Academic Appointments

Honors & Awards

  • Young Investigator Award Grant $25,000, Stanford University Immunity, Transplantation & Infection Institute (2016-2018)
  • NIH K01 Career Transition Grant, NIDDK (2016-2021)
  • Mass Spectrometry Seed Grant $8,000, Stanford University (2015-2016)
  • Charles J. Epstein Trainee Award for Excellence in Human Genetics Research – Semifinalist $750, American Society of Human Genetics (2016)
  • Best Presentation of 2016 $300, UCSF Liver Center Annual Symposium (2016)
  • Postdoc of the Year $200, Stanford Pediatrics Dept (2016)
  • Travel Award $500, American Society for Gene & Cell Therapy (2016)
  • NIH F32 NRSA Postdoctoral Fellowship, NHLBI (2014-17)
  • Helena Anna Henzl-Gabor Young Women in Science Travel Award $900, Stanford University (2014)
  • Hans Popper Memorial Postdoctoral Research Fellowship, American Liver Foundation (2013-14)
  • Genetics Idea of the Year - 1st Place, Stanford Genetics Dept (2013)
  • Stanford Dean's Postdoctoral Fellowship, Stanford University (2012-13)
  • Graduate Student Valedictorian, OHSU (2012)
  • Travel Award $500, American Society for Gene & Cell Therapy (2012)
  • Travel Award $500, American Society for Gene & Cell Therapy (2011)
  • Oregon Graduate Scholarship Fund $2000, Oregon State Legislature (2010-11)
  • Travel Award $500, NW Genome Engineering Consortium (2010)
  • Leslie S. Parker Memorial Scholarship $1000, Parker Family (2009-10)
  • Mary Horstkotte Memorial Scholarship $2000, Horstkotte Family (2009)
  • Travel Award $500, NW Genome Engineering Consortium (2009)
  • Travel Award $500, American Society for Gene Therapy (2008)
  • NIH F31 NRSA Predoctoral Fellowship, NCI (2007-12)
  • USA Funds Access to Education Academic Scholarship $12,000, USA Funds Access to Education (2007-10)
  • Mildred & CK Dart Memorial Scholarship $2000, Dart Family (2007-08)
  • Graduating Member, US National Dean's List (2006)
  • Brandon Koetje Memorial Community Service Scholarship $750, Koetje Family (2005-06)
  • Endowed Academic Scholarship $5000, Fred Meyer (2005-06)
  • Farrell Pre-Medical Academic Scholarship $5000, Farrell Family (2005-06)
  • Washington Award for Vocational Excellence $10,000, Washington State Legislature (2001-04)
  • Washington Promise Scholarship $3,500, Washington State Legislature (2001-03)
  • Academic Scholarship $1,500, Rotary Club of Mount Vernon, WA (2001)
  • Academic Scholarship $2,000, Kiwanis Club of Mount Vernon, WA (2001)
  • Student Service Scholarship $1,500, President George W. Bush (2001)

Boards, Advisory Committees, Professional Organizations

  • Co-Chair, ASGCT Trainee Committee (2016 - Present)
  • Member, ASGCT Viral Gene Transfer Vectors Committee (2016 - Present)
  • Member, ASGCT Outreach & Communications Committee -- Website Focus Group (2016 - Present)
  • Fellow, American Association for the Study of Liver Disease (2012 - Present)
  • Associate Member, American Society of Human Genetics (2014 - Present)
  • Associate Member, American Society of Gene and Cell Therapy (2007 - Present)
  • Trainee Member, Organization for the Study of Sex Differences (2015 - Present)
  • Member, Association for Women in Science (2013 - Present)
  • Member, American Association for the Advancement of Science (2007 - Present)
  • Associate Member, International Society for Stem Cell Research (2008 - 2009)
  • Member, Beta Beta Beta National Biological Honors Society (2004 - 2006)

Professional Education

  • BS, Central Washington University, Medical Microbiology, Chemistry Minor (2006)
  • PhD, Oregon Health & Science University, Cell & Developmental Biology (2012)


  • Nicole K. Paulk, Mark A. Kay. "United States Patent 62/268,428 Novel recombinant adeno-associated virus capsids with enhanced human skeletal muscle tropism", Stanford University
  • Nicole K. Paulk, Mark A. Kay. "United States Patent 62/296,046 Novel recombinant adeno-associated virus capsids resistant to pre-existing human neutralizing antibodies", Stanford University


All Publications

  • Promoterless gene targeting without nucleases ameliorates haemophilia B in mice. Nature BARZEL, A., Paulk, N. K., Shi, Y., Huang, Y., Chu, K., Zhang, F., Valdmanis, P. N., Spector, L. P., Porteus, M. H., Gaensler, K. M., Kay, M. A. 2015; 517 (7534): 360-364


