Browsing by Author "Yuan, Qichen"
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Item Single C-to-T substitution using engineered APOBEC3G-nCas9 base editors with minimum genome- and transcriptome-wide off-target effects(American Association for the Advancement of Science, 2020) Lee, Sangsin; Ding, Ning; Sun, Yidi; Yuan, Tanglong; Li, Jing; Yuan, Qichen; Liu, Lizhong; Yang, Jie; Wang, Qian; Kolomeisky, Anatoly B.; Hilton, Isaac B.; Zuo, Erwei; Gao, Xue; Center for Theoretical and Biological PhysicsCytosine base editors (CBEs) enable efficient cytidine-to-thymidine (C-to-T) substitutions at targeted loci without double-stranded breaks. However, current CBEs edit all Cs within their activity windows, generating undesired bystander mutations. In the most challenging circumstance, when a bystander C is adjacent to the targeted C, existing base editors fail to discriminate them and edit both Cs. To improve the precision of CBE, we identified and engineered the human APOBEC3G (A3G) deaminase; when fused to the Cas9 nickase, the resulting A3G-BEs exhibit selective editing of the second C in the 5′-CC-3′ motif in human cells. Our A3G-BEs could install a single disease-associated C-to-T substitution with high precision. The percentage of perfectly modified alleles is more than 6000-fold for disease correction and more than 600-fold for disease modeling compared with BE4max. On the basis of the two-cell embryo injection method and RNA sequencing analysis, our A3G-BEs showed minimum genome- and transcriptome-wide off-target effects, achieving high targeting fidelity.Item Therapeutic genome and cellular engineering with advanced programmable molecular tools(2023-04-17) Yuan, Qichen; Gao, Xue SherryNucleic acid engineering is a group of technologies that can change the script of life, such as genome and transcriptome, enabling a better understanding of human genomics, and can be developed as genetic medicines to treat diseases. Currently, there are three major types of gene editing approaches, including nuclease editing, base editing, and prime editing. Yet, the therapeutic applications of those technologies are still facing unmet needs. Although gene editing strategies have been demonstrated for monogenic disorders, such as sickle cell anemia, cystic fibrosis, Huntington disease, and Duchenne muscular dystrophy, the genetic or cellular treatment of polygenic disorder that caused by combined dysfunctions of more than one gene, such as coronary heart disease, diabetes, cancer, and neurological diseases, still needs to be well developed. How to further advance those technologies, or to develop next-generation gene editing tools that can perfectly address the emerging challenges from real-life medical issues? To approach a solution of the previous question, I focused my research on six topics: 1) Enable multiplex precision genome engineering with minimal delivery size, 2) Expand the type and number of genetic perturbations, 3) Manipulate cellular endogenous biological mechanisms to advance the performance of molecular tools, 4) Engineer the key components of molecular tools with improved activity, 5) Demonstrate therapeutic genome engineering on disease-relevant genes, 6) Deliver the therapeutic genetic payload using virial and non-viral approaches.