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.Construction of a prognostic model and drug prediction for clear cell renal cell carcinoma based on endoplasmic reticulum stress-related lncRNA
Yuan LI ; Zhuoyang LI ; Geliang LIU ; Chaoyang HU ; Peifeng HE ; Qi YU
Journal of Modern Urology 2024;29(2):158-167
【Objective】 To construct a prognostic model of clear cell renal cell carcinoma (ccRCC) based on endoplasmic reticulum stress (ERS)-related long non-coding ribonucleotides (lncRNA),so as to explore the correlation between immune cell infiltration and prognosis of ccRCC patients,and to search for new drugs for the treatment of ccRCC. 【Methods】 The transcriptome and clinical data of cancerous and paracancerous tissues of ccRCC were obtained from the TCGA database.The ERS-associated gene set was obtained from the MSigDB database.ERS co-expressed lncRNAs were screened with Pearson correlation analysis.ERS-related lncRNA (ERSRL) with prognostic significance were screened with Lasso regression,univariate and multivariate Cox regression analyses,and a prognostic model was constructed.The risk value of each sample was calculated according to the prognostic model formula.The patients were divided into high- risk and low- risk groups for survival difference analysis.The predictive performance of the prognostic model was evaluated with survival curve,receiver operating characteristic (ROC) curve and calibration curve.The infiltration of immune cells in high-and low-risk groups was analyzed with CIBERSORT database.The relationship between ERSRL and drug sensitivity was analyzed with GDSC database to identify drugs with potential efficacy against ccRCC. 【Results】 A total of 9 lncRNAs with independent prognostic significance were screened to construct the prognostic model.Kaplan-Meier analysis showed significant survival differences between the high- and low-risk groups.Univariate and multivariate Cox regression analyses showed that age,grade,stage and risk score could be used as independent prognostic factors.The area under the ROC curve (AUC) of the 1-,3-,and 5-year survival rates of the training set were 0.754 (95%CI:0.659-0.848),0.744 (95%CI:0.667-0.815),and 0.759 (95%CI:0.662-0.820),respectively,and the C-index was 0.777 (95%CI:0.759-0.796).Immune infiltration results showed that plasma cells,activated memory CD4+T cells,regulatory T cells,M0 macrophages,and activated mast cell infiltration levels were higher in the high-risk group than those in the low-risk group.Drug susceptibility analysis identified 12 drugs with potential curative effects on ccRCC,including AZD8055. 【Conclusion】 Based on 9 ERSRLs,a prognostic model for ccRCC patients was constructed,and 12 drugs with potential therapeutic effects were screened,including AZD8055.
3.Content Feature Mining of Medical Reviews and Its Impact on Patients' Utilization of Online Consultation Services
Zhilin JI ; Qi YU ; Jiao LU ; Peifeng HE ; Qichao GAO
Journal of Medical Informatics 2024;45(7):62-67,102
Purpose/Significance To expound the content features of online medical reviews and its impact on the utilization of pa-tients'online consultation services,and to provide references for the information management of online medical platforms.Method/Process The LDA topic model based on TF-IDF is constructed,the semantic analysis method based on sentiment dictionary is adopted to mine the content features of online medical reviews,and the principal component analysis(PC A)is applied to classify and explore them,and the regression analysis is carried out by binary logistic.Result/Conclusion The content features of online medical reviews are divided into 3 categories,including 9 indicators.Among them,the attributes of reviewers,timeliness,consultation process,service atti-tude and platform feedback have a significant impact on the utilization of efficient online consultation services by patients.It is suggested to improve the utilization level of online consultation services by optimizing related services of online medical platform review section.
4.Study on the strategy of medical security for rare diseases in China from the perspective of public concern and emotion:taking nosinasine as an example
Yangfang TAI ; Ying GUO ; Ziqiong WANG ; Junhui WANG ; Guomin HUA ; Huili YANG ; Xiaojie WANG ; Peifeng HE
China Pharmacy 2023;34(7):774-779
OBJECTIVE To mine the focus and emotional attitude of the public on rare diseases, and to provide decision- making reference for relevant departments to formulate and implement relevant policies, systems and strategies for medical security of rare diseases. METHODS Latent Dirichlet allocation (LDA) topic model and sentiment analysis method were used to analyze the comment text of short videos related to the “nosinasine” medical insurance admission event on the Bilibili video website, mine the theme and sentiment tendency of the text, and put forward relevant strategy suggestions. RESULTS A total of 8 videos with tens of thousands of playback and 7 109 text data were obtained. According to the LDA analysis, online public paid attention to 9 topics related to rare diseases (the price of rare disease drugs, the inclusion of rare disease drugs in medical insurance, the status quo of research and development of rare disease drugs, the scope of medical insurance and the medical security system, the plight of rare disease patients, the prevention and screening of rare diseases, the value of rare disease drugs in medical insurance, the Chinese and western medical methods of rare diseases, and the supply and demand status of rare disease drugs), which could be summarized into 4 categories according to the objects of concern (rare disease drugs, rare disease medical insurance, rare disease medical and health services and rare disease patient groups). On the whole, the emotional tendency of the Internet public towards each topic showed a low positive and high negative tendency. CONCLUSIONS The public paid more attention to the price, research and development, supply and demand of rare disease drugs, and was deeply worried about the current medical status of rare diseases in China. To strengthen and improve the medical security for patients with rare diseases, such as actively carrying out public health services for rare diseases, strengthening cooperation in the diagnosis and treatment of rare diseases, and researching rare disease drugs, etc. Chinese medical and health departments can make concerted efforts in medical and health services, drug supply security, medical security and other social security.
