1.Bioinformatics analysis of ferroptosis-related genes and immune infiltration in IgA nephropathy
Guiling XU ; Qinglin YE ; Chao XUE ; Liangping RUAN ; Wei LI
Chinese Journal of Immunology 2025;41(7):1673-1687
Objective:This study based on comprehensive bioinformatics technology aimed to investigate the pathogenesis of ferroptosis in IgA nephropathy(IgAN)from an immunological perspective,and to identify the key genes and functional pathways.Methods:Differentially expressed ferroptosis-related genes(DE-FRGs)were identified from GSE93798 and analyzed by Kyoto Ency-clopedia of Genes and Genomes(KEGG)and Gene Ontology(GO).STRING and Cytoscape were used to construct a protein-protein interaction(PPI)network.Degree and MCODE algorithm were run.Combining LASSO regression,SVM-RFE and PLS-DA machine learning to construct the optimal feature selection hub gene.Cibersort and ssGESA algorithms were used to assess the immune infiltra-tion,as well as to explore the relationship between hub genes and immune infiltration.Single cell RNA sequence(scRNA-seq)data was used to analyze the location of hub genes in IgAN cell populations.Gene Set Enrichment Analysis(GSEA)was performed on hub genes.The HPA database was used to obtain the position of the specific protein of the hub genes,and the DsigDB database was used to predict the target drug.The GSE37460,GSE116626 and GSE73953 were treated as validation sets and diagnostic effectiveness evalua-tion.Collecting IgAN and healthy kidney tissue for immunohistochemical testing of hub genes expression.Results:This study identi-fied 94 DE-FRGs and 3 hub genes(JJUN,EGR1 and DDR2).KEGG and GO analysis indicated that the DE-FRGs were mainly con-centrated in pathways of ferroptosis,reactive oxygen species,responsing to oxidative stress and metal particles,mitochondrion,and transcriptional regulatory complex.GESA analysis involved in amino acid and fatty acid metabolism.The analysis of immune cell infil-tration in IgAN revealed an increased ratio of naive B cells,mast cells,and CD4+T cells.Differential analysis of immune function re-vealed that mechanisms such as chemokine receptor signaling pathways,human leukocyte antigen signaling pathways,and inflamma-tion promotion were more active in IgAN.Furthermore,the correlation was observed between immune infiltration and hub genes.ScRNA-seq analysis demonstrated that hub genes were localized in monocytes,macrophages,poximal convoluted tubule cells,princi-pal cells,and smooth muscle cells.Validations set analysis suggested that JUN and SIRT1 had a diagnostic value.The HPA database analysis showed that JUN was mainly located in the nucleus,while EGR1 was located in the membrane and cytoplasm.The 2 278 po-tential drugs for the treatment of IgAN were predicted.Finally,the results of immunohistochemistry and bioinformatics analysis were consistent.Conclusion:Ferroptosis may be associated with immune cell infiltration and immune related function during the occur-rence and development of IgAN.
2.Clinical and endoscopic features of autoimmune gastritis with gastric neoplastic lesions
Shan LEI ; Xiaogang LIU ; Yan PAN ; Caiping GAO ; Liangping LI ; Yao HU ; Pu WANG
Chinese Journal of Internal Medicine 2025;64(7):652-659
Objective:Autoimmune gastritis (AIG) is characterized by the loss of acid-secreting glands, resulting in hypochlorhydria and hypergastrinemia, conditions that significantly increase the risk of developing gastric neuroendocrine tumors (NETs) and gastric adenocarcinoma. In recent years, AIG has garnered increasing attention in both clinical and research settings. However, comprehensive studies on the clinical and endoscopic characteristics of AIG particularly cases complicated by gastric neoplastic lesions remain limited in China. This study aims to comprehensively summarize the clinical and endoscopic features of AIG and its associated gastric neoplastic lesions.Methods:A retrospective analysis was conducted using medical records from patients with AIG diagnosed at Sichuan Provincial People′s Hospital between 2019 and 2024. Data collected included demographic information, medical history, serological test results, imaging findings, and endoscopic observations. The clinical and endoscopic features of AIG patients with gastric NETs or epithelial-derived tumors were compared to those without gastric neoplastic lesions to identify potential risk factors and diagnostic indicators for tumor development in AIG.Results:A total of 72 patients with AIG were included, of whom 62.5% (45/72) were female, with an age range of 30 to 79 years old (mean age: 57±11 years). Parietal cell antibody (PCA) positivity was observed in 93.1% (67/72), intrinsic factor antibody (IFA) positivity in 45.8% (33/72), and Helicobacter pylori ( H. pylori) co-infection in 48.6% (35/72). Endoscopically, 84.7% (61/72) showed prominent corpus-dominant advanced atrophy; 47.2% (34/72) had sticky adherent mucus; and 41.7% (30/72) displayed residual oxyntic mucosa in the gastric body or fundus. Only 23.6% (17/72) had normal antrum mucosa, and just 16.7% (12/72) showed a circular wrinkle-like pattern. Gastric neoplastic lesions were identified in 35 patients (48.6%), including 15 cases (20.8%) with NETs and 20 cases (27.8%) with epithelial-derived tumors (four adenocarcinomas, three adenomas, and 13 cases of intraepithelial neoplasia). No significant differences were found between tumor and non-tumor groups in terms of age, gender, PCA/IFA positivity, gastrin levels, anemia status, folic acid, or serum iron levels. However, patients with NETs had significantly lower vitamin B 12 levels compared to those without tumors (183±111 ng/L vs. 323±159 ng/L, t=2.47, P=0.042). Additionally, AIG patients with NETs were more likely to be H.pylori-negative compared to both the non-tumor group (66.7% vs. 35.1%, χ2=5.26, P=0.072) and the epithelial-derived tumor group (66.7% vs. 30.0%, χ2=5.80, P=0.055). The incidence of reverse atrophy in the epithelial-derived tumor group was significantly lower than that in the non-tumor group (65.0% vs. 91.9%, χ2=6.49, P=0.011) and the NETs group (65.0% vs. 93.3%, χ2=3.90, P=0.048).? Conclusion:In AIG patients with NETs, serum vitamin B 12 levels are significantly reduced, suggesting that vitamin B 12 deficiency may be a key risk factor or clinical indicator for NET development in AIG. Furthermore, NETs are more frequently observed in AIG patients without H.pylori infection, while epithelial-derived tumors are more commonly associated with H.pylori co-infection.
3.Bioinformatics analysis of ferroptosis-related genes and immune infiltration in IgA nephropathy
Guiling XU ; Qinglin YE ; Chao XUE ; Liangping RUAN ; Wei LI
Chinese Journal of Immunology 2025;41(7):1673-1687
Objective:This study based on comprehensive bioinformatics technology aimed to investigate the pathogenesis of ferroptosis in IgA nephropathy(IgAN)from an immunological perspective,and to identify the key genes and functional pathways.Methods:Differentially expressed ferroptosis-related genes(DE-FRGs)were identified from GSE93798 and analyzed by Kyoto Ency-clopedia of Genes and Genomes(KEGG)and Gene Ontology(GO).STRING and Cytoscape were used to construct a protein-protein interaction(PPI)network.Degree and MCODE algorithm were run.Combining LASSO regression,SVM-RFE and PLS-DA machine learning to construct the optimal feature selection hub gene.Cibersort and ssGESA algorithms were used to assess the immune infiltra-tion,as well as to explore the relationship between hub genes and immune infiltration.Single cell RNA sequence(scRNA-seq)data was used to analyze the location of hub genes in IgAN cell populations.Gene Set Enrichment Analysis(GSEA)was performed on hub genes.The HPA database was used to obtain the position of the specific protein of the hub genes,and the DsigDB database was used to predict the target drug.The GSE37460,GSE116626 and GSE73953 were treated as validation sets and diagnostic effectiveness evalua-tion.Collecting IgAN and healthy kidney tissue for immunohistochemical testing of hub genes expression.Results:This study identi-fied 94 DE-FRGs and 3 hub genes(JJUN,EGR1 and DDR2).KEGG and GO analysis indicated that the DE-FRGs were mainly con-centrated in pathways of ferroptosis,reactive oxygen species,responsing to oxidative stress and metal particles,mitochondrion,and transcriptional regulatory complex.GESA analysis involved in amino acid and fatty acid metabolism.The analysis of immune cell infil-tration in IgAN revealed an increased ratio of naive B cells,mast cells,and CD4+T cells.Differential analysis of immune function re-vealed that mechanisms such as chemokine receptor signaling pathways,human leukocyte antigen signaling pathways,and inflamma-tion promotion were more active in IgAN.Furthermore,the correlation was observed between immune infiltration and hub genes.ScRNA-seq analysis demonstrated that hub genes were localized in monocytes,macrophages,poximal convoluted tubule cells,princi-pal cells,and smooth muscle cells.Validations set analysis suggested that JUN and SIRT1 had a diagnostic value.The HPA database analysis showed that JUN was mainly located in the nucleus,while EGR1 was located in the membrane and cytoplasm.The 2 278 po-tential drugs for the treatment of IgAN were predicted.Finally,the results of immunohistochemistry and bioinformatics analysis were consistent.Conclusion:Ferroptosis may be associated with immune cell infiltration and immune related function during the occur-rence and development of IgAN.
