Academic Appointments

All Publications

  • Neuron Navigator 1 (Nav1) regulates the response to cocaine in mice. Communications biology Bagley, J. R., Tan, Y., Zhu, W., Cheng, Z., Takeda, S., Fang, Z., Arslan, A., Wang, M., Guan, Y., Jiang, L., Jian, R., Gu, F., Parada, I., Prince, D., Jentsch, J. D., Peltz, G. 2023; 6 (1): 1053


    Genetic variation accounts for much of the risk for developing a substance use disorder, but the underlying genetic factors and their genetic effector mechanisms are mostly unknown. Inbred mouse strains exhibit substantial and heritable differences in the extent of voluntary cocaine self-administration. Computational genetic analysis of cocaine self-administration data obtained from twenty-one inbred strains identified Nav1, a member of the neuron navigator family that regulates dendrite formation and axonal guidance, as a candidate gene. To test this genetic hypothesis, we generated and characterized Nav1 knockout mice. Consistent with the genetic prediction, Nav1 knockout mice exhibited increased voluntary cocaine intake and had increased motivation for cocaine consumption. Immunohistochemistry, electrophysiology, and transcriptomic studies were performed as a starting point for investigating the mechanism for the Nav1 knockout effect. Nav1 knockout mice had a reduced inhibitory synapse density in their cortex, increased excitatory synaptic transmission in their cortex and hippocampus, and increased excitatory neurons in a deep cortical layer. Collectively, our results indicate that Nav1 regulates the response to cocaine, and we identified Nav1 knockout induced changes in the excitatory and inhibitory synaptic balance in the cortex and hippocampus that could contribute to this effect.

    View details for DOI 10.1038/s42003-023-05430-9

    View details for PubMedID 37853211

    View details for PubMedCentralID PMC10584906

  • Innate immune cell activation causes lung fibrosis in a humanized model of long COVID. Proceedings of the National Academy of Sciences of the United States of America Cui, L., Fang, Z., De Souza, C. M., Lerbs, T., Guan, Y., Li, I., Charu, V., Chen, S. Y., Weissman, I., Wernig, G. 2023; 120 (10): e2217199120


    COVID-19 remains a global pandemic of an unprecedented magnitude with millions of people now developing "COVID lung fibrosis." Single-cell transcriptomics of lungs of patients with long COVID revealed a unique immune signature demonstrating the upregulation of key proinflammatory and innate immune effector genes CD47, IL-6, and JUN. We modeled the transition to lung fibrosis after COVID and profiled the immune response with single-cell mass cytometry in JUN mice. These studies revealed that COVID mediated chronic immune activation reminiscent to long COVID in humans. It was characterized by increased CD47, IL-6, and phospho-JUN (pJUN) expression which correlated with disease severity and pathogenic fibroblast populations. When we subsequently treated a humanized COVID lung fibrosis model by combined blockade of inflammation and fibrosis, we not only ameliorated fibrosis but also restored innate immune equilibrium indicating possible implications for clinical management of COVID lung fibrosis in patients.

    View details for DOI 10.1073/pnas.2217199120

    View details for PubMedID 36848564

  • Analysis of structural variation among inbred mouse strains. BMC genomics Arslan, A., Fang, Z., Wang, M., Tan, Y., Cheng, Z., Chen, X., Guan, Y., J Pisani, L., Yoo, B., Bejerano, G., Peltz, G. 2023; 24 (1): 97


    BACKGROUND: 'Long read' sequencing methods have been used to identify previously uncharacterized structural variants that cause human genetic diseases. Therefore, we investigated whether long read sequencing could facilitate genetic analysis of murine models for human diseases.RESULTS: The genomes of six inbred strains (BTBR T+Itpr3tf/J, 129Sv1/J, C57BL/6/J, Balb/c/J, A/J, SJL/J) were analyzed using long read sequencing. Our results revealed that (i) Structural variants are very abundant within the genome of inbred strains (4.8 per gene) and (ii) that we cannot accurately infer whether structural variants are present using conventional short read genomic sequence data, even when nearby SNP alleles are known. The advantage of having a more complete map was demonstrated by analyzing the genomic sequence of BTBR mice. Based upon this analysis, knockin mice were generated and used to characterize a BTBR-unique 8-bp deletion within Draxin that contributes to the BTBR neuroanatomic abnormalities, which resemble human autism spectrum disorder.CONCLUSION: A more complete map of the pattern of genetic variation among inbred strains, which is produced by long read genomic sequencing of the genomes of additional inbred strains, could facilitate genetic discovery when murine models of human diseases are analyzed.

