Person:
Newby, Gregory

Profile Picture

Email Address

AA Acceptance Date

Birth Date

Research Projects

Organizational Units

Job Title

Last Name

Newby

First Name

Gregory

Name

Newby, Gregory
Author's Publications: search.filters.isAuthorOfPublication.ca477bf1-b849-498c-b068-ef27902c2020

Search Results

Now showing 1 - 6 of 6
  • No Thumbnail Available
    Publication
    In vivo base editing restores sensory transduction and transiently improves auditory function in a mouse model of recessive deafness
    (American Association for the Advancement of Science (AAAS), 2020-06-03) Yeh, Wei Hsi; Shubina-Oleinik, Olga; Levy, Jonathan; Pan, Bifeng; Newby, Gregory; Wornow, Michael; Burt, Rachel; Chen, Jonathan C.; Holt, Jeffrey R.; Liu, David
    Most genetic diseases arise from recessive point mutations that require correction, rather than disruption, of the pathogenic allele to benefit patients. Base editing has the potential to directly repair point mutations and provide permanent therapeutic restoration of gene function. We developed a base editing strategy to treat Baringo mice, which carry a recessive, loss-of-function point mutation (c.A545G, resulting in the substitution p.Y182C) in transmembrane channel-like 1 (Tmc1) that causes deafness. Tmc1 encodes a protein that forms mechanosensitive ion channels in sensory hair cells of the inner ear and is required for normal auditory function. We found that sensory hair cells of Baringo mice have a complete loss of auditory sensory transduction that causes profound deafness. To repair the Baringo mutation, we tested several optimized cytosine base editors (CBEmax variants) and guide RNAs in Baringo mouse embryonic fibroblasts. We packaged the most promising CBE, derived from an activation-induced cytidine deaminase (AID), into dual AAV vectors using a split-intein delivery system. The dual AID-CBEmax AAVs were injected into the inner ears of Baringo mice at postnatal day 1. Injected mice showed up to 51% reversion of the Tmc1 c.A545G point mutation to wild type sequence (c.A545A) in Tmc1 transcripts. Repair of Tmc1 in vivo restored inner hair-cell sensory transduction, hair-cell morphology, and partial low-frequency hearing four weeks post-injection. These findings provide a foundation for a potential one-time treatment for recessive hearing loss and support further development of base editing to correct pathogenic point mutations.
  • No Thumbnail Available
    Publication
    Base editing of haematopoietic stem cells rescues sickle cell disease in mice
    (Springer Science and Business Media LLC, 2021-06-02) Newby, Gregory; Yen, Jonathan S.; Woodard, Kaitly J.; Mayuranathan, Thiyagaraj; Lazzarotto, Cicera R.; Li, Yichao; Sheppard-Tillman, Heather; Porter, Shaina N.; Yao, Yu; Mayberry, Kalin; Everette, Kelcee A.; Jang, Yoonjeong; Podracky, Christopher J.; Thaman, Elizabeth; Lechauve, Christophe; Sharma, Akshay; Henderson, Jordana M.; Richter, Michelle; Zhao, Kevin; Miller, Shannon; Wang, Tina; Koblan, Luke; McCaffrey, Anton P.; Tisdale, John F.; Kalfa, Theodosia; Pruett-Miller, Shondra M.; Tsai, Shengdar; Weiss, Mitchell J.; Liu, David
  • No Thumbnail Available
    Publication
    Search-and-Replace Genome Editing Without Double-Strand Breaks or Donor DNA
    (Springer Science and Business Media LLC, 2019-10-21) Anzalone, Andrew; Randolph, Peyton B.; Davis, Jessie R.; Sousa, Alexander; Koblan, Luke; Levy, Jonathan; Chen, Peter; Wilson, Christopher; Newby, Gregory; Raguram, Aditya; Liu, David R.
  • No Thumbnail Available
    Publication
    Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning
    (Springer Science and Business Media LLC, 2021-06-28) Koblan, Luke; Arbab, Mandana; Shen, Max; Hussmann, Jeffrey A.; Anzalone, Andrew; Doman, Jordan; Newby, Gregory; Yang, Dian; Mok, Beverly; Replogle, Joseph M.; Xu, Albert; Sisley, Tyler A.; Weissman, Jonathan S.; Adamson, Brittany; Liu, David
  • No Thumbnail Available
    Publication
    Continuous Evolution of Base Editors With Expanded Target Compatibility and Improved Activity
    (Springer Science and Business Media LLC, 2019-07-22) Zheng, Christine; Wilson, Christopher; Thuronyi, Benjamin; Koblan, Luke; Levy, Jonathan; Yeh, Wei-Hsi; Newby, Gregory; Bhaumik, Mantu; Shubina-Oleinik, Olga; Holt, Jeffrey; Liu, David
    Base editors use DNA-modifying enzymes targeted with a catalytically impaired CRISPR protein to precisely install point mutations. Here, we develop phage-assisted continuous evolution of base editors (BE–PACE) to improve their editing efficiency and target sequence compatibility. We used BE–PACE to evolve cytosine base editors (CBEs) that overcome target sequence context constraints of canonical CBEs. One evolved CBE, evoAPOBEC1-BE4max, is up to 26-fold more efficient at editing cytosine in the GC context, a disfavored context for wild-type APOBEC1 deaminase, while maintaining efficient editing in all other sequence contexts tested. Another evolved deaminase, evoFERNY, is 29% smaller than APOBEC1 and edits efficiently in all tested sequence contexts. We also evolved a CBE based on CDA1 deaminase with much higher editing efficiency at difficult target sites. Finally, we used data from evolved CBEs to illuminate the relationship between deaminase activity, base editing efficiency, editing window width and byproduct formation. These findings establish a system for rapid evolution of base editors and inform their use and improvement.
  • No Thumbnail Available
    Publication
    Engineered pegRNAs improve prime editing efficiency
    (Springer Science and Business Media LLC, 2021-10-04) Nelson, James W.; Randolph, Peyton B.; Shen, Simon; Everette, Kelcee A.; Chen, Peter; Anzalone, Andrew; An, Meirui; Newby, Gregory; Chen, Jonathan; Hsu, Alvin; Liu, David
    Prime editing enables the installation of virtually any combination of point mutations, small insertions or small deletions in the DNA of living cells. A prime editing guide RNA (pegRNA) directs the prime editor protein to the targeted locus and also encodes the desired edit. Here we show that degradation of the 3′ region of the pegRNA that contains the reverse transcriptase template and the primer binding site can poison the activity of prime editing systems, impeding editing efficiency. We incorporated structured RNA motifs to the 3′ terminus of pegRNAs that enhance their stability and prevent degradation of the 3′ extension. The resulting engineered pegRNAs (epegRNAs) improve prime editing efficiency 3–4-fold in HeLa, U2OS and K562 cells and in primary human fibroblasts without increasing off-target editing activity. We optimized the choice of 3′ structural motif and developed pegLIT, a computational tool to identify non-interfering nucleotide linkers between pegRNAs and 3′ motifs. Finally, we showed that epegRNAs enhance the efficiency of the installation or correction of disease-relevant mutations.