nature

Season 3, Episode 1: New CRISPR, New Function with Leo Vo

First Author: Leo Vo

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.

About the Author

  • Leo is a PhD candidate who performed this work under Professor Sam Sternberg at Columbia University in New York City. Dr. Sternburg and his team are world experts in CRISPR biology having discovered multiple new CRISPR systems, including the function of Cas9 during his time in Professor Jennifer Doudna’s lab.

  • Leo was driven to become a synthetic biologist after being exposed to all the ways nature has engineered biology to overcome problems.

Key Takeaways

  • A new class of CRISPRs have been discovered that don't cut DNA but instead integrate new DNA on the genome.

  • Leo hijacks this CRISPR’s novel functionality to integrate whatever new DNA he wants into whatever location on a genome he desires.

  • Through the tools of synthetic biology, the system generates extremely targeted integrations at high efficiency in bacterial cells.

  • This CRISPR tool allows for integration of huge genetic payloads, iterative integrations, and integration of payloads at multiple locations in a single step, all of which create entirely new options for strain engineering.

  • The tool can be applied to multiple bacterial species and has proven utility in engineering the microbiome in situ as well as modifying industrially sought after strains.

Translation

  • Leo demonstrates that the system is highly effective in laboratory settings and can be optimized to overcome new challenges in new bacterial hosts.

  • The tool is undergoing further development and optimization to do population scale engineering -- making targeted and useful modifications to bacteria in communities like those seen in our gut or in nature.

  • Further research is needed to move this powerful integration tool into human cells as a novel method to overcome genetic disease and engineer future cell therapies.

Paper: CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering, Nature Biotechnology, 2020

Season 2, Episode 5: What Regulates the Regulatory T cells? with Jessica Cortez

First Author: Jessica Cortez

Episode Summary: 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

  • Jessica performed this work in the lab of Professor Alex Marson at the University of California, San Francisco. The Marson lab is renowned for their work in building and applying synthetic biology tools to understand and improve the therapeutic value of immune cells.

  • Jessica is driven to understand and cure autoimmune diseases because her mother, her sister, and her have all been diagnosed with autoimmune diseases.

Key Takeaways

  • Regulatory T cells can suppress immune reactions, making them an attractive therapeutic to be used to cure any autoimmune disease.

  • These regulatory T cells do not easily maintain their suppressive function, necessitating some engineering to make sure they maintain their therapeutic value.

  • With CRISPR, Jessica turned every gene off one-by-one in regulatory T cells to find which genes were involved in maintaining its suppressive function.

  • Jessica found a gene, USP22, that when expressed, inhibited regulatory T cell function making it a useful target for both autoimmunity and cancer.

Translation

  • While Jessica focused on one of the hits from the screen, there were many more that have massive potential as drug targets or as engineering steps for T cell therapies against autoimmunity.

  • Maintaining a stable regulatory T cell is the vital first step to creating a world where all autoimmune diseases are cured using cells.

Paper: CRISPR screen in regulatory T cells reveals modulators of Foxp3

Season 2, Episode 4: Why CAR T Therapies are Such a Headache with Kevin Parker

First Author: Kevin Parker

Episode Summary: 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

  • Kevin recently received his PhD from Stanford University in the labs of Professor Howard Chang and Professor Ansuman Satpathy. These labs specialize in uncovering the molecular mechanisms of disease using advanced sequencing modalities.

  • Bridging both biology and computer science, Kevin’s background and expertise made him uniquely suited to hunt down the culprit of CAR T cell neurotoxicity.

Key Takeaways

  • CAR T cells are excellent at killing blood cancers but are not without side-effects -- they can cause severe neurotoxicities.

  • The receptor engineered into CAR T cells was thought to be specific to these blood cancers, ensuring the therapies don't attack healthy tissue.

  • Kevin looked at publically available single cell sequencing data to find a small subset of brain cells hiding in plain sight that the CAR T cells could attack. 

  • In mice, engineered “blood cancer specific” T cells attack the brain, demonstrating that neurotoxicity is an off-target effect of the therapy, not a byproduct.

Translation

  • The finding points to the potential need for different engineered receptors to be used to target these blood cancers.

  • As CAR T cells expand to other cancers and malignancies, this process can be run to ensure we engineer cells that minimize the opportunity for damage to healthy tissue.

Paper: Single-Cell Analyses Identify Brain Mural Cells Expressing CD19 as Potential Off-Tumor Targets for CAR-T Immunotherapies

Season 2, Episode 3: Brewing a Life-Saving Drug in Yeast with Prashanth Srinivasan

First Author: Prashanth Srinivasan

Episode Summary: 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 recapitulated 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

  • Prashanth is a graduate student at Stanford University and published this work in the lab of Professor Christina Smolke. Christina and her team are world experts in metabolic engineering and broke multiple records in generating yeast that perform complex biosynthesis.   

  • Prashanth’s love of science was fostered by his teacher who encouraged him to combine his fascination with biology and his unique perspective on chemistry. 

Key Takeaways

  • Drugs are often sourced from natural sources like plants that have extremely precarious supply chains.

  • The same biosynthetic pathways that make the drug in plants can be recapitulated in yeast so that the small molecule can be brewed anywhere.

  • Moving this biosynthetic pathway from one organism to another is not easy and still requires a ton of novel biology to be discovered in order to succeed.

  • Here, Prashanth had to hunt for new enzymes, cut-out wasted chemical reactions, and engineer ways to move the molecule and proteins to the specific parts of the cell.

Translation

  • Scaling these microbes to make them economically viable first requires maximizing the amount of drug that each yeast can make.

  • Directed evolution of useful enzymes, importing new molecular transporters, and optimizing growth conditions will be used to spin-out this microbe.

  • The strain will be licensed through Stanford to pharmaceutical companies.

Paper: Biosynthesis of medicinal tropane alkaloids in yeast

Season 2, Episode 2: A New Era of Antibiotic Discovery with James Martin

First Authors: James Martin, Benjamin Bratton, Joseph Sheehan

Episode Summary: 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

  • James Martin performed this work as a graduate student in Professor Zemer Getai’s lab at Princeton University.

  • James’s optimism and drive to understand a problem from all angles led him and his colleagues to develop one of the most potent antibiotics ever found.

Key Takeaways

  • Our arsenal of antibiotics will soon be worthless, as bacteria evolve ways to get around their killing effects.

  • Adding new antibiotics to this arsenal has been slow because they are challenging to discover and they have poor return on investment.

  • Synergizing a number of new biological tools available, like high throughput microscopy, CRISPR, and machine learning, new antibiotics can be developed and understood faster than ever before.

  • Applying this fresh take on antibiotic discovery, a novel drug is found that targets a wide-variety of bacteria and is difficult to evolve resistance to.

Translation

  • Moving this extremely potent compound to the clinic will require some smart biochemistry to make it a better drug.

  • The research of James and his colleagues demonstrates a paradigm shift in how antibiotic discovery pipelines are performed to more easily and rapidly find these new drugs.

Paper: A Dual-Mechanism Antibiotic Kills Gram-Negative Bacteria and Avoids Drug Resistance