1.Experimental validation of machine learning identification of KDELR3 as a signature gene for osteoarthritis hypoxia
Wenfei XU ; Chunyu MING ; Qijie MEI ; Changshen YUAN ; Jinrong GUO ; Chao ZENG ; Kan DUAN
Chinese Journal of Tissue Engineering Research 2024;28(21):3431-3437
BACKGROUND:Hypoxia is strongly associated with the development and progression of osteoarthritic chondrocyte injury,but the specific targets and regulatory mechanisms are unclear. OBJECTIVE:A machine learning approach was used to identify KDEL(Lys-Asp-Glu-Leu)receptor 3(KDELR3)as a characteristic gene for osteoarthritis hypoxia and immune infiltration analysis,to provide new ideas and methods for the treatment of osteoarthritis. METHODS:The osteoarthritis-related datasets were downloaded from the GEO database and the GSEA website to obtain hypoxia-related genes.The osteoarthritis datasets were batch-corrected and immune infiltration analyzed using R language,and osteoarthritis hypoxia genes were extracted for differential analysis.Differentially expressed genes were analyzed for GO function and KEGG signaling pathway.Weighted correlation network analysis(WGCNA)and machine learning were also used to screen osteoarthritis hypoxia signature genes,and in vitro cellular experiments were performed to validate expression and correlate immune infiltration analysis using the datasets and qPCR. RESULTS AND CONCLUSION:(1)8492 osteoarthritis genes were obtained by batch correction and principal component analysis,mainly strongly associated with immune cells such as Macrophages M2 and Mast cells resting;200 hypoxia genes were also obtained,resulting in 41 osteoarthritis hypoxia differentially expressed genes.(2)GO analysis involved mainly biological processes such as response to nutrient levels and glucocorticoids;cellular components such as lysosomal lumen and Golgi lumen;and molecular functions such as 14-3-3 protein binding and DNA-binding transcriptional activator activity.(3)KEGG analysis of osteoarthritis hypoxia differentially expressed genes was associated with signaling pathways such as PI3K-Akt,FoxO,and microRNAs in cancer.(4)The characteristic gene KDELR3 was obtained after using WGCNA analysis and machine learning screening.(5)The gene expression of KDELR3 was found to be higher in the test group than in the control group in the synovium(P=0.014)but lower in the meniscus(P=0.024)after validation by gene microarray.(6)In vitro chondrocyte assay showed that the expression of KDELR3 was higher in cartilage than in the control group(P=0.005),while KDELR3 was closely associated with Macrophages M0(P=0.014)and T cells follicular helper(P=0.014).Using a machine learning approach,we confirmed that KDELR3 can be used as a hypoxic signature gene for osteoarthritis and may intervene in osteoarthritis pathogenesis by improving hypoxia,expecting to provide a new direction for better treatment of osteoarthritis.
2.Identification of ferroptosis signature genes in osteoarthritis based on WGCNA and machine learning and experimental validation
Wenfei XU ; Chunyu MING ; Kan DUAN ; Changshen YUAN ; Jinrong GUO ; Qi HU ; Chao ZENG ; Qijie MEI
Chinese Journal of Tissue Engineering Research 2024;28(30):4909-4914
BACKGROUND:Ferroptosis is strongly associated with the occurrence and progression of osteoarthritis,but the specific characteristic genes and regulatory mechanisms are not known. OBJECTIVE:To identify osteoarthritis ferroptosis signature genes and immune infiltration analysis using the WGCNA and various machine learning methods. METHODS:The osteoarthritis dataset was downloaded from the GEO database and ferroptosis-related genes were obtained from the FerrDb website.R language was used to batch correct the osteoarthritis dataset,extract osteoarthritis ferroptosis genes and perform differential analysis,analyze differentially expressed genes for GO function and KEGG signaling pathway.WGCNA analysis and machine learning(random forest,LASSO regression,and SVM-RFE analysis)were also used to screen osteoarthritis ferroptosis signature genes.The in vitro cell experiments were performed to divide chondrocytes into normal and osteoarthritis model groups.The dataset and qPCR were used to verify expression and correlate immune infiltration analysis. RESULTS AND CONCLUSION:(1)12 548 osteoarthritis genes were obtained by batch correction and PCA analysis,while 484 ferroptosis genes were obtained,resulting in 24 differentially expressed genes of osteoarthritis ferroptosis.(2)GO analysis mainly involved biological processes such as response to oxidative stress and response to organophosphorus,cellular components such as apical and apical plasma membranes,and molecular functions such as heme binding and tetrapyrrole binding.(3)KEGG analysis exhibited that differentially expressed genes of osteoarthritis ferroptosis were related to signaling pathways such as the interleukin 17 signaling pathway and tumor necrosis factor signaling pathway.(4)After using WGCNA analysis and machine learning screening,we obtained the characteristic gene KLF2.After validation by gene microarray,we found that the gene expression of KLF2 was higher in the test group than in the control group in the meniscus(P=0.000 14).(5)In vitro chondrocyte assay showed that type Ⅱ collagen and KLF2 expression was lower in the osteoarthritis group than in the control group in chondrocytes(P<0.05),while in osteoarthritis ferroptosis,mast cells activated was closely correlated with dendritic cells(r=0.99);KLF2 was closely correlated with natural killer cells(r=-1,P=0.017)and T cells follicular helper(r=-1,P=0.017).(6)The findings indicate that using WGCNA analysis and machine learning methods confirmed that KLF2 can be a characteristic gene for osteoarthritis ferroptosis and may improve osteoarthritis ferroptosis by interfering with KLF2.