5.Protein-based Bioinformatics Analysis of Cervical Cancer Related Genes
Lingjing CHENG ; Hetong LI ; Shengxiao ZHANG ; Hongqi LIU ; Qi YU ; Chaoyue ZHENG ; Shuang FENG ; Teng KONG ; Xiangfei SUN ; Peifeng HE ; Xiaoping LYU
Journal of Medical Informatics 2023;44(12):47-54
Purpose/Significance To explore the characteristics and clinical significance of differentially expressed genes closely re-lated to HPV E6/E7 by using bioinformatics.Method/Process The cervical tissue and clinical information of cervical cancer in TCGA and GTEx of UCSC are used as the training set.The expression profile chip GSE63514 related to cervical cancer in GEO is used as the validation set.Firstly,the limma package of R software is used to screen DEGs of tumor and normal samples,and Venn map of genes re-lated to E6/E7 protein in MigDB is made.Survival analysis is performed by survival kit and verified by ROC and protein expression lev-els.Secondly,key genes are obtained by copy number variation and methylation correlation.Finally,the specific co-expression network is constructed and enrichment analysis and immune infiltration analysis are performed.Result/Conclusion There are 101 differentially expressed genes related to HPV E6/E7 protein,and three genes are found to have significance after screening,namely E2F1,MCM4 and PCNA.At the same time,it is found that the genes in the specific coexpression network are significantly enriched in the DNA replication and chromosome organization pathways.Immune correlation analysis shows that key genes are significantly associated with CD4 T cells,B cells and neutrophils.DNA replication,chromosome organization,etc.,are the molecular mechanisms and key genes significantly related to the development of cervical squamous cell carcinoma and HPV E6/E7 encoded proteins.
6.Effect of DMARDs on differentially expressed genes in synovium of rheumatoid arthritis
Lingjing CHENG ; Shengxiao ZHANG ; Qi YU ; Chaoyue ZHENG ; Shuang FENG ; Teng KONG ; Xiangfei SUN ; Peifeng HE ; Xuechun LU
Chinese Journal of Rheumatology 2023;27(8):541-544,C8-4-C8-6,F3
Objective:To identify differentially expressed genes (DEGs) associated with the progression of synovitis in RA by using bioinformatics analysis and explore the effects of DMARDs such as methotrexate, tocilizumab and rituximab on the DEGs in RA synovium.Methods:RA expression profile microarray data GSE7307、GSE12021、GSE55457、GSE55235、GSE77298、GSE89408 were acquired from the public gene chip database (GEO), including 113 synovial tissue samples from RA and 70 healthy controls (HC). At the same time, synovial expression microarrays GSE45867, GSE24742 and GSE97165 after DMARDs treatment were obtained. These data included 8 samples treated with methotrexate, 12 treated with tocilizumab, 12 treated with rituximab and 19 treated with combined tDMARDs. R software was used to screen DEGs and Venn plots using gene ontology function enrichment and Kyoto encyclopedia of genes and genomes pathway enrichment analysis. Hub genes were selected by STRING online analysis tool and Cytoscape software.Results:Compared with HC, 797 DEGs were up-regulated and 434 DEGs were down-regulated in the synovial tissue of RA. These DEGs were mainly enriched in T cell activation, immune response-activating cell surface receptor signaling pathway. Using Cytoscape and cytoHubba to obtain 5 sets of DEGs based on the STRING database model, the degree algorithm screened out 10 hub genes: LCK, SYK, PTPRC, HLA-DRA, LYN, NCAPG, TOP2A, JUN, CXCR4, CCNB1. Methotrexate treatment significantly up-regulated 20 DEGs and down-regulated 30 DEGs. Rituximab treatment up-regulated 100 DEGs and down-regulated 55 DEGs. Tocilizumab treatment up-regulated 91 DEGs and down-regulated 317 DEGs. These altered DEGs were enriched in regulating cell adhesion, leukocyte-cell adhesion, leukocyte transfer, and insulin-like growth factor receptor signaling pathways. It was worth noting that after treatment, a total of 306 high-expressing DEGs were down-regulated, and 36 low-expressing DEGs were up-regulated.Conclusion:LCK, insulin-like growth factor receptor signaling pathway, etc. are the responsible molecular mechanisms and key pivot genes for the occurrence and development of RA, and the treatment of DMARDs, which are closely related to the response of RA to the treatment of DMARDs.