    Site-specific gene addition can allow stable transgene expression for gene therapy. When possible, this is preferred over the use of promiscuously integrating vectors, which are sometimes associated with clonal expansion and oncogenesis. Site-specific endonucleases that can induce high rates of targeted genome editing are finding increasing applications in biological discovery and gene therapy. However, two safety concerns persist: endonuclease-associated adverse effects, both on-target and off-target; and oncogene activation caused by promoter integration, even without nucleases. Here we perform recombinant adeno-associated virus (rAAV)-mediated promoterless gene targeting without nucleases and demonstrate amelioration of the bleeding diathesis in haemophilia B mice. In particular, we target a promoterless human coagulation factor IX (F9) gene to the liver-expressed mouse albumin (Alb) locus. F9 is targeted, along with a preceding 2A-peptide coding sequence, to be integrated just upstream to the Alb stop codon. While F9 is fused to Alb at the DNA and RNA levels, two separate proteins are synthesized by way of ribosomal skipping. Thus, F9 expression is linked to robust hepatic albumin expression without disrupting it. We injected an AAV8-F9 vector into neonatal and adult mice and achieved on-target integration into ∼0.5% of the albumin alleles in hepatocytes. We established that F9 was produced only from on-target integration, and ribosomal skipping was highly efficient. Stable F9 plasma levels at 7-20% of normal were obtained, and treated F9-deficient mice had normal coagulation times. In conclusion, transgene integration as a 2A-fusion to a highly expressed endogenous gene may obviate the requirement for nucleases and/or vector-borne promoters. This method may allow for safe and efficacious gene targeting in both infants and adults by greatly diminishing off-target effects while still providing therapeutic levels of expression from integration.

    View details for DOI 10.1038/nature13864

    View details for PubMedID 25363772

  • AAV-Mediated Gene Targeting Is Significantly Enhanced by Transient Inhibition of Nonhomologous End Joining or the Proteasome In Vivo HUMAN GENE THERAPY Paulk, N. K., Loza, L. M., Finegold, M. J., Grompe, M. 2012; 23 (6): 658-665


    Recombinant adeno-associated virus (rAAV) vectors have clear potential for use in gene targeting but low correction efficiencies remain the primary drawback. One approach to enhancing efficiency is a block of undesired repair pathways like nonhomologous end joining (NHEJ) to promote the use of homologous recombination. The natural product vanillin acts as a potent inhibitor of NHEJ by inhibiting DNA-dependent protein kinase (DNA-PK). Using a homology containing rAAV vector, we previously demonstrated in vivo gene repair frequencies of up to 0.1% in a model of liver disease hereditary tyrosinemia type I. To increase targeting frequencies, we administered vanillin in combination with rAAV. Gene targeting frequencies increased up to 10-fold over AAV alone, approaching 1%. Fah(-/-)Ku70(-/-) double knockout mice also had increased gene repair frequencies, genetically confirming the beneficial effects of blocking NHEJ. A second strategy, transient proteasomal inhibition, also increased gene-targeting frequencies but was not additive to NHEJ inhibition. This study establishes the benefit of transient NHEJ inhibition with vanillin, or proteasome blockage with bortezomib, for increasing hepatic gene targeting with rAAV. Functional metabolic correction of a clinically relevant disease model was demonstrated and provided evidence for the feasibility of gene targeting as a therapeutic strategy.

    View details for DOI 10.1089/hum.2012.038

    View details for Web of Science ID 000306356700013

    View details for PubMedID 22486314

  • Adeno-Associated Virus Gene Repair Corrects a Mouse Model of Hereditary Tyrosinemia In Vivo HEPATOLOGY Paulk, N. K., Wursthorn, K., Wang, Z., Finegold, M. J., Kay, M. A., Grompe, M. 2010; 51 (4): 1200-1208


    Adeno-associated virus (AAV) vectors are ideal for performing gene repair due to their ability to target multiple different genomic loci, low immunogenicity, capability to achieve targeted and stable expression through integration, and low mutagenic and oncogenic potential. However, many handicaps to gene repair therapy remain. Most notable is the low frequency of correction in vivo. To date, this frequency is too low to be of therapeutic value for any disease. To address this, a point-mutation-based mouse model of the metabolic disease hereditary tyrosinemia type I was used to test whether targeted AAV integration by homologous recombination could achieve high-level stable gene repair in vivo. Both neonatal and adult mice were treated with AAV serotypes 2 and 8 carrying a wild-type genomic sequence for repairing the mutated Fah (fumarylacetoacetate hydrolase) gene. Hepatic gene repair was quantified by immunohistochemistry and supported with reverse transcription polymerase chain reaction and serology for functional correction parameters. Successful gene repair was observed with both serotypes but was more efficient with AAV8. Correction frequencies of up to 10(-3) were achieved and highly reproducible within typical dose ranges. In this model, repaired hepatocytes have a selective growth advantage and are thus able to proliferate to efficiently repopulate mutant livers and cure the underlying metabolic disease. Conclusion: AAV-mediated gene repair is feasible in vivo and can functionally correct an appropriate selection-based metabolic liver disease in both adults and neonates.

