genes between OA and normal samples. Subsequently, differentially expressed telomere-related genes (DETMRGs) were obtained, and their functional enrichment was analyzed. Feature genes for OA diagnosis were selected from DETMRGs using a combination of least absolute shrinkage and selection operator, support vector machine-recursive feature elimination, and Random Forest algorithms. The diagnostic value of these feature genes was then validated through receiver operating characteristic (ROC) curves and decision curve analysis. Additionally, CIBERSORT and xCell were employed to assess the infiltration of immune cells in OA tissues.Finally, potential drugs targeting candidate genes were predicted. Three telomererelated genes, PGD, SLC7A5, and TKT, have been identified as biomarkers for OA diagnosis and were confirmed through ROC diagnostic tests. The immune infiltration of mast cells, neutrophils, common lymphoid precursors, and eosinophils associated with PGD, SLC7A5, and TKT was reduced. Recognizing telomere-related genes PGD, SLC7A5, and TKT as potential diagnostic biomarkers for OA is significant, as it offers valuable insights into the role of telomere-related genes in OA. This discovery also provides valuable information for the diagnosis and treatment of OA.
5.Identification of telomere-related diagnostic markers in osteoarthritis based on bioinformatics analysis and machine learning
Sheng XU ; Jia YE ; Xiaochong CAI
The Korean Journal of Physiology and Pharmacology 2025;29(3):359-372
Osteoarthritis (OA) is one of the most prevalent joint disorders, with aging considered a primary, irreversible factor contributing to its progression. Telomere-related cellular senescence may be a crucial factor influencing the OA process, yet biomarkers for OA based on telomere-related genes have not been clearly identified. The datasets GSE51588, GSE12021, and GSE55457 were retrieved from the Gene Expression Omnibus database. Initially, R software was utilized to identify differentially expressed genes between OA and normal samples. Subsequently, differentially expressed telomere-related genes (DETMRGs) were obtained, and their functional enrichment was analyzed. Feature genes for OA diagnosis were selected from DETMRGs using a combination of least absolute shrinkage and selection operator, support vector machine-recursive feature elimination, and Random Forest algorithms. The diagnostic value of these feature genes was then validated through receiver operating characteristic (ROC) curves and decision curve analysis. Additionally, CIBERSORT and xCell were employed to assess the infiltration of immune cells in OA tissues.Finally, potential drugs targeting candidate genes were predicted. Three telomererelated genes, PGD, SLC7A5, and TKT, have been identified as biomarkers for OA diagnosis and were confirmed through ROC diagnostic tests. The immune infiltration of mast cells, neutrophils, common lymphoid precursors, and eosinophils associated with PGD, SLC7A5, and TKT was reduced. Recognizing telomere-related genes PGD, SLC7A5, and TKT as potential diagnostic biomarkers for OA is significant, as it offers valuable insights into the role of telomere-related genes in OA. This discovery also provides valuable information for the diagnosis and treatment of OA.
6.Development of an Analytical Software for Forensic Proteomic SAP Typing
Feng HU ; Meng-Jiao WANG ; Jia-Lei WU ; Dong-Sheng DING ; Zhi-Yuan YANG ; An-Quan JI ; Lei FENG ; Jian YE
Progress in Biochemistry and Biophysics 2025;52(9):2406-2416
ObjectiveThe proteome of biological evidence contains rich genetic information, namely single amino acid polymorphisms (SAPs) in protein sequences. However, due to the lack of efficient and convenient analysis tools, the application of SAP in public security still faces many challenges. This paper aims to meet the application requirements of SAP analysis for forensic biological evidence’s proteome data. MethodsThe software is divided into three modules. First, based on a built-in database of common non-synonymous single nucleotide polymorphisms (nsSNPs) and SAPs in East Asian populations, the software integrates and annotates newly identified exonic nsSNPs as SAPs, thereby constructing a customized SAP protein sequence database. It then utilizes a pre-installed search engine—either pFind or MaxQuant—to perform analysis and output SAP typing results, identifying both reference and variant types, along with their corresponding imputed nsSNPs. Finally, SAPTyper compares the proteome-based typing results with the individual’s exome-derived nsSNP profile and outputs the comparison report. ResultsSAPTyper accepts proteomic DDA mass spectrometry raw data (DDA acquisition mode) and exome sequencing results of nsSNPs as input and outputs the report of SAPs result. The pFind and Maxquant search engines were used to test the proteome data of 2 hair shafts of2 individuals, and both obtained SAP results. It was found that the results of the Maxquant search engine were