3.Fitting Degrees of Animal Models of Diarrhea-irritable Bowel Syndrome with Clinical Characteristics of Western Medicine and Traditional Chinese Medicine
Fengru JIANG ; Youcheng HE ; Yue WU ; Keyi PAN ; Chunyu ZHOU ; Shuyu CAI ; Jianye YUAN
Chinese Journal of Experimental Traditional Medical Formulae 2024;30(6):218-227
Diarrhea-irritable bowel syndrome (IBS-D) is one of the common functional bowel diseases in clinical practice. Since it pathogenesis is complex and has not been fully elucidated, effective treatment methods remains to be developed for this disease. Establishing the animal models of IBS-D in accordance with the clinical characteristics of traditional Chinese medicine (TCM) and Western medicine helps to reveal the pathogenesis of this disease and improve the treatment plan. The fitting degree of an animal model with clinical characteristics is an indicator to evaluate the effectiveness of the animal model in simulating the disease characteristics of Western medicine and the syndromes of TCM based on the latest diagnostic standards. By reviewing the relevant articles about the animal models of IBS-D, we discovered that rats were the preferred animals for modeling, and the models were mainly induced by single factors, double factors, or the combination of multiple factors. The established animal models mainly present symptoms or signs associated with visceral hypersensitivity or/and gastrointestinal motility abnormalities. The single factor-induced rat models of IBS-D had high fitting degrees with the clinical characteristics of Western medicine but low fitting degrees with the TCM syndromes. The animal models induced by two or more factors had high but varied fitting degrees with the clinical characteristics of Western medicine. In addition, the animal models of IBS-D considering TCM syndromes mainly focuses on the syndrome of liver depression and spleen deficiency, and few models were established for the syndromes of spleen-kidney Yang deficiency, spleen-stomach dampness-heat, spleen deficiency and dampness excess, and cold and heat in complexity. Therefore, it is essential to improve the existing or develop new animal models of IBS-D in the future, so as to provide more tools for deciphering the mechanisms of TCM and Western medicine and developing treatment methods for this disease.
4.Current status of cognition and skin care behavior in adolescent patients with acne: A survey in China.
Jing TIAN ; Hong SHU ; Qiufang QIAN ; Zhong SHEN ; Chunyu ZHAO ; Li SONG ; Ping LI ; Xiuping HAN ; Hua QIAN ; Jinping CHEN ; Hua WANG ; Lin MA ; Yuan LIANG
Chinese Medical Journal 2024;137(4):476-477
5.A Survey on the Mental Health Status of Social Workers Under Long-term Stress of COVID-19 and the Exploration of Associated Factors: A Case Study of Chaoyang District, Beijing
Han ZHANG ; Yuan GAO ; Wanxin MA ; Hongxin LIU ; Fanrui MENG ; Danping ZHANG ; Chunyu LIU ; Lu LIU ; Ying XING
Medical Journal of Peking Union Medical College Hospital 2024;15(4):845-854
To study the prevalence of depression, anxiety, and insomnia among social workers during the prolonged battle against the COVID-19 pandemic and explore the associated risk factors. Using a stratified cluster sampling method, we selected all social workers in the five streets of Chaoyang District, Beijing(Jiuxianqiao, Wangjing, Taiyanggong, Shibalidian, Sunhe) from November 2021 to March 2022 as the study population(social worker group), and the frontline medical staffs(medical professional group) of the same age range of the corresponding community hospitals of the same five streets, and the community residents(resident group) as the control population. The ratio of the social worker group, medical professional group, and resident group was 1∶1∶1. The Sojump platform was used to send electronic questionnaires to the wechat groups of social workers, healthcare workers, and community residents to carry out the survey. The screen positive rates for anxiety, depression, and sleep disorders were compared among the 3 groups. Multifactorial Logistic regression and decision tree were used to analyze the influencing factors of anxiety, depression, and sleep disorders among social workers. A total of 954 questionnaires were collected, of which 62 were disqualified and excluded. Finally, 892 valid questionnaires(93.5%) were included for data analysis. Among them, there were 372 questionnaires(41.7%) from the social worker group, 262(29.4%) from the medical professional group, and 258(28.9%) from the resident group. The prevalences of anxiety, depression, and sleep disorders among social workers group were found to be 15.3%, 22.0%, and 48.1%, respectively, which were significantly higher than those in the medical professional group(7.6%, 10.3%, and 30.5%) and the resident group(7.0%, 8.5%, and 29.5%), all Social workers exhibited significant levels of anxiety, depression, and sleep disorders during the long-term pandemic prevention, with CPSS being the most significant influencing factor.