4.Clinical and endoscopic features of autoimmune gastritis with gastric neoplastic lesions
Shan LEI ; Xiaogang LIU ; Yan PAN ; Caiping GAO ; Liangping LI ; Yao HU ; Pu WANG
Chinese Journal of Internal Medicine 2025;64(7):652-659
Objective:Autoimmune gastritis (AIG) is characterized by the loss of acid-secreting glands, resulting in hypochlorhydria and hypergastrinemia, conditions that significantly increase the risk of developing gastric neuroendocrine tumors (NETs) and gastric adenocarcinoma. In recent years, AIG has garnered increasing attention in both clinical and research settings. However, comprehensive studies on the clinical and endoscopic characteristics of AIG particularly cases complicated by gastric neoplastic lesions remain limited in China. This study aims to comprehensively summarize the clinical and endoscopic features of AIG and its associated gastric neoplastic lesions.Methods:A retrospective analysis was conducted using medical records from patients with AIG diagnosed at Sichuan Provincial People′s Hospital between 2019 and 2024. Data collected included demographic information, medical history, serological test results, imaging findings, and endoscopic observations. The clinical and endoscopic features of AIG patients with gastric NETs or epithelial-derived tumors were compared to those without gastric neoplastic lesions to identify potential risk factors and diagnostic indicators for tumor development in AIG.Results:A total of 72 patients with AIG were included, of whom 62.5% (45/72) were female, with an age range of 30 to 79 years old (mean age: 57±11 years). Parietal cell antibody (PCA) positivity was observed in 93.1% (67/72), intrinsic factor antibody (IFA) positivity in 45.8% (33/72), and Helicobacter pylori ( H. pylori) co-infection in 48.6% (35/72). Endoscopically, 84.7% (61/72) showed prominent corpus-dominant advanced atrophy; 47.2% (34/72) had sticky adherent mucus; and 41.7% (30/72) displayed residual oxyntic mucosa in the gastric body or fundus. Only 23.6% (17/72) had normal antrum mucosa, and just 16.7% (12/72) showed a circular wrinkle-like pattern. Gastric neoplastic lesions were identified in 35 patients (48.6%), including 15 cases (20.8%) with NETs and 20 cases (27.8%) with epithelial-derived tumors (four adenocarcinomas, three adenomas, and 13 cases of intraepithelial neoplasia). No significant differences were found between tumor and non-tumor groups in terms of age, gender, PCA/IFA positivity, gastrin levels, anemia status, folic acid, or serum iron levels. However, patients with NETs had significantly lower vitamin B 12 levels compared to those without tumors (183±111 ng/L vs. 323±159 ng/L, t=2.47, P=0.042). Additionally, AIG patients with NETs were more likely to be H.pylori-negative compared to both the non-tumor group (66.7% vs. 35.1%, χ2=5.26, P=0.072) and the epithelial-derived tumor group (66.7% vs. 30.0%, χ2=5.80, P=0.055). The incidence of reverse atrophy in the epithelial-derived tumor group was significantly lower than that in the non-tumor group (65.0% vs. 91.9%, χ2=6.49, P=0.011) and the NETs group (65.0% vs. 93.3%, χ2=3.90, P=0.048).? Conclusion:In AIG patients with NETs, serum vitamin B 12 levels are significantly reduced, suggesting that vitamin B 12 deficiency may be a key risk factor or clinical indicator for NET development in AIG. Furthermore, NETs are more frequently observed in AIG patients without H.pylori infection, while epithelial-derived tumors are more commonly associated with H.pylori co-infection.
