1.Analysis of transcriptome and chromatin accessibility changes during the differentiation of human embryonic stem cells into neural progenitor cells
Linying LI ; Xiaodong CAI ; Ran TONG ; Chen YANG ; Zhiming WANG ; Xiaoyu HE ; Ziyue MA ; Feng ZHANG ; Lingjie LI ; Junmei ZHOU
Journal of Shanghai Jiaotong University(Medical Science) 2025;45(4):387-403
Objective·To investigate the changes in transcriptome and chromatin accessibility during the differentiation of human embryonic stem cells(hESCs)into neural progenitor cells(NPCs)using in vitro differentiation models and high-throughput multi-omics sequencing technologies.Methods·hESCs were first induced to differentiate into NPCs in vitro using the embryoid body formation method,and cells at both stages were collected.The cell phenotypes were identified by reverse transcription-quantitative real-time PCR(RT-qPCR)and immunofluorescence(IF)staining.Transcriptome sequencing(RNA-seq)was conducted to detect and analyze the differentially expressed genes(DEGs)between hESCs and NPCs.The assay for transposase-accessible chromatin with high-throughput sequencing(ATAC-seq)was employed to assess chromatin accessibility changes between hESCs and NPCs.Motif enrichment analysis was performed on differentially accessible chromatin regions to discover potential regulatory transcription factors.Finally,an integrated analysis of RNA-seq and ATAC-seq data and the protein-protein interaction(PPI)network were performed to identify key genes and regulatory pathways involved in the early stages of neural differentiation in vitro.Results·Both RT-qPCR and IF results indicated that the expression levels of pluripotency markers(NANOG and POU5F1)were high at the hESC stage but significantly decreased at the NPC stage,while early neural differentiation markers(PAX6,SOX1,and NES)were minimally expressed at the hESC stage but markedly upregulated at the NPC stage.RNA-seq analysis revealed that compared to the hESC stage,there were 5 597 genes upregulated and 3 654 genes downregulated at the NPC stage.Gene function enrichment analysis showed that the upregulated genes at the NPC stage were enriched in the functions related to neural development.ATAC-seq analysis demonstrated a total of 27 491 genomic regions had significant changes in chromatin accessibility during the differentiation from hESC to NPC,with 12 381 regions showing increased accessibility and 15 110 regions showing decreased accessibility.Motif enrichment analysis revealed that transcription factor genes such as DLX1 and LHX2 might play an important role in the differentiation process from hESCs into NPCs.Integrated analysis of RNA-seq and ATAC-seq data revealed that overlapping genes with high expression at the NPC stage were mainly enriched in axon guidance,forebrain development,and neuron migration.After neural differentiation,the expression levels of CTNND2 and LHX2 genes increased,and the chromatin accessibility of related genomic regions also increased.PPI network analysis indentified candidate downstream genes including PRKACA,CDH2,and ERBB4.Conclusion·The in vitro differentiation model of hESCs combined with high-throughput multi-omics sequencing technologies can be used to depict the changes in transcriptome and chromatin accessibility during the differentiation of hESCs into NPCs.In this process,the expression levels of genes related to axon guidance,forebrain development,and neuronal migration pathways increase and related chromatin accessibility is enhanced.