7.Moving Rate of Positive Patient Results as a Quality Control Tool for High-Sensitivity Cardiac Troponin T Assays
Tingting LI ; Shunwang CAO ; Yi WANG ; Yujuan XIONG ; Yuting HE ; Peifeng KE ; Xianzhang HUANG
Annals of Laboratory Medicine 2021;41(1):51-59
Background:
A small shift in high-sensitivity cardiac troponin T (hs-cTnT) assays can lead to different result interpretation and consequent patient management. We explored whether a small bias could be detected using conventional internal quality control (QC) procedures, evaluated the performance of moving average (MA)-based QC procedures, and proposed a new QC procedure based on the moving rate (MR) of positive patient results of hs-cTnT assays.
Methods:
The ability of conventional QC to detect a 5 ng/L bias was examined using the 1 3s/ 22s/R4s multi-rule procedure as deviation rules.We developed MA and MR procedures for the hs-cTnT assay using eight months of patient data. The performance of different MA or MR procedures was investigated by calculating the median number of patient samples affected until a bias introduced into the dataset was detected (MNPed). After comparing the MNPed across different procedures, we selected an optimal MA or MR procedure for validation. Validation graphs were plotted using the minimum, median, and maximum number of results affected until bias detection.
Results:
Our conventional QC procedures could not detect a positive bias of 5 ng/L. When a positive bias was introduced, MNPed was much higher using MA than using MR, with cut-off values of 5 ng/L and 14 ng/L, respectively. MR validation charts for optimal procedures provided insight into the MR performance.
Conclusions
The MR procedure could detect different errors with few false alarms. In the hs-cTnT assay, the MR procedure with a smaller cut-off value outperformed MA and conventional QC procedures for small bias detection.
8.Construction of health data literacy education system characterized by knowledge map
Liang ZHANG ; Min ZHOU ; Peifeng HE ; Yanhua LÜ
Chinese Journal of Medical Education Research 2020;19(1):7-11
Thanks to the comprehension of health data literacy courses in medical colleges and universities at home and abroad, this paper proposed a multi-level health data literacy education system featuring knowledge maps for undergraduates, postgraduates and students majoring in medical informatics, from basic knowledge of health data, basic technology of knowledge maps, analysis methods and tools, application of knowledge maps and health data ethics. The study results have positive significances for improving students' data processing ability in medical colleges and universities, and promoting medical development fundamentally.
9.Efficacy and Safety of Colesevelam Hydrochloride Combined with Other Hypoglycemic Drugs in the Treatment of T 2DM: A Meta-analysis
Qi YU ; Chenchen JIA ; Pengli JIA ; Peifeng HE
China Pharmacy 2019;30(21):2998-3003
OBJECTIVE: To systematically review the efficacy and safety of colesevelam hydrochloride combined with other hypoglycemic drugs in the treatment of T2DM, and to provide evidence-based reference for clinical treatment of T2DM. METHODS: Retrieved from PubMed, Embase, Medline, Cochrane Library, CJFD, VIP and Wanfang database during database establishement-Jul. 2019, randomized controlled trials (RCT) about the efficacy and safety of colesevelam hydrochloride combined with other hypoglycemic drugs (trial group) vs. placebo or other hypoglycemic drugs (control group) in the treatment of T2DM were collected. After extracting data from clinical studies that met the inclusion criteria, the quality of the studies was evaluated by Cochrane System Evaluator Manual 5.1.0. Meta-analysis was conducted by using Rev Man 5.3 statistical software in respects of the levels HbA1c, FPG, LDL-C, the incidence of total ADR, incidence of hypoglycemia and incidence of gastrointestinal ADR. RESULTS: A total of 11 RCTs were included, involving 2 625 patients. Results of Meta-analysis showed that HbA1c levels [MD=-0.37, 95%CI(-0.51, -0.22),P<0.001], FPG level [MD=-0.47, 95%CI(-0.88, -0.07), P=0.02] and LDL-C level [MD=-0.38, 95%CI(-0.49, -0.28), P<0.001] in trial group were significantly lower than control group, with statistical significance. In terms of safety, the incidence of total ADR [OR=1.24, 95%CI(1.06, 1.45), P=0.007] and gastrointestinal ADR [OR=1.78,95%CI(1.05, 3.02),P=0.03] in trial group were significantly higher than control group, with statistical significance. There was no significant difference in the incidence of hypoglycemia [OR=1.03, 95%CI(0.62,1.72),P=0.90]. CONCLUSIONS: Colesevelam hydrochloride combined with other hypoglycemic drugs can effectively reduce the levels of HbA1c, FPG and LDL-C in T2DM patients, but attention should be paid to the occurrence of gastrointestinal ADR.
10.Key functions of mobile medical APP used in China and suggestions for their development
Ge ZHANG ; Qi YU ; Peifeng HE
Chinese Journal of Medical Library and Information Science 2017;26(4):21-25,33
The functions of the top 15 medical APP were compared.Their major functions of medical advice, information service and medical service were analyzed.The key functions of mobile medical APP used in China were described with suggestions for their development.

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