Julia / Yue Cui, PhD

Assistant Professor, Env. and Occ. Health Sciences (Primary department)
Julia received her B.S. Degree in Chukechen Honors College, Zhejiang University in Hangzhou, China, and received her Ph.D. Degree with honors in University of Kansas Medical Center. Julia currently is an Assistant Professor in Toxicology in the Department of Environmental and Occupational Health Sciences. She is a recipient of the Sheldon D. Murphy Endowed Chair, and a member of Center of Ecogenetics & Environmental Health. Julia is trained as a toxicologist, specializing in using toxicogenomic and toxicoepigenomic approaches to determine the effects of environmental chemical exposure and reprogramming the gut microbiome on the transcriptional and epigenetic regulation of genes involved in drug metabolism and obesity during development.

Contact Information

University of Washington
Office: Roo. 204
Box: 354695
4225 Roosevelt Way NE
Seattle, WA 98105-6099
Tel: 206-616-4331


Research Interests

  • 1) How developmental exposure to environmental chemicals reprograms the epigenetic memory and the nuclear receptor-signaling to modulate drug metabolism and transport during and beyond childhood; and 2) how the gut microbiome modulates the ontogeny of genes that are involved in drug metabolism and obesity, and how the developmental reprogramming of gut microbiome by probiotics and antibiotics modulate pediatric pharmacology and childhood obesity.
  • Toxicogenomics. Toxicoepigenomics. General principles and mechanisms of toxicology. Molecular toxicology. Hepatotoxicology.

Teaching interests

Toxicogenomics, toxicoepigenomics, , general principles and mechanisms of toxicology, hepatotoxicology, developmental toxicology


PhD, Toxicology, University of Kansas Medical Center, 2010
BS, Biological Sciences, Zhejiang University (China), 2005


Program/Grant Name: Developmental Regulation of Drug Processing Genes
Funding Agency: NIH/NIEHS (R01 ES019487)
Despite recent rapid progress in understanding the expression patterns and regulatory mechanisms of drug processing genes, namely drug metabolizing enzymes and transporters in adults, little is known about these in the pediatric period. The long-term goal is to understand mechanisms of ontogenic regulation of drug processing genes, so that efficacious and safe drug treatments can be achieved in children. Several factors are known to be essential for normal development, including hepatocyte nuclear factor 4 alpha (HNF4a), farnesoid X receptor (FXR), growth hormone (GH) signaling, and epigenetic influences. HNF4a, a master regulator of early liver development, regulates hepatic expression of a large battery of drug processing genes. Initiation of bile-acid signaling pathways, mediated largely via the FXR, is a hallmark of perinatal liver development. GH is essential for postnatal hepatic gene expression and maturation. The accessibility of transcription factors to the target genes is largely determined by the methylation/acetylation status of histones and DNA sequences. Preliminary studies illustrate that in developing mouse livers, drug processing genes and transcription factors are expressed in distinct dynamic patterns and correlate with epigenetic signatures. The objective of this proposal is to elucidate the regulatory mechanisms of ontogenic expression of drug processing genes in mice. The rationale of this proposal is that its successful completion will generate basic knowledge that will serve as the foundation for further understanding pediatric pharmacology in humans. The central hypothesis is: developmental regulation of drug processing genes is a sequential event regulated by hormones, which activate transcription factors to modify epigenetic signatures and regulate gene expression. This hypothesis will be tested in 2 aims. Aim 1 will determine the ontogenic expression patterns of drug processing genes and the correlation with transcription factors and epigenetic signatures. The relative mRNA expression of major phase I/II enzymes and drug transporters in male mouse livers versus intestine and kidney will be examined, and correlated with expression of transcription factors and chromosome modifications (genome-wide DNA methylation and histone modifications). Aim 2 will elucidate roles of transcription factors and GH in determining ontogenic hepatic expression of drug processing genes in HNF4a-null, FXR-null, and GH deficiency (lit/lit) mice using the same working strategy. This study is novel, because it will use a genome-wide approach to elucidate how alterations of hormones and transcription factors modulate epigenetic signatures and hepatic ontogenic expression of drug processing genes. This study is significant, because little is known about the regulation of hepatic drug processing genes in pediatric stages. Results from this study will: 1) provide basic knowledge on the ontogenic expression patterns of drug processing genes and nuclear receptors in liver, kidney, and intestine; and 2) help to understand how perinatal alterations in hormones and nuclear receptors, via modulating epigenetic signatures, affect stage-specific and long-term expression of drug processing genes.

