1.Identification and drug sensitivity analysis of key molecular markers in mesenchymal cell-derived osteosarcoma
Haojun ZHANG ; Hongyi LI ; Hui ZHANG ; Haoran CHEN ; Lizhong ZHANG ; Jie GENG ; Chuandong HOU ; Qi YU ; Peifeng HE ; Jinpeng JIA ; Xuechun LU
Chinese Journal of Tissue Engineering Research 2025;29(7):1448-1456
BACKGROUND:Osteosarcoma has a complex pathogenesis and a poor prognosis.While advancements in medical technology have led to some improvements in the 5-year survival rate,substantial progress in its treatment has not yet been achieved. OBJECTIVE:To screen key molecular markers in osteosarcoma,analyze their relationship with osteosarcoma treatment drugs,and explore the potential disease mechanisms of osteosarcoma at the molecular level. METHODS:GSE99671 and GSE284259(miRNA)datasets were obtained from the Gene Expression Omnibus database.Differential gene expression analysis and Weighted Gene Co-expression Network Analysis(WGCNA)on GSE99671 were performed.Functional enrichment analysis was conducted using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes separately for the differentially expressed genes and the module genes with the highest positive correlation to the disease.The intersection of these module genes and differentially expressed genes was taken as key genes.A Protein-Protein Interaction network was constructed,and correlation analysis on the key genes was performed using CytoScape software,and hub genes were identified.Hub genes were externally validated using the GSE28425 dataset and text validation was conducted.The drug sensitivity of hub genes was analyzed using the CellMiner database,with a threshold of absolute value of correlation coefficient|R|>0.3 and P<0.05. RESULTS AND CONCLUSION:(1)Differential gene expression analysis identified 529 differentially expressed genes,comprising 177 upregulated and 352 downregulated genes.WGCNA analysis yielded a total of 592 genes with the highest correlation to osteosarcoma.(2)Gene Ontology enrichment results indicated that the development of osteosarcoma may be associated with extracellular matrix,bone cell differentiation and development,human immune regulation,and collagen synthesis and degradation.Kyoto Encyclopedia of Genes and Genomes enrichment results showed the involvement of pathways such as PI3K-Akt signaling pathway,focal adhesion signaling pathway,and immune response in the onset of osteosarcoma.(3)The intersection analysis revealed a total of 59 key genes.Through Protein-Protein Interaction network analysis,8 hub genes were selected,which were LUM,PLOD1,PLOD2,MMP14,COL11A1,THBS2,LEPRE1,and TGFB1,all of which were upregulated.(4)External validation revealed significantly downregulated miRNAs that regulate the hub genes,with hsa-miR-144-3p and hsa-miR-150-5p showing the most significant downregulation.Text validation results demonstrated that the expression of hub genes was consistent with previous research.(5)Drug sensitivity analysis indicated a negative correlation between the activity of methotrexate,6-mercaptopurine,and pazopanib with the mRNA expression of PLOD1,PLOD2,and MMP14.Moreover,zoledronic acid and lapatinib showed a positive correlation with the mRNA expression of PLOD1,LUM,MMP14,PLOD2,and TGFB1.This suggests that zoledronic acid and lapatinib may be potential therapeutic drugs for osteosarcoma,but further validation is required through additional basic experiments and clinical studies.
