Current SPROUT Projects

Vaccines Targeting HIV Sugars for Broad Neutralization

Isaac Kraus, Dung Nguyen
Up to 20% of people infected with HIV develop antibodies against the virus. Many of these antibodies use a specific pathway to attack the disease, homing in on a particular carbohydrate on the virus’ envelope. Isaac Kraus and his team are working to replicate that natural antibody’s process to create an HIV vaccine.
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Although no HIV vaccine strategies have yet succeeded in eliciting a substantially-protective immune response, it is known that up to 20 % of HIV-infected individuals naturally develop broadly-neutralizing antibodies (bnAbs) to HIV. Of these bnAbs, roughly 40% bind to "high- mannose" sugars in a region of the HIV Env protein called the "high-mannose patch" (HMP). Thus, vaccines that stimulate HMP-targeted antibodies are desirable, and likely an achievable goal.

The Krauss lab has developed glycopeptide vaccine immunogens that recapitulate the presentation of high-mannose sugars in the HMP. They are currently testing alterations in the high-mannose sugars, in combination with alternate vaccine regimens, that may best target the immune response to the desired sugar epitopes. If successful, these tests would be a huge step toward development of a commercializable HIV vaccine.

Boosting rational drug design for Hepatitis B by large-scale production of the X antigen

Maria-Eirini Pandelia, Amy Milne, Chie Ueda, Michelle Langton
Chronic infection by Hepatitis B is one of the world’s leading causes of cancer. One of the virus’ proteins, HBx, is a major agent in how it damages cells, and has been shown to be instrumental in both cancer and cirrhosis development. Researchers around the world are targeting this protein as they seek new treatments for Hepatitis B, but it has been difficult to isolate, store, and study. Maria-Eirini Pandelia and her lab are developing new ways to purify this protein and scale up its production, making it easier for all researchers to study how Hepatitis B works.
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This project is focused on the heterologous overproduction of HBx, a protein from the Hepatitis B virus (HBV), to be employed as an immunogen for antibodies and anti-cancer drug development as well as for biochemical/structural studies. HBx is the smallest protein encoded in the HBV genome and has been shown to be a major agent in the progression of cirrhosis and hepatocellular carcinoma (HCC) that results from chronic HBV infection. HBx affects multiple cellular processes, either on its own or together with the proteins that it targets. Though its tumorigenic potential has been demonstrated, neither its structure nor the molecular mechanisms by which it mediates liver-associated diseases are known.

The Pandelia lab has developed methods and engineered new constructs to overcome the current limitations in HBx research, such as low protein solubility, stability and inhomogeneity. Additionally, they have identified an essential hidden cofactor, the presence of which may be critical for its biological activity. Their studies provide the possibility to overproduce this antigen in high yields and at concentrations that exceed the solubility limit of its commercially available lyophilized forms in a cost-efficient manner. The outcome of our studies is expected to provide the stepping stone to overcome the scant availability of the HBx protein, and will have the following impact: a) allow for extensive clinical trials, b) facilitate high-throughput drug and small molecule inhibitor screening, c) allow for structural studies making downstream development of pharmacological inhibitors targeting HBx by rational design possible. These milestones are of particular value, especially because chronic infection by HBV is a leading cause of human cancer worldwide. Therefore, the low-cost availability of highly pure and functionally homogeneous HBx will serve in accelerating development of novel antiviral therapies and provide much-needed new therapeutic approaches.

TRIBOX: Developing an assay kit for easy RNA-binding protein target identification

Michael Rosbash, Reazur Rahman, Weijin Xu
Damage or mutations to RNA-binding proteins in cells have been linked to many neurological conditions, from Fragile X Syndrome to ALS. Building on his Nobel Prize-Winning work on circadian rhythms, Michael Rosbash and his team have developed a method called TRIBE (Targets of RNA-binding proteins Identified By Editing) to better study these proteins and how they work when functioning normally, as well as how mutations affect the body. Once expensive, TRIBE is now within the reach of more labs, thanks to Rosbash’s new kit, which helps labs more affordably research the genetics of neurological diseases.
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Numerous human neuronal diseases have been linked to aberrations in RNA-binding proteins (RBPs), e.g., Amyotrophic Lateral Sclerosis (ALS), Fragile X Syndrome (FXS) etc. Therefore, identifying the biologically and pathologically relevant targets of RBPs is a hot topic in the biology. However, such endeavors have been throttled by the absence of effective tools to identify RBP targets specifically in a small number of neurons. Our recently developed method, TRIBE (Targets of RNA-binding proteins Identified By Editing) was designed to solve this problem and it has been proven to be effective even in a small numbers of circadian neurons of the Drosophila adult brain. Here we propose to develop a universal and user-friendly version of the TRIBE method by implementing the rapamycin-inducible dimerization system. The final product of this project would be an easy-to-use assay kit that would significantly lower the technical threshold for applying TRIBE method in research labs. With this assay kit, we hope to enable research labs over the world to decode the targets of various RBPs which would help design targeted therapies against RBP associated diseases, like ALS and FXS.