    View details for DOI 10.1002/hep.23481

    View details for Web of Science ID 000276538100016

    View details for PubMedID 20162619

  • Robust expansion of human hepatocytes in Fah(-/-)/Rag2(-/-)/Il2rg(-/-) mice NATURE BIOTECHNOLOGY Azuma, H., Paulk, N., Ranade, A., Dorrell, C., Al-Dhalimy, M., Ellis, E., Strom, S., Kay, M. A., Finegold, M., Grompe, M. 2007; 25 (8): 903-910


    Mice that could be highly repopulated with human hepatocytes would have many potential uses in drug development and research applications. The best available model of liver humanization, the uroplasminogen-activator transgenic model, has major practical limitations. To provide a broadly useful hepatic xenorepopulation system, we generated severely immunodeficient, fumarylacetoacetate hydrolase (Fah)-deficient mice. After pretreatment with a urokinase-expressing adenovirus, these animals could be highly engrafted (up to 90%) with human hepatocytes from multiple sources, including liver biopsies. Furthermore, human cells could be serially transplanted from primary donors and repopulate the liver for at least four sequential rounds. The expanded cells displayed typical human drug metabolism. This system provides a robust platform to produce high-quality human hepatocytes for tissue culture. It may also be useful for testing the toxicity of drug metabolites and for evaluating pathogens dependent on human liver cells for replication.

    View details for DOI 10.1038/nbt1326

    View details for Web of Science ID 000248725800029

    View details for PubMedID 17664939

  • In Vivo Selection of Transplanted Hepatocytes by Pharmacological Inhibition of Fumarylacetoacetate Hydrolase in Wild-type Mice MOLECULAR THERAPY Paulk, N. K., Wursthorn, K., Haft, A., Pelz, C., Clarke, G., Newell, A. H., Olson, S. B., Harding, C. O., Finegold, M. J., Bateman, R. L., Witte, J. F., McClard, R., Grompe, M. 2012; 20 (10): 1981-1987


    Genetic fumarylacetoacetate hydrolase (Fah) deficiency is unique in that healthy gene-corrected hepatocytes have a strong growth advantage and can repopulate the diseased liver. Unfortunately, similar positive selection of gene-corrected cells is absent in most inborn errors of liver metabolism and it is difficult to reach the cell replacement index required for therapeutic benefit. Therefore, methods to transiently create a growth advantage for genetically modified hepatocytes in any genetic background would be advantageous. To mimic the selective pressure of Fah deficiency in normal animals, an efficient in vivo small molecule inhibitor of FAH, 4-[(2-carboxyethyl)-hydroxyphosphinyl]-3-oxobutyrate (CEHPOBA) was developed. Microarray analysis demonstrated that pharmacological inhibition of FAH produced highly similar gene expression changes to genetic deficiency. As proof of principle, hepatocytes lacking homogentisic acid dioxygenase (Hgd) and hence resistant to FAH inhibition were transplanted into sex-mismatched wild-type recipients. Time course analyses of 4-6 weeks of CEHPOBA administration after transplantation showed a linear relationship between treatment length and replacement index. Compared to controls, recipients treated with the FAH-inhibitor had 20-100-fold increases in liver repopulation. We conclude that pharmacological inhibition of FAH is a promising approach to in vivo selection of hepatocytes.

    View details for DOI 10.1038/mt.2012.154

    View details for Web of Science ID 000309519000020

    View details for PubMedID 22871666

  • Ochronosis in a murine model of alkaptonuria is synonymous to that in the human condition OSTEOARTHRITIS AND CARTILAGE Taylor, A. M., Preston, A. J., Paulk, N. K., Sutherland, H., Keenan, C. M., Wilson, P. J., Wlodarski, B., Grompe, M., Ranganath, L. R., Gallagher, J. A., Jarvis, J. C. 2012; 20 (8): 880-886