2.Analysis of transcriptome and chromatin accessibility changes during the differentiation of human embryonic stem cells into neural progenitor cells
Linying LI ; Xiaodong CAI ; Ran TONG ; Chen YANG ; Zhiming WANG ; Xiaoyu HE ; Ziyue MA ; Feng ZHANG ; Lingjie LI ; Junmei ZHOU
Journal of Shanghai Jiaotong University(Medical Science) 2025;45(4):387-403
Objective·To investigate the changes in transcriptome and chromatin accessibility during the differentiation of human embryonic stem cells(hESCs)into neural progenitor cells(NPCs)using in vitro differentiation models and high-throughput multi-omics sequencing technologies.Methods·hESCs were first induced to differentiate into NPCs in vitro using the embryoid body formation method,and cells at both stages were collected.The cell phenotypes were identified by reverse transcription-quantitative real-time PCR(RT-qPCR)and immunofluorescence(IF)staining.Transcriptome sequencing(RNA-seq)was conducted to detect and analyze the differentially expressed genes(DEGs)between hESCs and NPCs.The assay for transposase-accessible chromatin with high-throughput sequencing(ATAC-seq)was employed to assess chromatin accessibility changes between hESCs and NPCs.Motif enrichment analysis was performed on differentially accessible chromatin regions to discover potential regulatory transcription factors.Finally,an integrated analysis of RNA-seq and ATAC-seq data and the protein-protein interaction(PPI)network were performed to identify key genes and regulatory pathways involved in the early stages of neural differentiation in vitro.Results·Both RT-qPCR and IF results indicated that the expression levels of pluripotency markers(NANOG and POU5F1)were high at the hESC stage but significantly decreased at the NPC stage,while early neural differentiation markers(PAX6,SOX1,and NES)were minimally expressed at the hESC stage but markedly upregulated at the NPC stage.RNA-seq analysis revealed that compared to the hESC stage,there were 5 597 genes upregulated and 3 654 genes downregulated at the NPC stage.Gene function enrichment analysis showed that the upregulated genes at the NPC stage were enriched in the functions related to neural development.ATAC-seq analysis demonstrated a total of 27 491 genomic regions had significant changes in chromatin accessibility during the differentiation from hESC to NPC,with 12 381 regions showing increased accessibility and 15 110 regions showing decreased accessibility.Motif enrichment analysis revealed that transcription factor genes such as DLX1 and LHX2 might play an important role in the differentiation process from hESCs into NPCs.Integrated analysis of RNA-seq and ATAC-seq data revealed that overlapping genes with high expression at the NPC stage were mainly enriched in axon guidance,forebrain development,and neuron migration.After neural differentiation,the expression levels of CTNND2 and LHX2 genes increased,and the chromatin accessibility of related genomic regions also increased.PPI network analysis indentified candidate downstream genes including PRKACA,CDH2,and ERBB4.Conclusion·The in vitro differentiation model of hESCs combined with high-throughput multi-omics sequencing technologies can be used to depict the changes in transcriptome and chromatin accessibility during the differentiation of hESCs into NPCs.In this process,the expression levels of genes related to axon guidance,forebrain development,and neuronal migration pathways increase and related chromatin accessibility is enhanced.
3.Clinical significance of group A streptococcal infection in pediatric patients with enthesitis related arthritis
Jing MA ; Junmei ZHANG ; Xiaohua TAN ; Yan LI ; Chao LI ; Yurong PIAO ; Shipeng LI ; Jiapeng SUN ; Tongxin HAN ; Weiying KUANG ; Caifeng LI
Chinese Journal of Rheumatology 2022;26(7):456-460
Objective:To demonstrate the clinical significance of group A streptococcal infection (GAS) in patients with enthesitis related arthritis (ERA).Methods:A retrospective study was conducted on ERA (136) and PolyRF-/Oligo juvenile idiopathic arthritis (JIA) (272) patients in Beijing Children's Hospital from 2016 to 2018. Anti-streptococcal hemolysin "O" (ASO) was tested and documented in all patients. The infection rate of GAS was compared between patients with ERA and PolyRF-/Oligo JIA. Patients with ERA were divided to two groups according to the result of ASO (ASO positive and ASO negative). All the clinical data were documented and compared within the two groups. The statistical methods used mainly include t test, rank sum test, chi-square test, and Spearman correlation analysis.Results:The GAS infection rate of patients with ERA was higher than patients with PolyRF-/Oligo JIA (17.6% vs 9.5%, χ2=5.52, P=0.019). In ERA patients, clinical data were analyzed, and a statistical significant difference was observed in the presence of human leukocyte antigen (HLA)-B27 between ASO positive and ASO negative group [75.0%(18/24) vs 49.1%(55/112), χ2=5.329, P=0.021]. Statistical differences were found in Patrick's sign positive rate between the two groups [100%(24/24) vs 67.0%(75/112), χ2=10.61, P=0.001]. There was statistically significant difference between the two groups regarding the radiogr-aphic grading at the sacroiliac joint. More patients with positive ASO had grade Ⅲ damage at the sacroiliac joint compare to patients with negative ASO [68.2%(15/22) vs 28.4%(29/102), χ2=12.49, P<0.001]. The logarithmic of the ASO was slightly correlated with the radiographic grade of sacroiliac joint ( r=0.26, P=0.005). Conclusion:Patients with ERA are prone to be infected by GAS. It's probably related to HLA-B27 postivity for antigen presentation. Patients who were infected by GAS fre-quently have sacroiliac joint involvement, and tend to be more sever. This indicates that GAS may play an important role in the pathogenesis of sacroiliac joint destruction.
