1.Machine learning combined with bioinformatics screening of key genes for pulmonary fibrosis associated with cellular autophagy and experimental validation
Yuehong GONG ; Mengjun WANG ; Hang REN ; Hui ZHENG ; Jiajia SUN ; Junpeng LIU ; Fei ZHANG ; Jianhua YANG ; Junping HU
Chinese Journal of Tissue Engineering Research 2025;29(35):7679-7689
BACKGROUND:Early diagnosis of pulmonary fibrosis is the foundation for timely antifibrotic drug therapy.Therefore,exploring and discovering ideal biomarkers that can be effectively used for the early diagnosis of pulmonary fibrosis is crucial for the treatment of the disease.OBJECTIVE:To conduct an in-depth analysis of key autophagy-related genes involved in the process of pulmonary fibrosis by means of bioinformatics and machine learning techniques,in order to investigate whether autophagy-related core genes of pulmonary fibrosis can be used as reliable biomarkers in the assessment of the progression of pulmonary fibrosis.METHODS:Two datasets of pulmonary fibrosis,GSE24206 and GSE110147,were downloaded from the Gene Expression Omnibus(GEO)database(a public database developed and maintained by the U.S.National Center for Biotechnology Information to store and share bioinformatics data),and the gene expression matrices of these two datasets were normalized by using the"limma"package in R software.The autophagy-related genes were extracted from GeneCards database(a database created by the U.S.National Center for Biotechnology Information,which automatically integrates gene-centric data from about 200 Web sources,including genomic,transcriptomic,proteomic,genetic,clinical,and functional information).Differential gene analysis was performed on the pulmonary fibrosis dataset,and the common genes were extracted by cross-comparing the differential genes with the autophagy genes,so as to identify autophagy genes that may play a role in the process of pulmonary fibrosis.The intersecting genes were analyzed for functional enrichment and cellular immune infiltration by gene ontology and Kyoto Encyclopedia of Genes and Genomes.Core genes of pulmonary fibrosis associated with autophagy were screened by protein-protein interactions and machine learning,and core genes were subjected to the enrichment analysis.Diagnostic models were constructed from the identified core genes.Calibration curves were used to assess the predictive ability of the line graph model.An external dataset,GSE21369,was used to perform a receiver operating characteristic curve analysis to validate the expression profiles of pulmonary fibrosis genes associated with autophagy,as well as to predict Chinese herbs associated with the genes IL6 and COL1A2 via the Coremine database.Finally,human embryonic lung fibroblasts were cultured and modelled by transforming growth factor-β1 treatment,and the relative expression of genes in the model cells was verified using qRT-PCR.RESULTS AND CONCLUSION:(1)A total of 51 pulmonary fibrosis differential genes and 25 genes intersecting with autophagy genes were obtained.Gene ontology analysis showed that the 25 intersecting genes were related to extracellular matrix tissue,collagen metabolism,collagen pro-fibroblasts,and growth factor binding,etc.The results of Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that they were mainly related to the Phosphatidylinositol 3-kinase/protein kinase B signaling pathway and the signaling pathway of the extracellular matrix-receptor interactions.(2)Immunoinfiltration analysis revealed that the expression of activated memory CD4+T cells,M0 macrophages,and resting dendritic cells was significantly elevated in the pulmonary fibrosis group(P<0.05),showing a strong correlation.(3)Two autophagy signature genes involved in the progression of pulmonary fibrosis were identified:COL1A2 and IL6.The column-line diagram model showed that the two core genes predicted the onset of pulmonary fibrosis more accurately,and the receiver operating characteristic curve analysis showed that the two characteristic genes had diagnostic significance.COL1A2 and IL6 were related to the cell-cycle pathway,mitogen-activated protein kinase signaling pathway,Janus kinase-signal transduction and activator of transcription signaling pathway and cytokine-cytokine receptor interactions.A total of 20 Chinese herbs were predicted to be related to COL1A2 and IL6 genes,and their efficacies were mainly to clear away heat and detoxify toxins and to invigorate blood and move qi.COL1A2 and IL6 were verified to be highly expressed in pulmonary fibrosis.To conclude,COL1A2 and IL6 may be potential diagnostic biomarkers for pulmonary fibrosis,but its specificity to pulmonary fibrosis needs to be further investigated.
