Compared with nucleic acids, the cancer proteome is more complex and dynamic, and better reflects the functional state of the cancer cell and tissue. Current mass spectrometry proteomic methods are bottlenecked in two aspects: (i) limited detection sensitivity and dynamic range, (ii) lack of information in detecting protein splicing isoforms and PTM patterns. These limitations make it difficult for studies of critical proteome changes during cancer progression, or in-depth proteomic profiling in small samples. The goal of this proposed research is to develop new proteomic methods to address these current bottlenecks, and apply them to study proteomic changes behind cancer progression, includ...

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Compared with nucleic acids, the cancer proteome is more complex and dynamic, and better reflects the functional state of the cancer cell and tissue. Current mass spectrometry proteomic methods are bottlenecked in two aspects: (i) limited detection sensitivity and dynamic range, (ii) lack of information in detecting protein splicing isoforms and PTM patterns. These limitations make it difficult for studies of critical proteome changes during cancer progression, or in-depth proteomic profiling in small samples. The goal of this proposed research is to develop new proteomic methods to address these current bottlenecks, and apply them to study proteomic changes behind cancer progression, including EMT and drug resistance. Specifically, there are two objectives for this research. First, building on the super-resolution microscopy, single-molecule biophysical methods and DNA bioengineering technologies that I previously developed and harnessing the exquisite single-molecule sensitivity and nanometer imaging resolution of our methods, my lab will develop new proteomic methods for splice isoform and PTM analysis on single molecules and proteomic analysis in complex samples. Second, my lab will apply these technologies to study proteomic changes behind EMT and cancer drug resistance. We will apply our new method to elucidate protein splice isoform switching during EMT with single-molecule sensitivity and exon specificity. We will also apply our method to study proteomic changes underlying drug-resistance, in an unbiased fashion and in single tumor cells. Upon completion of the project, our research will provide a new platform for highly sensitive analysis of protein isoforms and PTM modifications on single molecules. Additionally, our results will provide the first sequence-specific mapping of splicing isoforms at the protein level, as well as comprehensive proteomic profiling for cancer drug resistance, both with single-molecule sensitivity.

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