Superfund Publications

Search publications on site

Pandolfi, E.C., Breuer, J.A., Nguyen Huu, V.A., Talluri, T., Nguyen, D., Lee, J.S., Hu, R., Bharti, K., Skowronska-Krawczyk, D., Gorman, M.R., Mellon, P.L., Hoffmann, H.M. (2019) The Homeodomain Transcription Factors Vax1 and Six6 Are Required for SCN Development and Function. Mol Neurobiol. doi: 10.1007/s12035-019-01781-9. ( [Epub ahead of print]

PubMedID: 31705443
PubMed Central ID: 

Pai, R.K., Kleiner, D.E., Hart, J., Adeyi, O.A., Clouston, A.D., Behling, C.A., Jain, D., Kakar, S., Brahmania, M., Burgart, L., Batts, K.P., Valasek, M.A., Torbenson, M.S., Guindi, M., Wang, H.L., Ajmera, V., Adams, L.A., Parker, C.E., Feagan, B.G., Loomba, R., Jairath, V. (2019) Standardising the interpretation of liver biopsies in non-alcoholic fatty liver disease clinical trials. Aliment Pharmacol Ther. 50(10):1100-1111. doi: 10.1111/apt.15503. ( Epub 2019 Oct 3.

PubMedID: 31583739
PubMed Central ID: 

Wang, L., Mazagova, M., Pan, C., Yang, S., Brandl, K., Liu, J., Reilly, S.M., Wang, Y., Miao, Z., Loomba, R., Lu, N., Guo, Q., Liu, J., Yu, R.T., Downes, M., Evans, R.M., Brenner, D.A., Saltiel, A.R., Beutler, B., Schnabl, B. (2019) YIPF6 controls sorting of FGF21 into COPII vesicles and promotes obesity. Proc Natl Acad Sci U S A. 116(30):15184-15193. doi: 10.1073/pnas.1904360116. ( Epub 2019 Jul 9.

PubMedID: 31289229
PubMed Central ID: 

Mouzaki, M., Loomba, R. (2019) Insights into the evolving role of the gut microbiome in nonalcoholic fatty liver disease: rationale and prospects for therapeutic intervention. Therap Adv Gastroenterol. 12:1756284819858470. doi: 10.1177/1756284819858470. ( eCollection 2019. Review.

PubMedID: 31258623
PubMed Central ID: 

Pandolfi, E.C., Tonsfeldt, K.J., Hoffmann, H.M., Mellon, P.L. (2019) Deletion of the Homeodomain Protein Six6 From GnRH Neurons Decreases GnRH Gene Expression, Resulting in Infertility. Endocrinology. 160(9):2151-2164. doi: 10.1210/en.2019-00113. (

PubMedID: 31211355
PubMed Central ID: 

Sanchez-Lopez, E., Zhong, Z., Stubelius, A., Sweeney, S.R., Booshehri, L.M., Antonucci, L., Liu-Bryan, R., Lodi, A., Terkeltaub, R., Lacal, J.C., Murphy, A.N., Hoffman, H.M., Tiziani, S., Guma, M., Karin, M. (2019) Choline Uptake and Metabolism Modulate Macrophage IL-1β and IL-18 Production. Cell Metab. 29(6):1350-1362.e7. doi: 10.1016/j.cmet.2019.03.011. ( Epub 2019 Apr 11.

PubMedID: 30982734
PubMed Central ID: 

Baglieri J, Brenner DA, Kisseleva T. (2019) The Role of Fibrosis and Liver-Associated Fibroblasts in the Pathogenesis of Hepatocellular Carcinoma. Int J Mol Sci. 20(7). pii: E1723. doi: 10.3390/ijms20071723. Review. (

PubMedID: 30959975
PubMed Central ID: 

Mills, P.J., Caussy, C., Loomba, R. (2019) Glyphosate Excretion is Associated With Steatohepatitis and Advanced Liver Fibrosis in Patients With Fatty Liver Disease. Clin Gastroenterol Hepatol. pii: S1542-3565(19)30361-1. doi: 10.1016/j.cgh.2019.03.045. ( [Epub ahead of print]

PubMedID: 30954713
PubMed Central ID: 