5.Methods for Identifying Seeds of Chinese Medicinal Materials: A Review
Zhihao LIU ; Liangping ZHA ; Li LUO ; Yuyang ZHAO ; Xiaolin LI ; Yuan YUAN
Chinese Journal of Experimental Traditional Medical Formulae 2024;30(4):1-11
Seeds are the source for the production of Chinese medicinal materials. The seed authenticity and quality of directly affect the effectiveness and safety of Chinese medicinal materials. The seed quality is faced with the problems such as mixed sources, existence of adulterants and seeds stocked for years, low maturity, and low purity. To ensure the high-quality and sustainable development of the Chinese medicinal material industry, it is urgent to standardize the seed market and identify and evaluate the quality of the seeds circulating in the market. Seed identification methods include visual inspection, microscopic observation, micro-character identification, chemical fingerprinting, molecular identification, electronic nose, X-ray diffraction, electrochemical fingerprinting, spectral imaging, and artificial intelligence. These methods have different application scopes and unique advantages and disadvantages. According to the different species of Chinese herbal medicines and different requirements of testing sites, suitable methods can be selected to achieve rapid and accurate identification with low costs. In the future, the seed identification methods should be developed based on emerging technologies with interdisciplinary knowledge, and intelligent, nondestructive, and single-grain detection methods are needed for the modern Chinese medicinal material industry. This paper introduces the seed identification technologies currently applied in research and production, compares the principles, applicability, advantages, and disadvantages of different technologies, and provides an outlook on the future development of seed identification technologies, aiming to provide a reference for the identification and quality evaluation of seeds of Chinese medicinal material.
6.High expression of UBE2S promotes progression of hepatocellular carcinoma by increasing cancer cell stemness
Hao CHEN ; Zhenhan LI ; Mingting WANG ; Linming LU ; Qianli TANG ; Liangping LUO
Journal of Southern Medical University 2024;44(3):455-464
Objective To investigate the expression of the ubiquitination enzyme UBE2S in different cell types in hepatocellular carcinoma(HCC)microenvironment and its impact on proliferation and stemness of HCC cells.Methods TCGA and CPTAC database were used to analyze the transcriptional and promoter methylation levels and protein expressions of UBE2S in HCC.Specific expression patterns of UBE2S,intercellular communication and key transcription factors in different cell types were analyzed based on single-cell sequencing data from TISCH website.We further examined UBE2S expressions in clinical samples of HCC tissues,HCC cells and T cells using immunohistochemistry and immunofluorescence staining.We also tested the effects of UBE2S knockdown on stemness of HCC-LM3 and HepG2 cells using clone formation experiments and sphere formation assay.Results Analysis based on TCGA database suggested significant overexpression of UBE2S in both paired and non-paired tumor tissues(P<0.001),and its transcriptional level increased with tumor grades.The methylation level of UBE2S promoter was significantly decreased in HCC(P<0.001),and its transcription level increased obviously in HCC with TP53 mutation(P<0.001).Analysis of CPTAC database also demonstrated overexpression of UBE2S protein in HCC tissues(P<0.001).Three prognostic models suggested that HCC patients with high UBE2S expression had poorer prognosis(P<0.001).Single-cell sequencing data analysis revealed high expressions of UBE2S in T cells and high intensities of interaction between endothelial cells,epithelial cells and fibroblasts in HCC microenvironment.Immunohistochemistry and immunofluorescence staining demonstrated high UBE2S expressions in clinical samples of HCC tissues,HCC cells and T cells.In HCC-LM3 and HepG2 cells,UBE2S knockdown significantly inhibited cell clone formation and tumor sphere formation(P<0.05).Conclusion UBE2S is highly expressed in T cells in HCC microenvironment in close correlation with a poor prognosis.High UBE2S expression promotes the stemness of HCC cells.
7.High expression of UBE2S promotes progression of hepatocellular carcinoma by increasing cancer cell stemness
Hao CHEN ; Zhenhan LI ; Mingting WANG ; Linming LU ; Qianli TANG ; Liangping LUO
Journal of Southern Medical University 2024;44(3):455-464
Objective To investigate the expression of the ubiquitination enzyme UBE2S in different cell types in hepatocellular carcinoma(HCC)microenvironment and its impact on proliferation and stemness of HCC cells.Methods TCGA and CPTAC database were used to analyze the transcriptional and promoter methylation levels and protein expressions of UBE2S in HCC.Specific expression patterns of UBE2S,intercellular communication and key transcription factors in different cell types were analyzed based on single-cell sequencing data from TISCH website.We further examined UBE2S expressions in clinical samples of HCC tissues,HCC cells and T cells using immunohistochemistry and immunofluorescence staining.We also tested the effects of UBE2S knockdown on stemness of HCC-LM3 and HepG2 cells using clone formation experiments and sphere formation assay.Results Analysis based on TCGA database suggested significant overexpression of UBE2S in both paired and non-paired tumor tissues(P<0.001),and its transcriptional level increased with tumor grades.The methylation level of UBE2S promoter was significantly decreased in HCC(P<0.001),and its transcription level increased obviously in HCC with TP53 mutation(P<0.001).Analysis of CPTAC database also demonstrated overexpression of UBE2S protein in HCC tissues(P<0.001).Three prognostic models suggested that HCC patients with high UBE2S expression had poorer prognosis(P<0.001).Single-cell sequencing data analysis revealed high expressions of UBE2S in T cells and high intensities of interaction between endothelial cells,epithelial cells and fibroblasts in HCC microenvironment.Immunohistochemistry and immunofluorescence staining demonstrated high UBE2S expressions in clinical samples of HCC tissues,HCC cells and T cells.In HCC-LM3 and HepG2 cells,UBE2S knockdown significantly inhibited cell clone formation and tumor sphere formation(P<0.05).Conclusion UBE2S is highly expressed in T cells in HCC microenvironment in close correlation with a poor prognosis.High UBE2S expression promotes the stemness of HCC cells.
