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.Effects of branched-chain and aromatic amino acids on type 2 diabe-tes mellitus and the progress
Mengli ZHANG ; Fangfang WU ; Zhien TAN ; Min OU ; Lingjie LIU ; Na LU ; Liya QIAO ; Xia-onan YANG
Chinese Journal of Clinical Pharmacology and Therapeutics 2025;30(4):526-532
Type 2 diabetes mellitus is a metabol-ic disease characterized by high blood sugar levels.Traditionally,amino acids are primarily viewed as the basic building blocks for proteins and peptide synthesis.However,in recent years,amino acids have gained increased attention as signaling mole-cules that play crucial roles in the maintenance and regulation of metabolic homeostasis.It has been found that there is a close correlation between the metabolism of branched-chain and/or aromatic amino acids and the occurrence or development of type 2 diabetes mellitus.Furthermore,there have been successive reports on the regulation mecha-nism involved.This article will focus on the meta-bolic processes,mechanisms and clinical value of branched-chain and aromatic amino acids in type 2 diabetes mellitus.It will also summarize and pro-vide an outlook on the current state of amino acid metabolism in the treatment of diabetes mellitus,with the aim of offering new ideas for the treat-ment of type 2 diabetes mellitus.
3.Shear wave elastography for evaluating therapeutic effect of ultrasound-guided drug injection for muscle injury
Lingjie YANG ; Guoxiang SUN ; Ping HU ; Qizhi HE ; Ming LI ; Hai LI ; Zhuang TANG ; Bo SHEN
Chinese Journal of Interventional Imaging and Therapy 2025;22(7):463-466
Objective To observe the value of shear wave elastography(SWE)for evaluating therapeutic effect of ultrasound-guided drug injection for muscle injury.Methods Eighty patients with unilateral muscle injury were retrospectively included,including 40 cases underwent ultrasound-guided drug injection(group A)and 40 cases underwent electromagnetic wave physiotherapy plus external application of Yunnan Baiyao Gao(group B).Pain intensity was assessed using visual analogue scale(VAS)before treatment and 3 weeks after the final treatment,while the Young modulus(E)value of the injured muscle was measured before treatment and 1,2 and 3 weeks after final treatment,and the improvements of VAS scores and E values were compared between groups.Results The total effective rate in group A(35/40,87.50%)was higher than that in group B(21/40,52.50%;P<0.05).Before treatment,no significant difference of VAS score was found between group A(8.07±0.83)and group B(7.88±0.85)(P>0.05).After treatment,VAS scores decreased in both groups(both P<0.05),which in group A(2.30±1.07)was more obviously than that in group B(4.80±0.82)(P<0.05).After treatment,E values of injury muscles increased significantly in both groups(P<0.05),while group A had a greater increase in overall magnitude and overall rate than group B(P<0.05).Conclusion Ultrasound-guided drug injection therapy had significant therapeutic effect for muscle injuries,which could be dynamically monitored with SWE.
4.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.
5.Correlation Analysis between Different Vitamin D3 Levels and Immune Inflammatory Indicators in Elderly Patients with Sepsis
Congxin LI ; Haidong YUE ; Pengxi ZHU ; Guangxian HUANG ; Lingjie MU ; Yanan PENG ; Yijie WANG ; Yang YANG
Journal of Kunming Medical University 2025;46(2):51-58
Objective To explore the correlation between serum vitamin D(VD3)level differences and immune inflammatory markers in elderly sepsis patients.Methods A total of 103 elderly patients with sepsis(aged 65-99 years)in the ICU of the First Affiliated Hospital of Kunming Medical University from January 2020 to December 2022 were collected and divided into two groups according to the diagnostic criteria for VD3 deficiency:VD3 deficiency group(n=32)and VD3 severe deficiency group(n=71).Correlation analysis was conducted by comparing the differences in serum 25-(OH)-D3(VD3)levels,immune function-related indicators upon admission(blood routine,infection-related proteins,combined detection of 12 cytokines,absolute count analysis of lymphocytes and subgroups,quantitative determination of infection-related immune cells,immunoglobulin,and complement),illness severity,and prognostic indicators(APACHE-II score,SOFA score,duration of ICU stay,and 28-day mortality rate).Result(1)Serum VD3 levels were lower in elderly patients with sepsis.No patient was in the VD3 normal or insufficient group.Patients with severe VD3 deficiency had higher APACHE-II scores,SOFA scores,and 28-day mortality rates than those with VD3 deficiency,and these scores were negatively correlated with serum VD3 levels(P<0.001),while the difference in ICU stay duration between the two groups was not statistically significant(P>0.05);(2)WBC,PCT,CRP,and CD4/CD8 in the VD3 deficiency group were all lower than those in the VD3 severe deficiency group(P<0.05),while IL-6,IL-10,CD45+,CD3+/CD45+,and CD19+Abs were all higher than those in the VD3 severe deficiency group(P<0.05);In the VD3 deficiency group,VD3 levels were positively correlated with CD45+(P<0.05 for all),while negatively correlated with IL-6,IL-10,PCT,and CRP(P<0.05 for all);In the VD3 severe deficiency group,there were fewer corre-lation indicators and the correlation strength was not as strong as that in the VD3 deficiency group.Conclusion(1)Elderly patients with sepsis generally have lower levels of VD3,with lower levels associated with more severe illness and poorer prognosis;(2)In elderly sepsis patients,compared to patients with severe VD3 deficiency,patients with VD3 deficiency have lower levels of inflammation,stronger cellular immune response,and stronger correlation,suggesting that the effects of different VD3 levels on immune inflammatory responses may vary in elderly sepsis patients.
