The rapid advances in human genome sequencing has generated a large amount of data and consequently a large number of hypotheses. For psychiatric disease, a number of landmark studies have led to lists of genetic variations that are linked to specific diseases. However, functional testing of these hypotheses has remained challenging due to a lack of appropriate model systems and high-throughput functional assays. Here we propose to develop and apply a series of high-throughput genome perturbation methodologies to enable the rapid identification of causal genetic variants from large-scale genetics data. The technology we propose to develop will be very broadly applicable and has the potential to radically transform the scale and rate of discovery across different biomedical fields. Three complementary technologies will be developed as a part of this proposal: 1. Functional screening methods to enable rapid identification of reprogramming factors for specific cell types. By using genome-scale transcription activation or epigenetic reprogramming libraries, we will establish a systematic approach to reverse-engineer the sufficient combinations of reprogramming factors for neuron subtypes that are relevant for different neuropsychiatric diseases, such as parvalbumin positive interneurons in schizophrenia. 2. Large-scale and systematic genome perturbation tools to enable massively-parallel functional testing of genetic variants, to enable narrowing of the long lists of correlated genetic variants to a short list of causal variants. We will establish genetic perturbation technologies to enable multiplex and systematic deletion or mutational analysis of coding and non-coding genomic regions, as well as probing of their epigenetic states, to identify causal genetic variants. 3. Efficient and precise genome modification technologies to enable rapid introduction of causal variants into cellular or animal models to enable elucidation of their disease-causing mechanisms. Whereas nuclease-based genome editing systems enables efficient gene knockout, gene insertion or gene correction remains inefficient. We will characterize a novel programmed genome rearrangement mechanism and develop it into a technology for efficient and precise mammalian genome editing. This will significantly accelerate the generation of cellular and animal models Given the broad applicability of this technology, the impact of this proposed work will be far reaching and will radically transform existing experimental approaches for studying gene interactions in all fields of life science and medicine.
A major challenge facing the study of the genetic underpinning of psychiatric diseases is the lack of appropriate high-throughput models and functional testing methods to identify disease-causing genetic variants. Here we propose ways to develop high-throughput assays that will enable the derivation of specific neuronal subtypes and rapid and systematic functional genetic perturbations in cellular and animal models. The combination of technologies proposed here will establish a new and much-needed approach for the functional study of the genetic determinants of psychiatric disease.
| Nishimasu, Hiroshi; Shi, Xi; Ishiguro, Soh et al. (2018) Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science 361:1259-1262 |
| Myhrvold, Cameron; Freije, Catherine A; Gootenberg, Jonathan S et al. (2018) Field-deployable viral diagnostics using CRISPR-Cas13. Science 360:444-448 |
| Gootenberg, Jonathan S; Abudayyeh, Omar O; Kellner, Max J et al. (2018) Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360:439-444 |
| Tekin, Halil; Simmons, Sean; Cummings, Beryl et al. (2018) Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons. Nat Biomed Eng 2:540-554 |
| Gootenberg, Jonathan S; Abudayyeh, Omar O; Lee, Jeong Wook et al. (2017) Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356:438-442 |
| Smargon, Aaron A; Cox, David B T; Pyzocha, Neena K et al. (2017) Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28. Mol Cell 65:618-630.e7 |
| Yan, Winston X; Mirzazadeh, Reza; Garnerone, Silvano et al. (2017) BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks. Nat Commun 8:15058 |
| Nishimasu, Hiroshi; Yamano, Takashi; Gao, Linyi et al. (2017) Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1. Mol Cell 67:139-147.e2 |
| Shmakov, Sergey; Smargon, Aaron; Scott, David et al. (2017) Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol 15:169-182 |
| Gao, Linyi; Cox, David B T; Yan, Winston X et al. (2017) Engineered Cpf1 variants with altered PAM specificities. Nat Biotechnol 35:789-792 |
Showing the most recent 10 out of 43 publications