    View details for DOI 10.1186/s12864-023-09197-5

    View details for PubMedID 36864393

  • A human multi-lineage hepatic organoid model for liver fibrosis. Nature communications Guan, Y., Enejder, A., Wang, M., Fang, Z., Cui, L., Chen, S., Wang, J., Tan, Y., Wu, M., Chen, X., Johansson, P. K., Osman, I., Kunimoto, K., Russo, P., Heilshorn, S. C., Peltz, G. 2021; 12 (1): 6138


    To investigate the pathogenesis of a congenital form of hepatic fibrosis, human hepatic organoids were engineered to express the most common causative mutation for Autosomal Recessive Polycystic Kidney Disease (ARPKD). Here we show that these hepatic organoids develop the key features of ARPKD liver pathology (abnormal bile ducts and fibrosis) in only 21 days. The ARPKD mutation increases collagen abundance and thick collagen fiber production in hepatic organoids, which mirrors ARPKD liver tissue pathology. Transcriptomic and other analyses indicate that the ARPKD mutation generates cholangiocytes with increased TGFbeta pathway activation, which are actively involved stimulating myofibroblasts to form collagen fibers. There is also an expansion of collagen-producing myofibroblasts with markedly increased PDGFRB protein expression and an activated STAT3 signaling pathway. Moreover, the transcriptome of ARPKD organoid myofibroblasts resemble those present in commonly occurring forms of liver fibrosis. PDGFRB pathway involvement was confirmed by the anti-fibrotic effect observed when ARPKD organoids were treated with PDGFRB inhibitors. Besides providing insight into the pathogenesis of congenital (and possibly acquired) forms of liver fibrosis, ARPKD organoids could also be used to test the anti-fibrotic efficacy of potential anti-fibrotic therapies.

    View details for DOI 10.1038/s41467-021-26410-9

    View details for PubMedID 34686668

  • Engineered Matrices Enable the Culture of Human Patient-Derived Intestinal Organoids. Advanced science (Weinheim, Baden-Wurttemberg, Germany) Hunt, D. R., Klett, K. C., Mascharak, S., Wang, H., Gong, D., Lou, J., Li, X., Cai, P. C., Suhar, R. A., Co, J. Y., LeSavage, B. L., Foster, A. A., Guan, Y., Amieva, M. R., Peltz, G., Xia, Y., Kuo, C. J., Heilshorn, S. C. 2021; 8 (10): 2004705


    Human intestinal organoids from primary human tissues have the potential to revolutionize personalized medicine and preclinical gastrointestinal disease models. A tunable, fully defined, designer matrix, termed hyaluronan elastin-like protein (HELP) is reported, which enables the formation, differentiation, and passaging of adult primary tissue-derived, epithelial-only intestinal organoids. HELP enables the encapsulation of dissociated patient-derived cells, which then undergo proliferation and formation of enteroids, spherical structures with polarized internal lumens. After 12 rounds of passaging, enteroid growth in HELP materials is found to be statistically similar to that in animal-derived matrices. HELP materials also support the differentiation of human enteroids into mature intestinal cell subtypes. HELP matrices allow stiffness, stress relaxation rate, and integrin-ligand concentration to be independently and quantitatively specified, enabling fundamental studies of organoid-matrix interactions and potential patient-specific optimization. Organoid formation in HELP materials is most robust in gels with stiffer moduli (G' ≈ 1 kPa), slower stress relaxation rate (t1/2 ≈ 18 h), and higher integrin ligand concentration (0.5 × 10-3-1 × 10-3 m RGD peptide). This material provides a promising in vitro model for further understanding intestinal development and disease in humans and a reproducible, biodegradable, minimal matrix with no animal-derived products or synthetic polyethylene glycol for potential clinical translation.

    View details for DOI 10.1002/advs.202004705

    View details for PubMedID 34026461

    View details for PubMedCentralID PMC8132048

  • Engineered Matrices Enable the Culture of Human Patient-Derived Intestinal Organoids ADVANCED SCIENCE Hunt, D. R., Klett, K. C., Mascharak, S., Wang, H. Y., Gong, D., Lou, J., Li, X., Cai, P. C., Suhar, R. A., Co, J. Y., LeSavage, B. L., Foster, A. A., Guan, Y., Amieva, M. R., Peltz, G., Xia, Y., Kuo, C. J., Heilshorn, S. C. 2021
  • The Phosphatidylethanolamine Biosynthesis Pathway Provides a New Target for Cancer Chemotherapy. Journal of hepatology Guan, Y. n., Chen, X. n., Wu, M. n., Zhu, W. n., Arslan, A. n., Takeda, S. n., Nguyen, M. H., Majeti, R. n., Thomas, D. n., Zheng, M. n., Peltz, G. n. 2019


