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281 results on '"Zhou, Gangqiao"'

3. NRDE2 deficiency impairs homologous recombination repair and sensitizes hepatocellular carcinoma to PARP inhibitors

Author

Wang, Yahui, Liu, Xinyi, Zuo, Xianbo, Wang, Cuiling, Zhang, Zheng, Zhang, Haitao, Zeng, Tao, Chen, Shunqi, Liu, Mengyu, Chen, Hongxia, Song, Qingfeng, Li, Qi, Yang, Chenning, Le, Yi, Xing, Jinliang, Zhang, Hongxin, An, Jiaze, Jia, Weihua, Kang, Longli, Zhang, Hongxing, Xie, Hui, Ye, Jiazhou, Wu, Tianzhun, He, Fuchu, Zhang, Xuejun, Li, Yuanfeng, and Zhou, Gangqiao

Published
2024
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10. Plasma exosomal CD48 protein as a candidate diagnostic biomarker for hepatocellular carcinoma

Author

CHENG Yicai, DU Zhenhua, FAN Zhijuan, FENG Lan, CAO Pengbo, ZHOU Gangqiao

Subjects
hepatocellular carcinoma, exosome, proteome, diagnostic biomarker, cd48, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Background and purpose: Approximately 60% of patients with hepatocellular carcinoma (HCC) are diagnosed at an advanced stage, therefore cannot receive timely and effective treatment. At present, the sensitivity of serum biomarkers commonly used in the diagnosis of HCC is low. In this paper, through the differential expression analysis of plasma exosomal proteome, the candidate exosome protein markers which may be used in the diagnosis of HCC were identified. Methods: First, we performed shot-gun proteome mass spectrometry assays in the plasma exosomes from the discovery cohort [including 4 healthy control (HC) group and 4 HCC patients group], and identified differentially expressed proteins by qualitative and quantitative analyses. Then, we carried out enzyme-linked immunosorbent assay (ELISA) in plasma samples of an independent verification cohort [including 56 HCC patients group, 20 liver cirrhosis (LC) patients group and 48 HC group], and evaluated the diagnostic value of the candidate protein in HCC. Results: In the discovery cohort, we identified a total of 1 434 exosomal proteins, of which CD48 exhibited higher levels in HCC than in HC. We further verified in the validation cohort by ELISA that CD48 was markedly higher in HCC compared with LC and HC groups, with the area under receiver operating characteristic (ROC) curve (AUC) of 0.886. When combined with plasma alpha-fetoprotein (AFP), the AUC reached 0.970. Conclusion: The plasma exosomal CD48 protein can be used as a candidate diagnostic biomarker for HCC, and its combination with AFP may further improve the clinical diagnostic ability for HCC.

Published
2022
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14. Application of machine learning to associative scRNA-seq data gene expression and alternative polyadenylation sites clustering

Author

Hu Jiongsong, Ren Chao, Shu Wenjie, and Zhou Gangqiao

Subjects
Microbiology, QR1-502, Physiology, QP1-981, Zoology, QL1-991
Abstract

Cell type identification is a vital step in the analysis of scRNA-seq data. Transcriptome subtype pivotal information such as alternative polyadenylation (APA) obtained from standard scRNA-seq data can also provide valid clues for cell type identification with no alteration of experimental techniques or increased experimental costs. Furthermore, using multimodal analysis techniques and their methods, more confident cell type identification results can be obtained. For that purpose, we constructed a workflow framework: On five different scRNA-seq datasets, 18 methods based on machine learning that have not yet been applied to identify cell types by association APA and single-cell gene expression fusion were compared with three single-cell clustering methods, and compared these method against the advanced method scLAPA based on similarity network fusion (SNF). In our experiments, we used the adjusted Rand index (ARI) as a metric. We found that unsupervised methods like WMSC and supervised methods like MOGONET have more robust and excellent results in associating APA with single-cell gene expression clustering than methods based only on single-cell gene expression clustering and advanced scLAPA methods.

Published
2023
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17. Genome-wide association study of COVID-19 severity among the Chinese population

Author

Li, Yuanfeng, Ke, Yuehua, Xia, Xinyi, Wang, Yahui, Cheng, Fanjun, Liu, Xinyi, Jin, Xin, Li, Boan, Xie, Chengyong, Liu, Siyang, Chen, Weijun, Yang, Chenning, Niu, Yuguang, Jia, Ruizhong, Chen, Yong, Liu, Xiong, Wang, Zhihua, Zheng, Fang, Jin, Yan, Li, Zhen, Yang, Ning, Cao, Pengbo, Chen, Hongxia, Ping, Jie, He, Fuchu, Wang, Changjun, and Zhou, Gangqiao

Published
2021
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18. Germline Duplication of SNORA18L5 Increases Risk for HBV-related Hepatocellular Carcinoma by Altering Localization of Ribosomal Proteins and Decreasing Levels of p53