4.Antrodia cinnamomea exerts an anti-hepatoma effect by targeting PI3K/AKT-mediated cell cycle progression in vitro and in vivo.
Yan ZHANG ; Pin LV ; Junmei MA ; Ning CHEN ; Huishan GUO ; Yan CHEN ; Xiaoruo GAN ; Rong WANG ; Xuqiang LIU ; Sufang FAN ; Bin CONG ; Wenyi KANG
Acta Pharmaceutica Sinica B 2022;12(2):890-906
Antrodia cinnamomea is extensively used as a traditional medicine to prevention and treatment of liver cancer. However, its comprehensive chemical fingerprint is uncertain, and the mechanisms, especially the potential therapeutic target for anti-hepatocellular carcinoma (HCC) are still unclear. Using UPLC‒Q-TOF/MS, 139 chemical components were identified in A. cinnamomea dropping pills (ACDPs). Based on these chemical components, network pharmacology demonstrated that the targets of active components were significantly enriched in the pathways in cancer, which were closely related with cell proliferation regulation. Next, HCC data was downloaded from Gene Expression Omnibus database (GEO). The Cancer Genome Atlas (TCGA) and DisGeNET were analyzed by bioinformatics, and 79 biomarkers were obtained. Furtherly, nine targets of ACDP active components were revealed, and they were significantly enriched in PI3K/AKT and cell cycle signaling pathways. The affinity between these targets and their corresponding active ingredients was predicted by molecular docking. Finally, in vivo and in vitro experiments showed that ACDPs could reduce the activity of PI3K/AKT signaling pathway and downregulate the expression of cell cycle-related proteins, contributing to the decreased growth of liver cancer. Altogether, PI3K/AKT-cell cycle appears as the significant central node in anti-liver cancer of A. Cinnamomea.
5.Gut microbiota mediates the absorption of FLZ, a new drug for Parkinson's disease treatment.
Junmei SHANG ; Shurong MA ; Caixia ZANG ; Xiuqi BAO ; Yan WANG ; Dan ZHANG
Acta Pharmaceutica Sinica B 2021;11(5):1213-1226
The gut microbiota plays an important role in regulating the pharmacokinetics and pharmacodynamics of many drugs. FLZ, a novel squamosamide derivative, has been shown to have neuroprotective effects on experimental Parkinson's disease (PD) models. FLZ is under phase Ⅰ clinical trial now, while the underlying mechanisms contributing to the absorption of FLZ are still not fully elucidated. Due to the main metabolite of FLZ was abundant in feces but rare in urine and bile of mice, we focused on the gut microbiota to address how FLZ was metabolized and absorbed.
6.Evaluation of the performance of systems for whole blood C-reactive protein detection: a multi-center study
Juan CHENG ; Huaiyuan LI ; Haipeng LIU ; Yuxin WANG ; Jin XU ; Shangyang SHE ; Wei QU ; Yidong WU ; Guixia LI ; Junmei YANG ; Liya MO ; Yun XIANG ; Jiangwei KE ; Liyue KUI ; Lei ZHENG ; Hongbing CHEN ; Zhili YANG ; Xin LYU ; Hong ZHANG ; Zhenhua TANG ; Lijuan MA ; Hongquan LUO ; Xiangyang LI ; Wenli ZHANG ; Hui JIA ; Huiming YE ; Lijun TIAN ; Qiuhui PAN
Chinese Journal of Laboratory Medicine 2021;44(7):633-643
Objective:To explore the performance of the commonly used whole blood C-reactive protein (CRP) detection systems and give related recommendation on the performance requirements of detection systems.Methods:A total of 7 540 venous blood samples from 26 maternal, child and children′s hospitals were collected to conduct this multi-center study on the analytical performance of 5 commonly used whole blood CRP detection systems from March to April in 2019. The blank check, carryover, repeatability, intermediate precision, linearity, sample stability, influence of hematocrit/triglyceride/bilirubin, comparison with SIEMENS specific protein analyzer and trueness were evaluated. The 5 systems included BC-5390CRP autohematology analyzer, AstepPLUS specific protein analyzer, Ottoman-1000 Automated Specific Protein POCT Workstation, i-CHROMA Immunofluorometer equipment Reader and Orion