Summary

Protein abundance and post-translational modifications (PTMs) are tightly regulated to control cellular activities and developmental processes. Dysregulated protein function, either through abnormal protein levels or PTMs, disrupts normal cellular activities and can lead to complex diseases. Studies focusing on kinases and phosphatases involved in cancer development have identified targets, leading to many therapeutic discoveries. Targeting kinases, such as EGFR, ABL and more recently CDK4/6, has been an effective therapeutic strategy in many cancer types. Despite these advances, challenges remain.

How complex interactions between a patient’s genetic background and their environment influences protein and PTMs in cancer growth and treatment is largely unknown. Tumor heterogeneity, and drug resistance and the limitation of druggable targets remain problems in kinase-targeted cancer therapies. Therefore, an urgent need exists for target identification and drug discovery efforts. The continual development of more accurate, faster, comprehensive, and affordable proteomics and chemoproteomics technologies has greatly expanded our capacity to understand protein and PTMs regulation in disease models and to discover new therapeutic treatments.

In the Zhang Lab, we will integrate high-throughput proteomic, chemical, genetics and computational tools to investigate how related factors influence protein abundance and PTMs through diverse mechanisms to facilitate therapeutic treatment development for diseases, especially cancer.

1. Elucidate the effects of genetic variation on protein abundance and post translational modifications (PTMs)

We developed integrative multi-omics analysis in genetically diverse CC strains which provides a powerful tool to identify regulators of protein phosphorylation. Similar approaches could be used in combination with interventions, including mapping modifiers of transgenic models of disease. Moreover, it sets a precedent for future studies of regulatory mechanisms for other post translation modifications (PTMs) of proteins, such as methylation and ubiquitination. Coupled with advanced mass spectrometry technology for deeper coverage, we will use this strategy to provide a comprehensive regulatory map of PTMs.

2. A multi-pathway kinase activity assay to identify pathway modulators.

The limitation of druggable targets, the challenge of tumor heterogeneity and drug resistance to kinase inhibitors in cancer therapy highlight the urgent need of developing new high-throughput drug screening strategies to identify kinase modulators in complex cancer models. We developed a novel multi-pathway kinase activity assay and will apply it to profile a large cysteine-reactive covalent fragment library in 2D and 3D cancer cell culture models to identify kinase modulator leads. The findings from this study hold promise to not only advance kinase research overall, but also to identify candidate kinase modulators for future cancer drug development.

3. Probing cellular networks using proximity labeling tools

Interrogating Kinase-Substrate Relationships with Proximity Labeling and Phosphorylation Enrichment.

Time-resolved proximity labeling of protein networks associated with ligand-activated EGFR.