slightly less than those of pFind. This result shows that SAPTyper can achieve SAP fingding function. Moreover, the pFind search engine was used to test the proteome data of 3 hair shafts from 1 European person and 1 African person in the literature. Among the sites fully matched by the literature method, sites detected by SAPTyper are also included; for semi-matching sites, that is, nsSNPs are heterozygous, both literature method and SAPTyper method had the risk of missing detection for one type of the allele. Comparing the analysis results of SAPTyper with the SAP test results reported in the literature, it was found that some imputed nsSNP sites identified by the literature method but not detected by SAPTyper had a MAF of less than 0.1% in East Asian populations, and therefore they were not included in the common nsSNP database of East Asian populations constructed by this software. Since the database construction of this software is based on the genetic variation information of East Asian populations, it is currently unable to effectively identify representative unique common variation sites in European or African populations, but it can still identify SAP sites shared by these populations and East Asian populations. ConclusionAn automated SAP analysis algorithm was developed for East Asian populations, and the software named SAPTyper was developed. This software provides a convenient and efficient analysis tool for the research and application of forensic proteomic SAP and has important application prospects in individual identification and phenotypic inference based on SAP.
7.Inhibition of triggering receptor expressed on myeloid cells-1(TREM-1)attenuates chronic intermittent hypoxia-induced atherosclerosis in mouse models
Hanqiao YU ; Chao LI ; Yubin YU ; Lina FENG ; Xiaosheng SHENG ; Xiaoxia YE ; Linyan WANG
Basic & Clinical Medicine 2024;44(3):368-373
Objective To investigate the role of triggering receptor expressed on myeloid cells-1(TREM-1)in ath-erosclerosis induced by chronic intermittent hypoxia(CIH).Methods ApoE-/-mice were randomly divided into blank group,model group and experimental group.The mice in the model group and the experimental group were kept in a hypoxic environment and fed with a high-fat diet.After 4 weeks of high-fat feeding,mice in the experi-mental group were intraperitoneally injected with TREM-1 inhibitor LR12(5 mg/kg)for 8 weeks.After 12 weeks of feeding,the level of serum total cholesterol(TC),low density lipoprotein(LDL),triglyceride(TG),tumor necrosis factor-α(TNF-α),interleukin-1β(IL-1β)and interleukin-10(IL-10)were detected.Histological analysis of aortic TREM-1 expression,plaque area and macrophage level were examined.Results Compared with blank group,the expression of TREM-1 in the aorta of the model group significantly increased(P<0.05).Com-pared with model group,the aortic plaque,the level of lipids in serum(TC,LDL,TG)and inflammatory factors(TNF-α,IL-1β,IL-10),aortic plaque,the expression of TREM-1 and infiltrating macrophages in aortic plaque of the experimental group were all significantly reduced(P<0.05).Conclusions TREM-1 is involved in the develop-ment of CIH-induced AS.Inhibition of TREM-1 can alleviate CIH-induced AS and its mechanism is related to the inhibition of macrophage activation.
8.Sheng Guoguang's Stage Treatment of Metabolic Associated Fatty Liver Disease Based on"Earth-obstructing and Wood-stagnation,Phlegm and Blood Stasis"
Cheng LUO ; Yuanhang YE ; Xiaodong LI ; Jia KE ; Guoguang SHENG
Chinese Journal of Information on Traditional Chinese Medicine 2024;31(1):176-179
Metabolic associated fatty liver disease has become the most important chronic liver disease in China.Its mechanism is not completely clear.Professor Sheng Guoguang examines the symptoms and seek the cause,treats the disease by stages from the perspective of"earth-obstructing and wood-stagnation,phlegm and blood stasis",summarizes the core pathogenesis of each stage,and prescribes drugs for the pathogenesis.In the early stage,the disease is mainly caused by earth-obstructing and wood-stagnation and phlegm and blood stasis and the corresponding treatment method should be activating spleen to eliminate depression,relieving phlegm and promoting blood circulation,with common use of modified Sizhu Decoction combined with Erchen Decoction.In the middle stage,phlegm and blood stasis transform into heat are the main pathogenesis,and the appropriate treatment is clearing liver and purging fire,and relieving phlegm and promoting blood circulation,with common use of modified Xiaochaihu Decoction combined with Erchen Decoction.In the late stage,weakness of the internal organs is the main pathogenesis,and it is appropriate to nourish liver and fortify the spleen,tonifying the kidney and consolidate the root,supplementing with reducing phlegm and activating blood circulation,with common use of modified Yiguan Decoction combined with Liujunzi Decoction in modification,which has achieved confirmed clinical efficacy.
