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Ponomarev Lab

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Molecular mechanisms of cellular plasticity in models of AUD

The Ponomarev Lab in the School of Medicine investigates the molecular mechanisms of cellular plasticity in models of alcohol use disorder (AUD). The lab’s research explores changes in gene expression, epigenetic regulation and brain molecular networks associated with alcohol exposure, dependence and related behaviors, with the goal of advancing understanding of the biological mechanisms underlying AUD.

Research

See list of Publications
See list of Publications
  • Publications
    Presto P, Cardenas J, Ji G, Ponomareva O, Neugebauer V, Ponomarev I. Molecular signatures of maladaptive plasticity in the amygdala in a rat model of chronic neuropathic pain. bioRxiv. 2026 Jan 6;. doi: 10.64898/2026.01.05.697820. PubMed PMID: 41542620; PubMed Central PMCID: PMC12803241.
    Barnes RC, Banjara S, Oliver AG, Coulter M, Alanis A, Castro-Piedras I, Ponomarev I, Javed S, Almodovar S, Guindon J. Breast Cancer Cell Lines AT-3 and E0771 Decrease Mechanical and Cold Sensitivity, Along With Oestrous Cycle and Inflammatory Marker Alterations, in Wild-Type C57BL/6J Female Mice. Eur J Pain. 2025 Jul;29(6):e70066. doi: 10.1002/ejp.70066. PubMed PMID: 40580179; PubMed Central PMCID: PMC12205729.
    Bose C, Hindle A, Smith SC, Strickland J, Zhang C, Guzman I, Baker A, Ponomarev I, Manczak M, Shin AC, Pal R, Singh SP, Lawrence JJ. Low-dose dietary vorinostat increases brain histone acetylation levels and reduces oxidative stress in an Alzheimer's disease mouse model. J Alzheimers Dis. 2025 Aug;106(4):1360-1382. doi: 10.1177/13872877251352107. Epub 2025 Jul 1. PubMed PMID: 40598871; PubMed Central PMCID: PMC12322344.
    Kisby BR, Castro-Piedras I, Shanmugam S, Ponomarev I. Effects of innate immune activation by Toll-like receptor agonists on ethanol consumption and preference in FVB/NJ x C57BL/6J hybrid mice. bioRxiv. 2025 May 10;. doi: 10.1101/2025.05.06.652465. PubMed PMID: 40654825; PubMed Central PMCID: PMC12247976.
    Bailoo JD, Bergeson SE, Ponomarev I, Willms JO, Kisby BR, Cornwall GA, MacDonald CC, Lawrence JJ, Ganapathy V, Sivaprakasam S, Panthagani P, Trasti S, Varholick JA, Findlater M, Deonarine A. A bespoke water T-maze apparatus and protocol: an optimized, reliable, and repeatable method for screening learning, memory, and executive functioning in laboratory mice. Front Behav Neurosci. 2024;18:1492327. doi: 10.3389/fnbeh.2024.1492327. eCollection 2024. PubMed PMID: 39720305; PubMed Central PMCID: PMC11666379.
    Neugebauer V, Ponomarev I. Alcohol withdrawal and pain: Peripheral mechanisms join central circuits. Neuron. 2024 Jan 3;112(1):1-3. doi: 10.1016/j.neuron.2023.12.006. PubMed PMID: 38176389.
    Presto P, Ji G, Ponomareva O, Ponomarev I, Neugebauer V. Hmgb1 Silencing in the Amygdala Inhibits Pain-Related Behaviors in a Rat Model of Neuropathic Pain. Int J Mol Sci. 2023 Jul 26;24(15). doi: 10.3390/ijms241511944. PubMed PMID: 37569320; PubMed Central PMCID: PMC10418916.