Author

Cao, Pengbo, Yang, Aiqing, Wang, Rui, Xia, Xia, Zhai, Yun, Li, Yuanfeng, Yang, Fei, Cui, Ying, Xie, Weimin, Liu, Ying, Liu, Taotao, Jia, Weihua, Jiang, Zhengwen, Li, Zhuo, Han, Yuqing, Gao, Chengming, Song, Qingfeng, Xie, Bobo, Zhang, Luo, Zhang, Hongxing, Zhang, Jinxu, Shen, Xizhong, Yuan, Yunfei, Yu, Feng, Wang, Ying, Xu, Jing, Ma, Yilong, Mo, Zengnan, Yu, Wuzhong, He, Fuchu, and Zhou, Gangqiao

Published
2018
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22. Supplementary Methods, Supplementary Figures 1-10, Supplementary Tables 1-17, Supplementary References from Genome-Wide Association Study Identifies a New Locus at 7q21.13 Associated with Hepatitis B Virus–Related Hepatocellular Carcinoma

Author

Li, Yuanfeng, primary, Zhai, Yun, primary, Song, Qingfeng, primary, Zhang, Haitao, primary, Cao, Pengbo, primary, Ping, Jie, primary, Liu, Xinyi, primary, Guo, Bingqian, primary, Liu, Guanjun, primary, Song, Jin, primary, Zhang, Ying, primary, Yang, Aiqing, primary, Yan, Hongbo, primary, Yang, Liang, primary, Cui, Ying, primary, Ma, Yilong, primary, Xing, Jinliang, primary, Shen, Xizhong, primary, Liu, Taotao, primary, Zhang, Hongxin, primary, An, Jiaze, primary, Bei, Jin-Xin, primary, Jia, Weihua, primary, Kang, Longli, primary, Liu, Lijun, primary, Yuan, Dongya, primary, Hu, Zhibin, primary, Shen, Hongbing, primary, Lu, Lei, primary, Wang, Xuan, primary, Li, Hua, primary, He, Fuchu, primary, Zhang, Hongxing, primary, and Zhou, Gangqiao, primary

Published
2023
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24. Additional file 2 of The A-to-I editing of KPC1 promotes intrahepatic cholangiocarcinoma by attenuating proteasomal processing of NF-κB1 p105 to p50

Author

Gao, Chengming, Zhou, Guangming, Shi, Jie, Shi, Peipei, Jin, Liang, Li, Yuanfeng, Wang, Xiaowen, Liao, Song, Yan, Han, Wu, Junjie, Lu, Yiming, Zhai, Yun, Zhang, Jinxu, Zhang, Haitao, Zhang, Hongxing, Yang, Chenning, Cao, Pengbo, Cheng, Shuqun, and Zhou, Gangqiao

Abstract

Additional file 2: Supplementary file 2.

Published
2023
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25. Additional file 1 of The A-to-I editing of KPC1 promotes intrahepatic cholangiocarcinoma by attenuating proteasomal processing of NF-κB1 p105 to p50

Author

Gao, Chengming, Zhou, Guangming, Shi, Jie, Shi, Peipei, Jin, Liang, Li, Yuanfeng, Wang, Xiaowen, Liao, Song, Yan, Han, Wu, Junjie, Lu, Yiming, Zhai, Yun, Zhang, Jinxu, Zhang, Haitao, Zhang, Hongxing, Yang, Chenning, Cao, Pengbo, Cheng, Shuqun, and Zhou, Gangqiao

Abstract

Additional file 1: Supplementary file 1.

Published
2023
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29. Comprehensive assessment showed no associations of variants at the SLC10A1 locus with susceptibility to persistent HBV infection among Southern Chinese

Author

Zhang, Ying, Li, Yuanfeng, Wu, Miantao, Cao, Pengbo, Liu, Xiaomin, Ren, Qian, Zhai, Yun, Xie, Bobo, Hu, Yanling, Hu, Zhibin, Bei, Jinxin, Ping, Jie, Liu, Xinyi, Yu, Yinghua, Guo, Bingqian, Lu, Hui, Liu, Guanjun, Zhang, Haitao, Cui, Ying, Mo, Zengnan, Shen, Hongbing, Zeng, Yi-Xin, He, Fuchu, Zhang, Hongxing, and Zhou, Gangqiao

Published
2017
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36. Genomic gain of RRS1 promotes hepatocellular carcinoma through reducing the RPL11-MDM2-p53 signaling

Author

Cao, Pengbo, primary, Yang, Aiqing, additional, Li, Peiyao, additional, Xia, Xia, additional, Han, Yuqing, additional, Zhou, Guangming, additional, Wang, Rui, additional, Yang, Fei, additional, Li, Yuanfeng, additional, Zhang, Ying, additional, Cui, Ying, additional, Ji, Hongzan, additional, Lu, Lei, additional, He, Fuchu, additional, and Zhou, Gangqiao, additional