6.Carrier screening for 223 monogenic diseases in Chinese population:a multi-center study in 33 104 individuals
Wei HOU ; Xiaolin FU ; Xiaoxiao XIE ; Chunyan ZHANG ; Jiaxin BIAN ; Xiao MAO ; Juan WEN ; Chunyu LUO ; Hua JIN ; Qian ZHU ; Qingwei QI ; Yeqing QIAN ; Jing YUAN ; Yanyan ZHAO ; Ailan YIN ; Shutie LI ; Yulin JIANG ; Manli ZHANG ; Rui XIAO ; Yanping LU
Journal of Southern Medical University 2024;44(6):1015-1023
Objective To investigate the epidemiological characteristics and mutation spectrum of monogenic diseases in Chinese population through a large-scale,multicenter carrier screening.Methods This study was conducted among a total of 33 104 participants(16 610 females)from 12 clinical centers across China.Carrier status for 223 genes was analyzed using high-throughput sequencing and different PCR methods.Results The overall combined carrier frequency was 55.58%for 197 autosomal genes and 1.84%for 26 X-linked genes in these participants.Among the 16 669 families,874 at-risk couples(5.24%)were identified.Specifically,584 couples(3.50%)were at risk for autosomal genes,306(1.84%)for X-linked genes,and 16 for both autosomal and X-linked genes.The most frequently detected autosomal at-risk genes included GJB2(autosomal recessive deafness type 1A,393 couples),HBA1/HBA2(α-thalassemia,36 couples),PAH(phenylketonuria,14 couples),and SMN1(spinal muscular atrophy,14 couples).The most frequently detected X-linked at-risk genes were G6PD(G6PD deficiency,236 couples),DMD(Duchenne muscular dystrophy,23 couples),and FMR1(fragile X syndrome,17 couples).After excluding GJB2 c.109G>A,the detection rate of at-risk couples was 3.91%(651/16 669),which was lowered to 1.72%(287/16 669)after further excluding G6PD.The theoretical incidence rate of severe monogenic birth defects was approximately 4.35‰(72.5/16 669).Screening for a battery of the top 22 most frequent genes in the at-risk couples could detect over 95%of at-risk couples,while screening for the top 54 genes further increased the detection rate to over 99%.Conclusion This study reveals the carrier frequencies of 223 monogenic genetic disorders in the Chinese population and provides evidence for carrier screening strategy development and panel design tailored to the Chinese population.In carrier testing,genetic counseling for specific genes or gene variants can be challenging,and the couples need to be informed of these difficulties before testing and provided with options for not screening these genes or gene variants.
7.Current Research on the Effects of Vestibular Stimulation on Sleep
Chunyu YUAN ; Heng JING ; Weixia CHEN ; Xiaodomg LI ; Jimin WU ; Lujia WANG ; Lihong MA
Journal of Audiology and Speech Pathology 2024;32(6):559-563
Sleep is an important activity of daily life for individuals,and sleep disorders can seriously affect their physical and mental health.This article summarizes the impact of vestibular stimulation on sleep,and reviews feasible and effective intervention methods from swing movement,galvanic vestibular stimulation,and weighted blankets stimulation,in order to provide new ideas and methods for the diagnosis and treatment of sleep disorders.