Caussy, C., Tripathi, A., Humphrey, G., Bassirian, S., Singh, S., Faulkner, C., Bettencourt, R., Rizo, E., Richards, L., Xu, Z.Z., Downes, M.R., Evans, R.M., Brenner, D.A., Sirlin, C.B., Knight, R., Loomba, R. (2019) A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease. Nat Commun. 10(1):1406. doi: 10.1038/s41467-019-09455-9. (

PubMedID: 30926798
PubMed Central ID: 

Tonsfeldt, K.J., Schoeller, E.L., Brusman, L.E., Cui, L.J., Lee, J., Mellon, P.L. (2019) The Contribution of the Circadian Gene Bmal1 to Female Fertility and the Generation of the Preovulatory Luteinizing Hormone Surge. J Endocr Soc. 3(4):716-733. doi: 10.1210/js.2018-00228. ( eCollection 2019 Apr 1.

PubMedID: 30906911

Caussy, C., Bhargava, M., Villesen, I.F., Gudmann, N.S., Leeming, D.J., Karsdal, M.A., Faulkner, C., Bao, D., Liu ,A., Lo, M.T., Bettencourt, R., Bassirian, S., Richards, L., Brenner, D.A., Chen, C.H., Sirlin, C.B., Loomba, R. (2019) Collagen Formation Assessed by N-Terminal Propeptide of Type 3 Procollagen Is a Heritable Trait and Is Associated With Liver Fibrosis Assessed by Magnetic Resonance Elastography. Hepatology. 70(1):127-141. doi: 10.1002/hep.30610. ( Epub 2019 Apr 29.

PubMedID: 30859582
PubMed Central ID: 

Fu, T., Coulter, S., Yoshihara, E., Oh, T.G., Fang, S., Cayabyab, F., Zhu, Q., Zhang, T., Leblanc, M., Liu, S., He, M., Waizenegger, W., Gasser, E., Schnabl, B., Atkins, A.R., Yu, R.T., Knight, R., Liddle, C., Downes, M., Evans, R.M. (2019) FXR Regulates Intestinal Cancer Stem Cell Proliferation. Cell. 176(5):1098-1112.e18. doi: 10.1016/j.cell.2019.01.036. (

PubMedID: 30794774
PubMed Central ID: 

Hoffmann, H.M., Larder, R., Lee, J.S., Hu, R.J., Trang, C., Devries, B.M., Clark, D.D., Mellon, P.L. (2019) Differential CRE Expression in Lhrh-cre and GnRH-cre Alleles and the Impact on Fertility in Otx2-Flox Mice. Neuroendocrinology. 108(4):328-342. doi: 10.1159/000497791. Epub 2019 Feb 10.

PubMedID: 30739114
PubMed Central ID: 

Karin M. New insights into the pathogenesis and treatment of non-viral hepatocellular carcinoma: a balancing act between immunosuppression and immunosurveillance. (2018) Precis Clin Med. 1(1):21-28. doi: 10.1093/pcmedi/pby005. Epub 2018 Jun 4. Review.

PubMedID: 30687560

Castera, L., Friedrich-Rust, M., Loomba, R. (2019) Noninvasive Assessment of Liver Disease in Patients With Nonalcoholic Fatty Liver Disease. Gastroenterology. 156(5):1264-1281.e4. doi: 10.1053/j.gastro.2018.12.036. Epub 2019 Jan 18. Review.

PubMedID: 30660725
PubMed Central ID: 

Park, J., Kim, T.H., Takahashi, Y., Schwab, R., Dressano, K., Stephan, A.B., Ceciliato, P.H.O., Ramirez, E., Garin, V., Huffaker, A., Schroeder, J.I. (2019) Chemical genetic identification of a lectin receptor kinase that transduces immune responses and interferes with abscisic acid signaling. Plant J. 98(3):492-510. doi: 10.1111/tpj.14232. Epub 2019 Mar 7.

PubMedID: 30659683
PubMed Central ID: 

Febbraio, M.A., Reibe, S., Shalapour, S., Ooi, G.J., Watt, M.J., Karin, M.. (2019) Preclinical Models for Studying NASH-Driven HCC: How Useful Are They? Cell Metab. 29(1):18-26. doi: 10.1016/j.cmet.2018.10.012. Epub 2018 Nov 15. Review.