    Kisby BR, Farris SP, McManus MM, Varodayan FP, Roberto M, Harris RA, Ponomarev I. Alcohol Dependence in Rats Is Associated with Global Changes in Gene Expression in the Central Amygdala. Brain Sci. 2021 Aug 29;11(9). doi: 10.3390/brainsci11091149. PubMed PMID: 34573170; PubMed Central PMCID: PMC8468792.
    Hitzemann R, Bergeson SE, Berman AE, Bubier JA, Chesler EJ, Finn DA, Hein M, Hoffman P, Holmes A, Kisby BR, Lockwood D, Lodowski KH, McManus M, Owen JA, Ozburn AR, Panthagani P, Ponomarev I, Saba L, Tabakoff B, Walchale A, Williams RW, Phillips TJ. Sex Differences in the Brain Transcriptome Related to Alcohol Effects and Alcohol Use Disorder. Biol Psychiatry. 2022 Jan 1;91(1):43-52. doi: 10.1016/j.biopsych.2021.04.016. Epub 2021 May 1. Review. PubMed PMID: 34274109; PubMed Central PMCID: PMC8558111.
    Ferguson LB, Patil S, Moskowitz BA, Ponomarev I, Harris RA, Mayfield RD, Messing RO. A Pathway-Based Genomic Approach to Identify Medications: Application to Alcohol Use Disorder. Brain Sci. 2019 Dec 16;9(12). doi: 10.3390/brainsci9120381. PubMed PMID: 31888299; PubMed Central PMCID: PMC6956180.
    Ponomarev I. Alcohol use disorder: Role of epigenetics. In: Fitzgerald HE, Puttler LI, editors. Alcohol use disorders: A developmental science approach to etiology New York: Oxford University Press; 2018. p.69-80.
    Ferguson LB, Zhang L, Wang S, Bridges C, Harris RA, Ponomarev I. Peroxisome Proliferator Activated Receptor Agonists Modulate Transposable Element Expression in Brain and Liver. Front Mol Neurosci. 2018;11:331. doi: 10.3389/fnmol.2018.00331. eCollection 2018. PubMed PMID: 30283300; PubMed Central PMCID: PMC6156381.
    Ferguson LB, Zhang L, Kircher D, Wang S, Mayfield RD, Crabbe JC, Morrisett RA, Harris RA, Ponomarev I. Dissecting Brain Networks Underlying Alcohol Binge Drinking Using a Systems Genomics Approach. Mol Neurobiol. 2019 Apr;56(4):2791-2810. doi: 10.1007/s12035-018-1252-0. Epub 2018 Jul 30. PubMed PMID: 30062672; PubMed Central PMCID: PMC6459809.
    Ferguson LB, Ozburn AR, Ponomarev I, Metten P, Reilly M, Crabbe JC, Harris RA, Mayfield RD. Genome-Wide Expression Profiles Drive Discovery of Novel Compounds that Reduce Binge Drinking in Mice. Neuropsychopharmacology. 2018 May;43(6):1257-1266. doi: 10.1038/npp.2017.301. Epub 2017 Dec 18. PubMed PMID: 29251283; PubMed Central PMCID: PMC5916369.
    Ponomarev I, Stelly CE, Morikawa H, Blednov YA, Mayfield RD, Harris RA. Mechanistic insights into epigenetic modulation of ethanol consumption. Alcohol. 2017 May;60:95-101. doi: 10.1016/j.alcohol.2017.01.016. Epub 2017 Mar 12. PubMed PMID: 28433417; PubMed Central PMCID: PMC5550096.
    Kononenko O, Galatenko V, Andersson M, Bazov I, Watanabe H, Zhou XW, Iatsyshyna A, Mityakina I, Yakovleva T, Sarkisyan D, Ponomarev I, Krishtal O, Marklund N, Tonevitsky A, Adkins DL, Bakalkin G. Intra- and interregional coregulation of opioid genes: broken symmetry in spinal circuits. FASEB J. 2017 May;31(5):1953-1963. doi: 10.1096/fj.201601039R. Epub 2017 Jan 25. PubMed PMID: 28122917; PubMed Central PMCID: PMC5388547.
