Active Projects

Monoclonal antibody-based therapeutics for Argentine hemorrhagic fever

Brian Gowen (USU), Jonathan Abraham

Viral hemorrhagic fevers (VHFs) pose continuing threats to public health. Most have limited treatment options or vaccines, which underscores a point of vulnerability in public health. Passive immunization is an attractive treatment strategy; for example, transfusion of the monoclonal antibody (mAb) cocktail ZMappTM was a lead approach during the 2014-2016 Ebola virus outbreak. Results of testing in humans with ZMappTM did not reach statistical significance, suggesting that further studies would be required to fine-tune the approach. A mAb derived from the blood of an Ebola survivor, mAb114, was also recently deployed for testing in humans in the ongoing Ebola virus outbreak in the Democratic Republic of Congo.

While these investigational therapies are promising, there remains a large, unmet need for therapies against all agents that cause VHFs. We chose to focus on Argentine hemorrhagic fever (AHF) caused by the arenavirus Junin because antibody transfusions have a well-established track record of successfully treating this infection. We will isolate mAbs from the blood of AHF survivors, characterize the molecular basis for their antiviral activity, and test these for therapeutic effect in small animal models. We will also determine if the antibodies we isolate cross-react with Machupo, Guanarito, Sabia, and Chapare viruses, which are related arenaviruses that cause VHFs in South America and lack effective therapies. Once completed, the work would position candidate mAbs for pre-clinical testing in non-human primates, thus facilitating their translation into human use.

Targeting apoptotic pathways for ALS, Alzheimer’s Disease and Parkinson’s Disease

Clifford Woolf (BCH), Bruce Bean

The proposed work follows our recent discovery that targeting a class of voltage-dependent potassium Channels inhibits death of motor neurons derived from induced pluripotent stem cells (iPSCs) from patients with ALS. These experiments were motivated by single cell RNA-expression data showing altered expression of a channel regulatory subunit in ALS motor neurons compared to their isogenic controls. This discovery serendipitously converged with an ongoing project developing small molecule modulators of these channels as investigational tools. We have now found that one of these compounds mitigates cell death of ALS patient iPSC-derived motor neurons. We therefore propose to test its ability to delay disease progression in a mouse model of ALS, to develop more potent inhibitors with drug-like properties, and to test the efficacy of these modulators in animal models of Parkinson’s disease and Alzheimer’s disease as a new treatment paradigm for preventing neurodegeneration by inhibiting apoptosis.

“Bariatric surgery in a pill”: development of synthetic analogs of a sleeve gastrectomy-induced metabolite as a novel therapy for type 2 diabetes and obesity

Sloan Devlin, Eric Sheu (BWH)

New therapies are needed to address the related worldwide epidemics of obesity and type 2 diabetes (T2D). Bariatric surgery is currently the most effective and sustainable treatment for obesity. While weight loss occurs 6 months-1 year following surgery, patients see immediate resolution of their diabetic phenotypes within hours of surgery. This remarkable remission of T2D is maintained for over 7 years, suggesting that the change is durable. We have identified a metabolite whose levels are significantly increased in both mice and humans following surgery and that ameliorates diabetic phenotypes in vivo in an acute mouse model. The goal of this research is to develop analogs of this metabolite as a potential therapy for T2D and obesity.

Next-generation AAV therapies for management of intractable chronic pain

Aurel Nagy, Sinisa Hrvatin, Spencer Price, Michael Greenberg

Chronic pain represents an enormous unmet need (~$635 billion in the US in 2011). The primary treatment for severe chronic pain, opioid administration, causes unacceptable side effects including addiction and fatal respiratory depression while failing to provide therapeutic relief in patients seeking care.1 Without effective alternatives, opioid prescription

numbers continue to climb: there were 70,237 prescription-opioid-overdose-related deaths in 2017.2,3 The opioid epidemic highlights the urgent need for new therapeutics to manage chronic pain. Gene therapy, the delivery of genetic material to permanently change gene expression in target cells, could provide long-term pain management with a single dose and is

therefore, worthy of investigation. Recombinant adeno-associated virus (rAAV)-delivered gene therapies in particular have shown striking clinical success recently, suggesting a prime opportunity to develop rAAV-based therapeutics for treating chronic pain.

We propose to generate a rAAV that specifically targets nociceptors, the neurons that transduce pain, to deliver ligand-gated silencing ion channels that will allow patients to control pain without opioids. Current rAAV engineering approaches lack the cell-type-specificity required to selectively infect nociceptors while sparing non-nociceptor neuronal

subtypes however, and off-target silencing of these cells could cause unacceptable toxicity and anesthesia. We developed PESCA, the Paralleled Enhancer Single-Cell Assay, to overcome this limitation and engineer rAAVs that drive unprecedentedly cell-type-specific payload expression. Through PESCA, we aim to create a next-generation therapy that will provide lasting and patient-controlled relief upon administration of a single dose, revolutionizing treatment for the most debilitating and common chronic health condition in the world.

Developing novel therapeutic approaches for CNS drug delivery by targeting a newly identified key regulator of the blood brain barrier

Urs Langen, Chenghua Gu

A major obstacle in treating neurological diseases and brain tumors is to deliver drugs or antibodies across the ‘blood brain barrier’ (BBB). My lab’s recent discoveries have changed our understanding of how the BBB restricts blood-brain communication. The BBB is formed by a single layer of endothelial cells that lines the blood vessel walls and act as a gatekeeper for the brain. Historically, the restricted permeability of brain vasculature has been attributed to tight junctions. However, substances can also cross endothelial cells by transcytosis, and we discovered that transcytosis is actively inhibited in brain endothelial cells. We identified a

novel multi-transmembrane protein Mfsd2a as a key regulator for BBB function, and demonstrated that interfering with Mfsd2a and its downstream pathway upregulates transcytosis and causes the BBB to become permeable. We propose to develop therapeutic agents that specifically target Mfsd2a function as a strategy to facilitate drug delivery across the BBB.

Interleukin-17 as a novel erythropoiesis stimulating agent

Merav Socolovsky (UMASS), Jeffrey Way, Allon Klein

Anemia occurs in multiple clinical settings, including cancer, chronic inflammation or kidney disease, increasing morbidity and mortality. Existing treatments are limited to erythropoietin (Epo) and to glucocorticoids. Glucocorticoids have severe side effects, while Epo is contra-indicated in cancer-associated anemia, and is ineffective in conditions such as myelodysplastic syndrome. To address this gap, we undertook single-cell RNA-sequencing of early erythroid progenitors (Tusi et al., Nature 2018). We discovered they express an interleukin-17 receptor (Il-17ra); that IL-17a enhances the erythroid response to Epo, through an Il-17ra-dependent high affinity interaction, in both human and mouse cultures; and we have preliminary evidence of efficacy in vivo. Here we will determine how to translate these findings to the stimulation of erythropoiesis in vivo.

Engineered proteins for treatment of pancreatitis

Katherine Redfield, Jeff Way, Jungmin Lee, and Pamela Silver

We will develop a treatment for pancreatitis based on a protease inhibitor with enhanced pharmacokinetics and tissue distribution.

Evaluating novel transcription modulators for therapeutic impact in cohesin-mutant AML and MDS cells

Emily Kaye, Zuzana Tothova (DFCI), Karen Adelman

Cohesin is a multi-subunit protein complex that forms a ring-like structure around DNA. Cohesin is essential for sister chromatid cohesion, chromosome organization into looped domains, DNA damage repair and transcription regulation. Germline loss-of-function mutations in cohesin subunits cause a family of developmental disorders termed cohesinopathies. In addition, cohesin is one of the most frequently mutated protein complexes in cancer, including myeloid malignancies, with recurrent somatic loss-of-function mutations in core components of the cohesin ring and its modulators. Cancer-associated mutations in cohesin rarely affect chromosome integrity, but instead selectively impair gene-regulatory functions. However, how cohesin affects gene activity remains enigmatic, offering no clues towards intervention. There are therefore no targeted therapeutic approaches available to treat disease involving cohesin mutations. Recently, we discovered that cohesin mutations common in myeloid malignancies disrupt RNA splicing and render cells highly sensitive to broad-spectrum splicing inhibitors. We propose to use state-of-the-art approaches to characterize nascent transcription and RNA processing in cohesin-mutant cells, including transient transcriptome sequencing (TTSeq) assays, to define the aberrant RNA species that mediate this vulnerability. Our goal is to leverage this knowledge to develop high-throughput splicing reporter assays to screen for molecules that will selectively target cohesin-mediated disease. The findings from these studies have the potential to lead directly to one or more clinical trials within the next several years.

Multiplex editing the human genome

Eriona Hysolli, Yuting Chen, and George Church

We aim to make cells virus-resistant by recoding human stem cells. This universal ultrasafe and virus-resistant cell line will be utilized for safe manufacturing of therapeutics and avoid bioreactor contamination like the Genzyme incident of 2009.

A high-throughput platform for the non-invasive intracellular delivery of molecules for therapeutic applications

Martina Righi, Johan Paulsson

Existing methods for intracellular delivery of drugs, proteins or nucleic acids have either been system specific and inefficient, or based on methods like electroporation or chemical treatment that can greatly perturb cells. A recent method, now in co-development by a biotech startup and a pharma giant as a novel cell therapy platform, improved this process by squeezing cells through narrow constrictions, which slightly and temporarily deforms cells and porates the membrane. This allows for efficient uptake of many types of components while reducing the stress on cells. We developed, and Harvard patented, an alternative methodthat could more gently squeeze cells of varying sizes.

Target validation and in vivo testing of a broad-spectrum antiviral

Melissanne de Wispelaere and Priscilla Yang

Dengue virus (DENV) and other flaviviruses are human pathogens that cause significant disease. About 40% of the world lives in areas with substantial risk of DENV transmission. Up to 100 million people are infected annually with an estimated 500,000 hospitalizations and 20,000 deaths due to dengue hemorrhagic fever and dengue shock syndrome2. DENV presents a long-standing challenge for vaccine development due to antigenic diversity of the four DENV serotypes and the propensity of non-protective antibodies to enhance infection and disease severity4. There are no specific antivirals to counteract DENV.

We discovered QL47 and related tricyclic quinolones as potent covalent, host-targeted antivirals with broadspectrum activity against DENV and other RNA viruses of biomedical significance. Due to their broad-spectrum activity against the Flaviviridae and other viruses and their high natural barrier to resistance these compounds are of interest as antivirals. We have performed medicinal chemistry optimization to generate YKL-04-085, a candidate suitable for testing antiviral efficacy in vivo and have also performed chemoproteomic experiments to

identify the cellular targets responsible for antiviral activity. We propose to validate the antiviral target(s) of QL47/YKL-04-085 and to evaluate the antiviral activity of YKL-04-085 in a murine model of viral infection.

Development of a new precision therapeutic for an important cancer target
Jonathan LaRochelle and Stephen Blacklow

The focus of this proposal is to develop a new class of potent and selective small molecule inhibitors of a genetically validated cancer target for further therapeutic development by enhancing the potency of our initial hit. Our inhibitors will occupy a unique niche in the landscape of small molecule precision therapeutics in cancer.

Targeting neuro-immune signaling to treat bacterial infections
Felipe Pinho-Ribeiro, Pankaj Baral, Kimbria Blake, and Isaac Chiu

Bacterial skin and soft tissue infections (SSTIs) are increasingly common due to the rise in prevalence of multi-drug resistant pathogens, necessitating novel non-antibiotic based treatments. While methicillin-resistantStaphylococcus aureus (MRSA) and Streptococcus pyogenesare the two leading causes of SSTIs, up to 20% of SSTIs are also caused by gram-negative bacteria. We have found that skin-innervating neurons play a key role in suppressing neutrophil function and the innate immune response against SSTIs. We have developed an approach to treat bacterial infections by targeting this neuro-immune axis using botulinumneurotoxins (BoNTs), thereby enhancing host immunity. In this project, we determine whether this therapeutic approach is broadly applicable by testing BoNTs against S. pyogenes, MRSA, K. pneumoniae and P. aeruginosa infections. We are in active discussions to partner with companies that produce both of these products. Utilizing BoNTs to enhance host immunity could be a transformative approach to treat challenging bacterial infections.

Development of New Antiviral Compounds
Jim Hogle, Hari Arthanari, David Scott, Han Chen, and Donald Coen

Herpesviruses cause severe diseases, particularly in immunocompromised and immune-naive individuals. Currently approved anti-herpesvirus drugs have important drawbacks, including limited efficacy, toxicities, and drug resistance, driving a need for new, improved agents. We have been exploring new targets for anti-herpesvirus drugs starting with a combination of structural, biochemical, and genetic studies. Using high throughput screening, we have identified compounds that selectively inhibit such targets in vitro, with some compounds selectively inhibiting viral replication in cell culture. We have evidence that at least one of these compounds “hits the target” in infected cells. We propose to optimize this compound into leads for further development towards anti-herpesvirus drugs.