2.Investigation of the effects of Gabra3 gene knockout on sleep regulation in mouse neurons
Lizhong ZHANG ; Yujie TANG ; Yi SUN ; Qi YU ; Xuechun LU
Space Medicine & Medical Engineering 2025;36(3):206-213
Objective To construct a Gabra3 gene knockout cell model and explore transcriptomic and proteomic alterations in murine neuronal cells,in order to investigate the molecular mechanisms underlying the increased depth of slow-wave sleep observed following Gabra3 deletion.Methods Multiple sgRNA sequences were designed,and the CRISPR/Cas9 system was used to knock out the Gabra3 gene in the murine GT1-7 neuronal cell line.Gene sequencing was performed to assess knockout efficiency,and TA cloning was used to validate the knockout results.Protein immunoblotting experiments were conducted to confirm the knockout,while cell proliferation assays were used to validate the knockout phenotype.Total RNA and protein were extracted for transcriptomic and proteomic sequencing,respectively.A range of bioinformatics analyses was conducted to assess the functional consequences of Gabra3 knockout in GT1-7 neuronal cells.Results Following Gabra3 gene knockout,pathways related to cortisol and aldosterone synthesis and secretion,as well as circadian rhythm,were significantly enriched.Three key genes,BMP2,GLI2,and DLL1,were identified.Proteomic profiling revealed widespread disturbances in protein expression following Gabra3 knockout.Conclusion Gabra3 gene knockout may increase slow-wave sleep depth by modulating the expression of hormone secretion-related genes and altering circadian regulatory pathways.
3.Analysis of surveillance results of water-borne endemic fluorosis in Anhui Province from 2019 to 2022
Chen YU ; Xian XU ; Cuicui TIAN ; Zijian LIU ; Xuechun LU ; Tao ZHANG ; Weidong LI
Chinese Journal of Endemiology 2025;44(1):17-20
Objective:To investigate the current situation of water-borne endemic fluorosis in Anhui Province, and provide basic data for the adjusting the prevention and control measures.Methods:Using cross-sectional survey method, all villages in the water-borne endemic fluorosis areas were investigated in Anhui Province from 2019 to 2022. In water-borne endemic fluorosis village, the situation of water improvement project and the fluoride level of drinking water were investigated, and dental fluorosis of all children aged 8 - 12 was examined. The criteria for determining the achievement of control targets for water-borne endemic fluorosis in affected counties were based on the "Evaluation Measures for Control and Elimination of Key Endemic Diseases (2019 Edition)".Results:From 2019 to 2022, the rate of water improvement village in water-borne endemic fluorosis areas were 88.47% (1 527/1 726), 100% (1 726/1 726), 100% (1 726/1 726) and 100% (1 726/1 726), respectively. The qualified proportion of water fluoride in water-borne endemic fluorosis villages was 33.84% (584/1 726), 63.09% (1 089/1 726), 70.74% (1 221/1 726) and 74.33% (1 283/1 726), respectively. The prevalence rates of dental fluorosis in children aged 8 - 12 were 25.48% (45 461/178 440), 15.78% (27 959/177 200), 13.68% (23 505/171 880) and 12.66% (23 315/184 200), respectively. The proportion of affected counties that had achieved the control target of water-borne endemic fluorosis was 16% (4/25), 60% (15/25), 36% (9/25) and 40% (10/25), respectively.Conclusions:The water-borne endemic fluorosis areas in Anhui Province have improved the water fluoride qualification rate and reduced the incidence of fluorosis in children through prevention and control measures such as water improvement and fluoride reduction. However, the prevention and control efforts in key areas and counties need to be further improved.
