Rui graduated from pharmacology and obtained her bachelor and master degree from China Pharmaceutical University (2011-2018). During her master study, Rui was interested in elucidating the molecular mechanisms of cancer stem cell and inflammatory function during tumorigenesis. She also developed interests in chemoproteomics to identify the drug targets when she visited the National Center for Protein Science Center (Phoenix) during 2016-2017 as an exchange student in Dr. Jing Yang lab. Rui joined the Guomics team in 2018 as a PhD candidate. During this period, she mainly analyzed the proteomic characteristics of prostate and breast cancers to discover more precise prognostic biomarkers and therapeutic targets. She has made innovative contributions in sample pre-processing, development and optimization of the mass spectrometry method, and bioinformatics analysis for proteomics research. Rui received her Ph.D. degree at Westlake University in 2022 and served as a postdoctoral researcher from Augustin 2022 to July 2024, with a focused on establishing the workflow of perturbation proteomics. In August 2024, she joined Guomics laboratory for Proteome Complexity Science and became a research assistant professor in AI modeling. She is also core member of Westlake University Research Center of the State Key Laboratory of Medical Proteomics, Zhejiang-Switzerland Joint Laboratory on Clinical Proteomics.

 

Oral talks / posters / conferences (International)

1. Oral talks: 2023.09.17-22 HUPO (Busan, South Korea) title: “Perturbation proteomics: insights from 16,000 perturbated triple-negative breast cancer proteomes.”

2. Poster: 2019.06.02-06 ASMS (Atlanta, America) “Microflow DIA Using 15min Gradients Analyzes 40 Tumor Proteomes per Day and Effectively Detects Promising Protein Biomarkers.”

 

Representative Publications

[Note: *, co-corresponding; #, co-first author]

 

1 Perturbation proteomics

1.1 Rui Sun#, Weigang Ge#, Yi Zhu#, Azin Sayad#, Augustin Luna, Mengge Lyu, Shuang Liang, Luis Tobalina, Vinodh N. Rajapakse, Chenhuan Yu, Huanhuan Zhang, Jie Fang, Fang Wu, Hui Xie, Julio Saez-Rodriguez, Huazhong Ying, William C. Reinhold, Chris Sander, Yves Pommier, Benjamin G. Neel*, Ruedi Aebersold*, Tiannan Guo* Proteomic dynamics of breast cancer cell lines identifies potential therapeutic protein targets. Molecular & Cellular Proteomics.2023 Aug; 22(8):100602. doi.org/10.1016/j.mcpro.2023.100602. PMID: 37343696.

1.2 Liujia Qian, Rui Sun, Christ Sandar, Ruedi Aebersold, Peter Bühlmann, Tiannan Guo* Perturbation proteomics in complex biological systems. Cell Genomics.2024 Accepted.

 

2 Cancer studies

2.1 Rui Sun#, Jun A#, Haolan Yu #, Yan Wang#, Miaoxia He#, Lingling Tan, Jili Zhang, Yingrui Wang, Xiaochen Sun, Mengge Lyu, Min Qu, Lingling Huang, Zhenyang Dong, Weigang Ge, Yun Zhang, Honghan Cheng, Xuan Ding, Bo Yang, Jianguo Hou, Chuanliang Xu, Linhui Wang, Yi Zhu, Tiannan Guo*, Xu Gao*, Chenghua Yang*. Proteomic landscape profiling of primary prostate cancer reveals a 16-ptotein panel for prognosis prediction. Cell Reports Medicine. 2024 Aug 20;5(8):101679. doi: 10.1016/j.xcrm.2024.101679. PMID: 39168102

2.2 Jinsen Zhang#, Rui Sun#, Yingying Lyu#, Chaxian Liu#, Ying Liu, Feng Yuan, Minjie Fu, Peter Jih Cheng Wong, Zunguo Du, Tianming Qiu, Yi Zhang, Dongxiao Zhuang, Zhiyong Qin, Yu Yao, Wei Zhu, Tiannan Guo, Wei Hua#, Hui Yang#, Ying Mao# Proteomic Profiling of Gliomas Unveils Immune and Metabolism-Driven Subtypes with Implications for Anti-Nucleotide Metabolism Therapy. Nature Communications. 2024 Accepted.

2.3 Rui Sun*#, Lingling Tan#, Xuan Ding, Jun A, Zhangzhi Xue, Xue Cai, Sainan Li, Tiannan Guo* A pathway activity-based proteomic classifier stratifies prostate tumors into two subtypes. Clinical Proteomics. 2023 Nov 11;20(1):50. doi: 10.1186/s12014-023-09441-w. PMID: 37950160.