Optimization of HyperTRIBE Analysis

Michael Rosbash, Joshua Lepson, Reazur Rahman, Weijin Xu
RNA-binding proteins (RBP) plays an important role in the human genome: about 10% of all genes that code for proteins are RBPs. Mutations in RBPs have been implicated in many diseases, including cancer and ALS. Studying them has been challenging, however, as scientists need large samples of genes to accurately map the actions of RBPs. Colleagues of Nobel Prize Winner Michael Rosbash who work in his lab have developed HyperTRIBE, a software with an in vitro HyperTRIBE assay kit, to study even small samples of RBPs more accurately. This can lead to better understanding of many genetic diseases.
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We are developing a crucial computational component for HyperTRIBE, a technique recently developed at Rosbash Laboratory, which enables researchers to investigate the functional role of disease associated RNA-binding protein (RBP)-RNA interactions and aid in the discovery of novel drug targets. Because RBPs represent approximately 10% of protein-coding genes in humans and have been implicated in cancer and other neurological diseases, RBPs are of great research interest in both industry and academia. HyperTRIBE genetic construct expresses an RBP of interest fused to mutated catalytic domain of the RNA editing enzyme ADAR, which marks the target RNA transcript by editing and these transcripts can be identified by sequencing the transcriptome. HyperTRIBE is the only method capable of identifying cell-specific RBP & RNA interactions in as little as 150 cells, whereas the gold-standard method for characterizing RBP & RNA interactions, cross-linking immunoprecipitation (CLIP), requires millions of cells and has a potential false-positive problem. At the current state, both CLIP and HyperTRIBE software identifies a set of RNA transcripts that interact with the queried RBP but it is unable to rank these transcripts based on the RBP-RNA binding affinity.

This project aims to computationally characterize the RBP-RNA binding strength by analyzing the distribution and intensity of editing sites in a given transcript to develop a discriminative score, which will be capable of ranking transcripts based on their binding affinity to the queried RBP. We will further advance the HyperTRIBE software by improving the analysis for CLIP data and validating RNA targets that overlap in CLIP and HyperTRIBE. The ranked transcript list from HyperTRIBE will be tremendously beneficial to researchers investigating RBPs role in disease, as it will allow them to focus on selected targets implicated in disease states, catalyzing key advancements in pharmaceuticals and academic research. Because of the potential significance, we aim to either sell the HyperTRIBE ranking software with an in vitro HyperTRIBE assay kit described by the other HyperTRIBE team to a large scale company that sells kits, or to create a company dedicated to understanding all RBPs and their relationship to disease.

A New Strategy to Treat Chronic Infections

Liz Hedstrom, Devi Gollapalli
The reason bacteria become resistant to antibiotics is that no antibiotic kills all the bacteria causing an infection. Antibiotics are unable to kill certain dormant germs, which then stay behind, then can revive and evolve to resist antibiotics. Liz Hedstrom and her lab have found a way to make these “sleeper” bacteria awaken prematurely, so that they can be eliminated by antibiotic treatment before they can stay in the body to evolve into resistant strains.
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Most recurrent and difficult to treat infections are caused by bacteria that are susceptible to commonly used antibiotics. These infections persist because antibiotics are only effective against actively growing bacteria. However, a small number of bacteria in an infection are quiescent, and therefore survive treatment. These quiescent cells are known as persisters. We have discovered a compound, P226, that causes bacteria to initiate growth prematurely. We hypothesize that this compound will cause quiescent cells to become sensitive to commonly used antibiotics, thus providing a more effective treatment for chronic infections.

GreenLabs: Sustaining Science through Recycling

Brenda Lemos, David Waterman, both of Jim Haber’s Lab
More plastic has been manufactured in the last 10 years than all of the last century. This overplastification has had detrimental effects in our planet. Science—specifically laboratory work - is partly to blame. Much of the lab-grade plastics could not be recycled traditionally. Until now: Brenda Lemos and her team are working on a project to recycle America’s 6 Million tons of plastic lab waste.
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There are 20,500 research institutions world-wide that produce approximately 6 million tons of plastic waste per year – the equivalent weight of ~65 cruise ships. Of this 6 million tons, >85% ends up in landfills where it slowly degrades over centuries. GreenLabs will tackle this problem by collecting and recycling plastic lab waste and reintroducing it back into an $80 billon market as raw material. With over 10,000 research labs in the country, and over 300 in the greater Boston area, GreenLabs will both improve our planet and profit from an untapped market.

Drosophila "Flyght" Arena

Zachary Knecht, Tatevik Sarkissian, Eric Sun
Fruit flies are a mainstay of genetic research, thanks to their relatively simple genome and the ease of keeping them. Yet until now, different labs  Zachary Knecht and his team have made it easier than ever to observe fruit fly behavior with a 3D printed living environment for the insects.
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Our product is a 3-D printed arena in which to assess Drosophila melanogaster behavior. It will allow a wide variety of analyses, including control of specific neural circuits in awake, behaving animals via light (optogenetics). The arena will sit atop an LED bank inside an enclosed camera housing to allow visualization via infrared light, and optogenetic control of behavior.

The product will be marketed to professional researchers, for whom custom printed arenas can be matched to particular needs at little cost from the the flexibility of 3-D printing technology. It will also be marketed towards teaching labs, K-12 school science programs, and even for individuals, for which it will serve demonstration purposes of the principles underlying neural circuits and behavior, promoting STEM education. In this case, arenas and particular animals will be provided as a kit, allowing demonstrations of particular behaviors with reference to the underlying, cutting edge neuroscience research. In short, our product is poised to broach a largely untapped market existing in the space between the needs of educators, amateur and professional scientists, for whom a diverse set of needs is met by our flexible, modular platform.