QuikRead go detecting instrument. The 5 systems were labeled as a, b, c, d and e randomly.Results:Within the 5 systems, all values of blank check were less than 1.00 mg/L, the carryovers were lower than 1.00%. The repeatability of different ranges of CRP concentrations including 3.00-10.00, 10.00-30.00 and>30.00 mg/L were less than 10.00%, 6.00% and 5.00%, respectively, and the intermediate precision was less than 10.00%. The linearity correlation coefficients of the 5 systems were all above 0.975, while the slope was within 0.950-1.050. Whole blood samples were stable within 72 hours both at room temperature (18-25 ℃) and refrigerated temperature (2-8 ℃). The CRP results were rarely influenced by high triglyceride or bilirubin, except for the immmunoturbidimetric test based on microparticles coated with anti-human CRP F(ab) 2 fragments. When triglyceride was less than 15.46 mmol/L, the deviation of CRP was less than 10.00%. When bilirubin was less than 345.47 μmol/L, the deviation of CRP was less than 10.00%. CRP was more susceptible to Hct on the systems without Hct correction. The deviation of CRP between different Hct dilution concentration and 40% dilution concentration can reach as high as 67.48%. The correlation coefficients ( r) of 5 systems were all more than 0.975 in the range of 0-300.00 mg/L compared with Siemens specific protein analyzer. All systems passed the trueness verification using the samples with specified values of 12.89 and 30.60 mg/L. Conclusion:The performance of 5 systems can basically meet the clinical needs, but it is suggested that the whole blood CRP detection system without automatic Hct correction should be modified manually.
7.Application of video education combined with Teach-back in patients with rheumatoid arthritis
Kaimin ZHOU ; Xianxiu WEN ; Yuqiong CAO ; Junmei TAN ; Mao MA ; Shan ZENG ; Li LONG
Chinese Journal of Modern Nursing 2019;25(28):3583-3588
Objective? To explore the effect of video education combined with Teach-back on the compliance of patients with rheumatoid arthritis(RA) to exercise at home and the condition of disease activity. Methods? By convenience sampling, 80 patients with RA who were hospitalized in the Rheumatology and Immunology Department of Sichuan Provincial People's Hospital from March to November 2018 were included in the study. By random number table, the patients were divided into the intervention group and control group, the control group was given routine discharge instruction and the patients were taught about the functional exercise orally; on the basis of that, the intervention group was given the video education combined with Teach-back and assisted to download videos, Family Exercise Compliance Scale and Disease Activity Score in 28 Joints(DAS28) were used to evaluate the patients' compliance in functional exercise at home and disease activity condition before intervention, 1 month and 3 months after intervention. Results? Finally, 73 cases(37 cases in the control group, 36 cases in the intervention group) in two groups completed the research plan. One and 3 months after intervention, the compliance with family functional exercise of the intervention group was better than the control group from the same period with statistical significance(P<0.05); the scores of Tender Joint Coun(t TJC28), Swollen Joint Coun(t SJC28), Patient General Health(GH) of the intervention group were all lower than the control group from the same period with statistical significance (P<0.05), however, the scores of Erythrocyte Sedimentation Rate(ESR) and DAS28 didn't demonstrate obvious intervention effects (P>0.05). Conclusions? Video education combined with Teach-back can effectively improve the compliance of RA patients with home functional exercise, help to cultivate healthy behavior, and hence reduce the number of tender joint, swelling joints, reduce the degree of pain, improve the prognosis of patients.