PubMedID: 30449681
PubMed Central ID: 

Liang, S., Ma, H.Y., Zhong, Z., Dhar, D., Liu, X., Xu, J., Koyama, Y., Nishio, T., Karin, D., Karin, G., Mccubbin, R., Zhang, C., Hu, R., Yang, G., Chen, L., Ganguly, S., Lan, T., Karin, M., Kisseleva, T., Brenner, D.A. (2018) NADPH Oxidase 1 in Liver Macrophages Promotes Inflammation and Tumor Development in Mice. Gastroenterology. 156(4):1156-1172.e6. doi: 10.1053/j.gastro.2018.11.019. Epub 2018 Nov 13.

PubMedID: 30445007
PubMed Central ID: 

Hauser, F., Ceciliato, P.H.O., Lin, Y.C., Guo, D., Gregerson, J.D., Abbasi, N., Youhanna, D., Park, J., Dubeaux, G., Shani, E., Poomchongkho, N., Schroeder, J.I. (2019) A seed resource for screening functionally redundant genes and isolation of new mutants impaired in CO2 and ABA responses. J Exp Bot. 70(2):641-651. doi: 10.1093/jxb/ery363.

PubMedID: 30346611
PubMed Central ID: 

Zhang, Y., Nasser, V., Pisanty, O., Omary, M., Wulff, N., Di, Donato, M., Tal, I., Hauser, F., Hao, P., Roth, O., Fromm, H., Schroeder, J.I., Geisler, M., Nour-Eldin, H.H., Shani, E. (2018) A transportome-scale amiRNA-based screen identifies redundant roles of Arabidopsis ABCB6 and ABCB20 in auxin transport. Nat Commun. 9(1):4204. doi: 10.1038/s41467-018-06410-y.

PubMedID: 30310073
PubMed Central ID: 

Dow, M., Pyke, R.M., Tsui, B.Y., Alexandrov, L.B., Nakagawa, H., Taniguchi, K., Seki, E., Harismendy, O., Shalapour, S., Karin, M., Carter, H., Font-Burgada, J. (2018) Integrative genomic analysis of mouse and human hepatocellular carcinoma. Proc Natl Acad Sci U S A. 115(42):E9879-E9888. doi: 10.1073/pnas.1811029115. Epub 2018 Oct 4.

PubMedID: 30287485
PubMed Central ID: 

Hsu, P.K., Takahashi, Y., Munemasa, S., Merilo, E., Laanemets, K., Waadt, R., Pater, D., Kollist, H., Schroeder, J.I. (2018) Abscisic acid-independent stomatal CO2 signal transduction pathway and convergence of CO2 and ABA signaling downstream of OST1 kinase. Proc Natl Acad Sci U S A. 115(42):E9971-E9980. doi: 10.1073/pnas.1809204115. Epub 2018 Oct 3.

PubMedID: 30282744
PubMed Central ID: 

Hoffmann, H.M., Pandolfi, E.C., Larder, R., Mellon, P.L.. (2019) Haploinsufficiency of Homeodomain Proteins Six3, Vax1, and Otx2 Causes Subfertility in Mice via Distinct Mechanisms. Neuroendocrinology. 109(3):200-207. doi: 10.1159/000494086. Epub 2018 Sep 27. Review.

PubMedID: 30261489

Kim, J.Y., Garcia-Carbonell, R., Yamachika, S., Zhao, P., Dhar, D., Loomba, R., Kaufman, R.J., Saltiel, A.R., Karin, M. (2018) ER Stress Drives Lipogenesis and Steatohepatitis via Caspase-2 Activation of S1P. Cell. 175(1):133-145.e15. doi: 10.1016/j.cell.2018.08.020. Epub 2018 Sep 13.

PubMedID: 30220454
PubMed Central ID: 

Tõldsepp, K., Zhang, J., Takahashi, Y., Sindarovska, Y., Hõrak, H., Ceciliato, P.H.O., Koolmeister, K., Wang, Y.S., Vaahtera, L., Jakobson, L., Yeh, C.Y., Park, J., Brosche, M., Kollist, H., Schroeder, J.I. (2018) Mitogen-activated protein kinases MPK4 and MPK12 are key components mediating CO2 -induced stomatal movements. Plant J. 96(5):1018-1035. doi: 10.1111/tpj.14087. Epub 2018 Oct 23.