4.Identification of differential genes in systemic sclerosis and prediction of traditional Chinese medicine
Shuang FENG ; Yangfang TAI ; Shengxiao ZHANG ; Peifeng HE ; Chaoyue ZHENG ; Lingjing CHENG ; Teng KONG ; Xiangfei SUN ; Qi YU ; Xuechun LU
Chinese Journal of Immunology 2025;41(1):107-115,中插1-中插2
Objective:The differentially expressed genes(DEGs)and activated signaling pathways in systemic sclerosis(SSc)were screened by bioinformatics methods,and Chinese medicines for potential treatment of SSc were explored,providing a new theoretical basis for the study of SSc and the screening of potential markers.Methods:The data sets GSE58095,GSE130953,GSE33463 and GSE58613 were selected from GEO database and divided into skin group and peripheral blood group according to the sample source.The DEGs of SSc patients was analyzed by R language,and the Wayne diagram was drawn to take the intersection of the two groups.Metascape was used for GO enrichment analysis and KEGG pathway enrichment analysis,and STRING and Cytoscape were used for protein interaction network analysis to find key pathways and hub genes.The core genes were mapped to the medical on-tology information retrieval platform,and related Chinese medicines for SSc treatment were screened.The effective components of Chi-nese medicines were obtained through TCMSP and HERB databases,and the target letters of active ingredients were obtained through swiss database.The"drug-active ingredient-target"network was constructed by Cytoscape.Results:Total 218 DEGs were identified from the skin group of patients with SSc,and 283 DEGs were screened from peripheral blood of patients with SSc.Among them,there were 7 DEGs co-upregulated in skin and peripheral blood,namely ISG15,LGALS3BP,BST2,C1QB,IFI27,CEACAM1 and FBP1.CAMK2N1 was up-regulated in skin but down-regulated in peripheral blood,ARG1 was down-regulated in skin but up-regulated in pe-ripheral blood.GO and KEGG analysis of SSc DEGs showed that these genes were significantly enriched in inflammatory response,he-moglobin complex,immune receptor activity and extracellular matrix.The results of protein interaction network suggest that more than 10 genes such as COL1A1,CTGF12,IL1B,IFNG and JUN may be potential markers of SSc and core genes of therapeutic targets.The potential Chinese medicines screened for SSc treatment include ginseng,sanguisorba,convolvula,wolfberry,safflower,etc.The main components of these herbs were β-sitosterol,quercetin,kaempferol,stigmasterol,luteolin,sitosterol,Spinasterol,and the target were AKR1B1,AR,CYP1B1,XDH,etc.Conclusion:This study uses bioinformatics to screen out core genes that may be potential markers and therapeutic targets for SSc,which is expected to be a new target for the early diagnosis and mechanism research of SSc.Meanwhile,the mapped Chinese medicine and its effective components can provide ideas for the research and development of Chinese medicine compounds for the treatment of SSc.
5.Current status and standardization issues analysis of outcome indicators in randomized controlled trials of treating vascular dementia with acupuncture
Liang BAO ; Xuechun DING ; Zhenfeng ZHANG ; Zhenggang LU ; Chunning LI ; Wenshuai XU ; Qiucheng GUO ; Fei LI
Journal of Beijing University of Traditional Chinese Medicine 2025;48(10):1470-1480
Objective To analyze the current status of outcome measures in randomized controlled trials(RCTs)of acupuncture treatment for vascular dementia(VD)and promote the development of a standardized set of outcome measures.Methods Chinese and English literature databases were searched,including the Chinese Medical Periodical Full-Text Database,the Chinese Biology Medicine disc,China National Knowledge Infrastructure,Wanfang Data,VIP Database,PubMed,Embase,the Cochrane Library,MEDLINE,Web of Science,Chinese Clinical Trials Registry,and the International Traditional Medicine Clinical Trial Registry.Two researchers independently screened RCT literature on acupuncture treatment for VD between January 1,2015 and January 1,2025,risk of bias was assessed using the Cochrane Risk of Bias 2 tool.Extract basic study information,intervention measures,diagnostic criteria for both Chinese and Western medicine,TCM syndromes,and outcome measures.Summarize the indicator domains of RCT studies on acupuncture treatment for VD,and analyze the basic information and outcome measures of the included studies.Results A preliminary search identified 2,898 articles,of which 93 RCTs were ultimately included.These studies involved 84 outcome measures,covering six indicator domains:symptoms/signs(23.81%),traditional Chinese medicine(TCM)syndromes(3.57%),medical checkups(60.71%),quality of life(5.95%),safety assessment(4.76%),and prognosis follow-up(1.19%).A total of 91(97.85%)RCTs reported treatment duration,ranging from 2 to 24 weeks;72(77.42%)RCTs used clinical efficacy as the outcome indicator;11 studies(11.83%)reported safety assessments and adverse events.Conclusion Currently,the RCT study design for acupuncture treatment of VD lacks unified standards and has numerous methodological issues.These include insufficient description of sample size estimation processes,strong reliance on subjective rating scales,ambiguous definitions of primary and secondary outcome measures,incomplete integration of Chinese and Western medical indicators,and insufficient reflection of individualized syndrome differentiation and treatment characteristics.In addition,safety assessments and follow-up mechanisms remain relatively weak.Future research should focus on the essential nature of VD,establish a core set of indicators aligned with the clinical characteristics of traditional Chinese medicine,promote the scientific and standardized development of acupuncture research for VD,and provide more compelling evidence-based support for clinical practice.
