Matthew Levy, Ph.D. - US grants

High-throughput, automated selection methods will be employed by the Ellington lab at the University of Texas at Austin to generate aptamers against HIV-1 Rev, Tat, reverse transcriptase, Rnase H, and the RRE. Aptamers will be characterized by the company Accacia, and subsequently assayed in cell culture models of viral infection by the Prasad lab at the Albert Einstein College of Medicine, as well as in animal models by the Johnson lab at Harvard. The selected aptamers will also be used to generate chips for mapping epitopes and for the detection of resistance mutants. The development of viral resistance will be further addressed by conducting re-selections against proteins that have acquired resistance mutations. Ultimately, these selection experiments should potentiate the development of highly efficacious gene therapies for AIDS and will also provide unique insights into the evolution of viral resistance.

High-throughput, automated selection methods will be employed by the Ellington lab at the University of Texas at Austin to generate aptamers against HIV-1 Rev, Tat, reverse transcriptase, Rnase H, and the RRE. Aptamers will be characterized by the company Accacia, and subsequently assayed in cell culture models of viral infection by the Prasad lab at the Albert Einstein College of Medicine, as well as in animal models by the Johnson lab at Harvard. The selected aptamers will also be used to generate chips for mapping epitopes and for the detection of resistance mutants. The development of viral resistance will be further addressed by conducting re-selections against proteins that have acquired resistance mutations. Ultimately, these selection experiments should potentiate the development of highly efficacious gene therapies for AIDS and will also provide unique insights into the evolution of viral resistance.

DESCRIPTION (provided by applicant): We propose to develop a new system for site specific labeling proteins in live cells based on the bacterial transpeptidase sortase A (SrtA). Using a combination of protein engineering and directed evolution, we will develop SrtA variants capable of efficiently functioning within mammalian cells. We will also develop exceptionally small (<2KDa), brightly fluorescent membrane permeable labels as well as substrates which will fluoresce only upon attachment to the target protein. The reduced size of these labels coupled with their strong fluorescence will permit monitoring of proteins at lower, more physiological expression levels while reducing any potential for steric interference. Initial work will focus on labeling secretory proteins, but the technology will be applicable to almost any protein located in a number of cellular compartments. PUBLIC HEALTH RELEVANCE: We will develop a novel enzymatic method for labeling specific proteins with small fluorescent molecules in live cells.

Principal Investigators: GREALLY, J.M., LEVY, M. Project abstract IN VIVO IMAGING OF X INACTIVATION. We propose to develop a system for in vivo imaging of the epigenetic regulatory processes involved in X chromosome inactivation. X inactivation is a well-studied paradigm of epigenetic gene regulation, involving the silencing of the majority of the genes on one X chromosome in female cells, part of the process of dosage compensation in mammals. A number of epigenetic regulatory processes have been found to contribute to the inactivation process, which when imaged using immunofluorescence on fixed cells generate a signal throughout the chromosome territory of the inactive X. The robustness of this signal makes X inactivation an attractive system for the development of in vivo imaging approaches. The inactive X is characterized by the presence of repressive post-translational histone modifications such as histone H3 lysine 9 trimethylation (H3K9me3) and H3K27me3, modifications established by polycomb group proteins which, when mutated, are associated with the failure of X inactivation. There are, however, other regulatory mediators implicated with functions that are less obviously related to the establishment of these chromatin states, functions such as helicase activity, RNA-binding, matrix-attachment region DNA-binding, or those functions associated with chromosomal structural maintenance motifs. As a means of understanding how each component of the X inactivation system interacts functionally, an in vivo system would allow the observation of sequential localization of the protein mediators and histone modifications to the inactivating X chromosome, thus establishing a likely hierarchy of regulation in this complex epigenetic process. In order to develop such a system, a number of areas of expertise need to be assembled. The project starts with the in vitro generation of histone peptides (and eventually entire reconstituted nucleosomes) with methylation and ubiquitination marks (David Allis and Tom Muir, Rockefeller University) that are then used for in vitro selection by co-PI Matthew Levy (Einstein) to create RNA aptamers specifically binding to these post- translational modifications. These aptamers are then linked in an expression construct to RNA hairpins bound by fluorescently-tagged phage coat proteins, a system pioneered by co-investigator Robert Singer (Einstein) as a means of tracking RNA in vivo in transcription studies. This project represents the first use of the same system for epigenetic studies. The cell type in which the system will be optimized will be a female mouse embryonic stem cell line, allowing not only X inactivation studies but also the broader use of this system in pluripotent cells when made available to the scientific community. The X inactivation studies will be facilitated by the development of fluorescent tags for the candidate protein mediators of X inactivation (Edith Heard, Institut Curie, Paris, France). The project is thus based on a strong and multifaceted foundation of expertise and resources. PHS 398/2590 (Rev. 11/07) Continuation Format Page

DESCRIPTION (provided by applicant): We propose to use a combination of two powerful techniques: aptamer selection (systematic evolution of ligands by exponential enrichment; SELEX) and in vitro compartmentalization (IVC), to develop a new method of generating libraries of functionalized nanoparticles and that can be screened directly for function. While the goal of this application is to develop a novel system for the direct identification of targeted nanoparticles which localize to human tumors, we will develop a platform technology which extends beyond the detection and treatment of cancer and other diseases and will result in the generation of a novel class of capture agents that will find use in a variety of applications and fields of research.

