Representative publications

Representative Publication

Spatially resolved proteomics via tissue expansion

Lu Li#, Cuiji Sun#, Yaoting Sun#, Zhen Dong#, Runxin Wu, Xiaoting Sun, Hanbin Zhang, Wenhao Jiang, Yan Zhou, Xufeng Cen, Shang Cai, Hongguang Xia, Yi Zhu, Tiannan Guo* & Kiryl D. Piatkevich*

Nature Communications. 2022 Nov 30;13(1):7242. doi: 10.1038/s41467-022-34824-2. PMID: 36450705.

Representative Publication

Artificial intelligence defines protein-based classification of thyroid nodules

Yaoting Sun#, Sathiyamoorthy Selvarajan#, Zelin Zang#, Wei Liu#, Yi Zhu#, Hao Zhang#, Wanyuan Chen, Hao Chen, Lu Li, Xue Cai, Huanhuan Gao, Zhicheng Wu, Yongfu Zhao, Lirong Chen, Xiaodong Teng, Sangeeta Mantoo, Tony Kiat-Hon Lim, Bhuvaneswari Hariraman, Serene Yeow, Syed Muhammad Fahmy bin Syed Abdillah, Sze Sing Lee, Guan Ruan, Qiushi Zhang, Tiansheng Zhu, Yifan Hu, Zhen Dong, Weigang Ge, Qi Xiao, Weibin Wang, Guangzhi Wang, Junhong Xiao, Yi He, Zhihong Wang, Wei Sun, Yuan Qin, Jiang Zhu, Xu Zheng, Linyan Wang, Xi Zheng, Kailun Xu, Yingkuan Shao, Shu Zheng, Kexin Liu, Ruedi Aebersold, Haixia Guan, Xiaohong Wu, Dingcun Luo, Wen Tian, Stan Z. Li*, Oi Lian Kon*, N. Gopalakrishna Iyer*, Tiannan Guo*.

Cell Discovery. 2022 Sep 6;8(1):85. doi: 10.1038/s41421-022-00442-x. Erratum in: Cell Discov. 2022 Sep 30;8(1):100. PMID: 36068205.

Representative Publication

Multi-organ Proteomic Landscape of COVID-19 Autopsies

Xiu Nie#, Liujia Qian#, Rui Sun#, Bo Huang#, Xiaochuan Dong#, Qi Xiao#, Qiushi Zhang#, Tian Lu, Liang Yue, Shuo Chen, Xiang Li, Yaoting Sun, Li Lu, Luang Xu, Li Yan, 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*.

Cell. 2021 Feb.184(3): 775-791.e14. doi: 10.1016/j.cell.2021.01.004. PMID: 33503446.

Representative Publication

Proteomic and Metabolomic Characterization of COVID-19 Patient Sera

Bo Shen #, Xiao Yi #, Yaoting Sun #, Xiaojie Bi #, Juping Du #, Chao Zhang #, Sheng Quan #, Fangfei Zhang, Rui Sun, Liujia Qian, Weigang Ge, Wei Liu, Shuang Liang, Hao Chen, Ying Zhang, Jun Li, Jiaqin Xu, Zebao He, Baofu Chen, Jing Wang, Haixi Yan, Yufen Zheng, Donglian Wang, Jiansheng Zhu, Ziqing Kong, Zhouyang Kang, Xiao Liang, Xuan Ding, Guan Ruan, Nan Xiang, Xue Cai, Huanhuan Gao, Lu Li, Sainan Li, Qi Xiao, Tian Lu, Yi Zhu*, Huafen Liu*, Haixiao Chen*, Tiannan Guo*.

Cell. 2020 Jul 9;182(1):59-72.e15. doi: 10.1016/j.cell.2020.05.032. PMID: 32492406.

All publications

134

Integrated multiomic profiling of breast cancer in the Chinese population reveals patient stratification and therapeutic vulnerabilities

Yi-Zhou Jiang#, Ding Ma#, Xi Jin#, Yi Xiao#, Ying Yu#, Jinxiu Shi#, Yi-Fan Zhou, Tong Fu, Cai-Jin Lin, Lei-Jie Dai, Cheng-Lin Liu, Shen Zhao, Guan-Hua Su, Wanwan Hou, Yaqing Liu, Qingwang Chen, Jingcheng Yang, Naixin Zhang, Wen-Juan Zhang, Wei Liu, Weigang Ge, Wen-Tao Yang, Chao You, Yajia Gu, Virginia Kaklamani, François Bertucci, Claire Verschraegen, Anneleen Daemen, Nakul M. Shah, Ting Wang, Tiannan Guo, Leming Shi, Charles M. Perou, Yuanting Zheng*, Wei Huang* & Zhi-Ming Shao*

Nature Cancer. 2024 Apr;5(4):673-690. doi: 10.1038/s43018-024-00725-0. Epub 2024 Feb 12. PMID: 38347143.

