Translation

Episode Summary: Millions of people die every year from chronic diseases. Traditional drug discovery has failed in identifying solutions to many of these persistent health challenges. Functional genomics is offering a way forward by identifying gene networks and enabling the development of drugs with very specific targets. But, rather than just relying on gene targets within humans, Linda and her company, Fauna Bio, are casting a wider net across the animal kingdom. Extreme adaptation is common across many mammals, giving us an incredible pool of potential targets to go after. Whereas a single heart attack can kill a person, certain animals not only survive 25 heart attacks a year but also go on to thrive, living 2x longer than other mammals their size. By identifying and understanding the gene networks underlying these extreme adaptations, Fauna can identify novel targets across 415 different species, map them to human genes, and develop drugs that exploit our natural protective physiological mechanisms. About the Guest Key Takeaways Impact Company: Fauna Bio

Episode Summary The expression of genes in our genome to produce proteins and non-coding RNAs, the building blocks of life, is critical to enable life and human biology. So, the ability to predict how much of a gene is expressed based on that gene’s regulatory DNA, or promoter sequence, would help us both understand gene expression, regulation, and evolution, and would also help us design new, synthetic genes for better cell therapies, gene therapies, and other genomic medicines in bioengineering. However, the process by which gene transcription is regulated is incredibly complex; thus, prediction transcriptional regulation has been an open problem in the field for over half a century. In his work, Eeshit used neural networks to predict the levels of gene expression based on promoter sequences. Then, he reverse engineered the model to design specific sequences that can elicit desired expression levels. Eeshit’s work developing a sequence-to-expression oracle also provided a framework to model and test theories of gene evolution. About the Guest Key Takeaways Impact Paper: The evolution, evolvability and engineering of gene regulatory DNA

Episode Summary: In this very special episode of Translation, Seth is joined by Ash Trotman-Grant to demystify spinning out from academia. Much of this knowledge has so far only been available to select groups of academics and PhD founders are at a disadvantage – some potentially breakthrough technologies never saw the light of day and didn’t get a chance to have a real impact. We want to bring the power of the tech transfer process back to entrepreneurial scientists. Enter the Spinout Playbook – your complete guide to spinning out of academia. In this episode, we chat about the Playbook’s content and share useful tips for entrepreneurial academics eager to spin out their research into an impactful company. Ash shares his experience from spinning out Notch Therapeutics and, together with Seth, they offer brilliant insights into navigating the (up until now) stormy waters of the spinout process. About the Guests Key Takeaways Impact The Spinout Playbook

Episode Summary Chimeric antigen receptors, or CARs, repurpose the build-in targeting and homing signals of our immune system to direct T cells to find and eliminate cancers. Although CAR-T cells have transformed the care of liquid tumors in the circulating blood, like B cell leukemia and lymphoma, CAR-T therapy has shown limited efficacy against solid tumors. To unlock the full potential of CAR-T therapies, better receptor designs are needed. Unfortunately, the space of potential designs is too large to check one by one. To design better CARs, Dan and his co-author Camillia Azimi developed CAR Pooling, an approach to multiplex CAR designs by testing many at once with different immune costimulatory domains. They select the CARs that exhibit the best anti-tumor response and develop novel CARs that endow the T cells with better anti-tumor properties. Their methods and designs may help us develop therapies for refractory, treatment-resistant cancers, and may enable CAR-T cells to cure infectious diseases, autoimmunity, and beyond. About the Author Key Takeaways Impact Paper: Pooled screening of CAR T cells identifies diverse immune signaling domains for next-generation immunotherapies

Episode Summary: DNA is an ideal molecule for storing information in our genomes because it’s stable, programmable, and well understood. The same qualities make DNA a great building block or construction material for nanoscale biomolecular structures that have nothing to do with our genome, like molecular scaffolds created by folding DNA into 2D and 3D shapes. This technology is known as DNA origami. However, the practical applications of DNA origami are limited by spontaneous growth and poor reaction yields. Anastasia developed a method that uses crisscross DNA polymerization of single-stranded DNA slats or DNA origami tiles to assemble DNA structures in a seed-dependent manner. This work may be useful to produce ultrasensitive, next-generation diagnostics or in programmable biofabrication at the multi-micron scale. Search Keywords: fifty years, bio, translation, ayush noori, ashton trotman grant, dna origami, dna, monomers, anastasia ershova, structures, diagnostics, proteins, micron scale, nucleation, biology, nanoscale Episode Notes: About the Guest Impact Papers Robust nucleation control via crisscross polymerization of highly coordinated DNA slatsMulti-micron crisscross structures from combinatorially assembled DNA-origami slats