2.Machine learning combined with bioinformatics screening of key genes for pulmonary fibrosis associated with cellular autophagy and experimental validation
Yuehong GONG ; Mengjun WANG ; Hang REN ; Hui ZHENG ; Jiajia SUN ; Junpeng LIU ; Fei ZHANG ; Jianhua YANG ; Junping HU
Chinese Journal of Tissue Engineering Research 2025;29(35):7679-7689
BACKGROUND:Early diagnosis of pulmonary fibrosis is the foundation for timely antifibrotic drug therapy.Therefore,exploring and discovering ideal biomarkers that can be effectively used for the early diagnosis of pulmonary fibrosis is crucial for the treatment of the disease.OBJECTIVE:To conduct an in-depth analysis of key autophagy-related genes involved in the process of pulmonary fibrosis by means of bioinformatics and machine learning techniques,in order to investigate whether autophagy-related core genes of pulmonary fibrosis can be used as reliable biomarkers in the assessment of the progression of pulmonary fibrosis.METHODS:Two datasets of pulmonary fibrosis,GSE24206 and GSE110147,were downloaded from the Gene Expression Omnibus(GEO)database(a public database developed and maintained by the U.S.National Center for Biotechnology Information to store and share bioinformatics data),and the gene expression matrices of these two datasets were normalized by using the"limma"package in R software.The autophagy-related genes were extracted from GeneCards database(a database created by the U.S.National Center for Biotechnology Information,which automatically integrates gene-centric data from about 200 Web sources,including genomic,transcriptomic,proteomic,genetic,clinical,and functional information).Differential gene analysis was performed on the pulmonary fibrosis dataset,and the common genes were extracted by cross-comparing the differential genes with the autophagy genes,so as to identify autophagy genes that may play a role in the process of pulmonary fibrosis.The intersecting genes were analyzed for functional enrichment and cellular immune infiltration by gene ontology and Kyoto Encyclopedia of Genes and Genomes.Core genes of pulmonary fibrosis associated with autophagy were screened by protein-protein interactions and machine learning,and core genes were subjected to the enrichment analysis.Diagnostic models were constructed from the identified core genes.Calibration curves were used to assess the predictive ability of the line graph model.An external dataset,GSE21369,was used to perform a receiver operating characteristic curve analysis to validate the expression profiles of pulmonary fibrosis genes associated with autophagy,as well as to predict Chinese herbs associated with the genes IL6 and COL1A2 via the Coremine database.Finally,human embryonic lung fibroblasts were cultured and modelled by transforming growth factor-β1 treatment,and the relative expression of genes in the model cells was verified using qRT-PCR.RESULTS AND CONCLUSION:(1)A total of 51 pulmonary fibrosis differential genes and 25 genes intersecting with autophagy genes were obtained.Gene ontology analysis showed that the 25 intersecting genes were related to extracellular matrix tissue,collagen metabolism,collagen pro-fibroblasts,and growth factor binding,etc.The results of Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that they were mainly related to the Phosphatidylinositol 3-kinase/protein kinase B signaling pathway and the signaling pathway of the extracellular matrix-receptor interactions.(2)Immunoinfiltration analysis revealed that the expression of activated memory CD4+T cells,M0 macrophages,and resting dendritic cells was significantly elevated in the pulmonary fibrosis group(P<0.05),showing a strong correlation.(3)Two autophagy signature genes involved in the progression of pulmonary fibrosis were identified:COL1A2 and IL6.The column-line diagram model showed that the two core genes predicted the onset of pulmonary fibrosis more accurately,and the receiver operating characteristic curve analysis showed that the two characteristic genes had diagnostic significance.COL1A2 and IL6 were related to the cell-cycle pathway,mitogen-activated protein kinase signaling pathway,Janus kinase-signal transduction and activator of transcription signaling pathway and cytokine-cytokine receptor interactions.A total of 20 Chinese herbs were predicted to be related to COL1A2 and IL6 genes,and their efficacies were mainly to clear away heat and detoxify toxins and to invigorate blood and move qi.COL1A2 and IL6 were verified to be highly expressed in pulmonary fibrosis.To conclude,COL1A2 and IL6 may be potential diagnostic biomarkers for pulmonary fibrosis,but its specificity to pulmonary fibrosis needs to be further investigated.