    Alkaptonuria (AKU) is a rare genetic disease which results in severe early onset osteoarthropathy. It has recently been shown that the subchondral interface is of key significance in disease pathogenesis. Human surgical tissues are often beyond this initial stage and there is no published murine model of pathogenesis, to study the natural history of the disease. The murine genotype exists but it has been reported not to demonstrate ochronotic osteoarthropathy consistent with the human disease. Recent anecdotal evidence of macroscopic renal ochronosis in a mouse model of tyrosinaemia led us to perform histological analysis of tissues of these mice that are known to be affected in human AKU.The homogentisate 1,2-dioxygenase Hgd(+/)(-)Fah(-)(/)(-) mouse can model either hereditary tyrosinaemia type I (HT1) or AKU depending on selection conditions. Mice having undergone Hgd reversion were sacrificed at various time points, and their tissues taken for histological analysis. Sections were stained with haematoxylin eosin (H&E) and Schmorl's reagent.Early time point observations at 8 months showed no sign of macroscopic ochronosis of tissues. Macroscopic examination at 13 months revealed ochronosis of the kidneys. Microscopic analysis of the kidneys revealed large pigmented nodules displaying distinct ochre colouration. Close microscopic examination of the distal femur and proximal fibula at the subchondral junctions revealed the presence of numerous pigmented chondrocytes.Here we present the first data showing ochronosis of tissues in a murine model of AKU. These preliminary histological observations provide a stimulus for further studies into the natural history of the disease to provide a greater understanding of this class of arthropathy.

    View details for DOI 10.1016/j.joca.2012.04.013

    View details for Web of Science ID 000306988000010

    View details for PubMedID 22542924

  • Ploidy Reductions in Murine Fusion-Derived Hepatocytes PLOS GENETICS Duncan, A. W., Hickey, R. D., Paulk, N. K., Culberson, A. J., Olson, S. B., Finegold, M. J., Grompe, M. 2009; 5 (2)


    We previously showed that fusion between hepatocytes lacking a crucial liver enzyme, fumarylacetoacetate hydrolase (FAH), and wild-type blood cells resulted in hepatocyte reprogramming. FAH expression was restored in hybrid hepatocytes and, upon in vivo expansion, ameliorated the effects of FAH deficiency. Here, we show that fusion-derived polyploid hepatocytes can undergo ploidy reductions to generate daughter cells with one-half chromosomal content. Fusion hybrids are, by definition, at least tetraploid. We demonstrate reduction to diploid chromosome content by multiple methods. First, cytogenetic analysis of fusion-derived hepatocytes reveals a population of diploid cells. Secondly, we demonstrate marker segregation using ss-galactosidase and the Y-chromosome. Approximately 2-5% of fusion-derived FAH-positive nodules were negative for one or more markers, as expected during ploidy reduction. Next, using a reporter system in which ss-galactosidase is expressed exclusively in fusion-derived hepatocytes, we identify a subpopulation of diploid cells expressing ss-galactosidase and FAH. Finally, we track marker segregation specifically in fusion-derived hepatocytes with diploid DNA content. Hemizygous markers were lost by >or=50% of Fah-positive cells. Since fusion-derived hepatocytes are minimally tetraploid, the existence of diploid hepatocytes demonstrates that fusion-derived cells can undergo ploidy reduction. Moreover, the high degree of marker loss in diploid daughter cells suggests that chromosomes/markers are lost in a non-random fashion. Thus, we propose that ploidy reductions lead to the generation of genetically diverse daughter cells with about 50% reduction in nuclear content. The generation of such daughter cells increases liver diversity, which may increase the likelihood of oncogenesis.

    View details for DOI 10.1371/journal.pgen.1000385

    View details for Web of Science ID 000266320000025

    View details for PubMedID 19229314

  • Photochemistry of iron in simulated crustal aerosols with dimethyl sulfide oxidation products ENVIRONMENTAL SCIENCE & TECHNOLOGY Key, J. M., Paulk, N., Johansen, A. M. 2008; 42 (1): 133-139


    Iron contained in dust-derived aerosol particles deposited into remote oceans is essential for phytoplankton productivity, which controls photosynthesis rate and the uptake and release of climate forcing gases. Understanding chemical mechanisms that control iron bioavailability, that is, its speciation, is therefore crucial for global climate predictions. In the present study, the photoredox chemistry of iron in marine atmospheric aerosol particles was investigated by using ferrihydrite as a surrogate iron phase in the presence of dimethyl sulfide (DMS) derived oxidation products: dimethyl sulfoxide (DMSO), dimethyl sulfone (DMS02), methane sulfinic acid (MSIA), and methane sulfonic acid (MSA). Reactants and products were analyzed with UV-vis absorption spectroscopy, ion chromatography, and a hydrogen peroxide sensitive electrode. Results show that MSIA enhances the photoreductive dissolution of iron in a ligand-to-metal charge transfer reaction producing Fe(II), MSA, and H2O2. The rate law for Fe(II) is close to first order (0.79) with regard to adsorbed MSIA and has an empirical rate constant of 1.4 x 10(-4) s(-1). This mechanism may represent a significant pathway through which iron becomes more bioavailable, and it contributes to models of iron and sulfur chemistries in the marine atmosphere.

    View details for DOI 10.1021/es071469y

    View details for Web of Science ID 000252037400024

    View details for PubMedID 18350887