6.Research advances in immune regulation mediated by natural polysaccharides
Yuxuan ZHOU ; Leng HAN ; Dingyuan BAI ; Lingjie JING ; Cheng GUO ; Quanjun YANG
Journal of Chongqing Medical University 2025;50(7):940-944
Natural polysaccharides have important physiological effects on immune regulation,and their effects on natural and ac-quired immunity are worthy of further discussion.Natural polysaccharides can regulate the innate immune system by regulating macro-phages,natural killer cells,inflammatory response,physiological barrier,complement system,and oxidation of the body,and they can also regulate the adaptive immune system by regulating humoral immunity and cellular immunity.Therefore,this article reviews the re-search advances in the role of natural polysaccharides in innate immunity and adaptive immunity,in order to provide new ideas for fur-ther research.
7.Alterations of adenosine in tumor microenvironment and its impact on tumor treatment
Lingjie JING ; Leng HAN ; Dingyuan BAI ; Yuxuan ZHOU ; Xinting ZHU ; Jiayu ZHANG ; Cheng GUO ; Quanjun YANG
Journal of Chongqing Medical University 2025;50(9):1202-1211
Tumor microenvironment(TME)is the cellular environment for tumor development,growth,and metastasis.Adenosine(ADO)is an immunosuppressive metabolic product that is continuously upregulated in TME,with various types and wide distribution of receptors.The complex and dynamic interactions between ADO and tumor cells constantly influence tumor progression.ADO can di-rectly or indirectly promote tumor development and progression by promoting tumor generation and metastasis,mediating the immune escape of tumor,and modulating tumor-infiltrating immune cells.Based on the characteristics of ADOs in TME,this article reviews the latest advances in the dynamic alterations of ADO in TME,in order to provide insights into tumor treatment targeting the ADO pathway.
8.Multicenter study on the prediction of microvascular invasion in hepatocellular carcinoma using multiphase ultrasound imaging radiomics models
Yanhong HAO ; Juan CHEN ; Qin LU ; Ruining WANG ; Yuan SU ; Shanshan SHI ; Rui SHI ; Lingjie WANG ; Jianhong WANG ; Li YANG ; Liping LIU
Chinese Journal of Ultrasonography 2025;34(11):983-991
Objective:To construct and evaluate the predictive performance of a multiphase ultrasound radiomics model for microvascular invasion(MVI)in hepatocellular carcinoma(HCC).Methods:A total of 126 patients with pathologically confirmed HCC were retrospectively enrolled from 4 medical centers between May 2018 and July 2025,including the First Hospital of Shanxi Medical University,Shanxi Province Third People's Hospital,Changzhi People's Hospital,and the Organ Transplant Center of the Affiliated Hospital of Qingdao University. A total of 630 ultrasound images of the lesions in different phases were collected,from which 1 561 radiomic features were extracted. The patients from medical institutions in Shanxi Province were chosen as the training set( n=91),and the patients from the Organ Transplant Center of the Affiliated Hospital of Qingdao University were chosen as the validation set( n=35). In the training set,37.4%(34/91)patients presented MVI(+),whereas in the validation set,54.3%(19/35)patients presented MVI(+). Radiomics features were extracted from ultrasound images,and features related to the MVI(+)were selected through dimensionality reduction analysis. Five multiple machine learning algorithms were used to construct predictive models,which were then evaluated using an external validation set. The Radscore was calculated,and a nomogram was constructed combining Radscore with ultrasound and clinical characteristics to predict MVI. Results:The model combining radiomics features from the portal venous phase and the delay phase showed the best predictive performance in both the training and validation sets,with area under curve(AUC)values of 0.835 and 0.727,respectively. The prediction model developed using radiomics Radscore and clinical indicators could be represented and presented as a nomogram.Conclusions:The radiomics model based on multi-phase ultrasound offers a novel approach for non-invasive preoperative prediction of MVI in liver cancer. Furthermore,its integration with clinical features aids in optimizing clinical treatment strategies.