PubMedID: 30203878
PubMed Central ID: 

Chen, S., Tukey, R.H. (2018) Humanized UGT1 Mice, Regulation of UGT1A1, and the Role of the Intestinal Tract in Neonatal Hyperbilirubinemia and Breast Milk-Induced Jaundice. Drug Metab Dispos. 46(11):1745-1755. doi: 10.1124/dmd.118.083212. Epub 2018 Aug 9.

PubMedID: 30093417
PubMed Central ID: 

Zhong, Z., Liang, S., Sanchez-Lopez, E., He, F., Shalapour, S., Lin, X.J., Wong, J., Ding, S., Seki, E., Schnabl, B., Hevener, A.L., Greenberg, H.B., Kisseleva, T., Karin, M. (2018) New mitochondrial DNA synthesis enables NLRP3 inflammasome activation. Nature. 560(7717):198-203. doi: 10.1038/s41586-018-0372-z. Epub 2018 Jul 25.

PubMedID: 30046112
PubMed Central ID: 

Brenner, D.A. (2018) Of Mice and Men and Nonalcoholic Steatohepatits. Hepatology. 68(6):2059-2061. doi: 10.1002/hep.30186. Epub 2018 Nov 13. No abstract available.

PubMedID: 30033687

Roh, Y.S., Seki, E. (2018) Chemokines and Chemokine Receptors in the Development of NAFLD. Adv Exp Med Biol.1061:45-53. doi: 10.1007/978-987-10-8684-7_4. Review

PubMedID: 29956205
PubMed Central ID: 

Dhar, D., Antonucci, L., Nakagawa, H., Kim, J.Y., Glitzner, E., Caruso, S., Shalapour, S., Yang, L., Valasek, M.A., Lee, S., Minnich, K., Seki, E., Tuckermann, J., Sibilia, M., Zucman-Rossi, J., Karin, M. (2018) Liver Cancer Initiation Requires p53 Inhibition by CD44-Enhanced Growth Factor Signaling. Cancer Cell. 33(6):1061-1077.e6. doi: 10.1016/j.ccell.2018.05.003.

PubMedID: 29894692
PubMed Central ID: 

Que, X., Hung, M.Y., Yeang, C., Gonen, A., Prohaska, T.A., Sun, X., Diehl, C., Määttä, A., Gaddis, D.E., Bowden, K., Pattison, J., MacDonald, J.G., Ylä-Herttuala, S., Mellon, P.L., Hedrick, C.C., Ley, K., Miller, Y.I., Glass, C.K., Peterson, K.L., Binder, C.J., Tsimikas, S., Witztum, J.L. (2018) Oxidized phospholipids are proinflammatory and proatherogenic in hypercholesterolaemic mice. Nature. 558(7709):301-306. doi: 10.1038/s41586-018-0198-8. Epub 2018 Jun 6.

PubMedID: 29875409

Tripathi, A., Debelius, J., Brenner, D.A., Karin, M., Loomba, R., Schnabl, B., Knight, R. (2018) The gut-liver axis and the intersection with the microbiome. Nat Rev Gastroenterol Hepatol. 15(12):785. doi: 10.1038/s41575-018-0031-8.

PubMedID: 29785003
PubMed Central ID: 

Wei, Z., Yoshihara, E., He, N., Hah, N., Fan, W., Pinto, A.F.M., Huddy, T., Wang, Y., Ross, B., Estepa, G., Dai, Y., Ding, N., Sherman, M.H., Fang, S., Zhao, X., Liddle, C., Atkins, A.R., Yu, R.T., Downes, M., Evans, R.M. (2018) Vitamin D Switches BAF Complexes to Protect β Cells. Cell. 173(5):1135-1149.e15. doi: 10.1016/j.cell.2018.04.013. Epub 2018 May 10.

PubMedID: 29754817
PubMed Central ID: 

Li, Z., Takahashi, Y., Scavo, A., Brandt, B., Nguyen, D., Rieu, P., Schroeder, J.I. (2018) Abscisic acid-induced degradation of Arabidopsis guanine nucleotide exchange factor requires calcium-dependent protein kinases. Proc Natl Acad Sci U S A. 115(19):E4522-E4531. doi: 10.1073/pnas.1719659115. Epub 2018 Apr 23.