2.4 Qing Zhong#, Rui Sun#, Adel T. Aref#, Zainab Noor#, Asim Anees#, Yi Zhu, Natasha Lucas, Rebecca C. Poulos, Mengge Lyu, Tiansheng Zhu, Guo-Bo Chen, Yingrui Wang, Xuan Ding, Dorothea Rutishauser, Niels J. Rupp, Jan H. Rueschoff, Cédric Poyet, Thomas Hermanns, Christian Fankhauser, María Rodríguez Martínez, Wenguang Shao, Marija Buljan, Janis Frederick Neumann, Andreas Beyer, Peter G. Hains, Roger R. Reddel, Phillip J. Robinson, Ruedi Aebersold*, Tiannan Guo*, Peter J. Wild*. Proteomic-based stratification of intermediate-risk prostate cancer patients. Life Science Alliance. 2023 Dec 4;7(2):e202302146. doi: 10.26508/lsa.202302146. PMID: 38052461.

2.4 Rui Sun, Mengge Lyu, Shuang Liang, Weigang Ge, Yingrui Wang, Xuan Ding, Cheng Zhang, Yan Zhou, Shanjun Chen, Lirong Chen, Tiannan Guo#. A prostate cancer tissue specific spectral library for targeted proteomic analysis. Proteomics 2022 Apr;22(7):e2100147. doi: 10.1002/pmic.202100147. Epub 2021 Dec 1. PMID: 34799972.

2.6 Rui Sun#, Christie Hunter#, Chen Chen, Weigang Ge , Nick Morrice, Shuang Liang, Tiansheng Zhu, Chunhui Yuan, Guan Ruan, Qiushi Zhang, Xue Cai, Xiaoyan Yu, Lirong Chen, Shaozheng Dai, Zhongzhi Luan, Ruedi Aebersold, Yi Zhu*, Tiannan Guo*. Accelerated Protein Biomarker Discovery from FFPE tissue samplesusing Single-shot, Short Gradient Microflow SWATH MS. Journal of Proteome Research. 2020 Jul 2;19(7):2732-2741. doi: 10.1021/acs.jproteome.9b00671. PMID: 32053377.

2.7 Youming Wang#, Rui Sun# , Weigang Ge, Lei Xue, Qianwen Xu, Hui Xu, Sujun Li, Miaomiao Wu, Tiannan Guo*, Xingbing Wang*. Longitudinal Serum Proteomics Characterization of CD19-CAR-T Cell Therapy for B-Cell Malignancies. Journal of Proteome Research. 2023 Sep 1;22(9):2985-94. doi: 10.1021/acs.jproteome.3c00322. PMID: 37531193.

 

3 COVID-19 studies

3.1 Shaohua Tang#, Rui Sun#, Weigang Ge#,Tingting Mao#, Liujia Qian#, Chongquan Huang#, Zhouyang Kang#, Qi Xiao, Meng Luo, Qiushi Zhang, Sainan Li, Hao Chen, Wei Liu, Bingjie Wang, Shufei Li, Xiaoling Lin, Xueqin Xu, Huanzheng Li, Lianpeng Wu, Jianyi Dai, Huanhuan Gao, Lu Li, Tian Lu, Xiao Liang, Xue Cai, Guan Ruan, Fei Xu, Yan Li, Yi Zhu*, Ziqing Kong*, Jianping Huang*, Tiannan Guo*. Enhanced inflammation and suppressed adaptive immunity in COVID-19 with prolonged RNA shedding. Cell Discovery. 2022 Jul 25;8(1):70. doi: 10.1038/s41421-022-00441-y. PMID: 35879274.（The first author is the chief clinician.）

3.2 Jianfeng Bao#, Rui Sun#, Jingwen Ai#, Liujia Qian#, Fang Liu#, Hongyu Wang#, Lingling Tan, Xue Cai, Yingqiu Shi, Xiao Liang, Weigang Ge, Jing Wu, Chen Chen, Wenhong Zhang*, Jinsong Huang*, Tiannan Guo*. Proteomic characterization of Omicron SARS-CoV-2 host response. Cell Discovery. 2022 May 18;8(1):46. doi: 10.1038/s41421-022-00418-x. PMID: 35581179.（The first author is the chief clinician.）

3.3 Xiu Nie#, Liujia Qian#, Rui Sun#, Bo Huang#, Xiaochuan Dong#, Qi Xiao#, Qiushi Zhang#, Tian Lu, Liang Yue, Shuo Chen, Xiang Li, Yaoting Sun, Lu Li, Luang Xu, Yan Li, Ming Yang, Zhangzhi Xue, Shuang Liang, Xuan Ding, Chunhui Yuan, Li Peng, Wei Liu, Xiao Yi, Mengge Lyu, Guixiang Xiao, Xia Xu, Weigang Ge, Jiale He, Jun Fan, Junhua Wu, Meng Luo, Xiaona Chang, Huaxiong Pan, Xue Cai, Junjie Zhou, Jing Yu, Huanhuan Gao, Mingxing Xie, Sihua Wang, Guan Ruan, Hao Chen, Hua Su, Heng Mei, Danju Luo, Dashi Zhao, Fei Xu, Yan Li, Yi Zhu*, Jiahong Xia*, Yu Hu*, Tiannan Guo*. Multi-organ proteomic landscape of COVID-19 autopsies. Cell. 2021 Feb 4;184(3): 775-791.e14. doi: 10.1016/j.cell.2021.01.004. PMID: 33503446.（The first author is the chief clinician.）

