Hiroyuki Nakai, MD, PhD


Hiroyuki Nakai Headshot
Oregon Health & Science University
3181 SW Sam Jackson Park Road
Mail Code: L103
Portland, OR  97239
Office: 503 494-2256 | Lab: 503 494-9901
Fax: 503 494-6886


The two major focuses of our laboratory are the elucidation of the biology of recombinant adeno-associated virus (rAAV) vectors and cellular biology associated with rAAV infection/transduction, and development of new rAAV vector-mediated gene and cell therapies to treat various human diseases. To achieve this goal, we use tissue culture cells, rodents, large animals including non-human primates, bioinformatics, biostatistics, computer simulation and contemporary high-throughput approaches.

AAV is a non-pathogenic single-stranded DNA virus with the simplest viral structure. Recent studies have shown that single intravenous injection of rAAV serotype 8 or 9 vectors into experimental animals can efficiently deliver genetic payloads to many types of cells in the body, including the liver, heart, muscle and brain cells. Therefore, rAAV vectors have gained an increasing attention as promising gene delivery vehicle for human gene therapy. However, various issues need to be overcome to make rAAV gene therapy successful and broaden its application to a variety of human diseases. The issues include: (1) the presence of many extracellular and intracellular barriers (physical and biological) that hinder efficient gene delivery to target cells/tissues, necessitating administration of high vector doses for clinically beneficial outcomes; (2) substantial vector spillover to non-target cells/tissues at therapeutically effective vector doses due to promiscuous viral tropism; (3) efficacy-limiting host immune responses against viral proteins; (4) the high prevalence of preexisting anti-AAV neutralizing antibodies in humans; and (5) a potential risk of AAV-mediated insertional mutagenesis causing malignancy. The challenge in our laboratory has been to overcome these issues toward successful rAAV-mediated human gene and cell therapies by substantially understanding the rAAV vector biology and host responses. Despite the structural simplicity, the biology of this virus is very complicated and is not well understood. The basic biology of AAV and its translational application are both the subjects of our research.

In our laboratory, we have been studying AAV genome biology for many years. in this project, we focus on the interactions between viral genomes, host chromosomal DNA and host cellular DNA repair machinery in the in vivo context of various tissues. More recently, we have started putting significant efforts into mechanistically understanding the rAAV genotype-phenotype relationships. In this AAV capsid project, we have recently devised a paradigm-shifting non-traditional approach, termed AAV Barcode-Seq, that allows us to phenotypically characterize hundreds of different AAV strains in an unprecedented, comprehensive and high-throughput manner using only a small number of tissue culture replicates and animals. Using both traditional and non-traditional approaches, we are studying rAAV capsid amino acid sequence-phenotype relationships and engineering AAV capsids towards our ultimate research goals: (1) complete understanding of rAAV vector biology; (2) development of novel rAAV vectors endowed with biological phenotypes that are most ideal for clinical translation; and (3) successful application of rAAV for human gene therapy. We are also studying the viral-host protein interactions during the AAV capsid assembly. Moreover, we are conducting translational research projects in collaboration with the Oregon Stem Cell Center and the Oregon National Primate Research Center that focus on gene therapy for CNS diseases, gene therapy for diabetes by cell fate conversion, and reproduction control by means of gene delivery.


Earley, L.F., Kawano, Y., Adachi, K., Sun, X.X., Dai, M. S., Nakai, H. 2015 "Identification and characterization of nuclear and nucleolar localization signals in the adeno-associated virus serotype 2 assembly-activating protein" J. Virol. 89:3038-48 (highlighted in the Journal's Spotlight)

Adachi, K., Enoki, T., Kawano, Y., Veraz, M., Nakai, H. 2014 "Drawing a high-resolution functional map of adeno-associated virus capsid by massively parallel sequencing" Nat. Commun. 5:3075.

Kawano, Y., Neeley, S., Adachi, K., Nakai, H. 2013 "An experimental and computational evolution-based method to study a mode of co-evolution of overlapping open reading frames in the AAV2 viral genome" PLoS One 8:e66211.

Adachi, K., Nakai, H. 2011 "The Roles of DNA Repair Pathways in Adeno-Associated Virus Infection and Viral Genome Replication / Recombination / Integration" In Sofya Vengrova (ed), DNA Repair and Human Health, InTech, 2011 pp. 685-714.

Kotchey, N., Adachi, K., Zahid, M., Inagaki, K., Charan, R., Parker, P., Nakai, H. 2011 "A potential role of distinctively delayed blood clearance of recombinant adeno-associated virus serotype 9 in robust cardiac transduction" Mol. Ther. 19:1079-1089.

Adachi, K., Nakai, H. 2010 "A new recombinant adeno-associated virus (AAV)-based random peptide display library system: infection-defective AAV1.9-3 as a novel detargeted platform for vector evolution" Gene Ther. Regul. 5:31-55.

Dong, B., Nakai, H., Xiao, W. 2010. "Characterization of genome integrity for oversized recombinant AAV vector" Mol. Ther. 18:87-92.

Inagaki, K., Piao, C., Kotchey, N., Wu, X., Nakai, H. 2008. "Frequency and spectrum of genomic integration of recombinant adeno-associated virus serotype 8 vector in neonatal mouse liver" J. Virol. 82:9513-9524.

Inagaki, K., Ma, C., Storm, T.A., Kay, M. A., Nakai, H. 2007. "A Role of DNA-PKcs and Artemis in opening viral DNA hairpin termini in various tissues in mice" J. Virol. 81:11304-11321.

Inagaki, K., Lewis, S.M., Wu, X., Ma, C., Munroe, D.J., Fuess, S., Storm, T.A., Kay, M. A., Nakai, H. 2007. "DNA palindromes with a modest arm length of >~20 bp are a significant target for rAAV vector integration in the liver, muscle and heart in mice" J. Virol. 81:11290-11303.

Inagaki, K., Fuess, S., Storm, T.A., Gibson, G. A., Mctiernan, C. F., Kay, M. A., Nakai, H. 2006. "Robust systemic transduction with AAV9 vectors in mice: efficient global cardiac gene transfer superior to that of AAV8" Mol. Ther. 14:45-53.

Nakai, H., Montini, E., Fuess, S., Storm, T. A., Grompe, M., Kay, M. A. 2003. "AAV serotype 2 vectors preferentially integrate into active genes in mice" Nat. Genet. 34:297-302.