Episode Summary: Technologies like next-generation sequencing allow us to understand which RNA transcripts and proteins are expressed in biological tissues. However, it’s often equally important to understand how cells or molecules are positioned relative to one another! Whether it be a cell changing its shape, an organelle ramping up a metabolic process, or a DNA molecule traveling across the nucleus, understanding spatial context is critical. Current approaches for spatial sequencing are limited by cost, complicated equipment, sample damage, or low resolution. Recognizing this challenge, Josie and team developed Light-seq, a cheap and accessible method to combine sequencing and imaging in intact biological samples. Not only is the method inexpensive, but Light-seq can also achieve unprecedented spatial resolution by using light to add genetic barcodes to any RNA, allowing scientists to determine exactly where sequencing should occur with extreme precision. By helping researchers to understand spatial context, Light-seq-driven insights may illuminate cancer, neurodegeneration, and autoimmunity. Episode Notes: About the Author Key Takeaways whatwhereImpact Author: Josie Kishi Paper: Light-Seq: Light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing

Episode Summary: Antibodies are one of the greatest tools we have in our therapeutic arsenal and have transformed the way we treat cancer and autoimmunity. But we still largely develop these drugs using guess and check methods, massively slowing down the process. However, our own B cells are constantly making new antibodies against the pathogens and diseases we routinely suffer from, creating a gold mine of drugs floating around inside all of us. We just need to find them! Recognizing this challenge, Nima and his team at Avail Bio have leveraged their deep experience in computation and systems immunology to build a platform that massively screens the antibody repertoire of patients who have successfully cleared a disease. With it, they find ready-to-deploy antibody drugs that could treat everything from cancer to autoimmunity and even reprogram our own immune system! Search Keywords: fifty years, bio, translation, antibodies, B cells, cancer, autoimmunity, immunology, avail bio, nima emami Episode Notes: About the Guest Nima Emami is the CEO & co-founder of Avail Bio. He received a PhD in Bioinformatics from the UCSF Cancer Center, and studied Bioengineering, Electrical Engineering and Computer Science at UC Berkeley. Key Takeaways The immune system contains a massive diversity of antibodies that hold clues on how to fight disease. Avail has developed a platform to discover and develop these antibodies for cancer and autoimmune disease. Companies that spin out of universities can pair with accelerators early on to both raise funding and make progress with a small amount of capital. The most challenging part of pulling IP out of a university is speed. Public universities that generate many spinouts are often overwhelmed with the amount of inventions disclosed concurrently, which lengthens the time required for tech transfer. Avail’s platform combines synbio, machine learning and genomics to both discover and validate targets, and ultimately translate those targets into drugs. Failure of clinical stage programs in cancer trials can be traced back to the failure of mouse models to faithfully recapitulate the cancer biology or the immunobiology that we see in humans. The future that Avail hopes to create is one where drugs developed using their platform will reach patients, thereby changing the drug discovery paradigm to be more data-driven. Impact The platform that Avail is building peers inside the human immune response to find and develop novel antibodies to cure cancer and autoimmune disease. Company: Avail Bio

Episode Summary Imagine if every graphics design company built its own version of Photoshop in-house. That’s exactly what’s happening today in biology research. Ten-fold increases in data every two years are forcing every biology team to build out their own, in-house bioinformatics stack to store, clean, pipe, and manage the massive volumes of data generated by their experiments. All that work has to happen even before teams can analyze the results! Recognizing this obstacle to high-throughput biology research, Alfredo, Kenny and Kyle built LatchBio to bring the modern computing stack to biotech. By uniting wet lab experiments with dry lab processing, storage, and analyses, LatchBio is democratizing access to top-notch bioinformatics and empowering biologists to derive relevant insights from their data that can move our world forward. Tune in to learn more about their journey from Berkeley dropouts to entrepreneurs building no-code tools to power the biocomputing revolution. About the Team Key Takeaways SDKImpact Company: LatchBio

Episode Summary: Evolution is happening even at the cellular scale. Whether it's a virus, a bacterial pathogen, or a cancer cell, disease-causing agents are responding to the therapies we throw at them, updating their genes and molecular pathways to resist death. As a trained microbiologist, Nick Goldner and his co-founder Chris Bulow spent their years in grad school using -omics data to overcome antibiotic resistance in bacteria which led to their first company Viosera. As they struggled with the harsh realities of the antibiotics market, they stumbled upon the connection between bacterial and cancer resistance mechanisms. With this, they started resistanceBio which combines sophisticated tumoroids, intense patient sampling, and multi-omics to mimic the evolution of real tumors and ultimately find therapies that are irresistible. Episode Notes: About the Author Key Takeaways Impact Company: resistanceBio

