Past Projects

2018 Development Grants

Development of AAV-mediated Mini-Gene Therapy for Usher Syndrome Type 1F, a Combined Deafness and Blindness

Development of AAV-mediated Mini-Gene Therapy for Usher Syndrome Type 1F, a Combined Deafness and Blindness
Maryna Ivanchenko, Olga Strelkova, Pedro De La Torre, Daniel Hathaway, Marcos Sotomayor, Artur A. Indzhykulian, and David Corey.
Deafness and blindness are two of the most common and most devastating neurological disorders.  Seldom fatal, they separate patients from the world they live in and the people they love, for a lifetime.  In many cases, combined deafness and blindness result from a single gene defect, usually with a mutant gene copy inherited from both parents.  Usher syndrome is a hereditary deafness and blindness caused by mutation of any of nine genes. One gene, PCDH15, causes Usher syndrome type 1F, manifesting as profound congenital deafness and progressive blindness. There is no treatment.  Usher 1F occurs especially in the Ashkenazi Jewish population; there are ~3000 patients in the United States.
Following the striking success of Luxturna therapy for RPE65 blindness, gene addition for Usher 1F is an attractive approach. However the PCDH15 coding sequence, at 5.8 kb, is too large for AAV.  PCDH15 is a chain-like protein of 11 links, with binding domains at N- and C-termini.  We developed a number of mini-PCDH15 constructs that retain the binding domains but lack 3-8 links, and that consequently fit in AAV vectors.  Many mini-PCDH15 variants show normal binding in vitro. Since the deafness phenotype is more severe than blindness in mouse models, we assay function by testing cochlear receptor cells in vitro and hearing in vivo. AAVs encoding mini-PCDH15s have been assayed for their ability to preserve hearing in a Pcdh15-deficient mouse model that normally becomes completely deaf.   Some (but not all) of the minis, when injected into the cochleas of neonatal Pcdh15-deficient mice, produce substantial rescue of hearing. Because mechanical stress on PCDH15 is greater in the ear than in the eye, we believe that constructs that successfully rescue hearing will also rescue vision. In future work, we will test these constructs in the eye to assess rescue of the blindness phenotype.

Computationally designed therapy targeting inflammation in neurodegenerative diseases

Computationally designed therapy targeting lysosomal function and inflammation in neurodegenerative diseases
Jinkuk Kim, Yu-Han Huang, Timothy Yu, and Peter Park

Progranulin is a GRN-encoded protein that plays critical lysosomal and anti-neuroinflammatory functions. A therapy that boosts GRN expression would address the root genetic cause (GRN haploinsufficiency) of GRN-subtype frontotemporal dementia (GRN-FTD), a fatal and orphan neurodegenerative disease that affects 3,000-6,000 patients in the US alone. The therapy would also be effective for other neurodegenerative diseases including Alzheimer’s and Parkinson’s diseases. However, no such therapy is available currently. The recent remarkable success of Spinraza/nusinersen for spinal muscular atrophy has clearly demonstrated that antisense oligonucleotide (ASO)-based therapies can be highly effective for neuronal diseases. We have developed three ASOs that can increase the progranulin protein level in a human neuroblastoma cell line by multiple folds. These ASOs have the potential to become effective treatments for GRN-FTD and other neurodegenerative diseases.

2018 Pilot Grants

Small molecule modulators of gut bacterial bile acid metabolism to treat metabolic syndrome and associated NAFLD

Small molecule modulators of gut bacterial bile acid metabolism to treat metabolic syndrome and associated non-alcoholic fatty liver disease (NAFLD)
Arijit Adhikari and A. Sloan Devlin

Obesity is a growing worldwide health epidemic that is placing ever-growing medical and economic burdens on society. The prevalence of the associated condition non-alcoholic fatty liver disease (NAFLD) is also rising, and this condition is now the leading cause of chronic liver disease in the West. As a result of the multifaceted nature of these diseases and the lack of mechanistic understanding of their molecular underpinnings, doctors must resort to “trial and error” to identify effective treatments. The goal of this research is to develop small molecules that modulate gut bacterial metabolism of bile acids, compounds that play crucial roles in human metabolism, as new potential treatments for metabolic syndrome and NAFLD. These first-in-class molecules that target the microbiota will also allow us to better understand how the human microbiome contributes to obesity on a molecular level, knowledge that will pave the way for the development of future microbiome-based therapies.