PubMedID: 29686103
PubMed Central ID: 

Ajmera, V., Park, C.C., Caussy, C., Singh, S., Hernandez, C., Bettencourt, R., Hooker, J., Sy, E., Behling, C., Xu, R., Middleton, M.S., Valasek, M.A., Faulkner, C., Rizo, E., Richards, L., Sirlin, C.B., Loomba, R. (2018) Magnetic Resonance Imaging Proton Density Fat Fraction Associates With Progression of Fibrosis in Patients With Nonalcoholic Fatty Liver Disease. Gastroenterology. 155(2):307-310.e2. doi: 10.1053/j.gastro.2018.04.014. Epub 2018 Apr 13.

PubMedID: 29660324
PubMed Central ID: 

McNulty, R., Cardone, G., Gilcrease, E.B., Baker, T.S., Casjens, S.R., Johnson, J.E. (2018) Cryo-EM Elucidation of the Structure of Bacteriophage P22 Virions after Genome Release. Biophys J. 114(6):1295-1301. doi: 10.1016/j.bpj.2018.01.026.

PubMedID: 29590587
PubMed Central ID: 

Pandolfi, E.C., Hoffmann, H.M., Schoeller, E.L., Gorman, M.R., Mellon, P.L. (2018) Haploinsufficiency of SIX3 Abolishes Male Reproductive Behavior Through Disrupted Olfactory Development, and Impairs Female Fertility Through Disrupted GnRH Neuron Migration. Mol Neurobiol. 55(11):8709-8727. doi: 10.1007/s12035-018-1013-0. Epub 2018 Mar 27.

PubMedID: 29589282

Caussy, C., Hsu, C., Lo, M.T., Liu, A., Bettencourt, R., Ajmera, V.H., Bassirian, S., Hooker, J., Sy, E., Richards, L., Schork, N., Schnabl, B., Brenner, D.A., Sirlin, C.B., Chen, C.H., Loomba, R.; Genetics of NAFLD in Twins Consortium. (2018) Link between gut-microbiome derived metabolite and shared gene-effects with hepatic steatosis and fibrosis in NAFLD. Hepatology. doi: 10.1002/hep.29892.

PubMedID: 29572891
PubMed Central ID: 

Ahmadian, M., Liu, S., Reilly, S.M., Hah, N., Fan, W., Yoshihara, E., Jha, P., De Magalhaes Filho, C.D., Jacinto, S., Gomez, A.V., Dai, Y., Yu, R.T., Liddle, C., Atkins, A.R., Auwerx, J., Saltiel, A.R., Downes, M., Evans, R.M. (2018) ERRγ Preserves Brown Fat Innate Thermogenic Activity. Cell Rep. 22(11):2849-2859. doi: 10.1016/j.celrep.2018.02.061.

PubMedID: 29539415
PubMed Central ID: 

Fan, W., He, N., Lin, C.S., Wei Z., Hah, N., Waizenegger, W., He, M.X., Liddle, C., Yu, R.T., Atkins, A.R., Downes, M., Evans, R.M. (2018) ERRγ Promotes Angiogenesis, Mitochondrial Biogenesis, and Oxidative Remodeling in PGC1α/β-Deficient Muscle. Cell Rep. 22(10):2521-2529. doi: 10.1016/j.celrep.2018.02.047.

PubMedID: 29514081
PubMed Central ID: 

Desai, A.P., Mohan, P., Roubal, A.M., Bettencourt, R., Loomba, R. (2018) Geographic Variability in Liver Disease-Related Mortality Rates in the United States. Am J Med. 131(7):728-734. doi: 10.1016/j.amjmed.2018.01.047. Epub 2018 Feb 26.

PubMedID: 29496501
PubMed Central ID: 

Xu J., Ma H.Y., Liang S., Sun M., Karin G., Koyama Y., Hu R., Quehenberger O., Davidson N.O., Dennis E.A., Kisseleva T., Brenner D.A. (2017) The role of human cytochrome P450 2E1 in liver inflammation and fibrosis. Hepatol Commun. 1(10):1043-1057. doi: 10.1002/hep4.1115. eCollection 2017 Dec.