Episode Summary: When COVID-19 hit and society decided to use mRNA vaccines for the first time, many questions remained about whether RNA itself was ready for the challenge. But three scientists at Stanford University who had barely worked with each other before the pandemic realized that RNA’s limitations were merely a design challenge and not an issue with the substrate itself. Through emails and zooms, Kathrin, Gun, and Hannah built a tool to massively test RNA designs. With it, they screened for RNA with better functionality, increasing the stability and expression of the protein they encode and ultimately creating a platform to improve these life-saving vaccines. Episode Notes: About the Authors Key Takeaways Translation First Authors: Kathrin Leppek, Gun Woo Byeon, and Hannah Wayment-Steele Paper: Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

Episode Summary: COVID-19 tests have become synonymous with jamming a swab up our nose to find out whether we have an active infection. But as we progress through this pandemic, a test that tells us whether people have antibodies against the virus will be massively important to creating public health initiatives and deciding who to vaccinate next. Unfortunately, these serology tests are exceedingly tedious to perform, inhibiting their widespread use. Realizing this problem, Susanna talks us through how she utilized protein engineering to create a novel serology test that is massively easier and quicker than traditional methods. Importantly, this test can be used in resource low settings to help end the pandemic worldwide. Episode Notes: About the Author Key Takeaways Translation First Author: Susanna Elledge Paper: Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection

Episode Summary: Brain machine interfaces untangle the complex web of neurons firing in our brains and relay the underlying meaning to a computer. These devices are being adapted to help patients regain motor control, monitor our mental well being, and may one day even make us more empathetic. State of the art methods to do this have massive trade-offs, either being high resolution yet requiring devices to be embedded in our heads or low resolution but non-invasive. Finding a key middle ground, Sumner uses advances in ultrasound to monitor the brain activity of monkeys performing specific tasks. With this data, he can not only record the brain activity associated with performing the task itself but also the intention of doing it before the subject even has a chance to move. Episode Notes: About the Author Key Takeaways Translation First Author: Sumner Norman Paper: Single-trial decoding of movement intentions using functional ultrasound neuroimaging

Episode Summary: Enzymes that break down other proteins, or proteases, could be used as a powerful therapeutic if they could specifically chew-up disease causing entities. However many proteases are non-specific, breaking any protein in their path, while the specific ones target proteins that would provide no therapeutic benefit. Travis and his colleagues developed a riff on the method known as PANCE that utilizes bacteria and bacterial viruses known as phages to evolve proteins toward a specific goal. With it, he retrains the sequence-specific protease, botulinum neurotoxin, toward new targets and away from its original ones. The novel enzymes Travis generates have the potential to not only stimulate nerve regeneration but also deliver itself to the correct cell types for a whole new type of therapy. Episode Notes: About the Author Key Takeaways Translation First Author: Travis Blum Paper: Phage-assisted evolution of botulinum neurotoxin proteases with reprogrammed specificity

Episode Summary: Novel drugs that boost the immune system to fight cancer have become pharma darlings in the few short years since their approval. These drugs, known as immunotherapies, have so far focused on improving T cell responses and can be used to cure a multitude of different cancer types. Yet more often than not, immunotherapies have no effect on a patient, leaving doctors guessing on whether to prescribe the drug. To find the reason why some people respond while others don’t, Kevin and his team create a huge database of sequences derived from immunotherapy-treated patients. With it, he discovers biomarkers, mutational signatures, and immune profiles that correlate to response with the hopes that one day, these measurements form a diagnostic to ensure we treat the right patients. Episode Notes: About the Author Key Takeaways Translation First Author: Kevin Litchfield Paper: Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition

Episode Summary: In a single decade, CRISPR has made a dramatic impact on literally every facet of biotechnology. This game-changing system is traditionally programmed to make cuts at very specific parts of the genome, altering the code to cure disease. But a new class of CRISPRs discovered by Leo’s colleagues don’t simply cut DNA -- they integrate entirely new genetic material at targeted locations. With it, Leo generates a new method to perform very specific and highly efficient genome engineering on bacteria and describes the multitude of ways it can generate strains that revolutize commodity molecule synthesis and medicine. Episode Notes: About the Author Key Takeaways in situTranslation First Author: Leo Vo Paper: CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering, Nature Biotechnology, 2020.