Program/Grant Name: Developmental Regulation of Drug Metabolism by Targeting the Gut Microbiome
Funding Agency: NIH/NIGMS (R01 GM111381)
Very little is known about the developmental regulation of drug-metabolizing enzymes and transporters (together called "drug-processing genes" [DPGs]) in liver, placing newborns and children at a much higher risk of adverse drug reactions (ADRs). Using RNA-Seq, we have shown that drug metabolism is the top most differentially regulated pathway in the entire liver transcriptome of germ-free (GF) mice, suggesting that there is a novel interaction between gut microbiome and hepatic DPGs. One of the key functions of gut microbiome is to produce secondary bile acids (BAs), which can activate two most critical xenobiotic-sensing nuclear receptors in liver, namely the pregnane X receptor (PXR) and constitutive androstane receptor (CAR). During development, profound changes occur in the intestinal bacteria and the secondary BA profiles, suggesting that gut microbiome may at least in part contribute to the developmental regulation of DPGs in liver. No systematic studies have been performed to characterize the regulation of all DPGs by gut microbiome during development, and little is known regarding how targeting the gut microbiome by antibiotics or probiotics reprograms the ontogeny of DPGs in liver. Therefore the goal of this research is to utilize multidisciplinary approaches, including GF and genetically-engineered mice, BA metabolomics, Next-Generation Sequencing, and human fecal samples, to unveil the role of gut microbiota in modulating PXR and CAR signaling and the subsequent ontogenic re-programming of DPGs in liver. The proposed work will unveil a novel link between the ontogeny of gut microbiome and the developmental changes of drug processing capacities during development, and will lead to a paradigm shift in pediatric pharmacology, by establishing a new concept in considering ADRs in children, which is the "bug-drug" interactions, in addition to the known "drug-drug" and "food-drug" interactions.

Funding Agency: NIH/NIEHS/(R01ES025708)
Developmental exposure to the flame-retardant polybrominated diphenyl ethers (PBDEs) has attracted growing concerns recently, because these highly persistent environmental toxicants are accumulated much more in infants through breast milk, and produce multiple detrimental effects. Although a growing body of research has been done regarding the toxicities of PBDEs themselves, little is known about the potential involvement of PBDEs in modulating the pharmacokinetics of drugs in newborns and children, who are at a much higher risk of adverse drug reactions. More importantly, there is no information regarding whether developmental exposure to PBDEs produces long lasting modifications of drug metabolism beyond childhood. We and others have identified that PBDEs are novel activators of the major xenobiotic-sensing nuclear receptors pregnane X receptor (PXR) and constitutive and rostane receptor (CAR). Neonatal activation of CAR results in epigenetic memory on histone methylation signatures and permanent change of drug metabolism in mouse liver, whereas PXR also regulates distinct epigenetic modifiers. Thus the objective of this research is to utilize multidisciplinary approaches to strategically investigate he epigenetic mechanisms of PBDEs in modulating the transcriptional activities of PXR and CAR and drug-processing capacities during and beyond the neonatal period on a genome-wide scale. Our central hypothesis is: neonatal exposure to PBDEs activates CAR and/or PXR, which in turn reprograms the ontogeny of critical chromatin epigenetic modifiers (such as DNA and histone methylation as well as histone acetylation), leading to epigenetic memory and altered ontogeny of drug-processing genes (DPGs), and long-term alterations in the pharmacokinetics and toxicokinetics beyond childhood. We will test this hypothesis in 3 specific aims: Aim 1 will use xeno-sensor null mice and second- generation sequencing to determine the roles of PXR and CAR in modulating the chromatin epigenetic signatures and expression of DPGs following neonatal exposure to PBDEs; Aim 2 will determine the effect of silencing key chromatin epigenetic modifiers on the expression of PXR- and CAR-target genes in PBDE- treated primary hepatocytes; Aim 3 will determine the role of neon