Published
2021
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38. Genetic variants in five novel loci including CFB and CD40 predispose to chronic hepatitis B

Author

Jiang, De-Ke, Ma, Xiao-Pin, Yu, Hongjie, Cao, Guangwen, Ding, Dong-Lin, Chen, Haitao, Huang, Hui-Xing, Gao, Yu-Zhen, Wu, Xiao-Pan, Long, Xi-Dai, Zhang, Hongxing, Zhang, Youjie, Gao, Yong, Chen, Tao-Yang, Ren, Wei-Hua, Zhang, Pengyin, Shi, Zhuqing, Jiang, Wei, Wan, Bo, Saiyin, Hexige, Yin, Jianhua, Zhou, Yuan-Feng, Zhai, Yun, Lu, Pei-Xin, Zhang, Hongwei, Gu, Xiaoli, Tan, Aihua, Wang, Jin-Bing, Zuo, Xian-Bo, Sun, Liang-Dan, Liu, Jun O., Yi, Qing, Mo, Zengnan, Zhou, Gangqiao, Liu, Ying, Sun, Jielin, Shugart, Yin Yao, Zheng, Lilly S., Zhang, Xue-Jun, Xu, Jianfeng, and Yu, Long

Published
2015
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42. Additional file 1 of Genome-wide association study identifies new loci associated with noise-induced tinnitus in Chinese populations

Author

Xie, Chengyong, Niu, Yuguang, Ping, Jie, Wang, Yahui, Yang, Chenning, Li, Yuanfeng, and Zhou, Gangqiao

Abstract

Additional file 1: Supplementary Figure 1. The principal components analyses (PCA) of the population in the discovery stage in this study and reference populations from the 1,000 Genomes Project. Supplementary Figure 2. The genotypes of rs2846071 are significantly associated with the expression levels of WNT11 in several types of brain tissues from GTEx. Supplementary Figure 3. Colocalization analyses of the association signals from GWAS and brain eQTL data at the 11q13.5 and 12p13.31 loci. Supplementary Figure 4. Chromatin state segmentations for rs1800692 and rs4149570 using the ENCODE data. Supplementary Figure 5. The genotypes of rs4149577 are significantly associated with the expression levels of TNFRSF1A in several types of brain tissue from GTEx. Supplementary Figure 6. Proxy plots for 11q13.5 and 12p13.31 regions in Chinese Han Chinese and European populations. Supplementary Figure 7. Linkage disequilibrium plots for 11q13.5 and 12p13.31 regions in Chinese Han Chinese and European populations. Supplementary Figure 8. Power to detect the genetic effects of rs2846071 and rs4149577. Supplementary Table 1. Summary of the case/control populations used in this study. Supplementary Table 2. Summary of the genotyped and imputed SNPs in the discovery stage. Supplementary Table 3. Summary of the SNPs that have been reported to be associated with tinnitus in previous studies. Supplementary Table 4. Summary of the top 22 SNPs in the discovery stage. Supplementary Table 5. Primers used for SNPs genotyping in the replication stage. Supplementary Table 6. Summary of the association results in the replication stage. Supplementary Table 7. Stratification analyses of rs2846071 and rs4149577 by age. Supplementary Table 8. The predicted functional relevance of rs2846071, rs4149577 and the other SNPs in strong or moderate LD with them. Supplementary Table 9. Pathway analyses based on i-GSEA4GWAS. Supplementary Table 10. The allele and genotype frequencies of rs2846071 and rs4149577 in different populations.

Published
2021
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48. A genome wide association study of genetic loci that influence tumour biomarkers cancer antigen 19-9, carcinoembryonic antigen and α fetoprotein and their associations with cancer risk

Author

He, Meian, Wu, Chen, Xu, Jianfeng, Guo, Huan, Yang, Handong, Zhang, Xiaomin, Sun, Jielin, Yu, Dianke, Zhou, Li, Peng, Tao, He, Yunfeng, Gao, Yong, Yuan, Jing, Deng, Qifei, Dai, Xiayun, Tan, Aihua, Feng, Yingying, Zhang, Haiying, Min, Xinwen, Yang, Xiaobo, Zhu, Jiang, Zhai, Kan, Chang, Jiang, Qin, Xue, Tan, Wen, Hu, Yanling, Lang, Mingjian, Tao, Sha, Li, Yuanfeng, Li, Yi, Feng, Junjie, Li, Dongfeng, Kim, Seong-Tae, Zhang, Shijun, Zhang, Hongxing, Zheng, S Lilly, Gui, Lixuan, Wang, Youjie, Wei, Sheng, Wang, Feng, Fang, Weimin, Liang, Yuan, Zhai, Yun, Chen, Weihong, Miao, Xiaoping, Zhou, Gangqiao, Hu, Frank B, Lin, Dongxin, Mo, Zengnan, and Wu, Tangchun

Published
2014
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