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.Effect and mechanism of dabrafenib combined with tremelimumab on melanoma
Xiaosong WANG ; Yunjiao LIU ; Jin ZHOU ; Qianqian ZHANG ; Lingjie MENG
Journal of Pharmaceutical Practice and Service 2025;43(10):496-502
Objective To investigate the effect and mechanism of dabrafenib (DAB) combined with tremelimumab (TREM) on melanoma. Methods The effects of DAB combined with TREM on cell viability, cytotoxicity and cell migration of A375 cells were evaluated by Cell Counting Kit-8 (CCK-8) method, lactate dehydrogenase (LDH) method and scratch assay. The levels of reactive oxygen species (ROS), adenosine triphosphate (ATP), malondialdehyde (MDA), and superoxide dismutase (SOD) were detected to evaluate the effects of combined drugs on oxidative stress and energy metabolism. In addition, A375 tumor-bearing nude mice model was used to evaluate the inhibitory effect of the combined treatment on tumor growth in vivo, and the degree of cell apoptosis and cell proliferation in tumor tissues were analyzed by terminal deoxynucleotidyl transferase-mediated dutP Nick end labeling (TUNEL) and proliferating cell nuclear antigen (PCNA) immunohistochemical staining. Results The combined treatment significantly inhibited the survival rate and migration ability of A375 cells and enhanced the cytotoxicity. The combined intervention also significantly increased ROS level, decreased ATP, SOD and MDA levels. It effectively inhibited tumor growth in tumor-bearing nude mice, increased the apoptosis rate of tumor cells and inhibited cell proliferation. Conclusion DAB combined with TREM may improve the therapeutic effect of melanoma by enhancing oxidative stress, inhibiting energy metabolism, and promoting cell apoptosis. This combination therapy may provide a new therapeutic strategy to overcome the limitations of singledrug therapy.
4.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.
5.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.
6.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.
7.The NO-sGC-cGMP pathway and heart failure
Dilu LI ; Yuanyuan PEI ; Wuchao WANG ; Lingjie CAO ; Fengtao YANG ; Shuangkui SHI ; Guyue ZHOU ; Kunyu YANG ; Jihong ZHU
Chinese Journal of Clinical Pharmacology and Therapeutics 2025;30(5):702-708
Heart failure,as a global public health challenge,is experiencing an increasingly severe disease burden.Given the close relationship be-tween the Nitric Oxide-Soluble Guanylate Cyclase-Cyclic Guanosine Monophosphate(NO-sGC-cGMP)signaling pathway and heart failure,this study,through a comprehensive search and review of re-cent literature on the NO-sGC-cGMP pathway and heart failure,aims to outline the mechanism of ac-tion of this signaling pathway and its connection with heart failure,in order to explore new avenues for the treatment of heart failure.
8.The NO-sGC-cGMP pathway and heart failure
Dilu LI ; Yuanyuan PEI ; Wuchao WANG ; Lingjie CAO ; Fengtao YANG ; Shuangkui SHI ; Guyue ZHOU ; Kunyu YANG ; Jihong ZHU
Chinese Journal of Clinical Pharmacology and Therapeutics 2025;30(5):702-708
Heart failure,as a global public health challenge,is experiencing an increasingly severe disease burden.Given the close relationship be-tween the Nitric Oxide-Soluble Guanylate Cyclase-Cyclic Guanosine Monophosphate(NO-sGC-cGMP)signaling pathway and heart failure,this study,through a comprehensive search and review of re-cent literature on the NO-sGC-cGMP pathway and heart failure,aims to outline the mechanism of ac-tion of this signaling pathway and its connection with heart failure,in order to explore new avenues for the treatment of heart failure.
9.The advancement of cuproptosis in hematological tumors
Lingjie ZHOU ; Yanying LI ; Liuyun ZHANG ; Juan ZHANG
Chinese Journal of Hematology 2024;45(10):965-969
Cuproptosis is a type of independent cell death form, that differs from apoptosis, necroptosis and ferroptosis. It is mediated by Copper (Cu), and mainly affects the lipoylation of proteases in the mitochondrial tricarboxylic acid (TCA) cycle and exhibits cytotoxicity through oligomerization; however, its specific mechanism, signal transduction process and regulation mode are still not clear. Mitochondria affect the sensitivity of cells to copper toxicity and play a central role in the occurrence and development of copper-related death. In recent years, though hematological tumors have achieved better remission through targeted therapy and immunotherapy, they are associated with high recurrence rates and poor prognoses. It is therefore imperative to find better prognostic indicators and new treatment ideas. This paper summarizes the interaction between Cu and mitochondria in the development of tumors and provides ideas for further exploration of the mechanism of copper death and coping with hematological tumors.
10.Effects of extended latissimusdorsi musculocutaneous flap combined with precision surgery for breast cancer in stage Ⅰ breast reconstruction
Xiaochun ZHOU ; Cuicui GE ; Yong DENG ; Hui CHEN ; Lingjie LI ; Xiyu CHEN ; Lanlan YAN ; Jing LU
Chinese Journal of Medical Aesthetics and Cosmetology 2024;30(4):332-336
Objective:To evaluate the application value of extended latissimusdorsi musculocutaneous flap combined with breast precision hand in stage Ⅰ breast reconstruction.Methods:Twelve cases of extended latissimusdorsi musculocutaneous flap combined with stage Ⅰ breast reconstruction for breast cancer precision surgery were collected from January 2022 to February 2023 in our department, the postoperative complications of surgical techniques were analyzed, and the cosmetic effects of breast reconstruction were evaluated according to Harris standards.Results:All 12 cases underwent breast reconstruction with extended latissimusdorsi musculocutaneous flap, and the survival rate of the flap was 100%. There was local cutaneous margin necrosis in 1 case of back incision, partial ischemic necrosis of the nipple in 1 case, and effusion in the donor area of the back in 5 cases. Harris evaluation of cosmetic effect of breast reconstruction was excellent in 3 cases, good in 6 cases, and fair in 3 cases. Follow-up time was 4-16 months (median was 12 months), and no local recurrence or distant metastasis was observed during follow-up.Conclusions:The extended latissimusdorsi musculocutaneous flap combined with precision mastectomy stage Ⅰ reconstruction is a safe and feasible treatment method for breast cancer.

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