3.Construction and initial application of a intervention programme for breastfeeding in infants with congenital heart disease
Qi ZHANG ; Ying GU ; Huimei WANG ; Yu SUN ; Xueping ZHANG ; Yuehong REN ; Mengxin ZHU ; Lan XING
Chinese Journal of Nursing 2024;59(22):2700-2709
Objective To construct an intervention programme for breastfeeding among mothers of infants with congenital heart disease and to verify its effect.Methods Taking the capability-opportunity-motivation-behaviour model as the theoretical basis,the first draft of the intervention programme was formed through literature search and semi-structured interviews,and 8 experts in the relevant fields were selected to conduct expert validation and determine the content of the program.By the consecutive sampling method,infants and their mothers who attended the cardiothoracic disease clinic of a tertiary-level children's specialist hospital in Shanghai from 4 May to 24 June 2023,with a day-old age of≤14 d and a confirmed diagnosis of CHD,were selected as the study subjects.They were divided into an experimental group and a control group,with 16 cases in each group,by the method of randomized grouping by district.The experimental group received breastfeeding intervention for mothers of infants with CHD on the basis of routine care;the control group received routine care and basic disease education and breastfeeding counselling.At 1 and 3 months of the infants with CHD,the 2 groups were compared in terms of exclusive breastfeeding rate,daily human milk as a percentage of total feeds,weight for age Z-score and height for age Z-score.Results A total of 1 round of expert validation was conducted,with a valid questionnaire recovery rate of 100%and an expert authority coefficient of 0.94.The breastfeeding intervention programme for mothers of infants with CHD is a comprehensive approach that encompasses 3 key dimensions,including capability,opportunity,and motivation.The programme is designed to enhance mothers'ability to recognize feeding signals,master breastfeeding techniques,and maintain successful breastfeeding practices.It also addresses common breastfeeding challenges and provides effective solutions.Additionally,it includes strategies for breastmilk management and fosters family support for breastfeeding.The programme offers medical information support on breastfeeding and aims to elevate mothers'understanding of its benefits.It involves systematic monitoring and recording of breastfeeding volumes,as well as thorough assessments and guidance on infant growth and development,including but not limited to the 10 specific entries related to the infant's progress.The results of the generalized estimating equations and repeated measures analysis of variance revealed statistically significant between-group differences(P<0.05)in the rates of exclusive breastfeeding,the proportion of daily human milk as a percentage of total feeds,and the weight-for-age(WAZ)and height-for-age(HAZ)z-scores of infants across the 2 groups at various time points.The results of simple effect analysis showed that the differences in exclusive breastfeeding rate,the proportion of daily human milk as a percentage of total feeds,WAZ and HAZ between the 2 groups before intervention were not statistically significant(P>0.05).At the age of 3 months of the infants after the intervention,the rate of exclusive breastfeeding in the experimental group was higher than that in the control group,and the difference was statistically significant(P=0.003).The proportion of daily human milk as a percentage of total feeds for infants in the intervention group at 1 and 3 months of age was higher than that in the control group,with a statistically significant difference(P<0.05).At 3 months of age,WAZ of the experimental group was higher than that of the control group,and the difference was statistically significant(P=0.037);HAZ of the experimental group was higher than that of the control group at 1 and 3 months of age after intervention,and the difference was statistically significant(P<0.05).Conclusion The breastfeeding intervention programme for mothers of infants with CHD,constructed on the basis of the COM-B model in this study,was comprehensive,feasible and acceptable.Implementation of the programme has potential positive effects on increasing exclusive breastfeeding rates and the daily human milk as a percentage of total feeds,and may also have a positive impact on WAZ and HAZ of infants.
4.The feasibility of oral targeted drug delivery: Gut immune to particulates?
Yuehong REN ; Wei WU ; Xingwang ZHANG
Acta Pharmaceutica Sinica B 2023;13(6):2544-2558
Targeted drug delivery is constantly updated with a better understanding of the physiological and pathological features of various diseases. Depending on high safety, good compliance and many other undeniable advantages, attempts have been undertaken to complete an intravenous-to-oral conversion of targeted drug delivery. However, oral delivery of particulates to systemic circulation is highly challenging due to the biochemical aggressivity and immune exclusion in the gut that restrain absorption and access to the bloodstream. Little is known about the feasibility of targeted drug delivery via oral administration (oral targeting) to a remote site beyond the gastrointestinal tract. To this end, this review proactively contributes to a special dissection on the feasibility of oral targeting. We discussed the theoretical basis of oral targeting, the biological barriers of absorption, the in vivo fate and transport mechanisms of drug vehicles, and the effect of structural evolution of vehicles on oral targeting as well. At last, a feasibility analysis on oral targeting was performed based on the integration of currently available information. The innate defense of intestinal epithelium does not allow influx of more particulates into the peripheral blood through enterocytes. Therefore, limited evidence and lacking exact quantification of systemically exposed particles fail to support much success with oral targeting. Nevertheless, the lymphatic pathway may serve as a potentially alternative portal of peroral particles into the remote target sites via M-cell uptake.