133

The 2023 Report on the Proteome from the HUPO Human Proteome Project

Gilbert S Omenn, Lydie Lane, Christopher M Overall, Cecilia Lindskog, Charles Pineau, Nicolle H Packer, Ileana M Cristea, Susan T Weintraub, Sandra Orchard, Michael H A Roehrl, Edouard Nice, Tiannan Guo, Jennifer E Van Eyk, Siqi Liu, Nuno Bandeira, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch.

Journal of Proteome Research.  2024 Jan 17. doi: 10.1021/acs.jproteome.3c00591. Epub ahead of print. PMID: 38232391.

129

Risk stratification of papillary thyroid cancers using multidimensional machine learning

Li, Yuanhui#; Wu, Fan#; Ge, Weigang#; Zhang, Yu #; Hu, Yifan; Zhao, Lingqian; Gou, Wanglong; Shi, Jingjing; Ni, Yeqin; Li, Lu; Fu, Wenxin; Lin, Xiangfeng; Yu, Yunxian; Han, Zhijiang; Chen, Chuanghua; Xu, Rujun; Zhang, Shirong; Zhou, Li; Pan, Gang; Peng, You; Mao, Linlin; Zhou, Tianhan; Zheng, Jusheng; Zheng, Haitao*; Sun, Yaoting*; Guo, Tiannan*; Luo, Dingcun*

International Journal of Surgery. 2024 Jan 1;110(1):372-384. doi: 10.1097/JS9.0000000000000814. PMID: 37916932.

126

Proteomic-based stratification of intermediate-risk prostate cancer patients

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*

Life Science Alliance. 2023 Dec 4;7(2):e202302146. doi: 10.26508/lsa.202302146. PMID: 38052461.

125

Multitissue Circadian Proteome Atlas of WT and Per1-/-/Per2-/- mice

Liujia Qian#, Yue Gu#, Qiaocheng Zhai#, Zhangzhi Xue#, Youqi Liu, Sainan Li, Yizhun Zeng, Rui Sun, Qiushi Zhang, Xue Cai, Weigang Ge, Zhen Dong, Huanhuan Gao, Yan Zhou, Yi Zhu*, Ying Xu*, Tiannan Guo*

Mol Cell Proteomics. 2023 Dec;22(12):100675. doi: 10.1016/j.mcpro.2023.100675. PMID: 37940002.

124

Immunotherapy targeting isoDGR-protein damage extends lifespan in a mouse model of protein deamidation

Pazhanichamy Kalailingam, Khalilatul-Hanisah Mohd-Kahliab, SoFong Cam Ngan, Ranjith Iyappan, Evelin Melekh, Tian Lu, Gan Wei Zien, Bhargy Sharma, Tiannan Guo, Adam J MacNeil, Rebecca EK MacPherson, Evangelia Litsa Tsiani, Deborah D O’Leary, Kah Leong Lim, I Hsin Su, Yong-Gui Gao, A Mark Richards, Raj N Kalaria, Christopher P Chen, Neil E McCarthy & Siu Kwan Sze

EMBO Molecular Medicine. 2023 Dec 7;15(12):e18526. doi: 10.15252/emmm.202318526. PMID: 37971164.

121

Forager-farmer transition at the crossroads of East and Southeast Asia 4900 years ago

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*

Science Bulletin. 2024 Jan 15;69(1):103-113. doi: 10.1016/j.scib.2023.10.015. Epub 2023 Oct 16. PMID: 37914610.

120

Population serum proteomics uncovers a prognostic protein classifier for metabolic syndrome

Xue Cai#, Zhangzhi Xue#, Fang-Fang Zeng#, Jun Tang#, Liang Yue#, Bo Wang#, Weigang Ge, Yuting Xie, Zelei Miao, Wanglong Gou, Yuanqing Fu, Sainan Li, Jinlong Gao, Menglei Shuai, Ke Zhang, Fengzhe Xu, Yunyi Tian, Nan Xiang, Yan Zhou, Peng-Fei Shan, Yi Zhu*, Yu-ming Chen*, Ju-Sheng Zheng*, Tiannan Guo*

Cell Reports Medicine. 2023 Sep 19;4(9). doi: https://doi.org/10.1016/j.xcrm.2023.101172. PMID: 37652016.