9.Preparation and optimization of novel targeted nanobubbles carrying exosomes
Ying ZHAO ; Yuming MU ; Shangke CHEN ; Lina GUAN ; Lingjie YANG
Chinese Journal of Ultrasonography 2025;34(6):525-532
Objective:To prepare novel targeted lipid nanobubbles(MEB-NBs)that can be loaded with exosomes(Exo),and test the property and explore the specific invitro target-seeking ability of MEB-NBs. Methods:The core lipid nanobubbles(NBs)were prepared using mechanical oscillation methods,and Exo was connected to the NBs through membrane fusion. The target antibody MYH6 was linked to the NBs using a phospholipid coupling covalent method,resulting in the preparation of targeted lipid nanobubbles MEB-NBs loaded with Exo. The morphology,particle size,and surface potential of the prepared lipid nanobubbles MEB-NBs were observed,and the co-loading of Exo and NBs was verified using laser confocal and fluorescence resonance energy transfer techniques. The in vitro imaging capability and biosafety of MEB-NBs were evaluated,and the loading rate and drug content of Exo carried by MEB-NBs were measured. The ability of MEB-NBs to specifically target hiPSC-CMs cells was observed using flow cytometry,small animal in vivo imaging systems,and laser confocal microscopy. Results:The average particle size of the prepared MEB-NBs was(597.10 ± 47.70)nm,the surface potential was(-11.70 ± 0.21)mV,and the concentration was(2.43 ± 0.06)×10 7/ml. Laser confocal microscopy and FRET results confirmed that the Exo was effectively connected with the NBs;When the Exo concentration was 250 μg/ml,the Exo loading rate and drug loading of MEB-NBs were both 73.8%,and the results of laser confocal microscopy showed that MEB-NBs could be effectively targeted to hiPSC-CMs cells. MEB-NBs were well developed in vitro and had good biological safety. Conclusions:This study constructs novel Exo-loaded targeted lipid nanobubbles(MEB-NBs)that demonstrate stable physicochemical properties and ultrasound imaging capabilities. The developed MEB-NBs precisely target hiPSC-CMs cells,providing an innovative drug delivery system with enhanced therapeutic efficacy for Exo-based therapies.
10.Analysis of bacterial colonization pathways and predictive factors of epidural analgesia catheters in patients with chronic pain
Zhuang TANG ; Liming ZHOU ; Ping HU ; Lin ZHAO ; Weipeng HONG ; Xingli SHEN ; Xingyu LI ; Lingjie YANG ; Qizhi HE
Journal of Clinical Medicine in Practice 2025;29(12):67-70,76
Objective To analyze the incidence,colonization pathways,and predictive factors of bacterial colonization of epidural analgesia catheters in patients with chronic pain.Methods A total of 150 patients with chronic pain who underwent continuous epidural catheterization(catheter in-dwelling time of 7 to 10 days)were selected as study subjects.Samples from three sites were collect-ed for bacterial culture.Clinical data of the patients were collected,and the positive rate of bacterial culture,characteristics of bacterial species distribution,and bacterial colonization pathways were ana-lyzed.The efficacy of predictive factors was assessed using the receiver operating characteristic(ROC)curve.Results The positive rates of bacterial culture in samples from the skin swabbing fluid around the puncture site,the subcutaneous segment of the catheter,and the catheter tip were 22.0%,7.3%,and 8.7%,respectively.Staphylococcus epidermidis was the predominant colonizing bacterial species.Spearman correlation coefficient analysis showed a significant correlation between the results of bacterial culture from the skin around the puncture site and catheter tip colonization(r=0.47,P<0.01).ROC curve analysis revealed that the area under the curve of bacterial culture results from the skin around the puncture site in predicting catheter tip bacterial colonization was 0.843,with a sensitivity of 84.9%and a specificity of 84.6%.Conclusion Bacterial migra-tion along the catheter is the main pathway for catheter tip bacterial colonization,and the results of bacterial culture from the skin around the puncture site are an effective predictive factor for the risk of bacterial colonization.

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