8.Effects of seamless nursing on the quality of timely vaccination in community floating children
Xia LIU ; Guozhen MA ; Junmei DENG ; Xiaochun YE ; Yanping DENG
Chinese Journal of Modern Nursing 2018;24(5):536-540
Objective To explore the effects of seamless nursing on timely vaccination in community floating children, so as to provide references for the management of the immunization nurses and the implementation of timely vaccination in community health service center. Methods Totally 155 cases of floating children (parents) from 2 community health service centers were recruited in the research by convenience sampling method, and assigned into intervention group and control group for each community health service center. Routine nursing management was applied in the control group. Based on the routine nursing management, the intervention group received seamless nursing by the contract between family doctor team and the children's family, collective health seminars on vaccination day, specialist health education of prescription into the family, remote guidance about home skills. The parents' health belief of timely immunization, the timely immunization rate and the parents' satisfaction were compared between the two groups. Results After the intervention, the score of the parents' health belief of the control group was (58.42±6.90), which was lower than that of the intervention group (99.07±7.23), and the difference was statistically significant (t=-50.637, P< 0.001). The timely vaccination rates of the control group and the intervention group were 81.94% and 94.84% respectively, and the difference was statistically significant (χ2=12.571, P< 0.001). There was a significantly higher satisfaction rate in the intervention group (95.48%) than in the control group (87.10%) (χ2=6.856,P< 0.001). Conclusions The seamless management could effectively improve the quality of timely children vaccination and the parents' satisfaction rate.
9.Clinical study of umbilical compress using anti-cancer Xiaogu formula in the management of malignant ascites
Yingjie WEI ; Beibei SHAN ; Junmei YAN ; Xiaolin WANG ; Lihua WANG ; Rui QIANG ; Dayan ZHANG ; Jinlong MA ; Jing WANG ; Zhenzhen CHU
International Journal of Traditional Chinese Medicine 2018;40(12):1134-1137
Objective To observe the clinical efficacy of umbilical compress with anti-cancer Xiaogu formula in managing malignant ascites. Methods A total of 56 patients with malignant ascites who met the inclusion criteria were randomized into 28 patients in the treatment group and 28 patients in the control group. The control group was treated with one type of diuretic, and the treatment group was given umbilical compress using Anti-Cancer Xiaogu formula and diuretics. Both groups were treated for 14 days. The changes of abdominal girth, 24 h urine volume, ascites efficacy, TCM syndrome scores, quality of life and adverse reactions were observed. Results The decrease in the maximum depth difference of the ascites in the treatment group was significantly greater than that of the control group (1.16 ± 1.29 vs. 0.00 ± 1.34, Z=-2.553). The difference was statistically significant (P<0.05). The decrease in abdominal girth in the treatment group was significantly larger than that in the control group (0.57 ± 0.55 vs. 2.61 ± 0.28, Z=-2.264). The difference was statistically significant (P<0.05). The in 24-hour urine volume in the treatment group after intervention (-800.18 ± 64.12 vs.-683.57 ± 55.38, Z=-1.770) was no statistically significant (P>0.05). The response rate in the treatment group was 92.9% (26/28), while that of the control group was 89.3% (25/28).treatment group was 71.4%, while that of the control group was 35.7%. The difference was statistically significant (P<0.05). The increase in KPS in the treatment group was significantly higher than that of the control group. The difference was statistically significant (P<0.05). Conclusions Anti-cancer Xiaogu umbilical cord combined with diuretic can reduce the degree of malignant ascites, alleviate clinical symptoms, improve quality of life and decrease the occurrence of adverse reactions when used concomitantly with diuretics in the management of malignant ascites.
10.Effect of health education improvement on promotion of timely vaccination among migrant children in community
Guozhen MA ; Beirong MO ; Pengjun JIANG ; Honglin SHEN ; Junmei DENG
Chinese Journal of Nursing 2017;52(1):87-92
Objective To explore the effect of health education improvement on promotion of timely vaccination among migrant children in community and to provide references for community health service center.Methods A total of 155 migrant children's parents were recruited from July 2015 to February 2016,and improved health education intervention was carried out on the basis of routine health education to promote parents' health belief on timely vaccination.The compliance of parents' participation in health education activities,the health belief of parents themselves on timely vaccination at different stages of intervention and parents' satisfaction,and the rate of timely vaccination of migrant children before and after intervention were evaluated.Results Regarding the compliance of health education activities for parents in 12 weeks,the first 3 weeks was 85% ~ 91%,the last 4 weeks were 95% and above.Six months after intervention,the score of parents' health belief on timely vaccination was higher than that after 3 months of intervention and before intervention,and the difference was statistically significant (P<0.05).The timely vaccination rates in the study group for migrant children was higher than that in the historical groups (P<0.05).After intervention,the satisfaction rate for parents was 95.484%.Conclusion Health education improvement could effectively promote parents' health belief on timely vaccination,satisfaction rate and rate of timely vaccination among migrant children.

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