- cell cycle, mitosis, protein stability, ubiquitin, cancer, genetics, cell biology
Multi-disciplinary research approaches
- Systems biology, cell and molecular biology, biochemistry, genetics
Challenges interpreting proteome landscape
Human cells encode more than twenty thousand unique proteins. The protein landscape, or “proteome” (which proteins are expressed, and the respective levels of each), can be vastly different between different cell types, and different stages of development, and throughout our lifetimes. In addition, cells rapidly reorganize their own protein landscape in response to environmental changes, following stress, as part of normal proliferation, and in the setting of cancer. Simplistically, the proteome is determined at any given time by which proteins are being made (transcription and translation), and which ones are being destroyed (degradation). While there are robust genomics based techniques that analyze global changes in transcription and translation, limited tools are available to assess global changes in protein degradation. This poses a significant challenge to understanding the networks and signaling pathways that allow cells to grow and divide normally, respond to stress, and prevent genome instability and cancerous transformation.
Systematic examination of proteome organization
To address these challenges in a systematic way, we are implementing technologies that can assess global, proteome wide changes in protein stability. Global Protein Stability Profiling (GPS) is a genetic platform that utilizes fluorescent reporters together with cell sorting to assess changes in protein stability (see reference 1 below). The GPS system employs a collection of more than 15,000 human ORFs (based on the human ORFeome collection) expressed from a retroviral reporter construct that encodes red fluorescent protein (DsRed) and green fluorescent protein (GFP) fused to the protein of interest. Importantly, GPS can simultaneously assess changes in the stability of these 15,000 proteins, and effectively analyzes low abundance proteins often missed by proteomic techniques. As a complement to GPS, we utilize a quantitative proteomic approach that interrogates the ubiquitin modified proteome. Together, these emerging technologies will provide a deep snap shot in the regulated proteome.
Ubiquitin system in cell cycle control and cancer
Protein degradation is regulated primarily through the ubiquitin proteasome system. Ubiquitin is a versatile post-translation modification that, among other things, targets its substrates for degradation. The ubiquitin system is essential for normal proliferation and genome stability, and is rewired in many cancers, where it is known to play a causative role. Since cancer is primarily a disease of uncontrolled cell proliferation, we are focused on the role of ubiquitin signaling in both normal cell proliferation and in the uncontrolled growth observed in disease. We expect that by applying systems biology approaches (above) and following up specific signaling nodes with direct cell, molecular and biochemical assays, we provide key insights into physiological indicators of disease, and present unforeseen therapeutic vulnerabilities to be exploited in the future.
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