8.Chinese Translation of Benefits and Challenges in Implementation of Artificial Intelligence in Colonoscopy:World Endoscopy Organization Position Statement
Chinese Journal of Gastroenterology 2023;28(9):545-550
The number of artificial intelligence(AI)tools for colonoscopy on the market is increasing with supporting clinical evidence.Nevertheless,their implementation is not going smoothly for a variety of reasons,including lack of data on clinical benefits and cost-effectiveness,lack of trustworthy guidelines,uncertain indications,and cost for implementation.To address this issue and better guide practitioners,the World Endoscopy Organization has provided its perspective about the status of AI in colonoscopy as the position statement.
9.Clinical features of non-B, non-C hepatocellular carcinoma
Journal of Clinical Hepatology 2023;39(10):2358-2365
ObjectiveTo investigate the change in the proportion of non-B, non-C hepatocellular carcinoma (NBNC-HCC) in hepatocellular carcinoma, and to compare and analyze the clinicopathological features of NBNC-HCC. MethodsA total of 3 090 patients with hepatocellular carcinoma (HCC) who were diagnosed in Sichuan Provincial People’s Hospital from January 2011 to December 2021 were enrolled, and according to the hepatitis markers, they were divided into hepatitis virus infection-associated HCC group with 2 472 patients and NBNC-HCC group with 618 patients. According to the liver disease and metabolic risk factors, the NBNC-HCC group was further divided into metabolic disorder HCC group with 289 patients, alcoholic liver disease (ALD)-associated HCC group with 174 patients, and other HCC group with 155 patients. General information, laboratory markers, and pathological findings were collected from all HCC patients. The Mann-Whitney U test was used for comparison of continuous data between two groups, and the Kruskal-Wallis H test was used for comparison between three groups; the chi-square test was used for comparison of categorical data between groups, and the chi-square trend test was used to investigate the trend of the change in the proportion of NBNC-HCC in HCC. ResultsThe proportion of patients with NBNC-HCC in HCC increased from 13.7% in 2011 to 20.1% in 2021 (χ2=5.529, P=0.019), and compared with the hepatitis virus infection-associated HCC group, the NBNC-HCC group had a significantly higher proportion of patients with diabetes (28.0% vs 10.3%, χ2=129.482, P<0.001) or hypertension (33.2% vs 15.2%, χ2=105.079, P<0.001), a significantly lower proportion of patients with liver cirrhosis (44.5% vs 68.4%, χ2=122.563, P<0.001) or vascular invasion (20.4% vs 29.6%, χ2=7.749, P=0.005), and a significantly higher body mass index (BMI) (Z=-4.015, P<0.001). Compared with the ALD-HCC group, the metabolic disorder HCC group had a significantly higher BMI, a significantly lower FIB-4 index, and a significantly lower proportion of patients with liver cirrhosis (all P<0.05). ConclusionThere is a tendency of increase in the proportion of patients with NBNC-HCC in HCC, and NBNC-HCC often coexists with metabolic risk factors such as obesity, diabetes, and hypertension. Patients in the metabolic disorder HCC group may develop liver cancer in the absence of liver cirrhosis or in the early stage of liver fibrosis.
10.Chinese translation of benefits and challenges in implementation of artificial intelligence in colonoscopy: World Endoscopy Organization position statement
Chinese Journal of Digestion 2023;43(6):365-370
The number of artificial intelligence (AI) tools for colonoscopy on the market is increasing with supporting clinical evidence. Nevertheless, their implementation is not going smoothly for a variety of reasons, including lack of data on clinical benefits and cost-effectiveness, lack of trustworthy guidelines, uncertain indications, and cost for implementation. To address this issue and better guide practitioners, the World Endoscopy Organization has provided its perspective about the status of AI in colonoscopy as the position statement.

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