113

Proteomic Dynamics of Breast Cancer Cell Lines Identifies Potential Therapeutic Protein Targets

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*

Mol Cell Proteomics. 2023 Jun 19:100602. doi.org/10.1016/j.mcpro.2023.100602. PMID: 37343696.

110

Multi-omics blood atlas reveals unique features of immune and platelet responses to SARS-CoV-2 Omicron breakthrough infection

Hong Wang#*, Cuicui Liu#, Xiaowei Xie#, Mingming Niu#, Yingrui Wang#, Xuelian Cheng#, Biao Zhang#, Dong Zhang, Mengyao Liu, Rui Sun, Yezi Ma, Shihui Ma, Huijun Wang, Guoqing Zhu, Yang Lu, Baiming Huang, Pei Su, Xiaoyuan Chen, Jingjing Zhao, Hongtao Wang, Long Shen, Lixia Fu, Qianqian Huang, Yang Yang, He Wang, Chunlong Wu, Weigang Ge, Chen Chen, Qianyu Huo, Qingping Wang, Ying Wang, Li Geng, Yan Xie, Yi Xie, Lijun Liu, Jianwei Qi, Huaiyong Chen, Junping Wu, Erlie Jiang, Wentiao Jiang, Ximo Wang*, Zhongyang Shen*, Tiannan Guo*, Jiaxi Zhou*, Ping Zhu*, Tao Cheng*

Immunity. 2023 Jun 13;56(6):1410-1428.e8. doi.org/10.1016/j.immuni.2023.05.007. PMID: 37257450.

108

An immunometabolism subtyping system identifies S100A9+ macrophage as an immune therapeutic target in colorectal cancer based on multiomics analysis

Xuanwen Bao#*, Danyang Wang#, Xiaomeng Dai#, Chuan Liu#, Hangyu Zhang, Yuzhi Jin, Zhou Tong, Bin Li, Chuchu Tong, Shan Xin, Xin Li, Yanfang Wang, Lulu Liu, Xudong Zhu, Qihan Fu, Yi Zheng, Jingwen Deng, Weihong Tian, Tiannan Guo, Peng Zhao, Wenbin Chen*, and Weijia Fang*

Cell Reports Medicine. 2023 Apr 18;4(4):100987. doi: 10.1016/j.xcrm.2023.100987. PMID: 36990096.

104

Genome-wide genotype-serum proteome mapping provides insights into the cross ancestry differences in cardiometabolic disease susceptibility

Fengzhe Xu#, Evan Yi-Wen Yu#, Xue Cai#, Liang Yue#, Li-peng Jing#, Xinxiu Liang#, Yuanqing Fu, Zelei Miao, Min Yang, Menglei Shuai, Wanglong Gou, Congmei Xiao, Zhangzhi Xue, Yuting Xie, Sainan Li, Sha Lu, Meiqi Shi, Xuhong Wang, Wensheng Hu, Claudia Langenberg, Jian Yang, Yu-ming Chen*, Tiannan Guo* & Ju-Sheng Zheng*

Nature Communications. 2023 Feb 16;14(1):896. doi: 10.1038/s41467-023-36491-3. PMID: 36797296.

102

Proteomics Investigation of Diverse Serological Patterns in COVID-19

Xiao Liang#, Rui Sun, Jing Wang, Kai Zhou, Jun Li, Shiyong Chen, Mengge Lyu, Sainan Li, Zhangzhi Xue, Yingqiu Shi, Yuting Xie, Qiushi Zhang, Xiao Yi, Juan Pan, Donglian Wang, Jiaqin Xu, Hongguo Zhu, Guangjun Zhu, Jiansheng Zhu, Yi Zhu, Yufen Zheng*, Bo Shen*, and Tiannan Guo*

Mol Cell Proteomics. 22(2): 100493. doi: 10.1016/j.mcpro.2023.100493. PMID: 36621767.

100

Longitudinal proteomic investigation of COVID-19 vaccination

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*

Protein & Cell. 2023 Sep 14;14(9):668-682. doi: 10.1093/procel/pwad004. PMID: 36930526.

99

DPHL v2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins

Zhangzhi Xue#, Tiansheng Zhu#, Fangfei Zhang, Cheng Zhang, Nan Xiang, Liujia Qian, Xiao Yi, Yaoting Sun, Wei Liu, Xue Cai, Linyan Wang, Xizhe Dai, Liang Yue, Lu Li, Thang V. Pham, Sander R.Piersma, Qi Xiao, Meng Luo, Cong Lu, Jiang Zhu, Yongfu Zhao, Guangzhi Wang, Junhong Xiao, Tong Liu, Zhiyu Liu, Yi He, Qijun Wu,Tingting Gong, Jianqin Zhu, Zhiguo Zheng, Juan Ye, Yan Li , Connie R.Jimenez*, Jun A*, Tiannan Guo*

Patterns. 2023 Jul 5;4(7):100792. doi: 10.1016/j.patter.2023.100792. PMID: 37521047.