6.Mechanism of bexarotene in suppressing double hit lymphoma via modulation of the c-Myc pathway:Insights from WGCNA
Tiantian HE ; Hongyi LI ; Jie GENG ; Chuandong HOU ; Hong ZHANG ; Hui ZHANG ; Peng ZHAO ; Xuechun LU ; Peifeng HE
Chinese Journal of Cancer Biotherapy 2025;32(7):716-722
Objective:To investigate the molecular mechanisms of bexarotene in treating double hit lymphoma(DHL)based on Weighted Gene Co-expression Network Analysis(WGCNA),thereby providing potential targets and experimental evidence for DHL treatment.Methods:The gene expression datasets GSE44164 and GSE43677 were downloaded from the Gene Expression Omnibus(GEO)database,and differentially expressed genes(DEGs)were identified.WGCNA was employed to identify gene modules associated with DHL.A protein-protein interaction(PPI)network was constructed to screen for key hub genes.Drug-gene association analysis was conducted using the EpiMed platform to identify potential targeted drugs for DHL.The effects of bexarotene on DHL cell proliferation and key protein expression were evaluated using the CCK-8 assay and Western blotting(WB),and its effects on cell apoptosis was evaluated using flow cytometry.Results:WGCNA identified a turquoise module highly associated with DHL,and 10 hub genes(COL1A2,COL3A1,MMP2,COL5A2,DCN,BGN,FN1,MMP9,FBN1,and LUM)were screened from the PPI network.Drug association analysis nominated bexarotene as a potential therapeutic agent.In vitro validation demonstrated that bexarotene significantly inhibited U2932 cell viability(P<0.05),promoted cell apoptosis(P<0.001),and downregulated c-Myc and COL1A2 expression(P<0.05).Conclusion:Bexarotene may exert anti-DHL effects by suppressing the c-Myc signaling pathway and modulating extracellular matrix-related genes.Further studies are warranted to validate its in vivo efficacy and potential for combination therapy.
7.Current status and standardization issues analysis of outcome indicators in randomized controlled trials of treating vascular dementia with acupuncture
Liang BAO ; Xuechun DING ; Zhenfeng ZHANG ; Zhenggang LU ; Chunning LI ; Wenshuai XU ; Qiucheng GUO ; Fei LI
Journal of Beijing University of Traditional Chinese Medicine 2025;48(10):1470-1480
Objective To analyze the current status of outcome measures in randomized controlled trials(RCTs)of acupuncture treatment for vascular dementia(VD)and promote the development of a standardized set of outcome measures.Methods Chinese and English literature databases were searched,including the Chinese Medical Periodical Full-Text Database,the Chinese Biology Medicine disc,China National Knowledge Infrastructure,Wanfang Data,VIP Database,PubMed,Embase,the Cochrane Library,MEDLINE,Web of Science,Chinese Clinical Trials Registry,and the International Traditional Medicine Clinical Trial Registry.Two researchers independently screened RCT literature on acupuncture treatment for VD between January 1,2015 and January 1,2025,risk of bias was assessed using the Cochrane Risk of Bias 2 tool.Extract basic study information,intervention measures,diagnostic criteria for both Chinese and Western medicine,TCM syndromes,and outcome measures.Summarize the indicator domains of RCT studies on acupuncture treatment for VD,and analyze the basic information and outcome measures of the included studies.Results A preliminary search identified 2,898 articles,of which 93 RCTs were ultimately included.These studies involved 84 outcome measures,covering six indicator domains:symptoms/signs(23.81%),traditional Chinese medicine(TCM)syndromes(3.57%),medical checkups(60.71%),quality of life(5.95%),safety assessment(4.76%),and prognosis follow-up(1.19%).A total of 91(97.85%)RCTs reported treatment duration,ranging from 2 to 24 weeks;72(77.42%)RCTs used clinical efficacy as the outcome indicator;11 studies(11.83%)reported safety assessments and adverse events.Conclusion Currently,the RCT study design for acupuncture treatment of VD lacks unified standards and has numerous methodological issues.These include insufficient description of sample size estimation processes,strong reliance on subjective rating scales,ambiguous definitions of primary and secondary outcome measures,incomplete integration of Chinese and Western medical indicators,and insufficient reflection of individualized syndrome differentiation and treatment characteristics.In addition,safety assessments and follow-up mechanisms remain relatively weak.Future research should focus on the essential nature of VD,establish a core set of indicators aligned with the clinical characteristics of traditional Chinese medicine,promote the scientific and standardized development of acupuncture research for VD,and provide more compelling evidence-based support for clinical practice.
