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High Throughput Chemical Biology

Stanford ChEM-H solicited seed grant proposals from Stanford faculty members in the area of High Throughput Chemical Biology. In December 2013, three projects were funded based on their potential to result in transformative methods and/or resources that can be used by the broader Stanford research community to advance our understanding of human physiology or disease. Each seed grant provides $80,000 for one year of research funding.

"Development of an automated bioreactor platform for rapid genome-wide screening and identification of single and combination drug targets"

Principal Investigators:

Michael Bassik, Genetics
Michael Cleary, Pathology, Pediatrics
Michael Wei, Pediatrics

Project Summary:

Major limitations in drug development are identification of targets for novel drugs, and discovery of effective drug combinations to combat rapidly evolving diseases. Furthermore, drug screens require extensive handling, which limits throughput and increases variability.  The purpose of this proposal is to address these issues by (1) dramatically enhancing the speed, accuracy, and scale of pooled genome-wide screens using bioreactors to automate cell culture, and (2) developing a first-in-class set of tools to examine pairwise genetic interactions between drug targets in high-throughput.  We have shown in pilot studies that our novel high-complexity shRNA libraries (25 shRNAs/gene) can be used to identify the target of a cancer-killing drug with remarkable specificity (Matheny et al 2013). Such libraries can also be used to simultaneously measure genetic interactions between 100,000’s of gene pairs (Bassik et al, 2013). We will combine these strategies to (a) conduct a complete genome screen for modifiers of a NAMPT inhibitor in a leukemia model together with the lab of Michael Cleary, and (b) identify synthetic lethal interactions between druggable genes in the context of stress.  Beyond these initial studies, we expect these tools will be broadly useful for genetic screening and drug development efforts at Stanford, and will serve as the basis of a future core resource. 


"Primary organoid screening platforms for solid tumor therapeutics discovery"

Principal Investigators:

Calvin Kuo, Medicine

Project Summary:

The in vitro culture of primary, non-transformed tissues as three-dimensional (3D) organoids that accurately recapitulate tissue structure, multilineage differentiation and physiology has diverse applications ranging from basic biology to therapy.  This project attempts to develop organoid models of mouse and human tissues using an air-liquid interface in which culture is performed in a gel that is directly exposed to air rather than cell culture medium.   The overall goal is to perform process development for organoid screening platforms usable for therapeutics discovery and toxicology applications.   


"Probing Protein-Protein Interactions with High-Throughput GMR Protein Arrays"

Principal Investigators:

Shan Wang, Materials Science & Engineering, Electrical Engineering, Radiology

Project Summary:

The grand promises of genomic revolution, including curing cancer and lowering healthcare cost, remain largely unfulfilled, even many years after the completion of Human Genome Project. It is now widely recognized that relentless innovation and the convergence of physical science and biomedicine are urgently needed to bring about truly paradigm-shifting progress in healthcare. Identifying and characterizing protein-protein interactions and entire interaction networks is the key to understanding drug targeting or side effects, but major hurdles remain. We propose to create a non-optical array-based approach for ultrasensitive investigation of protein-protein interactions relevant to therapeutic response and drug discovery. The ultra-sensitivity (~femtomolar) will be provided by the giant magnetoresistance (GMR) biosensors previously developed in Wang Lab and Stanford Center for Cancer Nanotechnology Excellence (CCNE). Better specificity and faster assay time will be achieved due to much better signal to noise ratios. Deep multiplexing to probe tens of thousands of proteins is possbile with large scale GMR sensor array. By using high avidity (multivalent) magnetic nanotags, we will be able to detect transient low affinity extracellular protein-protein interactions as multiple ECDs (baits) can react with multiple binding sites of prey proteins simultaneously. We will engineer giant magnetoresistive (GMR) biosensors with femtomolar sensitivity in a high-throughput array format. During this SICB seed project, we will demonstrate the ability to detect protein-protein binding events in real time in a highly multiplexed array format with unprecedented sensitivities based on nanoparticle labeling and GMR sensing.