Selected Publications

1.    Aleksunes, L. M., Cui, Y., and Klaassen, C. D. (2008) Prominent expression of xenobiotic efflux transporters in mouse extraembryonic fetal membranes compared with placenta. Drug Metab Disp 36: 960-70.  PMID: 18566041, PMCID: PMC2574899
2.    Cui, Y.J., Yeager, R.L., Zhong, X.B., and Klaassen, C.D. (2009) Ontogenic expression of hepatic Ahr mRNA correlates with histone H3K4 di-methylation during mouse liver development. Toxicol Lett. 189: 1840190.  PMID: 19481593, PMCID: PMC2762423
3.    Cui, Y. J., Cheng, X., Weaver, Y. M., and Klaassen, C. D. (2009) Tissue distribution, gender divergent expression, ontogeny, and chemical induction of multidrug resistance transporter genes (Mdr1a, Mdr1b, Mdr2) in mice. Drug Metab Disp 37: 203-10.  PMID: 18854377, PMCID: PMC2683659
4.    Cui, Y., Aleksunes, L.M., Tanaka, Y., Goedken, M.J., and Klaassen, C.D. (2009) Compensatory induction of liver efflux transporters in response to ANIT-induced liver injury is impaired in FXR-null mice. Toxicol Sci. 110: 47-60. PMID: 19407337, PMCID: PMC2696329
5.    Li, Y., Cui, Y., Hart, S. N., Klaassen, C. D., and Zhong, X. (2009) Dynamic patterns of histone methylation are associated with ontogenic expression of the Cyp3a genes during mouse liver maturation. Mol Pharmacol. 75: 1171-1179.  PMID:19188337, PMCID: PMC2672803
6.    Hart, S.N., Li, Y., Cui, Y., Klaassen, C., and Zhong, X.B. (2009) Dynamic DNA and histone methylation influences the ontogeny of xenobiotic metabolizing genes during postnatal mouse liver maturation. FASEB J. 23: 752.4. PMID: N/A, PMCID: N/A
7.    Hart, S. N., Cui, Y., Klaassen, C. D., and Zhong, X. B. (2009) Three patterns of cytochrome P450 gene expression during liver maturation in mice. Drug Metab Disp 37: 116-21. PMID: 18845660, PMCID: PMC2672803
8.    Tanaka, Y., Aleksunes, L. M., Cui, Y. J., and Klaassen, C. D. (2009) ANIT-induced intrahepatic cholestasis alters hepatobiliary transporter expression via Nrf2 dependent and independent signaling. Toxicol Sci.  108: 247-257.  PMID: 19181614, PMCID: PMC2664692
9.    Choudhuri, S., Cui, Y., and Klaassen, C.D. (2010) Molecular targets of epigenetic regulation and effectors of environmental influences. Toxicol and Appl Pharmacol. 245: 378-93. PMID: 20381512, PMCID:  PMC2911443
10.    Cui, Y.J., Gunewardena, S.S., and Klaassen, C.D. (2010) ChIPing the cistrome of PXR in mouse liver. Nucleic Acids Research 38:7943-63.  PMID: 20693526, PMCID: PMC3001051
11.    Staudinger, JL, Xu, CS, Cui, Y.J., and Klaassen, C.D. (2010) Nuclear receptor mediated regulation of carboxylesterase expression and activity. Expert Opin on Drug Metab and Toxicol. 261-71 PMID: 20163318, PMCID: PMC2826721
12.    Cui, Y.J., Choudhuri, S., House-Knight, T, and Klaassen, C.D. (2010) Genetic and epigenetic regulation and expression signatures of glutathione S-transferases in developing mouse liver. Toxicol Sci. 115: 32-43. PMID: 20395309, PMCID: PMC2886863
13.    Klaassen, C.D., Lu, H., and Cui, J.Y. (2011) Epigenetic regulation of drug processing genes. Toxicol Mech Methods 21: 312-24.  PMID: 21495869, PMCID: PMC2886863
14.    Wu, K.C., Cui, J.Y., and Klaassen, C.D. (2011) Beneficial Role of Nrf2 in Regulating NADPH Generation and Consumption Toxicol Sci. PMID: 21775727, PMCID: PMC3179677
15.    Renaud, H.J., Cui, J.Y., and Klaassen, C.D. (2011) Tissue distribution and gender-divergent expression of 78 cytochrome P450 mRNAs in mice Toxicol Sci. 124: 261-277.  PMID: 21920951, PMCID: PMC3216415
16.    Cui, J.Y., Gunewardena, S.S., Yoo, B., Renaud, H.J., Lu, H., Zhong, X.B., and Klaassen, C.D. (2012) RNA-Seq Reveals different mRNA abundance of transporters and their alternative transcript isoforms during liver Development Toxicol Sci. 127: 592-609. PMID: 22454430, PMCID: PMC3355312
17.    Aleksunes, L.M., Yeager R.L., Wen X., Cui, J.Y., and Klaassen, C.D. (2012) Repression of hepatobiliary transporters and differential regulation of classic and alternative bile acid pathways in mice during pregnancy. Toxicol Sci. 130: 257-268. PMID: 22903823, PMCID: PMC3498745