    Since iPSC human develop into hepatic organoids through stages that resemble human embryonic liver development, they can be used to study developmental processes and disease pathology. Therefore, we examined the early stages of hepatic organoid formation to identify key pathways affecting early liver development.Single cell RNA-sequencing and metabolomic analysis was performed on developing organoid cultures at the iPSC, hepatoblast (day 9) and mature organoid stage. The importance of the phosphatidyl-ethanolamine biosynthesis pathway to early liver development was examined in developing organoid cultures using iPSC with a CRISPR-mediated gene knockout and an over the counter medication (meclizine) that inhibits the rate-limiting enzyme in this pathway. Meclizine's effect on the growth of a human hepatocarcinoma cell line in a xenotransplantation model and on the growth of acute myeloid leukemia cells in vitro was also examined.Transcriptomic and metabolomic analysis of organoid development indicated that the phosphatidyl-ethanolamine biosynthesis pathway is essential for early liver development. Unexpectedly, early hepatoblasts were selectively sensitive to the cytotoxic effect of meclizine. We demonstrate that meclizine could be repurposed for use in a new synergistic combination therapy for primary liver cancer: a glycolysis inhibitor reprograms cancer cell metabolism to make it susceptible to the cytotoxic effect of meclizine. This combination inhibited the growth of a human liver carcinoma cell line in vitro; and in a xenotransplantation model without causing significant side effets. This drug combination was also highly active against acute myeloid leukemic cells.Our data indicates that the phosphatidyl-ethanolamine biosynthesis is a targetable pathway for cancer; and that meclizine may have clinical efficacy as a repurposed anti-cancer drug when used as part of a new combination therapy.

    View details for DOI 10.1016/j.jhep.2019.11.007

    View details for PubMedID 31760071

  • Human hepatic organoids for the analysis of human genetic diseases. JCI insight Guan, Y., Xu, D., Garfin, P. M., Ehmer, U., Hurwitz, M., Enns, G., Michie, S., Wu, M., Zheng, M., Nishimura, T., Sage, J., Peltz, G. 2017; 2 (17)


    We developed an in vitro model system where induced pluripotent stem cells (iPSCs) differentiate into 3-dimensional human hepatic organoids (HOs) through stages that resemble human liver during its embryonic development. The HOs consist of hepatocytes, and cholangiocytes, which are organized into epithelia that surround the lumina of bile duct-like structures. The organoids provide a potentially new model for liver regenerative processes, and were used to characterize the effect of different JAG1 mutations that cause: (a) Alagille syndrome (ALGS), a genetic disorder where NOTCH signaling pathway mutations impair bile duct formation, which has substantial variability in its associated clinical features; and (b) Tetralogy of Fallot (TOF), which is the most common form of a complex congenital heart disease, and is associated with several different heritable disorders. Our results demonstrate how an iPSC-based organoid system can be used with genome editing technologies to characterize the pathogenetic effect of human genetic disease-causing mutations.

    View details for DOI 10.1172/jci.insight.94954

    View details for PubMedID 28878125

    View details for PubMedCentralID PMC5621886

  • Treating Liver Fibrosis: (Re)Programmed to Succeed. Cell stem cell Guan, Y., Xu, D., Peltz, G. 2016; 18 (6): 683-4


    Two papers (Rezvani et al., 2016; Song et al., 2016) in this issue of Cell Stem Cell use transcription-factor-mediated reprogramming to convert liver myofibroblasts into hepatocyte-like cells in mice. Moreover, murine models of fibrotic and cholestatic liver injury were used to demonstrate that this approach has potential for treatment of liver cirrhosis.

    View details for DOI 10.1016/j.stem.2016.05.007

    View details for PubMedID 27257752

  • Chimeric TK-NOG Mice: A Predictive Model for Cholestatic Human Liver Toxicity. journal of pharmacology and experimental therapeutics Xu, D., Wu, M., Nishimura, S., Nishimura, T., Michie, S. A., Zheng, M., Yang, Z., Yates, A. J., Day, J. S., Hillgren, K. M., Takeda, S. T., Guan, Y., Guo, Y., Peltz, G. 2015; 352 (2): 274-280


    Due to the substantial interspecies differences in drug metabolism and disposition, drug-induced liver injury (DILI) in humans is often not predicted by studies performed in animal species. For example, a drug (bosentan) used to treat pulmonary artery hypertension caused unexpected cholestatic liver toxicity in humans, which was not predicted by preclinical toxicology studies in multiple animal species. In this study, we demonstrate that NOG mice expressing a thymidine kinase transgene (TK-NOG) with humanized livers have a humanized profile of biliary excretion of a test (cefmetazole) drug, which was shown by an in situ perfusion study to result from interspecies differences in the rate of biliary transport and in liver retention of this drug. We also found that readily detectable cholestatic liver injury develops in TK-NOG mice with humanized livers after 1 week of treatment with bosentan (160, 32, or 6 mg/kg per day by mouth), whereas liver toxicity did not develop in control mice after 1 month of treatment. The laboratory and histologic features of bosentan-induced liver toxicity in humanized mice mirrored that of human subjects. Because DILI has become a significant public health problem, drug safety could be improved if preclinical toxicology studies were performed using humanized TK-NOG.

    View details for DOI 10.1124/jpet.114.220798

    View details for PubMedID 25424997

    View details for PubMedCentralID PMC4293443