A novel system for rational discovery of Polycystic Kidney Disease therapeutics

A novel system for rational discovery of Polycystic Kidney Disease therapeutics
Cherry Liu and Adrian Salic

Polycystic kidney disease (PKD) is the most frequent life-threatening genetic disease, affecting almost 1 million people in the US alone. It is characterized by growth of numerous cysts that progressively replace normal kidney tissue, which eventually leads to kidney failure, requiring chronic dialysis or transplantation. Currently without treatment, PKD constitutes a very large unmet medical need. PKD is caused by inhibitory mutations in PKD1 or PKD2, two interacting membrane proteins that activate a poorly understood signal transduction pathway (hereby, the PKD pathway) that is normally required for suppressing cyst formation. An attractive therapeutic strategy would be to rescue signaling activity downstream of defective PKD1 and PKD2. A major barrier has been the lack of a tractable system for dissecting the PKD pathway. We have recently developed a robust cell-based system that recapitulates PKD signaling, which allows, for the first time, rapid and quantitative measurements of PKD signaling, in a manner not possible in more complicated animal or tissue models. Currently, we are using this powerful system to comprehensively identify and dissect PKD pathway components. Here, we propose to use this novel system to discover small molecules capable of correcting defective signaling in PKD.

Development of an inexpensive at-home influenza kit and detection technology

Development of an inexpensive at-home influenza kit and detection technology
Sarah Boswell, Jason Qian, Zhixiang Lu, Mary Pettit, and Michael Springer

Influenza is a major drain on the US economy. Antiviral drugs are most effective against influenza when taken early, often before patients seek medical help. Tests exist for influenza but are only effective when influenza titer is high and/or require sophisticated medical equipment. Here we will build off of methods we are combining and developing for the specific detection of barcoded microorganisms (a DARPA funded project) to develop and optimize a quantitative, cheap, rapid, sensitive, selective, and field-deployable method for detecting influenza. We aim to develop this influenza detection system into an affordable ‘at-home’ system allowing individuals to detect influenza early, thereby increasing the efficacy of antiviral drugs and eliminating unnecessary trips to the ER.


2017 Development Grants

Developing therapeutics for treating Rett Syndrome by correcting neuronal long-gene misregulation

Developing therapeutics for treating Rett Syndrome by correcting neuronal long-gene misregulation – Lead compound optimization and in vivo validation
Rock Liao and Michael Greenberg

Disruption of X-linked methyl CpG-binding protein 2 (MECP2) causes Rett syndrome (RTT) - a devastating neurodevelopmental disorder leading to nonsyndromic mental retardation, learning disability, and autism. Currently there is no cure. We recently identified a molecular defect that is a likely cause of RTT – the mis-regulation of long highly methylated genes through MECP2 dysfunction. Notably, many of the mis-regulated highly methylated long genes are required for proper neuronal functions including synapses that underlie learning and memory. We hypothesize that restoring the expression of mis-regulated long genes and synaptic development may be key to treating RTT. A score of hits were identified and the majority were successfully validated by a series of in vitro experiments. Moreover, structural, pharmacokinetic (PK) and blood-brain-barrier (BBB) permeability analyses suggest favorable chemistry for therapeutics. In the next phase of study, we plan to further the drug development by focusing on behavioral testing while starting to investigate potential drug targets and mechanism of action (MOA).

Identification of dengue virus inhibitors

Identification of dengue virus inhibitors
Jared Pitts, Lorilee Tallorin, Marc-Philipp Pfeil, Chih-Yun (Angela) Hsia, and Priscilla L. Yang

  1. Zika, and other members of the Flavivirus genus are major human pathogens for which we lack effective countermeasures. Development of safe and effective vaccines against dengue virus (DENV) has been complicated by the propensity of non-neutralizing antibodies to worsen disease through antibody-dependent enhancement of infection. Antibody responses to the four DENV serotypes and Zika virus (ZIKV) cross-react to a significant extent but do not cross-neutralize. Antibody responses elicited by a vaccine can thus worsen disease upon subsequent infection. Antivirals provide an alternative approach to reduce disease and transmission of DENV and ZIKV. Persistence of ZIKV in immune-privileged sites, as evidenced by detection of ZIKV in semen and saliva for months, represents an additional opportunity for antiviral intervention. We are developing novel assays to identify flavivirus antivirals that act by both established and new mechanisms.