9.Relationship between lifestyle and the comorbidity of myopia and depressive symptoms among primary and secondary school students in Nanjing
LI Juntong, LIU Hui, YE Sheng, YANG Yue, LU Xuelei, LIU Li
Chinese Journal of School Health 2024;45(5):630-634
Objective:
To explore the relationship between lifestyle and myopia and depressive symptoms comorbidity among primary and secondary school students in Nanjing, so as to provide a scientific basis for developing effective prevention measures.
Methods:
In October 2022, a stratified cluster random sampling method was used to select primary and secondary school students aged 9-19 years in 4 urban and 4 suburban districts in Nanjing as the research subjects. A total of 10 498 students were included for physical examination and questionnaire survey by using the student health condition and influencing factors questionnaire. Chisquare test was used for univariate analysis, and multifactor Logistic regression analysis was used to analyze the relationship between students lifestyle and the cooccurrence of myopia and depressive symptoms.
Results:
The prevalence of comorbidity of screening positive myopia and depression among primary and secondary school students in Nanjing was 18.11%. The prevalence of comorbidity was higher in girls (20.97%) than in boys (15.47%), higher in boarding students (31.31%) than in nonboarding students (16.51%), and higher in high school students than in middle and primary school students (28.63%, 19.10%, 7.76%), with statistically significant differences (χ2=53.49, 149.31, 522.55, P<0.01). Multivariate Logistic regression results showed that smoking (OR=1.51), drinking (OR=2.36), looking at electronic screens in dim conditions (OR=2.40), screen time ≥2 h/d(OR=1.50), afterschool homework time ≥2 h/d(OR=1.48) were positively correlated with the prevalence of comorbidity of screening positive myopia and depressive symptoms, healthy diet (OR=0.67), outdoor activities during breaks (OR=0.80), sufficient sleep (OR=0.64), meeting physical activity standards (OR=0.74) and outdoor activity time ≥2 h/d(OR=0.84) were negatively correlated with the prevalence of comorbidity of screening positive of myopia and depressive symptoms (P<0.05).
Conclusions
The lifestyle of primary and secondary school students in Nanjing is related to the comorbidity of myopia and depressive symptoms. Schools and families should carry out relevant education and intervention measures to promote students to develop good living habits and jointly prevent the occurrence of myopia and depressive symptoms.
10.Research status of premyopia
Yitong LIN ; Ziyang CHEN ; Zhaoda YE ; Sheng CHEN ; Yanhong HU
International Eye Science 2024;24(7):1102-1105
The visual impairment and blindness caused by myopia have become a global burden, and the World Health Organization has included the prevention and control of myopia in the global program for preventing blindness. In China, the development of myopia is showing a trend with higher incidence, younger age, and higher refractive errors. Moving forward the port of prevention and control myopia has become an important strategy to address the current predicament. Premyopia refers to the stage in children where the refractive power is ≤+0.75 D and >-0.50 D, and there are multiple risk factors during this stage that can potentially lead to myopia. Currently, the incidence of premyopia and its transformation into myopia is high, and the key prevention and control measures include building a predictive model for the transformation of premyopia into myopia, emphasizing the reduction of exposure to risk factors, using low-concentration atropine eye drops, red light therapy, and optical defocus intervention. This article provides a comprehensive review of the current situation regarding the incidence of premyopia and its transformation into myopia, as well as the research progress on existing prevention and control measures, with the aim of providing relevant references for the prevention and control of myopia during the premyopia stage.


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