Stanford ChEM-H solicited proposals from Stanford faculty and postdoctoral scholars who are seeking to pursuing a potentially transformative new idea at the interface of chemistry and human biology. Three faculty proposals and three postdoctoral scholar proposals were selected for one year of funding beginning in August 2014.
Faculty Track Awards:
"ChEM-H Medicinal Chemistry: Pharmacologic Manipulation of EGFR Presentation to the Cell Surface for the Treatment of Human Solid Tumors "
Anson Lowe, Medicine
Mark Smith, ChEM-H Medicinal Chemistry Knowledge Center
EGFR is the prototypical receptor tyrosine kinase that has an established role in development and human cancers. Current therapeutic strategies targeting EGFR have focused on inhibiting either ligand binding or the tyrosine kinase activity. We have recently established that delivery of EGFR to the plasma membrane is determined by the activity of AGR2, an endoplasmic reticulum-based thioredoxin. In the absence of AGR2 activity, EGFR is unable to achieve the appropriate confirmation that enables delivery to the plasma membrane where signal transduction occurs. The focus of this project is to enhance the structure activity relationship of candidate compounds that inhibit AGR2 activity. Compounds will be developed with the goal of optimizing pharmacokinetics, safety, and specificity. Success will result in a therapeutic agent with potentially far greater efficacy that currently employed drugs used for treating neoplasms dependent on EGFR-mediated signaling. This project establishes a collaboration between Dr. Anson Lowe, Associate Profess of Medicine, Division of Gastroenterology and Hepatology and Dr. Mark Smith, Head of Medicinal Chemistry at the Stanford ChEM-H Medicinal Chemistry Knowledge Center.
"Design Principles for Improved Far-Red Fluorescent Proteins "
Todd Martinez, Chemistry
Michael Lin, Pediatrics & Bioengineering
Vijay Pande, Chemistry, Structural Biology, & Computer Science
"High-throughput Scintillation Counting and Sorting of Single Cells "
Guillem Pratx, Radiation Oncology
Sindy Tang, Mechanical Engineering
Methods that can analyze the heterogeneous states and phenotypes of single cells have garnered increased attention in recent years. Flow cytometry has long been used to interrogate cellular states by detecting fluorescence emissions from single cells. This detection process is however not applicable to many small-molecule compounds that are neither intrinsically fluorescent nor amenable to fluorescence labeling. We are developing a novel method that could potentially measure how single cells interact with virtually any small molecule, with high sensitivity and quantitative accuracy. We utilize the fact that many small molecules can be labeled with a beta-emitting radionuclide such as 3H, 11C, 18F, 32P, and 35S. However, detecting radionuclides within a flow cytometer poses a major challenge. Due to the high throughput required, each singe cell can only be measured for a few milliseconds, which is too short for a significant number of radioactive decays to occur. Thus we are investigating a novel approach that effectively converts ionizing radiation into an integrated signal that can be readily measured within a standard flow cytometer. We are using the fact that certain materials undergo a change in their optical properties proportional to exposure to ionizing radiation. While many such materials exist, we plan to focus our investigation on photostimulable phosphors. These phosphors become fluorescent upon exposure to radiation, and there they could be read out using a standard flow cytometer. In order to measure single cells, we plan to co-encapsulate single cells and phosphors into calcium alginate alginate droplets. This project establishes a collaboration between the division of Radiation Physics within the School of Medicine (PI: Guillem Pratx, PhD; assistant professor) and the department of Mechanical Engineering within the School of Engineering (co-PI: Sindy Tang, PhD; assistant professor). The focus of Dr. Pratx’ lab is on novel optical and radionuclide approaches for improving cancer therapy and imaging. Dr. Tang’s lab works on solving problems at the interface of engineering, soft matter, and biology using microfluidics technology.
Postdoctoral Scholar Track Awards:
"Human Induced Neuronal Cells for Mechanism-Based Therapeutic Application"
Thomas Südhof, Molecular and Cellular Physiology and HHMI
Marius Wernig, Institute for Stem Cell Biology and Regenerative Medicine and Pathology
A major challenge in developing in vitro platform to conduct therapeutic drug screening for human neurological disorders is the difficulties of studying human neurons, for example: (i) ethical reasons forbid performing neurophysiological experiments on live brain tissues biopsied from individuals, (ii) culturing neurons from adult mammalian organisms is virtually impossible. As an alternative technique, human fibroblast and embryonic stem (ES) cells can be directly converted into induced neuronal (iN) cells by forced expression of transcription factors. This approach provides an excellent opportunity to study pathophysiology of disease-associated molecular mutations in human cellular environment. Dr. Chanda will use human ES cell derived iN (hES-iN) cells to decipher the underlying pathomechanisms of an epilepsy-associated molecule. To take a step further towards clinical studies, Dr. Chanda will reverse the molecule-specific pathogenic phenotype with mechanism-based targeted screening of candidate drugs. Dr. Chanda is advised by Drs. Thomas C. Südhof and Marius Wernig who provide a firm foundation and great opportunity to explore this new scientific field using molecular biology, stem cell biology, electrophysiology, and chemical biology.
"A Catalytic Approach to Remove Formaldehyde Crosslinks in FFPE Tissues"
David S. Hewings
Eric Kool, Chemistry
Ash Alizadeh, Oncology & Hematology
Formalin fixation and paraffin embedding (FFPE) is used universally to preserve tissue samples from biopsies and surgery. A vast archive of FFPE samples, often with long-term pa- tient follow-up, constitutes an invaluable resource for the study of disease and the investigation of biomarkers. FFPE tissues are routinely used for histopathology, but their application for the molecular characterization of diseased tissue specimens is hindered by the degradation or modification of the biomolecular analytes. Dr. Hewing is working with Prof. Eric Kool (Department of Chemistry) and Prof. Ash Alizadeh (School of Medicine) to develop a novel approach to remove formaldehyde-induced crosslinks in preserved tissue specimens. He aims to reverse these crosslinks under mild conditions using chemical knowledge of their mechanism of formation. Crosslinks limit the effectiveness of techniques such as qRT-PCR and immunohistochemistry on preserved samples, and improved techniques for their removal will benefit molecular diagnosis and biomarker identification. Dr. Hewing joined Stanford from the University of Oxford where he completed his PhD in Organic Chemistry under the supervision of Dr. Stuart Conway.
"Hierarchical Device Arrays for Single-Cell Chemical and Genetic Control"
J. Nathan Hohman
Nicholas Melosh, Materials Science and Engineering
Craig Garner, Psychiatry and Behavioral Sciences
The cell membrane is the fundamental interface of life. It is soft, flexible, yet is surprisingly strong. This structure represents the primary impediment that must be addressed when delivering molecules to or sampling contents from the cell’s interior. Nanowire array-based methodologies for cell penetration have demonstrated the ability to promote uptake of material loaded on the nanowire surface and pressed against a cell, but there remains a need for a controllable access port. We employ hybrid nanolithography to construct hierarchical structures designed to interact with and seal against the cell membrane. Within this microscale reaction environment in contact with the cell, biodegradable polymer nanoparticles encapsulating a chemical payload (viral vectors, plasmids, proteins) are trapped in an electrochemical composite. Degradation slowly releases the targets into the internal volume of the microreactor, enabling the concentration to build up within the trapped volume for efficient cellular uptake or electrochemical assay. A simple voltage pulse can rapidly deliver the contents of the reaction vessel to the cell without damaging its viability.