3.4 Yingrui Wang#, Qianru Zhu#, Rui Sun#, Xiao Yi#, Lingling Huang, Yifan Hu, Weigang Ge, Huanhuan Gao , Xinfu Ye , Yu Song, Li Shao, Yantao Li, Jie Li*, Tiannan Guo*, Junping Shi*. Longitudinal proteomic investigation of COVID-19 vaccination. Protein & Cell. 2023 Sep 14;14(9):668-682. doi: 10.1093/procel/pwad004. PMID: 36930526.

3.5 Xiuqin Zhang#, Dan Li#, Rui Sun#, Xinli Hu#, Zhiqi Song#, Xiaotian Ni, Hua Zhu, Tiannan Guo*, Chuan Qin*, Rui-Ping Xiao*. sRAGE alleviates SARS-CoV-2-induced pneumonia in hamster. Signal Transduction and Targeted Therapy. 2022 Feb 2;7(1):36. doi: 10.1038/s41392-022-00883-6. PMID: 35110523.

 

4 Chemoproteomics studies

a) Rui Sun#, Ling Fu#, Keke Liu, Caiping Tian, Yong Yang, Tallman KA, Porter NA, Liebler DC, Jing Yang*. Chemoproteomics Reveals Chemical Diversity and Dynamics of 4-Oxo-2-nonenal modifications in cells. Molecular cell Proteomics. 2017. 16 (10), 1789-1800. PMID: 28814509.

b) Rui Sun#, Fuguo Shi#, Keke Liu, Ling Fu, Caiping Tian, Yong Yang, Tallman KA, Porter NA, Jing Yang*. Chemoproteomic platform to assess bioactivation potential of drugs. Chemical Research in Toxicology. 2017. 30 (10), 1797-1803. PMID: 28960974.

 

5 Others studies

a) Minmin Ma#, Minxia Lu#, Rui Sun#, Zhonghua Zhu#, Dorian Q. Fuller, Jianxin Guo, Guanglin He, Xiaomin Yang, Lingling Tan, Yongxiu Lu, Jiajia Dong, Ruiliang Liu, Jishuai Yang, Bo Li, Tiannan Guo, Xiaorui Li, Dongyue Zhao, Ying Zhang, Chuan-Chao Wang*, Guanghui Dong*. Forager-farmer transition at the crossroads of East and Southeast Asia 4900 years ago. Science Bulletin. 2024 Jan 15;69(1):103-113. doi: 10.1016/j.scib.2023.10.015. Epub 2023 Oct 16. PMID: 37914610.

b) Chunguang Guo#, Rui Sun#, Xiao Wang, Ye Yuan, Yan Xv, Shihan Li, Xueting Sun, Yuting Lu, Jue Wang, Xinli Hu, Xiao-Wei Chen, Tiannan Guo*, Rui-Ping Xiao*, Xiuqin Zhang*. Intestinal SURF4 is essential for lipid homeostasis by regulating apolipoprotein trafficking. Molecular Metabolism. 2024 Jan;79:101847. doi: 10.1016/j.molmet.2023.101847. Epub 2023 Nov 30. PMID: 38042368.

 

Grants

1. National Natural Science Foundation of China (Young Scientist Fund): Graph neural networks solve differential equations for protein network inference of drug combinations and analyze the therapeutic effects of drug perturbations (Grant No. 32401239 to Dr Rui Sun) 2025.01-2027.12

2. National Natural Science Foundation of China (Key Joint Research Program): Systematic identification and functional characterization of understudied proteins in multiple cancers using proteomics (Grant No. U24A20476) 2025.1-2028.12

3. National Natural Science Foundation of China (Major Research Plan): Exploring colorectal cancer and its microenvironment evolution and accurate molecular classification via expansion microscopy and spatial proteomics (Grant No. 92259201) 2023.01-2026.12

4. National Natural Science Foundation of China (General Program): Discovery and Verification of Novel Protein Biomarkers and Drug Targets for Triple Negative Breast Cancers using PCT-SWATH Proteomic Big Data Technology (Grant No. 81972492) 2020.01-2023.12

5. Zhejiang Provincial Natural Science Foundation of China: A sensitization study of EGFR/mTOR/AKT targeted drugs for the treatment of triple-negative breast cancer based on multi-mics network analysis (Grant No. LQ24C050002 to Dr Rui Sun) 2024.01-2026.12