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.Study on analgesic effect of anterior quadratus lumborum block at lateral supra-arcuate ligament and transversus abdominis plane block in analgesia in patients undergoing laparoscopic partial hepatectomy
Lingling JIANG ; Yun LI ; Kui SHENG ; Lili ZHANG ; Yang HU ; Ye ZHANG
Tianjin Medical Journal 2024;52(3):302-306
Objective To observe the effect of ultrasound-guided anterior quadratus lumborum block at lateral supra-arcuate ligament(QLB-LSAL)and transversus abdominis plane block(TAPB)on analgesia and recovery quality after laparoscopic partial hepatectomy(LPH).Methods Fifty-eight patients underwent elective LPH were selected and divided into the quadratus lumborum group or the transversus abdominis group randomly,with 29 patients in each group.The quadratus lumborum group received bilateral QLB-LSAL,and the transversus abdominis group received bilateral subcostal TAPB block before surgery.Both groups received 20 mL of 0.33%ropivacaine on each side.All patients used patient-controlled intravenous analgesia(PCIA)postoperatively.The numeric rating scale(NRS)scores for rest and movement were recorded at 2,4,6,12,24 and 48 hours postoperatively,as well as the Quality of Recovery-15(QoR-15)scores at 1 day preoperatively,1 and 3 days postoperatively.The perioperative anesthetic agent consumption,PCIA pressing frequency,remedial analgesia use in 48 h,postoperative nausea and vomiting(PONV)incidence and time of first out-of-bed mobilization were also recorded.Results Compared with the transversus abdominis group,the quadratus lumborum group had lower movement NRS scores at 2,4,6,12,24 and 48 hours postoperatively,and lower rest NRS scores at 2,4,6,12 and 24 hours postoperatively(P<0.05).The quadratus lumborum group had higher QoR-15 scores at 1 and 3 days postoperatively(P<0.05).Patients in the quadratus lumborum group had reduced perioperative remifentanil and sufentanil consumption,postoperative 48-hour rescue analgesia use,PCIA pressing frequency,PONV incidence and time of first out-of-bed mobilization(P<0.05).Conclusion QLB-LSAL block provides superior analgesic effects and recovery quality compared to TAPB block after LPH.
9.The role of PINK1/Parkin-mediated mitophagy in mechanical imbalance-induced endplate cartilage degeneration
Quan ZHENG ; Ming-Fan WU ; Song SHAO ; Liang-Ye SUN ; Jun-Sheng XU
Journal of Regional Anatomy and Operative Surgery 2024;33(3):189-193
Objective To detect the changes of mitophagy level in rats with endplate cartilage degeneration induced by spinal instability,and explore the role of PINK1/Parkin-mediated mitophagy in endplate cartilage and intervertebral disc degeneration.Methods The rat spinal instability model was established by surgically removing the superspinal and interspinal ligaments of L2 to L5,and cleaning the bilateral articular processes of the L2 to L5.Eighteen SD rats were divided into the normal group,the degenerative group,and the carbonyl cyanide 3-chlorophenylhydrazone(CCCP)group,with 6 rats in each group.The rats in the normal group had no special treatment,the rats in the degenerative group constructed a rat spinal instability model,and the rats in the CCCP group were injected with 5 μL of CCCP(10 μmol/L)in the intervertebral disc after the construction of spinal instability model.The changes of histomorphology in the endplate cartilage and intervertebral disc were abserved by HE staining,and the change of extracellular matrix of endplate cartilage was observed by safranin O-fast green staining.RT-PCR detected the mRNA expression of type Ⅱ collagen(COL-2A),aggrecan(ACAN),PINK1 and Parkin in each group.The changes of the protein expression levels of COL-2A,ACAN,PINK1,Parkin and mitochondrial membrane proteins of Tomm20 and Timm23 were detected by Western blot.Results Compared with the normal group,the intervertebral disc nucleus pulposus of rats in the degenerative group was significantly destroyed and the secretion of extracellular matrix of endplate chondrocytes decreased;while the structure of intervertebral discs for rats in the CCCP group was more intact,and the secretion of extracellular matrix of endplate chondrocytes was significantly increased compared with that in the degenerative group.Compared with the normal group,the expression of COL-2A and ACAN in endplate cartilage tissues of rats in the degenerative group were significantly down-regulated(P<0.05),the expression of mitochon-drial autophagy-related genes of PINK1 and Parkin were significantly decreased(P<0.05),and the expression of mitochondrial membrane proteins of Tomm20 and Timm23 were increased(P<0.05).Compared with the degenerative group,the expression of COL-2A,ACAN,PINKI and Parkin in the endplate cartilage tissue of rats in the CCCP group were significantly up-regulated(P<0.05),and the protein levels of Tomm20 and Timm23 were significantly down-regulated(P<0.05).Conclusion Rat spinal instability leads to a decrease level of mitophagy mediated by PINK1/Parkin signaling pathway in endplate cartilage,thereby inducing endplate cartilage and intervertebral disc degeneration,and the activation of mitophagy can significantly reduce endplate cartilage and intervertebral disc degeneration.
10.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.

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