Our Research

Proteogenomics, Bioinformatics and Precision Medicine

We are seeking empirical evidence for the existence of genetic variations at protein levels, revealing molecular subtypes of cancers and their associated markers relying on both genomic and proteomic data, identifying disrupted pathways linked to subtypes and nominating potential drug targets for oncology drug development. We have developed multiple proteomic variant callers to identify undocumented proteoforms that may play a key role in certain physiological events.

Further reading:

a. Xu J*, Zhang C*, Wang X*, Zhai L*, Ma Y*, et al. Integrative proteomic characterization of human lung adenocarcinoma. Cell, 2020; 182(1):245-261. (Cover Article, co-first authorship, I developed proteomic variant callers for mutations and fusions and led the bioinformatic/statistical analyses).

b. Gong T*, Zhang C* et al. A Time-resolved Multi-omic Atlas of the Developing Mouse Liver. Genome Res, 2020; 30(2):263-275. (co-first authorship)

c. Li X*, Zhang C* et al. A Time-resolved Multi-omic Atlas of the Developing Mouse Stomach. Nature Communications, 2018; 9(1):4910. (co-first authorship. I developed a bioinformatic pipeline to identify novel alternative splicing by integrating multi-omics data sets).

d. Ni X *, Tang Z *, Ding C *, Zhang C et al. A region-resolved mucosa proteome of the human stomach. Nature Communications, 2019; 10(39):1.

Cancer Immunotherapy

We are working on single cell-based biomarker discovery and therapeutical targets mining for engineering T cell therapies in multiple cancers. The goal is to identify tumor specific antigens for novel cancer immunotherapies.

Further reading:

a. Andras Heczey, Xin Xu, Amy N Courtney, Gengwen Tian, Gabriel A Barragan, Linjie Guo, Claudia Martinez Amador, Nisha Ghatwai, Purva Rathi, Michael S Wood, Yanchuan Li, Chunchao Zhang, Thorsten Demberg, Erica J Di Pierro, Andrew C Sher, Huimin Zhang, Birju Mehta, Sachin G Thakkar, Bambi Grilley, Tao Wang, Brian D Weiss, Antonino Montalbano, Meena Subramaniam, Chenling Xu, Chirag Sachar, Daniel K Wells, Gianpietro Dotti, Leonid S Metelitsa. Anti-GD2 CAR-NKT cells in relapsed or refractory neuroblastoma: updated phase 1 trial interim results. Nat Med. 2023 Jun;29(6):1379-1388.

b. H Ngai, GA Barragán, G Tian, JC Balzeau, C Zhang, et al. LEF1 drives a central memory program and supports antitumor activity of natural killer T cells. Cancer Immunol Res. 2022, CIR-22-0333.

c. Yang Yu, Yanling Zhao, Jongmin Choi, Zhongcheng Shi, Linjie Guo, John Elizarraras, Andy Gu, Feng Cheng, Yanxin Pei, Dai Lu, Muller Fabbri, Saurabh Agarwal, Chunchao Zhang, Sung Yun Jung, Jennifer H Foster, Jianhua Yang. Cancers. 2022, 10;14(22):5534.

d. Tomolonis JA, Xu X, Dholakia KH, Zhang C, et al. Interaction between tumor-cell TNFR2 and monocyte membrane TNFα triggers tumorigenic inflammation in neuroblastoma. Journal for ImmunoTherapy of Cancer. 2023; 11(3): e005478.

e. Y Yu†, WM Cao†, F Cheng, Z Shi, L Han, JL Yi, EM Da Silva, H Dopeso, H Chen, J Yang, X Wang, C Zhang*, H Zhang*. FOXK2 amplification and overexpression promotes breast cancer development and chemoresistance. bioRxiv May 30, 2023 (Co-corresponding author)