18.    Lu, H., Cui, J.Y., Gunewardena, S., Yoo, B., Zhong, X.B., and Klaassen, C.D. (2012) Hepatic ontogeny and tissue distribution of mRNAs of epigenetic modifiers in mice using RNA-sequencing. Epigenetics 7: 914-29. PMID: 22772165, PMCID: PMC3427287
19.     Cui, J.Y., Renaud, H.J., and Klaassen, C.D. (2012) Ontogeny of novel cytochrome P450 gene isoforms during postnatal liver maturation in mice. Drug Metab Dispos. 49:1226-1237. PMID: 22446519, PMCID: PMC3362787
20.    Cui, J.Y., Aleksunes, L.M., Tanaka, Y., Fu, Z.D., Guo, Y., Guo, G.L., Lu, H., Zhong, X.B., and Klaassen, C.D. (2012) Bile acids via FXR initiate the expression of major transporters involved in the enterohepatic circulation of bile acids in newborn mice. Am J Physiol Gastrointest Liver Physiol. 302: G979-G996. PMID: 22268101, PMCID: PMC3362079
21.    Wu, K.C., Cui, J.Y., and Klaassen, C.D. (2012) Effect of graded Nrf2 activation on phase-I and –II drug metabolizing enzymes and transporters in mouse liver. PLoS One. 7:e39006. PMID: 22808024, PMCID: PMC3395627
22.    Lu, H., Gunewardena, S., Cui, Y., Yoo, B., Zhong, X.B., and Klaassen, C.D. (2013) RNA-Sequencing quantification of hepatic ontogeny and tissue distribution of mRNAs of phase-II enzymes in mice. Drug Metab Dispos. PMID: 23382457, PMCID: PMC3608454
23.    Peng, L., Cui, J.Y., Yoo, B., Gunewardena, S., Lu, H., Zhong, X.B., and Klaassen, C.D. (2013) RNA-Sequencing Quantification of Hepatic Ontogeny of Phase-I Enzymes in mice. Drug Metab Dispos. PMID: 24080161, PMCID: PMC3834128
24.    Fu ZD, Cui JY, Klaassen CD (2014) Atorvastatin induces bile-acid synthetic enzyme Cyp7a1 by suppressing FXR signaling in both liver and intestine in mice. J Lipid Res. PMID: 25278499, PMCID: PMC4242450
25.    Liu J, Lu H, Lu YF, Lei X, Cui JY, Ellis E, Strom SC, Klaassen CD (2014) Potency of individual bile acids to regulate bile acid synthesis and transport genes in primary human hepatocyte cultures. Toxicol Sci. PMID: 25055961, PMCID: PMC4271050
26.    Song P, Rockwell CE, Cui JY, Klaassen CD (2015) Individual bile acids have differential effects on bile acid signaling in mice.  Toxicol App Pharmacol.  PMID: 25582706, PMCID: N/A
27.    Guo Y, Cui JY, Lu H,  Klaassen CD (2015) Effect of various diets on the expression of phase-I drug-metabolizing enzymes in livers of mice.  Xenobiotica.  PMID: 2573328
28.    Guo Y, Cui JY, Lu H,  Klaassen CD (2015) Effect of nine diets on xenobiotic transporters in livers of mice.  Xenobiotica.  PMID: 25566878
29.  Selwyn FP, Cui JY, Klaassen CD (2015) RNA-Seq Quantification of Hepatic Drug
       Processing Genes in Germ-Free mice. 43: 1572-80. PMID: 25956306; PMCID: PMC4576678
30. Selwyn FP, Cheng SL, Bammler TK, Prasad B, Vrana M, Klaassen C, and Cui JY* (2015) Developmental Regulation of Drug-processing Genes in Livers of Germ-free Mice. Toxicol Sci. 147: 84-103. PMID: 26032512; PMCID: PMC4560037
31. Fu ZD, Cui JY, and Klaassen CD (2015) The Role of Sirt1 in Bile Acid Regulation during Calorie Restriction in Mice. Drug Metab Dispos. e0138307. PMID: 26372644; PMCID: PMC4570809
32. Klaassen CD, and Cui JY (2015) Review: Mechanisms of How the Intestinal Microbiota Alters the Effects of Drugs and Bile Acids. Drug Metab Dispos. 43: 1505-21. PMID: 26261286; PMCID: PMCID: PMC4576672.
33. Gunewardena SS, Yoo B, Peng L, Lu H, Zhong X, Klaassen CD, and Cui JY* (2015) Deciphering the Developmental Dynamics of the Mouse Liver Transcriptome. PloS One. e0141220. PMID: 26496202; PMCID: PMC4619800
34. Li YF, Renaud H, Klaassen CD, and Cui JY* (2015) Age-specific Regulation of Drug-processing Genes in Mouse Liver by Ligands of Xenobiotic-sensing Transcription Factors. Drug Metab Dispos. (in press) PMID: 26577435; PMCID: N/A.
35. Selwyn FP, Cheng SL,  Klaassen CD, and Cui JY* (2016) Regulation of Hepatic Drug-metabolizing Enzymes in Germ-free Mice by Conventional and Probiotics. Drug Metab Dispos. 44: 262-74. PMID: 26586378; PMCID: N/A.

Review date: