Active Projects

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

Benjamin Martin, Zuzana Tothova (DFCI), and 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. Importantly, 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. Consequently, there are no targeted therapeutic approaches available to treat disease involving cohesin mutations. Recently, we discovered that cohesin mutations common in myeloid malignancies such as myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) disrupt RNA splicing. We propose to define the aberrant RNA species generated in cohesin-mutant AML cells, using state-of-the-art molecular and computational approaches to capture nascent transcripts and characterize RNA processing. Through detailed investigation of gene activity and splicing profiles in cohesin-mutant AML cells, we hope to discover genes with alternative splicing events that may present opportunities for therapeutic targeting. Our goal is to leverage this knowledge to develop targeted approaches that will selectively kill 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.

Application of the SPLANDID Antigen Presentation Technology to HIV-1 Vaccine Development

Alessandro Piai, Yongfei Cai, Bing Chen, and James J. Chou.

The HIV-1 envelope glycoprotein (Env) is a transmembrane protein sitting in the viral membrane and it is also a major target for B-cell based vaccine development. Previous large clinical trials of vaccine candidates involving recombinant Env preparations mostly focused on various soluble forms of its ectodomain. These efforts have been disappointing, however, probably because we do not fully understand how effective antibodies are generated in some infected patients and what is the best form of the Env that can induce such an antibody response by vaccination. To facilitate Env immunogen design, we have recently developed an antigen presentation technology known as SPLANDID that allows presentation of transmembrane immunogens in a membrane environment on nanoparticles suitable for in vivo immunogenicity studies. This HMS patented technology now affords the opportunity to test novel HIV-1 Env immunogens that include the membrane-related components in a membrane environment and better mimic the native Env on the virion surface. We plan to use the new technology to display membrane-bound Env immunogens and evaluate their potential as vaccine candidates by defining their antigenicity in vitro and testing their immunogenicity in animals.

A novel biologic and therapeutic target for the treatment of diabetes

José Rivera-Feliciano, Timothy R. Kunz, Elias S. Peterson and Douglas A. Melton

It is estimated that more than 422 million people in the world have diabetes; by 2021 the cost burden of diabetes in the United States is on track to be $512 billion. Diabetes, characterized by elevated blood glucose (sugar) levels, results from either beta-cell malfunction (Type 2) or beta-cell demise after an autoimmune attack (Type 1). The hormone insulin, produced by pancreatic beta-cells, reduces circulating levels of glucose after a meal primarily by shuttling glucose to muscle and fat. Current strategies to treat diabetics include insulin injection, augmenting endogenous insulin secretion, increasing glucose absorption, or increasing glucose excretion. Hypoglycemic (low blood glucose) episodes after insulin injection are life threatening and this risk usually results in patients underdosing. Here we describe the discovery of a novel peptide hormone, we call ERSEQ08, present in human beta-cells, that can reduce blood glucose levels in mice. Importantly, this effect is independent of insulin action. Surprisingly, ERSEQ08 lowers blood glucose, in a glucose dependent manner, without causing hypoglycemia—thus overcoming one of the major setbacks with current diabetic treatments. While it is well known that pancreatic beta cells make Insulin, this new finding may represent a second system by which beta cells regulate glucose metabolism.

The potential to bypass insulin resistance presents a novel therapeutic paradigm to treat diabetes. As a biologic, this hormone may complement or replace some of the therapies used as the current standard of care in diabetes treatment. As an inroad into a novel signaling system controlling glucose homeostasis, this discovery has the potential to lead to a new kind of drug for diabetics.

Our main objectives using the Q-FASTR funds are: to test the activity of recombinant human ERSEQ08 protein to lower blood glucose levels in mice; to develop a cell-based assay to identify ERSEQ08’s mechanism of action; and, to find the minimal active fragment required for ERSEQ08’s function.

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.

Protein therapeutics for treatment of chronic and inflammatory pain

Bruce Bean, Clifford Woolf, Jeff Way, and Peter Sorger

Chronic and inflammatory pain affect millions and new treatments are urgently

needed. Despite significant investment in opioid safety and formulation, there is little exploration of drugs with fundamentally novel mechanisms of action. Our goal is to develop such medicines based on novel protein therapeutics that block pain sensation by silencing multiple NaV sodium channels in nociceptors. The failure of NaV1.7 inhibitors as analgesics1 suggests that blocking more than one channel will be necessary. We will therefore take an approach involving a multivalent scaffold and small proteins that inhibit several NaV channels with tunable selectivity and potency. Activity will be measured by differential screening against human iPSC-derived sensory, cortical, and motor neurons. Over a two year period we expect to achieve hit/lead generation for 10-30 distinct molecules and optimization of the most active for testing in animals.

Target Identification of Neuroprotective Kinase Inhibitors for Alzheimer’s and Related Dementias

Mark Albers, Peter Sorger, Gary Bradshaw

Alzheimer’s dementia (AD) affects nearly 6 million US patients and costs > $250B/year. No therapies slow its devastating course. We have discovered a root cause of neuronal cell death in disease-relevant regions of autopsied AD brains: inflammation caused by cytoplasmic double stranded RNA (cdsRNA). cdsRNA triggers neurodegeneration in mouse models that can be recapitulated in cultured human neural cells. This proposal focuses on small molecule kinases inhibitors that we have shown to block cdsRNA-mediated neuronal death. The active molecules (some of which are approved therapeutics) are annotated as JAK kinase inhibitors but this class of compounds is known to have a complex poly-pharmacology. Moreover, not all JAK inhibitors on signal transduction in neurons rescue cell death. We have therefore conducted a genome-wide CRISPR/Cas9 screen and found than none of the three members of the JAK family rescue cdsRNA-mediated neuronal death when knocked down. Thus, JAK kinase inhibition does not appear to be sufficient (and perhaps not even necessary) to rescue neuronal death. We propose to identify “off-target” proteins – most likely kinases - that are preferentially bound by neuroprotective JAK inhibitors relative to inactive molecules. We will confirm the relevance of these targets by generating knockout human neural cells using CRISPR/Cas9 and then proceed to small molecule screening. This will allow us to leverage extensive experience in kinase inhibitors, particularly those exhibiting therapeutically relevant poly-pharmacology, to target AD and other neurodegenerative diseases.

Identifying novel therapeutic targets for treating pain and chronic itch

David Ginty, Nikhil Sharma, Jing Peng

The perception of painful stimuli begins with detection of noxious stimuli by somatosensory neurons called nociceptors. Itch-inducing compounds, on the other hand, are detected by neurons called pruriceptors. We have recently identified the genes expressed in all somatosensory neuron subtypes, including nociceptors and pruriceptors, throughout development and into adulthood. This analysis revealed six transcriptionally distinct subtypes of nociceptors and two subtypes of pruriceptors, each with strikingly distinct gene expression profiles. Importantly, our findings reveal new candidate therapeutic targets to block nociceptors and pruriceptors. We found that select members of the GPCR superfamily, which account for nearly 1/3 of known drug targets, are expressed in nociceptors and pruriceptors, but not other sensory neuron subtypes. We will to leverage our knowledge of somatosensory neurons and the newly identified GPCRs they express to develop new drugs for treating pain and chronic itch while avoiding undesirable side effects. We will focus on drugs that activate G_i/o-coupled GPCRs expressed in nociceptors and pruriceptors because activation of these GPCR subtypes silence neuronal activity.

Structure-guided discovery of novel antibiotics inhibiting bacterial cell wall formation

Francois Thelot and Maofu Liao

The emergence of drug-resistant Gram-negative bacteria causes a significant global health problem, because the available antibiotics are limited and the discovery of new compounds cannot keep pace with the emergence of drug-resistant strains. The difficulty to combat these pathogens is largely due to their unique dual-membrane cell wall which efficiently blocks the entry of antibiotics. Lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria plays key roles in cell wall formation and antibiotic resistance. Thus, LPS biosynthesis is a particularly attractive target for developing new classes of antibiotics. LPS is synthesized in the inner membrane and subsequently transported to the outer membrane, a process critically dependent on two ATP-binding cassette transporters (MsbA and LptB₂FGC). My laboratory has made important contributions in characterizing the structure and function of these LPS transporters. Here we propose to leverage our experience and mechanistic insights of MsbA to develop novel antibiotics. This will be achieved by establishing a targeted screening pipeline that comprises chemical screen, cryo-electron microscopy (cryo-EM), computational docking, and activity assays. Once established, this pipeline can be applied to target many other bacterial membrane transporters.

Monoclonal antibody-based therapeutics for Argentine hemorrhagic fever

Lars Clark, Brian Gowen (USU), and 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

Sooyeon Jo, Laurel Heckman (BCH), Clifford Woolf (BCH), and 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.

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

Urs Langen and 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.

Development of a new precision therapeutic for an important cancer target
Vidyasiri Vemulapalli, 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.