5.Effects of the improved cattle-tongue model in the training of senior midwives
Hong LIU ; Ping REN ; Yuehong LI ; Na WU
Chinese Journal of Modern Nursing 2022;28(3):408-410
Objective:To explore the effect of the improved cattle-tongue model in the training of senior midwives.Methods:From August 2018 to August 2019, convenience sampling was adopted to select 140 senior midwives from the east, west, and south hospitals of Shanghai First Maternity and Infant Hospital and other provinces and cities for training as the research object. Midwives were trained in theoretical knowledge and operation, and an improved cattle-tongue model was used for operation training. This study compared the midwife's theoretical and skill assessment results before and after the training and their satisfaction with the training.Results:After the training, the midwife's theoretical and skill assessment scores were higher than those before the training, and the differences were statistically significant ( P<0.01) . The 140 midwives were very satisfied with the training program. Conclusions:The application of the improved cattle-tongue model for training can improve the theoretical and operational skills of senior midwives, and is worthy of clinical application.
6.Discovery of potential biomarkers for human atherosclerotic abdominal aortic aneurysm through untargeted metabolomics and transcriptomics
JI LEI ; CHEN SILIANG ; GU GUANGCHAO ; WANG WEI ; REN JINRUI ; XU FANG ; LI FANGDA ; WU JIANQIANG ; YANG DAN ; ZHENG YUEHONG
Journal of Zhejiang University. Science. B 2021;22(9):733-745
Abdominal aortic aneurysm (AAA) and atherosclerosis (AS) have considerable similarities in clinical risk factors and molecular pathogenesis. The aim of our study was to investigate the differences between AAA and AS from the perspective of metabolomics, and to explore the potential mechanisms of differential metabolites via integration analysis with transcriptomics. Plasma samples from 32 AAA and 32 AS patients were applied to characterize the metabolite profiles using untargeted liquid chromatography-mass spectrometry (LC-MS). A total of 18 remarkably different metabolites were identified, and a combination of seven metabolites could potentially serve as a biomarker to distinguish AAA and AS, with an area under the curve (AUC) of 0.93. Subsequently, we analyzed both the metabolomics and transcriptomics data and found that seven metabolites, especially 2'-deoxy-D-ribose (2dDR), were significantly correlated with differentially expressed genes. In conclusion, our study presents a comprehensive landscape of plasma metabolites in AAA and AS patients, and provides a research direction for pathogenetic mechanisms in atherosclerotic AAA.
7.Effect of propofol on HMGB1/TLR4 signaling pathway during hepatic ischemia-reperfusion injury in rats
Shuzhen YU ; Weiwei ZHANG ; Junming REN ; Jianfeng WEI ; Yu ZHANG ; Lina ZHENG ; Lijun HAO ; Yuehong QI ; Tiane LUO ; Yongqing GUO
Chinese Journal of Anesthesiology 2019;39(7):870-872
Objective To evaluate the effect of propofol on high-mobility group box 1 protein (HMGB1)/Toll-like receptor 4 (TLR4) signaling pathway during hepatic ischemia-reperfusion (I/R) injury in rats.Methods Thirty-six clean-grade healthy male Sprague-Dawley rats,aged 3 months,weighing 250 -300 g,were divided into 3 groups (n=12 each) using a random number table method:sham operation group (group S),hepatic I/R group (group I/R) and propofol group (group P).Hepatic I/R injury was induced by occluding the portal vein and hepatic artery supplying the left and middle lobes of the liver for 1 h followed by 6-h reperfusion in anesthetized rats.Propofol was infused via the tail vein at a rate of 12 mg ·kg-1 · h-1 starting from 20 min before ischemia until 6 h of reperfusion in group P.The rats were sacrificed at 6 h of reperfusion,and the left lobe of the liver was removed for microscopic examination of the pathological changes which were scored and for determination of the expression of HMGB1,TLR4,tumor necrosis factor-alpha (TNF-α) and interleukin-1 beta (IL-6) in liver tissues (by Western blot).Results Compared with group S,pathological scores of liver tissues were significantly increased,and the expression of HMGB1,TLR4,TNF-α and IL-6 was up-regulated in I/R and P groups (P<0.05).Compared with group I/R,pathological scores of liver tissues were significantly decreased,and the expression of HMGB1,TLR4,TNF-α and IL-6 was down-regulated in group P (P< 0.05).Conclusion The mechanism by which propofol reduces liver I/R injury is associated with blocking HMGB-1/TLR4 signaling pathway and inhibiting inflammatory responses in rats.
