Professional Education


  • Doctor of Philosophy, Harvard University (2019)
  • Bachelor of Science, Colorado State University (2012)

Stanford Advisors


All Publications


  • Reply to "Efficient Nuclease-free HR by Clade F AAV Requires High MOIs with High Quality Vectors". Molecular therapy : the journal of the American Society of Gene Therapy Dudek, A. M., Porteus, M. H. 2019

    View details for DOI 10.1016/j.ymthe.2019.11.004

    View details for PubMedID 31735604

  • Genome-Wide CRISPR/Cas9 Screening Identifies GPR108 as a Highly Conserved AAV Entry Factor Dudek, A. M., Zinn, E., Pillay, S., Zengel, J., Carette, J. E., Vandenberghe, L. H. CELL PRESS. 2019: 313–14
  • GPR108 Is a Highly Conserved AAV Entry Factor. Molecular therapy : the journal of the American Society of Gene Therapy Dudek, A. M., Zabaleta, N., Zinn, E., Pillay, S., Zengel, J., Porter, C., Franceschini, J. S., Estelien, R., Carette, J. E., Zhou, G. L., Vandenberghe, L. H. 2019

    Abstract

    Adeno-associated virus (AAV) is a highly promising gene transfer vector, yet major cellular requirements for AAV entry are poorly understood. Using a genome-wide CRISPR screen for entry of evolutionarily divergent serotype AAVrh32.33, we identified GPR108, a member of the G protein-coupled receptor superfamily, as an AAV entry factor. Of greater than 20 divergent AAVs across all AAV clades tested in human cell lines, only AAV5 transduction was unaffected in the GPR108 knockout (KO). GPR108 dependency was further shown in murine and primary cells in vitro. These findings are further validated in vivo, as the Gpr108 KO mouse demonstrates 10- to 100-fold reduced expression for AAV8 and rh32.33 but not AAV5. Mechanistically, both GPR108 N- and C-terminal domains are required for transduction, and on the capsid, a VP1 unique domain that is not conserved on AAV5 can be transferred to confer GPR108 independence onto AAV2 chimeras. In vitro binding and fractionation studies indicate reduced nuclear import and cytosolic accumulation in the absence of GPR108. We thus have identified the second of two AAV entry factors that is conserved between mice and humans relevant both in vitro and in vivo, further providing a mechanistic understanding to the tropism of AAV gene therapy vectors.

    View details for DOI 10.1016/j.ymthe.2019.11.005

    View details for PubMedID 31784416

  • AAV6 Is Superior to Clade F AAVs in Stimulating Homologous Recombination-Based Genome Editing in Human HSPCs. Molecular therapy : the journal of the American Society of Gene Therapy Dudek, A. M., Porteus, M. H. 2019

    View details for DOI 10.1016/j.ymthe.2019.09.005

    View details for PubMedID 31537456

  • Identification and Characterization of an Alternate, AAVR Independent, AAV Entry Mechanism Using a Genome-Wide CRISPR/Cas9 Knock-Out Screen Dudek, A. M., Zinn, E. M., Pillay, S., Puschnik, A. S., Nagamine, C. M., Cheng, F., Qiu, J., Carette, J. E., Vandenberghe, L. H. CELL PRESS. 2018: 323
  • Delayed Onset and Altered Biodistribution of a Non-Canonical AAV Entry Pathway Dudek, A. M., Pillay, S., Puschnik, A. S., Nagamine, C. M., Carette, J. E., Vandenberghe, L. H. CELL PRESS. 2018: 188
  • An alternate route for adeno-associated virus entry independent of AAVR. Journal of virology Dudek, A. M., Pillay, S., Puschnik, A. S., Nagamine, C. M., Cheng, F., Qiu, J., Carette, J. E., Vandenberghe, L. H. 2018

    Abstract

    Determinants and mechanisms of cell attachment and entry steer the Adeno-Associated Virus (AAV) in its utility as a gene therapy vector. Thus far a systematic assessment of how diverse AAV serotypes engage their proteinaceous receptor AAVR (KIAA0319L) to establish transduction has been lacking, despite potential implications for cell and tissue tropism. Here, a large set of human and simian AAVs as well as in silico reconstructed ancestral AAV capsids were interrogated for AAVR usage. We identified a distinct AAV capsid lineage comprised of AAV4 and AAVrh32.33 that can bind and transduce cells in the absence of AAVR, independent of multiplicity of infection. Viral overlay assays and rescue experiments in non-permisive cells demonstrate that these AAVs are unable to bind to or use the AAVR protein for entry. Further evidence for a distinct entry pathway was observed in vivo, as AAVR knock out mice were equally permissive to transduction by AAVrh32.33 compared to wild type mice upon systemic injection. We interestingly observe that some AAV capsids undergo a low level of transduction in the absence of AAVR, both in vitro and in vivo, suggesting that some capsids may have a multi-modal entry pathway. In aggregate, our results demonstrate that AAVR usage is conserved amongst all primate AAVs except for those in the AAV4 lineage, and a non-AAVR pathway may be available to other serotypes. This work furthers our understanding of entry of AAV, a vector system of broad utility in gene therapy.Importance: Adeno-Associated Virus (AAV) is a non-pathogenic virus that is used as a vehicle for gene delivery. Here, we have identified several situations in which transduction is retained in both cell lines and a mouse model in the absence of a previously defined entry receptor, AAVR. Defining the molecular determinants of the infectious pathway of this highly relevant viral vector system can help refine future applications and therapies of this vector.

    View details for PubMedID 29343568