Hua Yu Lab

Principle Investigator

Dr. Hua Yu, Supervisor of PhD student

Distinguished Professor of Nanchang University

Dr. Hua Yu received his Ph.D. degree from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences in 2017. He was employed as lecturer, assistant researcher and associate researcher in Nantong University, Zhejiang University and Westlake University. He is currently a distinguished professor at the School of Basic Medical Sciences of Nanchang University, an independent PI of the Laboratory of Non-coding RNA Function Research and Translation, and a leader of the omics and big data platform of the Medical Science and Technology Innovation Center. In recent years, Professor Hua Yu has published a total of 22 SCI academic papers in high-level journals such as Nature Communications, Nature Metabolism, Protein & Cell, Genome Biology, Bioinformatics.

Research Directions

The mission of our group is to elucidate the functions and mechanisms of non-coding RNA in totipotent stem cells and human cancers by combining both dry and wet research strategies. On the one hand, our group will develop novel computational software to systematically predict and infer the functions of non-coding RNAs and phenotype-related non-coding RNAs. On the other hand, we will carry out biological experiments to discover key non-coding RNAs driving the fate transition of totipotent stem cells and the occurrence and development of human cancers, and further screening potential drugs targeting key non-coding RNAs.

Lab member

Zhiming Chen, Undergraduate

Basic Medicine, Nanchang University

Huiquan Wang, Undergraduate

Basic Medicine, Nanchang University

Selected Publications

(#) Co-first author; (*) Corresponding author

[1] Hua Yu#, Zhen Sun#, Tianyu Tan#, Hongru Pan#, Jing Zhao, Ling Zhang, Jiayu Chen, Yuqing Zhu, Lang Chen, Yuyan Xu, Shaorong Gao, George Q. Daley, Jin Zhang*. rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin. Nature Communications, 2021 12(6365). https://doi.org/10.1038/s41467-021-26576-2.

[2] Zhen Sun#, Hua Yu#, Jing Zhao#, Tianyu Tan, Hongru Pan, Bo Gao, Yuqing Zhu, Lang Chen, Cheng Zhang, Li Zhang, Anhua Lei, Yuyan Xu, Xianju Bi, Xin Huang, Cristina Correia, Ming Chen, Qiming Sun, Li Shen, Longfei Wang, Yu Feng, Jianlong Wang, Xiaohua Shen, Hu Li, Hao Wu, George Q. Daley, Jin Zhang*. LIN28 coordinately promotes nucleolar/ribosomal functions and represses the 2C-like transcriptional program in pluripotent stem cells. Protein & Cell, 2021. https://doi.org/10.1007/s13238-021-00864-5.

[3] Jing Zhao#, Ke Yao#, Hua Yu#, Ling Zhang, Yuyan Xu, Lang Chen1, Zhen Sun, Yuqing Zhu, Chen Zhang, Yuli Qian, Zhuyan Ji, Min Zhang, Jie Chen, Cristina Correia, Taylor Weiskittel, Dan Zhang, Hu Li, Wei Xie, Zeping Hu*, Jin Zhang* Metabolic reprogramming during mouse early embryo development. Nature Metabolism，2021 3(1). https://doi.org/10.1038/s42255-021-00464-x.

[4] Lin Yang, Yuqing Zhu#, Hua Yu#, Xiaolong Cheng, Sitong Chen, Yulan Chu, He Huang, Jin Zhang*, Wei Li*. scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens. Genome Biology, 2020 21(19). https://doi.org/10.1186/s13059-020-1928-4.

[5] Li Zhang#, Lin Tian#, Xiaoyang Dai#, Hua Yu#, Jiajia Wang#, Anhua Lei, Mengmeng Zhu, Jianpo Xu, Wei Zhao, Yuqing Zhu, Zhen Sun, Hao Zhang, Yongxian Hu, Yanlin Wang, Yuming Xu, George M. Church, He Huang, Qinjie Weng*, Jin Zhang*. Pluripotent stem cell-derived CAR-macrophage cells with antigen-dependent anti-cancer cell functions. Journal of Hematology and Oncology, 2020 13(153). https://doi.org/10.1186/s13045-020-00983-2.

[6] Hua Yu#*, Lu Lu#, Bingke Jiao, Chengzhi Liang*. Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples. Bioinformatics, 2018, bty642. https://doi.org/10.1093/bioinformatics/bty642.

[7] Hua Yu*, Biaoke Jiao, Lu Lu, Pengfei Wang, Shuangcheng Chen, Chengzhi Liang*, Wei Liu*, NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples. PLoS ONE, 2018, 13(2): e019261. https://doi.org/10.1371/journal.pone.0192613.

[8] Hua Yu#*, Lu Lu#, Ming Chen, Chen Li*, Jin Zhang*, Genome-wide discovery of hidden genes mediating known drug-disease association using KDDANet. npj Genomic Medicine, 2021 6(50). https://doi.org/10.1038/s41525-021-00216-6.

[9] Hua Yu#, Jianxin Chen#, Xue Xu, Yan Li, Huihui Zhao, Xiuxiu Li, Wei Zhou, Wei Wang* and Yonghua Wang*. A systematic prediction of multiple drug-target interactions from chemical, genomic and pharmacological data. PLoS ONE, 2012, 7(5): e37608. https://doi.org/10.1371/journal.pone.0037608.