Development of AAV-mediated Gene Therapy for Usher Syndrome Type 1F, a Combined Deafness and Blindness
Killian Hanlon, Olga Strelkova, Artur A. Indzhykulian, Casey A. Maguire, Marcos Sotomayor, David Corey

Usher syndrome is a devastating recessive hereditary syndrome of deafness and blindness, caused by mutations in any of 12 genes. One Usher gene, PCDH15 (encoding protocadherin-15) 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 ~1500 patients in the United States and ~5000 in the world.

Following the striking success of the Luxturna therapy for blindness by Spark Therapeutics, gene addition for Usher 1F is an attractive approach. Because the deafness phenotype is more severe than blindness in mouse models, we will assay successful rescue by testing cochlear function in vitro and hearing in vivo.  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 to assess rescue of the blindness phenotype. 

Isoguvacine and benzodiazepine derivatives for the treatment of tactile hypersensitivity and anxiety in Autism Spectrum Disorders
Lauren Orefice and David Ginty

Autism spectrum disorders (ASD) are neurodevelopmental disorders characterized by impairments in social communication and interactions, and restricted and repetitive behaviors. ASD is well-established to be associated with aberrant reactivity in multiple sensory domains, including touch, and indeed aberrant sensory reactivity is now considered a key diagnostic feature of ASD. We have used a range of mouse genetic models of ASD combined with behavioral testing, synaptic analyses, and electrophysiology to define both the etiology of aberrant tactile sensitivity in ASD and the contribution of somatosensory dysfunction to the expression of ASD-like traits (Orefice et al., Cell, 2016; Orefice et al., unpublished; Tasnim et al., unpublished). We found that mutations in genes associated with both syndromic and non-syndromic forms of ASD cause tactile dysfunction, and that the RTT- and autism-associated genes Mecp2, Shank3, and Gabrb3 function cell autonomously in peripheral somatosensory neurons for normal tactile behaviors. Remarkably, these somatosensory deficits during development contribute to aberrant social behaviors, including anxiety-like behaviors and social interactions, in adulthood. Our findings raise the exciting possibility that GABAA receptor agonists, which attenuate the activity of peripheral mechanosensory neurons, may be useful for treating tactile hypersensitivity and thus anxiety and social impairments in ASD patients. A key consideration for our work is that physicians are reluctant to prescribe GABAA receptor agonists and positive allosteric modulators because of undesirable side effects, including sedation, and serious complications associated with interference of brain development. Therefore, we aim to use peripherally-restricted GABAA receptor agonists and modulators, compounds that do not cross the blood-brain barrier, to treat tactile dysfunction and core ASD behaviors. Importantly, peripherally-restricted GABAA receptor drugs should not promote undesirable side effects observed with all currently used, FDA-approved GABAA receptor agonists that act in the brain. Thus, for this Q-FASTR application, we propose to determine the efficacy of isoguvacine, a known peripherally-restricted GABAA receptor agonist, as well as novel isoguvacine and nonbenzodiazepine derivatives designed to be peripherally-restricted, for treating tactile hypersensitivity and core ASD behaviors in animal models of ASD.

Computationally designed therapy targeting inflammation in neurodegenerative diseases
Jinkuk Kim, Timothy Yu, and Peter Park

By 2020, more than twenty million people will suffer from neurodegenerative diseases, including Alzheimer and Parkinson's diseases. One of the major hallmarks of neurodegeneration is spurious activation of neuronal inflammation, called microgliosis. Recent studies showed that normalization of the disrupted expression of a key immunoregulatory factor in the central nervous system can reverse the pathology. Through the integrative computational analysis of a massive body of genomic datasets, we found a key mechanism regulating the expression of the factor. We have designed a set of molecules that are predicted to correct the expression based on our algorithm. A screening experiment to identify a lead molecule is underway.

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
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
Jason Qian, Zhixiang Lu, Victoria Jones, Sarah Boswell, Michael Baym, 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.