8.Change of Serum Angiopoietin-like Protein 2 and Its Significance in Patients with Arteriosclerotic Occlusion.
Yue LIANG ; Hao NIE ; Hualiang REN ; Fangda LI ; Cui TIAN ; Huihua LI ; Yuehong ZHENG
Acta Academiae Medicinae Sinicae 2017;39(2):188-195
Objective To investigated the changes of angiopoietin-like protein 2(Angptl2) in patients with arteriosclerotic occlusion (ASO). Methods A total of 140 subjects including 75 ASO patients (ASO group) and 65 healthy subjects (control group) were enrolled in this study. Angptl2 and adiponectin were evaluated by using enzyme-linked immunosorbent assay. Biochemical data and high sensitive C reactive protein were measured and recorded as well. Results Compared to the control group,the ASO group presented with significantly higher level of plasma Angptl2 [(13.55±9.17) μg/L vs. (9.04±4.79) μg/L,P=0.010]. Plasma Angptl2 level of critical limb ischemia subjects was significantly higher than that of intermittent claudication subjects [(17.01±10.20)μg/L vs. (10.53±6.97) μg/L,P=0.003]. The best diagnostic cutoff value of Angptl2 was 13.67 μg/L,with a sensitivity of 60.34% and a specificity of 81.25%. In addition,type 2 diabetes mellitus patients with ASO exhibited significantly higher serum Angptl2 levels [(18.67±9.84)μg/L] than those without ASO [(13.01±3.47) μg/L] (P=0.021). In ASO group,serum Angptl2 levels were negatively correlated with ankle brachial index (r=-0.244,P=0.035). Conclusion The plasma level of Angptl2 increases in ASO patients. Its level is remarkably increased when the disease progressions to critical limb ischemia. Angptl2 can be a potential biological marker of disease progression.
9.Genetic analysis and prenatal diagnosis for patients with non-syndromic hearing impairment
Yuehong LIANG ; Chenchun REN ; Wenjing WANG ; Haixia ZHANG ; Weiwei YANG ; Deming LI ; Yuexiang ZHANG
Tianjin Medical Journal 2017;45(9):953-957
Objective To explore the genetic pathogen of patients with non-syndromic hearing impairment and to provide prenatal diagnosis for the families of hereditary deafness. Methods Mutation screening of GJB2, SLC26A4, GJB3 and mitochondrial 12 S rRNA genes was performed in 208 patients with non-syndromic hearing impairment by gene chip. Then direct sequencing was used in 41 patients who were found one mutation of GJB2 or SLC26A4 gene. And prenatal diagnosis was carried out in two families by direct sequencing. Results Eighty-six patients (41.35%) were found at least one mutation by gene chip. Among them, 40 patients were found to carry two mutations and 46 patients were found to carry one mutation. The most frequent mutation was 235delC, which was found in 46 patients. And 12 cases were found the second mutation through direct sequencing. A total of 52 (25.00%) patients were detected two mutations. Prenatal diagnosis showed that one fetus carried compound mutations of 299-300delAT and 235delC, and another one carried heterozygous mutation of IVS7-2A>G. Conclusion Patients with non-syndromic hearing impairment can be accurately diagnosed by gene chip and Sanger sequencing. The prenatal diagnosis is primary means for high-risk fetuses.
10.Construction and Management of Official Websites of Medical Institutions
Ziming MAI ; Bin LI ; Yuehong SU ; Zhongmin REN ; Caisheng HE
Journal of Medical Informatics 2017;38(7):68-71
The paper summarizes the significance of the construction of official websites of medical institutions,introduces the requirements of Guangdong Health and Family Planning Commission for the construction of official websites of medical institutions,and describes the construction thought,safety protection and deployment,website management,etc.of the Cancer Hospital Affiliated to Sun Yat -Sen University,in order to provide reference for website construction and management in the industry.

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