DESCRIPTION (provided by applicant): Secretory proteins are often robust markers of changes in disease-relevant cellular states including ER stress and metastasis. The absence of technologies for detecting specific luminal secretory proteins in live cells represents a major gap in cell imaging tools. Our goal is to develop and deliver highly sensitive reporters that can detec differences in the expression of diagnostic secretory proteins within a population of live cells. T do this, we will combine three existing technologies to create a new class of imaging tools, STABs (Secretory Targeting Aptamer Beacons). More specifically, by combining modified bacterial toxins with nuclease stabilized aptamer beacons specific for secreted proteins such as VEGF or the UPR-induced endoplasmic reticulum proteins Ero1 and ERdj4, we aim to generate reagents which, when added directly to cells or tissues, will enter the secretory pathway and report the presence of these proteins. Theoretically, up to four distinct fluorescent dyes can be paired with unique aptamers to report on the expression of four different secretory proteins. We envision the probe technology will have utility for basic research and rapid clinical analysis of tissue samples.

DESCRIPTION (provided by applicant): We propose to develop a novel platform technology that will produce high-affinity and high-specificity ligands to target carbohydrate binding protein (CBPs), a diverse class of proteins which possess a wide range of biological functions, playing roles cancer tumorigeneisis, immune modulation and viral infection. Our method builds upon advances in sequencing technologies and leverages the natural, low affinity, interactions of monovalent sugars for CBPs combined with the ease of synthesis of nucleic acids. Our glycan-anchored libraries will thus possess many of the attributes of nucleic acids - in particular structural rigidity, ease of synthesis and the ease with which they can be amplified and characterized - but with the enhanced chemical functionality observed in peptides, proteins and small molecule ligands. Because these reagents are based on nucleic acids, the resulting affinity agents can be readily synthesized at relatively low cost and can be easily modified with a variety of fluorophores or chemical moieties for diagnostic, therapeutic and research purposes.

DESCRIPTION (provided by applicant): The prevalence of HIV-associated neurological disorders (HAND) is on the rise despite Highly Active Anti-Retroviral Therapy (HAART). The pathogenesis of HAND is primarily due to neurotoxic viral proteins such as HIV-1 gp120 and Tat due to the replication of HIV in the brain. Antiretrovirals have variable efficiencies in crossing he blood brain barrier and thus being unable to eliminate HIV-1 in the CNS or in reducing the neurotoxic viral proteins. To overcome this problem, we propose to employ a modular, aptamer-based approach to deliver therapeutics designed to neutralize HIV-1 and inhibit neurotoxic viral proteins hiding behind the blood brain barrier (BBB). We will develop the next generation of delivery agents that can transcytose the BBB, specifically target HIV and consequently achieve higher effective drug concentrations in the CNS to be able to combat and neutralize HIV-1 and its toxic byproducts. There will be two specific aims. In Aim 1, we will target HIV reservoirs in te CNS using previously selected anti-transferrin receptor (hTfR) aptamers that can cross an in vitro model BBB composed of Human Brain Microvascular Endothelial Cells (HBMECs). Using these aptamers and our in vitro BBB model, we will develop a strategy to deliver therapeutic antibodies, aptamers or other molecules across the BBB and attempt to neutralize recombinant gp120 or Tat protein-mediated neuronal killing or to prevent HIV-infection of macrophages. In Aim 2, using a novel cell-based SELEX approach (selective evolution of ligands by exponential amplification) and using a flow-based dynamic in vitro blood brain barrier (DIV-BBB; Flowcel Inc.) which accurately reproduces the BBB in vivo, we seek to identify RNA aptamers that can specifically cross the BBB and will subsequently adapt these for drug delivery across the BBB.

The broader impact/commercial potential of this Small Business Innovation Research (SBIR) Phase I project is to reduce the impact of preventable vision loss caused by retinal diseases such as the wet form of advanced macular degeneration (wAMD) and diabetic macular edema (DME). Vision loss has a significant impact on the lives of those who experience it as well as on society as a whole. The retinal therapeutics market was $13 B in 2018 and is projected to grow to $28B in 2025. The proposed project develops a new technology to address multiple aspects of eye disease, which is expected to improve clinical outcomes at reduced cost.

This Small Business Innovation Research (SBIR) Phase I project will identify the best approach to combining anti-VEGF and anti-IL8 aptamers to generate a bispecific aptamer. Two different approaches will be evaluated: 1) direct chemical synthesis, in which the individual aptamer components are used to form a bispecific aptamer synthesized as a single compound, and 2) assembly by hybridization, in which individual aptamer components are synthesized separately with complementary extensions subsequently used for assembly. This project will assess the effect of linker identity and length on function, as well as the inhibitory activity, which will be compared with that of the individual aptamer components. The best performing bispecific aptamers will be PEGylated using at least two different PEG variants, and further evaluated. The biophysical properties of the PEGylated compounds will be assessed. These properties are key to establishing parameters for bispecific aptamer formulation and predicting intravitreal half-life. The best performing PEGylated bispecific aptamer function will be evaluated in vivo, to confirm its ability to engage its targets in an established animal model of retinal disease.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.