[10] Hua Yu#*, Xiaojun Chen#*, Lu Lu. Large-scale prediction of microRNA-disease associations by combinatorial prioritization algorithm. Scientific Reports, 2017, 7:43792. https://doi.org/10.1038/srep43792.

[11] Lu Lu#, Jiale Qin#, Jiandong Chen, Hao Wu, Qiang Zhao, Satoru Miyano, Yaozhong Zhang*, Hua Yu* and Chen Li*. DDIT: An Online Predictor for Multiple Clinical Phenotypic Drug-Disease Associations. Frontier in Pharmacology, 2022, 12:772026. https://doi.org/10.3389/fphar.2021.772026

[12] Lu Lu*, Hua Yu*. DR2DI: a powerful computational tool for predicting novel drug-disease associations. Journal of Computer-Aided Molecular Design (2018) 32: 633. https://doi.org/10.1007/s10822-018-0117-y.

[13] Lingtong Liu#, Yunlong Lu#, Liqin Wei#, Hua Yu#, Yinghao Cao, Yan Li, Ning Yang, Yunyun Song, Chengzhi Liang*, Tai Wang*, Transcriptomics analyses reveal the molecular roadmap and long noncoding RNA landscape of sperm cell lineage development. The Plant Journal, 2018, 96(2):421-437. https://doi.org/10.1111/tpj.14041.

[14] Chengzhen Liang#, Aifu Li#, Hua Yu#, Wenzhen Li, Chengzhi Liang, Sandui Guo, Rui Zhang, Chengcai Chu. Melatonin Regulates Root Architecture by Modulating Auxin Response in Rice. Frontier in Plant Science, 2017, 8:134. https://doi.org/10.3389/fpls.2017.00134.

[15)] Hong-Qing Ling#*, Bin Ma#, Xiaoli Shi#, Hui Liu#, Lingli Dong#, Hua Sun#, Yinghao Cao, Qiang Gao, Shusong Zheng, Ye Li, Ying Yu, Huilong Du, Ming Qi, Yan Li, Hongwei Lu, Hua Yu, Yan Cui, Ning Wang, Chunlin Chen, Huilan Wu, Yan Zhao, Juncheng Zhang, Yiwen Li, Wenjuan Zhou, Bairu Zhang, Weijuan Hu, Michiel J. T. van Eijk, Jifeng Tang, Hanneke M. A. Witsenboer, Shancen Zhao, Zhensheng Li, Aimin Zhang*, Daowen Wang*, Chengzhi Liang*. Genome sequence of the progenitor of wheat A subgenome Triticum Urartu. Nature, 2018, 557:424-428. https://doi.org/10.1038/s41586-018-0108-0.

[16] Li Chen#, Qiaoqiao Tong#, Xiaowen Chen#, Penglei Jiang, Hua Yu, Qianbing Zhao, Lingang Sun, Chao Liu, Bin Gu, Yuping Zheng, Lijiang Fei, Xiao Jiang, Wenjuan Li, Giacomo Volpe, Mazid MD. Abdul, Guoji Guo, Jin Zhang, Pengxu Qian, Qiming Sun, Dante Neculai, Miguel A. Esteban, Chen Li, Feiqiu Wen, Junfeng Ji. PHC1 maintains pluripotency by organizing genome-wide chromatin interactions of the Nanog locus. Nature Communications, 2021, 12: 2829. https://doi.org/10.1038/s41467-021-22871-0.

[17] Lu Su#, Linkang Zhou#, Feng-Jung Chen, Huimin Wang, Hui Qian, Yuanyuan Sheng, Yuangang Zhu, Hua Yu, Xinqi Gong, Lie Cai, Xuerui Yang, Li Xu, Tong-Jin Zhao, John Zhong Li, Xiao-Wei Chen*, Peng Li*. Cideb controls sterol-regulated ER export of SREBP/ SCAP by promoting cargo loading at ER exit sites. The EMBO Journal, 2019, 38(8):e100156. https://doi.org/10.15252/embj.2018100156.

[18] Xue Li#, Xin Guo#, Yuqing Zhu#, Guoqing Wei, Yanlei Zhang, Xia Li, Huijun Xu, Jiazhen Cui, Wenjun Wu, Jingsong He, Matthew E.Ritchie, M.Weiskittel, Hu Li, Hua Yu, Lijuan Ding, Mi Shao, Qian Luo, XiaoxiaoXu, Xinyi Teng, Alex H.Chang, Jin Zhang*, He Huang*, Yongxian Hu*, Single cell transcriptomic analysis reveals BCMA CAR-T cell dynamics in a patient with refractory primary plasma cell leukemia. Molecular Therapy, 2021, 29(2):645-657. https://doi.org/10.1016/j.ymthe.2020.11.028.

Grants Approved

(1) National Natural Science Foundation of China, rRNA Biogenesis Regulates Mouse ES/2C-like State Homeostasis, 32100632, 2022/01-2024/12.

(2) Natural Science Foundation of Zhejiang Province, Nucleolar Stress Regulates Fate Decision of Mouse Embryonic Stem Cells, LQ21C120002, 2021/01-2023/12.

(3) Postdoctoral Science Foundation of China, Application of network flow intelligence algorithm in prediction of gene pathways bridging drugs and diseases, 2018M642441, 2018/11-2021/04.

E-mail: huayu@ncu.edu.cn

Office: Room 504, the fourth experimental building of Medical College of Nanchang University, No. 1299, Xuefu Avenue, Honggutan District, Nanchang City.

Phone number: 18758008246