8.Analysis of surveillance results of water-borne endemic fluorosis in Anhui Province from 2019 to 2022
Chen YU ; Xian XU ; Cuicui TIAN ; Zijian LIU ; Xuechun LU ; Tao ZHANG ; Weidong LI
Chinese Journal of Endemiology 2025;44(1):17-20
Objective:To investigate the current situation of water-borne endemic fluorosis in Anhui Province, and provide basic data for the adjusting the prevention and control measures.Methods:Using cross-sectional survey method, all villages in the water-borne endemic fluorosis areas were investigated in Anhui Province from 2019 to 2022. In water-borne endemic fluorosis village, the situation of water improvement project and the fluoride level of drinking water were investigated, and dental fluorosis of all children aged 8 - 12 was examined. The criteria for determining the achievement of control targets for water-borne endemic fluorosis in affected counties were based on the "Evaluation Measures for Control and Elimination of Key Endemic Diseases (2019 Edition)".Results:From 2019 to 2022, the rate of water improvement village in water-borne endemic fluorosis areas were 88.47% (1 527/1 726), 100% (1 726/1 726), 100% (1 726/1 726) and 100% (1 726/1 726), respectively. The qualified proportion of water fluoride in water-borne endemic fluorosis villages was 33.84% (584/1 726), 63.09% (1 089/1 726), 70.74% (1 221/1 726) and 74.33% (1 283/1 726), respectively. The prevalence rates of dental fluorosis in children aged 8 - 12 were 25.48% (45 461/178 440), 15.78% (27 959/177 200), 13.68% (23 505/171 880) and 12.66% (23 315/184 200), respectively. The proportion of affected counties that had achieved the control target of water-borne endemic fluorosis was 16% (4/25), 60% (15/25), 36% (9/25) and 40% (10/25), respectively.Conclusions:The water-borne endemic fluorosis areas in Anhui Province have improved the water fluoride qualification rate and reduced the incidence of fluorosis in children through prevention and control measures such as water improvement and fluoride reduction. However, the prevention and control efforts in key areas and counties need to be further improved.