Development of small molecule modulators of autophagy and ER stress as novel therapeutics for AD

Development of small molecule modulators of autophagy and ER stress as novel therapeutics for AD
Jiefei Geng, Mingzhi Jin, Slawomir Dziedzic, Albert D. Yu, Hong Zhu, Amanda Tomie Ouchida, Jiachen Chu, and Junying Yuan

The goal of this project is to isolate inhibitors of apoptosis that can activate autophagy. Apoptosis has been implicated in a wide array of human inflammatory and degenerative diseases. However, after more than 30 years of research, the field failed to deliver a target that can be pharmacologically manipulated to inhibit apoptosis, as direct inhibition of caspases leads to necroptosis. Activating autophagy will support cell survival under stress condition.

2017 Pilot Grants

Developing CRISPR-Cas9 Reagents for Editing Lytic and Latent Herpes Simplex Virus Genomes

Developing CRISPR-Cas9 Reagents for Editing Lytic and Latent Herpes Simplex Virus Genomes
Hyungsuk Oh and David Knipe

Herpes simplex virus (HSV) 1 and 2 cause significant morbidity and mortality, and HSV-2 infection increases the risk of HIV infection. Furthermore, HSV-1 infection is associated with increased risk of Alzheimer’s disease. HSV undergoes an acute lytic infection at the mucosal epithelium and spreads to establish a latent infection in sensory and central nervous system neurons for the life of the individual. Reactivation from latent infection is a major cause of herpetic disease. Drugs that target lytic infection are available, but drugs that target latent infection are not available. Thus, a therapeutic targeting HSV latent infection could reduce HSV latent infection and reactivation and the associated herpetic disease, Alzheimer’s disease, and AIDS.

We have identified a highly active CRISPR-Cas9 reagent that effectively edits lytic and latent HSV-1 genomes in cell culture. Therefore, we propose experiments to further refine the use of this approach for prophylactic and therapeutic treatment of acute and latent HSV infection in animal models. Commercial entities have expressed interest in latent HSV targets, and there is obviously a large market and demand for a “cure” for herpes as well as preventatives for AIDS and Alzheimer’s disease.

2016 Development Grants

Developing a ubiquitin-dependent proteasome activity reporter

Developing a ubiquitin-dependent proteasome activity reporter to screen for activators and inhibitors
Ying Lu and Marc Kirschner

The 26S proteasome mediates both ubiquitin-dependent and ubiquitin-independent protein degradation and plays critical roles in the immune response, stress response and gene regulation. Current proteasome inhibitors, targeting only the rather nonspecific core particle, have nevertheless shown efficacy in cancer but they indiscriminately affect most functions of the proteasomes. With the help of Q-FASTR grant, we have successfully invented a novel and powerful screening platform for testing inhibitors that distinguish between ubiquitin-dependent and independent activities. We have performed initial screening and identified novel inhibitors with such specificity. By precisely modulating selected activities of the proteasome, these new classes of inhibitors could advance the treatment of cancer, inflammation and neurodegenerative disease. Currently, we are looking for partners to bring the project to the next phase.

Restoring Cortical Function and Plasticity Treatment of AD

Restoring Cortical Function and Plasticity for the Treatment of Alzheimer’s Disease
Brian Chow, Adam Granger, Sarah Melzer, and Bernardo Sabatini

Alzheimer’s disease (AD)is characterized by degeneration and dysfunction of the brain. In particular, a large folded expanse of the brain known as cortex is severely affected. Treatments for AD can aim at either stopping the degeneration or at maximizing the function of the remaining cortex. Here we proposed a new approach for the latter. We proposed to manipulate a specific cell type in cortex, known as VIP cells, which have the ability to regulate cortical function, plasticity, and blood flow. We have identified a molecular regulator that is uniquely expressed in VIP cells that provides a means to control these cells, and thereby cortex. We have been working to characterize the regulation of cortex by this pathway and establish it as a preclinical model for the enhancement of cortical function. If our hypotheses are correct, we will have identified a druggable pathway to enhance cognitive function in disease states