Whether it's Multiple Sclerosis, Type 1 Diabetes, Lupus, or Crohn's Disease, autoimmunity is a rapidly growing problem that traditional pharmaceuticals have failed to completely cure. While these diseases have very different symptoms, they all have the same root cause -- the body’s immune system is attacking its own healthy organs. Lurking within ourselves are a group of T cells called regulatory T cells that have the power to suppress immune function. These cells have huge potential to be engineered and utilized as a platform to cure any autoimmune disease. Unfortunately, they easily lose their suppressive abilities and can even exacerbate autoimmunity if handled incorrectly. Looking to stabilize regulatory T cells, Jessica and her colleagues perform a CRISPR screen to map which genes are responsible for maintaining their suppressive function. Using this data, Jessica takes the first step to bring this incredibly powerful cell type to the clinic to help millions of patients suffering from a myriad of diseases. About the Author Key Takeaways Translation First Author: Jessica Cortez Paper: CRISPR screen in regulatory T cells reveals modulators of Foxp3

Engineered T cells that hunt and kill blood cancers have recently obtained three landmark FDA approvals, forever changing the way we treat this disease. Even with its massive clinical success, these cells come with life-threatening neurotoxicities. But is neurotoxicity a set feature of using T cell therapies or is our engineering accidentally targeting the brain? Utilizing advances in bioinformatics and the huge sequencing datasets available to science, Kevin uncovers similarities between a cell type in our brain and the cancer we target with engineered cells. Finding this needle in a haystack, Kevin creates a link between how we engineer these cells and the neurotoxicities we see, discovering a potential root cause of the problem and generating a rule for how to engineer around it. About the Author Key Takeaways Translation First Author: Kevin Parker Paper: Single-Cell Analyses Identify Brain Mural Cells Expressing CD19 as Potential Off-Tumor Targets for CAR-T Immunotherapies

Small molecules are a pillar of human health, making up a majority of the drugs we have in our healthcare arsenal. Many of these drugs are obtained by utilizing synthetic chemistry to modify the composition of some small molecule found in nature. Derivatives of tropane alkaloids, for example, alleviate neuromuscular disorders and are derived from a chemical found in nightshade plants. However, sourcing these plants have become exceedingly difficult as climate change, the pandemic, and geopolitics ravage the supply chain. Looking to overcome these challenges, Prashanth recapitualed the biochemical pathway that makes these tropane alkaloids in yeast. In the most complex feat of metabolic engineering to date, Prashanth can make these life-saving drugs in a bioreactor, insulated from the issues that make them expensive and in short-supply. About the Author Key Takeaways Translation First Author: Prashanth Srinivasan Paper: Biosynthesis of medicinal tropane alkaloids in yeast

Bacteria are rapidly evolving ways to resist antibiotics, causing minor infections to become life-threatening events. Compounding the problem, new antibiotics have been incredibly challenging to develop and pharma is economically disincentivized to invest in finding them. James Martin and his colleagues Joseph Sheehan and Benjamin Bratton took on this challenge, developing an extremely potent antibiotic that targets multiple different classes of bacteria. James tells the story of identifying this antibiotic, understanding its potential, and pinpointing how its structure begets its function. Describing the state-of-the art CRISPR screens, proteomics, and machine learning methods they used, James calls for a new era of antibiotic discovery to meet the impending wave of superbugs. About the Author Key Takeaways Translation First Authors: James Martin, Benjamin Bratton, Joseph Sheehan Paper: A Dual-Mechanism Antibiotic Kills Gram-Negative Bacteria and Avoids Drug Resistance Follow Fifty Years on Twitter! If you’re an author of an upcoming paper in bio or know of any interesting papers dropping soon and want to hear from the authors, drop us an email at translation [AT] fifty [DOT] vc.

Hundreds of iterations of immune cells that are engineered to kill cancer have already been designed. Corina reached outside of this box to use the same synthetic biology principles to engineer T cells to attack senescent cells, a cell type that contributes to diseases of aging. Corina walks us through how her engineered T cells know the difference between a diseased cell and healthy tissue, how she stumbled upon the chimeric antigen receptor that made this possible, and how these new T cells are being moved from academia to the clinic. About the Author Key Takeaways Translation First Author: Corina Amor Vegas Paper: Senolytic CAR T cells reverse senescence-associated pathologies. Nature, 2020. Follow Fifty Years on Twitter! If you’re an author of an upcoming paper in bio or know of any interesting papers dropping soon and want to hear from the authors, drop us an email at translation [AT] fifty [DOT] vc.