98

FAM3C in circulating tumor-derived extracellular vesicles promotes non-small cell lung cancer growth in secondary sites

Win Lwin Thuya#, Li Ren Kong#, Nicholas L. Syn#, Ling-Wen Ding#, Esther Sok Hwee Cheow, Regina Tong Xin Wong, Tingting Wang, Robby Miguel Wen-Jing Goh, Hongyan Song, Migara K. Jayasinghe, Minh TN Le, Jian Cheng Hu, Wei-Peng Yong, Soo-Chin Lee, Andrea Li-Ann Wong, Gautam Sethi, Huynh The Hung, Paul Chi-Lui Ho, Jean-Paul Thiery, Siu Kwan Sze, Tiannan Guo, Ross A. Soo, Henry Yang, Yaw Chyn Lim, Lingzhi Wang*, Boon-Cher Goh*

Theranostics. 13(2): 621-638. doi: 10.7150/thno.72297. PMID: 36632230.

Representative Publication

Spatially resolved proteomics via tissue expansion

Lu Li#, Cuiji Sun#, Yaoting Sun#, Zhen Dong#, Runxin Wu, Xiaoting Sun, Hanbin Zhang, Wenhao Jiang, Yan Zhou, Xufeng Cen, Shang Cai, Hongguang Xia, Yi Zhu, Tiannan Guo* & Kiryl D. Piatkevich*

Nature Communications. 2022 Nov 30;13(1):7242. doi: 10.1038/s41467-022-34824-2. PMID: 36450705.

95

The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

Gilbert S. Omenn*, Lydie Lane, Christopher M. Overall, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Cecilia Lindskog, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L. Moritz, and Eric W. Deutsch

Journal of Proteome Research. 2023 Apr 7;22(4):1024-1042. doi: 10.1021/acs.jproteome.2c00498. PMID: 36318223.

94

Integrated proteogenomic characterization of medullary thyroid carcinoma

Xiao Shi#, Yaoting Sun#, Cenkai Shen#, Yan Zhang#, Rongliang Shi#, Fan Zhang#, Tian Liao#, Guojun Lv, Zhengcai Zhu, Lianghe Jiao, Peng Li, Tiansheng Xu,  Ning Qu, Naisi Huang, Jiaqian Hu, Tingting Zhang, Yanzi Gu, Guangqi Qin, Haixia Guan, Weilin Pu, Yuan Li, Xiang Geng, Yan Zhang, Tongzhen Chen, Shenglin Huang, Zhikang Zhang, Shuting Ge, Wu Wang, Weibo Xu, Pengcheng Yu, Zhongwu Lu, Yulong Wang, Liang Guo, Yu Wang*, Tiannan Guo*, Qinghai Ji* & Wenjun Wei*

Cell Discovery. 2022 Nov 8;8(1):120. doi: 10.1038/s41421-022-00479-y. PMID: 36344509.

Representative Publication

Artificial intelligence defines protein-based classification of thyroid nodules

Yaoting Sun#, Sathiyamoorthy Selvarajan#, Zelin Zang#, Wei Liu#, Yi Zhu#, Hao Zhang#, Wanyuan Chen, Hao Chen, Lu Li, Xue Cai, Huanhuan Gao, Zhicheng Wu, Yongfu Zhao, Lirong Chen, Xiaodong Teng, Sangeeta Mantoo, Tony Kiat-Hon Lim, Bhuvaneswari Hariraman, Serene Yeow, Syed Muhammad Fahmy bin Syed Abdillah, Sze Sing Lee, Guan Ruan, Qiushi Zhang, Tiansheng Zhu, Yifan Hu, Zhen Dong, Weigang Ge, Qi Xiao, Weibin Wang, Guangzhi Wang, Junhong Xiao, Yi He, Zhihong Wang, Wei Sun, Yuan Qin, Jiang Zhu, Xu Zheng, Linyan Wang, Xi Zheng, Kailun Xu, Yingkuan Shao, Shu Zheng, Kexin Liu, Ruedi Aebersold, Haixia Guan, Xiaohong Wu, Dingcun Luo, Wen Tian, Stan Z. Li*, Oi Lian Kon*, N. Gopalakrishna Iyer*, Tiannan Guo*.

Cell Discovery. 2022 Sep 6;8(1):85. doi: 10.1038/s41421-022-00442-x. Erratum in: Cell Discov. 2022 Sep 30;8(1):100. PMID: 36068205.