Targeted protein degradation as a strategy for potent antivirals

Assessment of targeted protein degradation as a strategy for potent antivirals with high barriers to resistance
Mélissanne de Wispelaere, Deirdre Costello, Tinghu Zhang, Guangyan Du, Nathaniel J. Henning, Supanee Potisopon, Eric S. Fischer, Radoslaw Nowak, Matthew Ponthier, Bethany Berry, Nathanael S. Gray, and Priscilla L. Yang

There is a major need for antivirals to combat the diverse viral pathogens causing human disease. Drugs that potently inhibit one or more related viruses with high natural barriers to resistance remain a much-desired but elusive goal. “Degronimids” represent a new class of inhibitors that induce degradation of their targets through recruitment of the E3 ubiquitin ligase cereblon. This inhibitory strategy can alleviate the need for stoichiometric target engagement and also suppress drug resistance. Recent examples in cancer biology demonstrate that degronimids against kinases and transcriptional enzymes deplete their requisite targets and have superior efficacy and resistance profiles relative to the parental compounds. Here, we propose to develop and evaluate degronimids that inhibit hepatitis C virus and dengue virus through inhibition and targeted degradation of specific viral targets. The goal of this work is to provide proof of concept that degronimid antivirals have superior antiviral potency and resistance profile when compared to the parental compounds. Viral targets and parent inhibitors have been judiciously selected to allow synthesis and characterization of antiviral degronimids on a relatively short time scale by leveraging our virological tools and expertise as well as by taking advantage of resistance mutations that have already been well-documented in the literature

2016 Pilot Grants

Building Better Screens and Identifying Ligands for Human MS4A

Building Better Screens and Identifying Ligands for Human MS4A proteins
Maria Lissitsinya Bloom, Talya Kassessian, and Sandeep Robert Datta

In the nose, a family of proteins called the MS4As act as small molecule detectors. These receptors detect ethologically relevant molecules from the environment, including nitrogenous heterocyclics and long chain fatty acids. The MS4As have been strongly implicated by human genetic studies in the development of Alzheimer’s Disease, although the mechanism through which the MS4As are linked to disease are completely unknown. The MS4As are expressed within microglia, a chemosensory cell type within the brain that have been associated with AD progression. We hypothesize that the ability of the MS4As to detect endogenous ligands found in the brain might mediate neuroinflammation associated with AD; if true, this suggests that the MS4As might define a completely new molecular mechanism underlying the AD progression. However, a major challenge in de-orphanizing the MS4As and in identifying chemical activators and inhibitors is the poor behavior of these receptors when expressed on their own in typical reconstitution systems like HEK cells. With support from Q-FASTR, we screened through a variety of cell lines and tested several chaperone candidates, in an attempt to convert our single cell screen for MS4A-dependent responses into a platform useful for high-throughput screening. This work continues, in the hope that identified ligands will be important starting templates for the development of molecules that manipulate MS4A activity, which may have significant therapeutic potential for treating AD.

Microtubule stabilizing drugs-neurodegenerative disease and SCI

Microtubule stabilizing drugs for neurodegenerative disease and spinal cord injury
Yuyu Song and Timothy Mitchison

Our 3-5 year goal is to develop small molecules drugs for neurodegenerative diseases and/or spinal cord injury that bind directly to microtubules and stabilize them in CNS neurons and glia. This well-defined pharmacological mechanism protects neurons from degenerative pathologies, and promotes axon growth in damaged spinal cord. It showed considerable promise in rodent models of neurodegeneration, spinal cord injury and schizophrenia using epothilone-D and -B as CNS-penetrating tool compounds. The potential efficacy of epothilones in man is limited by high peripheral toxicity. They kill dividing cells by stabilizing mitotic spindle microtubules and were originally developed as cytotoxic cancer drugs, making them a poor starting point for neurology drugs, despite their promising mechanism. To develop fundamentally less toxic microtubule stabilizing drugs that retain neuro-protective and neuro–regenerative activities we will adopt approaches from GPCR pharmacology that have never been applied to microtubule drugs. We will use ligand displacement assays as our primary screen, and then evaluate neuroprotective, cytotoxic and microtubule stabilizing activities in follow-up assays. In a 1-year pilot we propose to test the concept that we can obtain scaffolds which bind to the epothilone site and exhibit superior neuroprotective to cytotoxic ratios compared to current tool compounds. If we validate this concept, we will pursue a drug development project based using the assays and concepts we develop during the pilot phase.