9.Identification of differential genes in systemic sclerosis and prediction of traditional Chinese medicine
Shuang FENG ; Yangfang TAI ; Shengxiao ZHANG ; Peifeng HE ; Chaoyue ZHENG ; Lingjing CHENG ; Teng KONG ; Xiangfei SUN ; Qi YU ; Xuechun LU
Chinese Journal of Immunology 2025;41(1):107-115,中插1-中插2
Objective:The differentially expressed genes(DEGs)and activated signaling pathways in systemic sclerosis(SSc)were screened by bioinformatics methods,and Chinese medicines for potential treatment of SSc were explored,providing a new theoretical basis for the study of SSc and the screening of potential markers.Methods:The data sets GSE58095,GSE130953,GSE33463 and GSE58613 were selected from GEO database and divided into skin group and peripheral blood group according to the sample source.The DEGs of SSc patients was analyzed by R language,and the Wayne diagram was drawn to take the intersection of the two groups.Metascape was used for GO enrichment analysis and KEGG pathway enrichment analysis,and STRING and Cytoscape were used for protein interaction network analysis to find key pathways and hub genes.The core genes were mapped to the medical on-tology information retrieval platform,and related Chinese medicines for SSc treatment were screened.The effective components of Chi-nese medicines were obtained through TCMSP and HERB databases,and the target letters of active ingredients were obtained through swiss database.The"drug-active ingredient-target"network was constructed by Cytoscape.Results:Total 218 DEGs were identified from the skin group of patients with SSc,and 283 DEGs were screened from peripheral blood of patients with SSc.Among them,there were 7 DEGs co-upregulated in skin and peripheral blood,namely ISG15,LGALS3BP,BST2,C1QB,IFI27,CEACAM1 and FBP1.CAMK2N1 was up-regulated in skin but down-regulated in peripheral blood,ARG1 was down-regulated in skin but up-regulated in pe-ripheral blood.GO and KEGG analysis of SSc DEGs showed that these genes were significantly enriched in inflammatory response,he-moglobin complex,immune receptor activity and extracellular matrix.The results of protein interaction network suggest that more than 10 genes such as COL1A1,CTGF12,IL1B,IFNG and JUN may be potential markers of SSc and core genes of therapeutic targets.The potential Chinese medicines screened for SSc treatment include ginseng,sanguisorba,convolvula,wolfberry,safflower,etc.The main components of these herbs were β-sitosterol,quercetin,kaempferol,stigmasterol,luteolin,sitosterol,Spinasterol,and the target were AKR1B1,AR,CYP1B1,XDH,etc.Conclusion:This study uses bioinformatics to screen out core genes that may be potential markers and therapeutic targets for SSc,which is expected to be a new target for the early diagnosis and mechanism research of SSc.Meanwhile,the mapped Chinese medicine and its effective components can provide ideas for the research and development of Chinese medicine compounds for the treatment of SSc.
10.Causal Relationship Between Gut Microbiota and Duodenal Ulcer:A Two-sample Mendelian Randomization Study
Yaqi HOU ; Yuan LI ; Lixuan YAN ; Wanli GONG ; Yang WANG ; Xuechun LU ; Peifeng HE ; Qi YU
Chinese Journal of Gastroenterology 2024;29(5):276-282
Background:The diversity and function of gut microbiota have been regarded as crucial factors affecting human health.With the advances in genetics and epidemiology,especially the application of Mendelian randomization analysis,a novel perspective has been provided for profoundly uncovering the causal relationship between gut microbiota and duodenal ulcer.Aims:To investigate the causal relationship between gut microbiota and duodenal ulcer through two-sample Mendelian randomization analysis.Methods:Genetic variation samples of the gut microbiota were screened from the MiBioGen database.Genetic loci related to duodenal ulcer were selected as instrumental variables from genome-wide association study.The inverse-variance weighted method,weighted median method,and MR-Egger regression analysis were used to assess the causal relationship between gut microbiota and duodenal ulcer.Tests for heterogeneity and horizontal pleiotropy were conducted to ensure the stability of the results.Results:Bacteroides(OR=0.998,95%CI:0.996-1.000,P=0.014),Prevotella_7(OR=0.999,95%CI:0.998-1.000,P=0.043)and Terrisporobacter(OR=0.998,95%CI:0.997-1.000,P=0.029)exhibited negative causal relationship with duodenal ulcer,while Bifidobacterium(OR=1.001,95%CI:1.000-1.003,P=0.046),Lachnoclostridium(OR=1.002,95%CI:1.001-1.004,P=0.007)and Olsenella(OR=1.001,95%CI:1.000-1.002,P=0.018)presented positive causal relationship with duodenal ulcer.The sensitivity analysis indicated that the influences of heterogeneity and horizontal pleiotropy on the causal relationship could be excluded.Conclusions:The two-sample Mendelian randomization analysis revealed that Bacteroides,Prevotella_7 and Terrisporobacter were protective factors for duodenal ulcer,while Bifidobacterium,Lachnoclostridium and Olsenella were risk factors.

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