8.Carrier screening for 223 monogenic diseases in Chinese population:a multi-center study in 33 104 individuals
Wei HOU ; Xiaolin FU ; Xiaoxiao XIE ; Chunyan ZHANG ; Jiaxin BIAN ; Xiao MAO ; Juan WEN ; Chunyu LUO ; Hua JIN ; Qian ZHU ; Qingwei QI ; Yeqing QIAN ; Jing YUAN ; Yanyan ZHAO ; Ailan YIN ; Shutie LI ; Yulin JIANG ; Manli ZHANG ; Rui XIAO ; Yanping LU
Journal of Southern Medical University 2024;44(6):1015-1023
Objective To investigate the epidemiological characteristics and mutation spectrum of monogenic diseases in Chinese population through a large-scale,multicenter carrier screening.Methods This study was conducted among a total of 33 104 participants(16 610 females)from 12 clinical centers across China.Carrier status for 223 genes was analyzed using high-throughput sequencing and different PCR methods.Results The overall combined carrier frequency was 55.58%for 197 autosomal genes and 1.84%for 26 X-linked genes in these participants.Among the 16 669 families,874 at-risk couples(5.24%)were identified.Specifically,584 couples(3.50%)were at risk for autosomal genes,306(1.84%)for X-linked genes,and 16 for both autosomal and X-linked genes.The most frequently detected autosomal at-risk genes included GJB2(autosomal recessive deafness type 1A,393 couples),HBA1/HBA2(α-thalassemia,36 couples),PAH(phenylketonuria,14 couples),and SMN1(spinal muscular atrophy,14 couples).The most frequently detected X-linked at-risk genes were G6PD(G6PD deficiency,236 couples),DMD(Duchenne muscular dystrophy,23 couples),and FMR1(fragile X syndrome,17 couples).After excluding GJB2 c.109G>A,the detection rate of at-risk couples was 3.91%(651/16 669),which was lowered to 1.72%(287/16 669)after further excluding G6PD.The theoretical incidence rate of severe monogenic birth defects was approximately 4.35‰(72.5/16 669).Screening for a battery of the top 22 most frequent genes in the at-risk couples could detect over 95%of at-risk couples,while screening for the top 54 genes further increased the detection rate to over 99%.Conclusion This study reveals the carrier frequencies of 223 monogenic genetic disorders in the Chinese population and provides evidence for carrier screening strategy development and panel design tailored to the Chinese population.In carrier testing,genetic counseling for specific genes or gene variants can be challenging,and the couples need to be informed of these difficulties before testing and provided with options for not screening these genes or gene variants.
9.Discussion on the Connotation and Clinical Practice of Prevention and Treatment of Syndrome of Dampness-heat of Spleen and Stomach Based on"Attacking it According to Its Combination"
Youcheng HE ; Fengru JIANG ; Yue WU ; Keyi PAN ; Chunyu ZHOU ; Shuyu CAI ; Jianye YUAN
Chinese Journal of Information on Traditional Chinese Medicine 2024;31(6):175-180
Syndrome of dampness-heat of spleen and stomach is one of the complex syndromes of the spleen and stomach,which is difficult to differentiate and treat in TCM.According to the theoretical connotation of"attacking it according to its combination",it is suggested that the syndrome of dampness-heat of spleen and stomach should be comprehensively differentiated and treated from five aspects,including"attacking the visible pathogens combined with the invisible ones"(removing dampness and warming yang),"treating the fu-organs sharing interior-exterior relationship with zang-organs"(clearing away damp-heat pathogens of stomach with drugs of bitter taste and cold property),"formulating the treatment according to the likes and dislikes of the five internal organs"(developing a life adjustment plan favored by the spleen and stomach),"administrating drug according to the five organs"(medications according to the spleen and stomach),"weighing the severity and applying the treatment"(pay attention to the details,and treating according to syndrome differentiation).A clinical case is exampled,with the purpose to provide reference for the prevention and treatment of syndrome of dampness-heat of spleen and stomach.
10.Development of shared traditional Chinese medicine pharmacy from the perspective of primary medical care
Qianqian SUN ; Chunyu LIU ; Siyu LI ; Man YUAN ; Chunjin LI ; Yixuan LI ; Tao WU ; Weiyong ZHOU ; Huaqiang ZHAI
China Pharmacy 2023;34(3):269-274
In order to make the shared traditional Chinese medicine (TCM) pharmacy develop more efficiently and normatively at the grass-roots level, using the “shared TCM pharmacy” as the retrieval word, this paper uses the literature research method to retrieve the reports, documents and policies from CNKI, the websites of people’s governments at all levels, the official websites of the State Administration of Traditional Chinese Medicine, people.com, China News Network, Xinhua News and other platforms before May 20, 2022, sort out the development mode and history of two “Internet plus” TCM pharmacies, namely “shared TCM pharmacies” and “smart TCM pharmacies”, and compare them with each other. Combined with the actual work of community hospitals and community service centers (stations), the necessity and advantages (such as reducing the costs of the intermediate links of drug circulation and standardizing the grass-roots drug use process) of the development of “shared TCM pharmacy” are obtained from the perspective of primary medical care. Combined with the current situation of the promotion and application of shared TCM pharmacy in county medical communities, it is concluded that the shared TCM pharmacy should be further constructed from four aspects: improving the work process of drug centralized procurement under the background of normalization, improving the compatibility and synchronization of the whole process dispensing information system module, unifying pharmaceutical services and personnel training, defining the authority of data query and clarifying the boundaries of patient privacy to further build a shared TCM pharmacy. Finally, it integrates information technology, summarizes the definition of shared TCM pharmacy and its future construction direction, and provides reference for the next development of shared TCM pharmacy at the grass-roots level.

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