Two weekends ago, approximately 300 scientists, industry professionals, and students gathered at MIT Building 26 for The Mammalian Synthetic Biology Workshop 2.0. On Twitter, the hashtag #msbw2 was used to cover the event live. The first mSBW workshop took place two years ago, and there were many new developments to be discussed in that short time span. Dozens of labs since 2013 have made use of CRISPR/Cas9-based genomic editing to pioneer everything from logic gates implemented with designer proteins to customized immune cells and in vitro disease modeling with organoids. Descriptions of these advancements were spread over more than 25 talks during the day-and-a-half meeting, and recurring trends arose quickly in the domain of immunological engineering, biocomputation, and ex vivo disease modeling.
Circuits and Pathways
President Emeritus and Robert Andrews Millikan Professor of Biology at Caltech, Dr. David Baltimore, started the second day with his perspective on engineering the immune system. After accepting the title of synthetic biologist, Dr. Baltimore reflected on the recent paper by Liang et al on using CRISPR/Cas9 system to edit genes in human tripronuclear zygotes, showing us that while this publication proves a point of how far we can take this technology, it also goes far in telling us how much we still need to learn. He spent the rest of his talk illuminating his research on reprogramming the immune system. Specifically, he spoke about therapies based on lentviral vector transfers that encode siRNA, and vectors that carry antigen genes to dendritic cells. His group used adeno-associated virus (AAV) vectors that carry genes encoding antibodies so that they could use them in the muscle cells of mice to make specific antibodies, such as those that fight against HIV and influenza.
Professor Joshua Leonard of Northwestern University followed by telling us about his group’s research on engineering robust cell therapies using a design-driven approach. Most notably, he described MESA (Modular Extracellular Sensor Architecture), which is a tool developed by his lab to tune the gene expression response of cell surface receptors based on the environment. Furthermore, he showed how MESA can be used to recognize exogenous physiologically relevant ligands (for example in tumor microenvironments) in order to induce expression of endogenous genes.
Keeping in line with discussing design challenges in engineering biology in mammalian systems was MIT Professor Timothy Lu’s talk on massively parallel combinatorial genetics. The talk began with strategies to start deciphering biological networks, such as going through the network, perturbing various nodes, and understanding what are the specific design rules that make each node different. This understanding of biological networks gave rise to CombiGEM, or combinatorial genetics en masse, which is a technique to allow regenerative one-pot cloning, generate pool lentiviral vectors, and combinatorial miRNA libraries. The example that Dr. Lu used to describe this method regarded strategies to overcome cancer chemoresistance, since many times tumors can become resistant, thereby limiting therapeutic efficacy. Using their model of ovarian cancer cell lines, Dr. Lu’s group experimented with pairwise and 3-wise combinations of miRNA to enhance cancer-killing effects. One thing that Dr. Lu stressed was the need to use such synthetic biology techniques to aid systems biology research; that is, dealing with issues such as how we can use these tools to answer questions about network interactions, how we can map genotypes to phenotypes, and more.
A word from the industry
The industry research session brought companies from several areas that ranged from xenotransplantation, which is the medical procedure of taking the tissue or organs of one species and embedding or grafting it within another, to efficient and high throughput DNA synthesis technologies. The talks commenced with Sean Stevens from Synthetic Genomics, Inc., who spoke on how synthetic biology and cell engineering methods can be used in applications for xenotransplantation with pig organs to induce strong immune response involving inflammatory, innate, and adaptive mechanisms. With such technology, Stevens and his team would like to target systems for applications in coagulation, and antibody- and cell- mediated destruction.
Jon Chestnut from Thermo Fischer Scientific talked about their work on DNA editing tools in designing engineered effectors (activators, repressors, nucleases) to create double-stranded breaks as efficiently as possible to improve transfection efficiency with Cas9 in a variety of cell lines. Jose-Carlos Gutierrez-Ramos from Pfizer BioTherapeutics then spoke about their work on streamlining the development of next generation CHO production cell lines to define the best in-class drugs. He was followed by Phillip Gregory from Sangamo Biosciences, who gave us an industrial perspective on therapeutic genome editing with his companys work on the ZFN genome-editing platform with mRNA delivery to reduce HIV infection. The last talk of the industry session was given by Bill Peck ofTwist Biosciences, which focused on their work on new technology for synthesizing large DNA, as well as their successes in oligo synthesis and gene assembly.
The last session of the conference on progress of cell-based therapies started with Dr. Michel Sadelain from the Memorial Sloan Kettering Cancer Center. He told us about a newly formed biotechnology company that has partnered with Sloan Kettering, called Juno Therapeutics, that focuses on the development of technologies that take a patient’s own T cells and and engineer them to recognize a protein, CD-19, that appears on the surface of cancer cells and induce remission. By taking cell’s from different sources, he and his colleagues believes medical applications of T cells can overcome many histocompatibility problems, and they recently published the sources they believe could be used. These T cells would them be infused back into the patient’s blood to attack the precise cancer cells.
UCLA Professor Yvonne Chen closed out the conference, wrapping up the topics discussed quite nicely with her talk titled Engineering Smarter and Stronger T cells for Cancer Therapy. She started her presentation reiterating some of the main issues regarding this space. In particular, she talked abut problems controlling cell proliferation, issues related to on-target/off-tumor toxicity, antigen escape, immunosuppression, and cytokine release syndrome. She also touched on advantages, such as discrimination in tumor targets, systemic mobility, and modular CAR composition. Chen spoke in depth about two main projects her group is working on, starting with logical computation with CAR, such as an OR-Gate CAR, in order to decrease possibility of antigen escape. Specifically, her group has developed techniques and models to use design principles for CAR molecules, as opposed to using trial and error, in order to get better data and synergy with bispecific receptors. Among the models used by her lab is yeast, which can serve as an initial testing platform for gene-control in mammalian organisms. The second project Professor Chen spoke about focused on targeting intracellular oncoproteins. Her group has developed a synthetic zymogen, SUMO-Granzyme B (GrB), which is a tumor protease cleavage sequence that can be activated in the cell by SENP1. They have been able to show cleavage activity scaling with SENP1 dosage.