PubMedID: 29404441
PubMed Central ID: 

Fujiwara R., Mitsugi R., Uemura A., Itoh T., Tukey R.H. (2017) Severe Neonatal Hyperbilirubinemia in Crigler-Najjar Syndrome Model Mice Can Be Reversed With Zinc Protoporphyrin. Hepatol Commun. 1(8):792-802. doi: 10.1002/hep4.1082. Epub 2017 Aug 10.

PubMedID: 29399656
PubMed Central ID: 

Song, N.Y., Zhu, F., Wang, Z., Willette-Brown, J., Xi, S., Sun, Z., Su, L., Wu, X., Ma, B., Nussinov, R., Xia, X., Schrump, D.S., Johnson, P.F., Karin, M., Hu, Y. (2018) IKKα inactivation promotes Kras-initiated lung adenocarcinoma development through disrupting major redox regulatory pathways. Proc Natl Acad Sci U S A. 115(4):E812-E821. doi: 10.1073/pnas.1717520115. Epub 2018 Jan 8.

PubMedID: 29311298
PubMed Central ID: 

Tapper, E.B., Loomba, R. (2018) Nonalcoholic fatty liver disease, metabolic syndrome, and the fight that will define clinical practice for a generation of hepatologists. Hepatology. 67(5):1657-1659. doi: 10.1002/hep.29722. Epub 2018 Apr 1.

PubMedID: 29222913
PubMed Central ID: 

Dickey A.S., Sanchez D.N., Arreola M., Sampat K.R., Fan W., Arbez N., Akimov S., Van Kanegan M.J., Ohnishi K., Gilmore-Hall S.K., Flores A.L., Nguyen J.M., Lomas N., Hsu C.L., Lo D.C., Ross C.A., Masliah E., Evans R.M., La Spada A.R. PPARδ activation by bexarotene promotes neuroprotection by restoring bioenergetic and quality control homeostasis. (2017) Sci Transl Med. 9(419). pii: eaal2332. doi: 10.1126/scitranslmed.aal2332.

PubMedID: 29212711

Hartmann P., Hochrath K., Horvath A., Chen P., Seebauer C.T., Llorente C., Wang L., Alnouti Y., Fouts D.E., Stärkel P., Loomba R., Coulter S., Liddle C., Yu R.T., Ling L., Rossi S.J., DePaoli A.M., Downes M., Evans R.M., Brenner D.A., Schnabl B. (2017) Modulation of the intestinal bile acid-FXR-FGF15 axis improves alcoholic liver disease in mice. Hepatology. doi: 10.1002/hep.29676.

PubMedID: 29159825
PubMed Central ID: 

Shalapour, S., Lin, X.J., Bastian, I.N., Brain, J., Burt, A.D., Aksenov, A.A., Vrbanac, A.F., Li, W., Perkins, A., Matsutani, T., Zhong, Z., Dhar, D., Navas-Molina, J.A., Xu, J., Loomba, R., Downes, M., Yu, R.T., Evans, R.M., Dorrestein, P.C., Knight, R., Benner, C., Anstee, Q.M., Karin, M. (2017). Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. Nature. 551, 340-345. doi: 10.1038/nature24302.

PubMedID: 29144460
PubMed Central ID: 

Cao Q., Zhao X., Bai J., Gery S., Sun H., Lin D.C., Chen Q., Chen Z., Mack L., Yang H., Deng R., Shi X., Chong L.W., Cho H., Xie J., Li Q.Z., Müschen M., Atkins A.R., Liddle C., Yu R.T., Alkan S., Said J.W., Zheng Y., Downes M., Evans R.M., Koeffler H.P. (2017) Circadian clock cryptochrome proteins regulate autoimmunity. Proc Natl Acad Sci U S A. 114(47):12548-12553. doi: 10.1073/pnas.1619119114.

PubMedID: 29109286
PubMed Central ID: 

He N., Fan W., Henriquez B., Yu R.T., Atkins A.R., Liddle C., Zheng Y., Downes M., Evans R.M. (2017) Metabolic control of regulatory T cell (Treg) survival and function by Lkb1. Proc Natl Acad Sci U S A. 114(47):12542-12547. doi: 10.1073/pnas.1715363114.

PubMedID: 29109251