David R. Liu
Core Institute Member, Vice Chair of the Faculty, The Broad Institute of MIT and Harvard
Investigator, Howard Hughes Medical Institute
DNA-TEMPLATED SMALL MOLECULES The discovery, synthesis, delivery and testing of small bioactive molecules remains an active focus of chemists in both academic and industrial settings. The discovery of these bioactive molecules provide important insights into basic cellular function and are critical to identifying cellular targets implicated in human diseases. The Liu group developed and applied DNA-templated synthesis (DTS) to program chemical reactions of organic small molecules and sequence-defined synthetic polymers. By combining DTS and Darwinian selections, the Liu group has discovered several families of bioactive synthetic small molecules, such as inhibitors of kinases implicated in cancer, and inhibitors of insulin-degrading enzyme (IDE), which has been associated with diabetes. The Liu group has also applied the principles of DNA-programmed reactivity and DNA encoding to develop a new approach to reaction discovery, resulting in the discovery of several new chemical reactions.
PROTEIN EVOLUTION Biological evolution has efficiently solved many challenging molecular problems. By harnessing the power of biological evolution, researchers have started to address problems of their own choosing, rather than of nature‘s choosing. The Liu group has developed a method that enables proteins to evolve continuously in the laboratory known as phage-assisted continuous evolution (PACE), increasing the speed of laboratory evolution by more than 100-fold over other methods. We applied PACE to evolve more than a dozen diverse classes of proteins including proteases, genome editing proteins, polymerases, antibodies, biosynthetic enzymes, and insecticidal proteins. PACE is now used both in academic and industry settings to evolve proteins with dramatically altered activities and specificities, and to reveal new basic scientific insights into the nature of biological evolution.
GENOME EDITING Most genetic mutations that contribute to human genetic disease are challenging to efficiently correct without an excess of undesired editing byproducts. Modern genome editing technologies are constantly being improved to enable targeted changes in the genome of any living cell or organism with improved specificity, targeting scope and deliverability to tissues of therapeutic relevance. To this end, the Liu group has comprehensively evaluated DNA cleavage specificity of various nucleases (ZFNs, TALENs and CRISPR/Cas9), and used the resulting insights to engineer TALENs and Cas9 variants with improved DNA-modification specificity.
In 2016 the Liu group developed base editing, a genome editing method that efficiently converts one base pair to a different base pair without inducing double-stranded DNA breaks or extensive insertions and deletions (indels). The two classes of base editors (adenine base editors or ABEs and cytosine base editors or CBEs) developed by the Liu group can correct all four transition mutations, which collectively account for more than 60% of human pathogenic point mutations. These base editor constructs have been distributed by Addgene more than 9,000 times to more than 3,000 laboratories around the world, resulting in more than 200 published studies using base editing in organisms including bacteria, plants, insects, fish, mice, and primates.
In 2019 the Liu group developed prime editing, a new approach to genome editing in which a reverse transcriptase directly copies edited DNA sequences into a specified target site from an extended guide RNA without requiring double-stranded DNA breaks or donor DNA templates. Prime editing is highly versatile, and can mediate all possible base-to-base conversions, insertions, deletions, and combinations thereof, at target locations near or far from PAM sequences, in a variety of human cell lines and primary mouse cortical neurons. Prime editing shows higher or similar efficiency and fewer byproducts than homology-directed repair, complementary strengths and weaknesses compared to base editing, and much lower off-target editing than Cas9 nuclease at known Cas9 off-target sites. Prime editing substantially expands the scope and capabilities of genome editing, and in principle can correct the vast majority of known genetic variants associated with human diseases.
“Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein” Pak, C. W.; Kosno, M.; Holehouse, A.S.; Padrick, S.B.; Mittal, A.; Ali, R.; Yunus, A.A.; Lu, D.R.; Pappu, R.V.; Rosen, M.K. Mol. Cell 63, 72-85 (2016).
“Structural and Biochemical Basis for Inhibition of Breast Cancer Cell Migration and Drug-Resistance Mutations by Src-Specific Macrocyclic Inhibitors” Aleem, A.; Georghiou, G.; Kleiner, R.; Guja, K.; Garcia-Diaz, M.; Miller, W.T.; Liu, D.R.; Seeliger, M.A. Cell Chem. Biol. 23, 1103-1112 (2016).
“A Programmable Cas9-Serine Recombinase Fusion Protein That Operates on DNA Sequences in Mammalian Cells” Chaikind, B.; Bessen, J.L.; Thompson, D.B.; Hu, J.H.; Liu, D.R. Nucl. Acids Res. 44, 9758- 9770 (2016).
“CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes” Komor, A.C.; Badran, A.H.; Liu, D.R. Cell 168, 20-36 (2017).
“Increasing the Genome-Targeting Scope and Precision of Base Editing With Engineered Cas9-Cytidine Deaminase Fusions” Kim, Y.B.; Komor, A.C.; Levy, J.M.; Packer, M.S.; Liu, D.R. Nature Biotechnol. 35, 371- 376 (2017).
Broad Institute of Harvard and MIT
Cambridge, MA 02142