    Tulisiak CT, Harris RA, Ponomarev I. DNA modifications in models of alcohol use disorders. Alcohol. 2017 May;60:19-30. doi: 10.1016/j.alcohol.2016.11.004. Epub 2016 Nov 9. Review. PubMed PMID: 27865607; PubMed Central PMCID: PMC5420490.
    Marballi K, Genabai NK, Blednov YA, Harris RA, Ponomarev I. Alcohol consumption induces global gene expression changes in VTA dopaminergic neurons. Genes Brain Behav. 2016 Mar;15(3):318-26. doi: 10.1111/gbb.12266. Epub 2015 Dec 28. PubMed PMID: 26482798; PubMed Central PMCID: PMC4785873.
    Farris SP, Harris RA, Ponomarev I. Epigenetic modulation of brain gene networks for cocaine and alcohol abuse. Front Neurosci. 2015;9:176. doi: 10.3389/fnins.2015.00176. eCollection 2015. PubMed PMID: 26041984; PubMed Central PMCID: PMC4438259.
    Marballi K, Ponomarev I, Mayfield RD, Harris RA. Alcohol and the brain: An epigenetic viewpoint.. In: Neurobiology of alcohol dependence Oxford, UK: Academic Press, Elsevier; 2014. 349-358p.
    Ponomarev I. Epigenetic control of gene expression in the alcoholic brain. Alcohol Res. 2013;35(1):69-76. doi: 10.35946/arcr.v35.1.08. Review. PubMed PMID: 24313166; PubMed Central PMCID: PMC3860426.
    Reilly MT, Faulkner GJ, Dubnau J, Ponomarev I, Gage FH. The role of transposable elements in health and diseases of the central nervous system. J Neurosci. 2013 Nov 6;33(45):17577-86. doi: 10.1523/JNEUROSCI.3369-13.2013. Review. PubMed PMID: 24198348; PubMed Central PMCID: PMC3818539.
    Osterndorff-Kahanek E, Ponomarev I, Blednov YA, Harris RA. Gene expression in brain and liver produced by three different regimens of alcohol consumption in mice: comparison with immune activation. PLoS One. 2013;8(3):e59870. doi: 10.1371/journal.pone.0059870. Epub 2013 Mar 29. PubMed PMID: 23555817; PubMed Central PMCID: PMC3612084.
    Ozburn AR, Mayfield RD, Ponomarev I, Jones TA, Blednov YA, Harris RA. Chronic self-administration of alcohol results in elevated ΔFosB: comparison of hybrid mice with distinct drinking patterns. BMC Neurosci. 2012 Oct 29;13:130. doi: 10.1186/1471-2202-13-130. PubMed PMID: 23102405; PubMed Central PMCID: PMC3504532.
    Ponomarev I, Wang S, Zhang L, Harris RA, Mayfield RD. Gene coexpression networks in human brain identify epigenetic modifications in alcohol dependence. J Neurosci. 2012 Feb 1;32(5):1884-97. doi: 10.1523/JNEUROSCI.3136-11.2012. PubMed PMID: 22302827; PubMed Central PMCID: PMC3564514.
    Blednov YA, Ponomarev I, Geil C, Bergeson S, Koob GF, Harris RA. Neuroimmune regulation of alcohol consumption: behavioral validation of genes obtained from genomic studies. Addict Biol. 2012 Jan;17(1):108-20. doi: 10.1111/j.1369-1600.2010.00284.x. Epub 2011 Feb 11. PubMed PMID: 21309947; PubMed Central PMCID: PMC3117922.
    Mulligan MK, Rhodes JS, Crabbe JC, Mayfield RD, Harris RA, Ponomarev I. Molecular profiles of drinking alcohol to intoxication in C57BL/6J mice. Alcohol Clin Exp Res. 2011 Apr;35(4):659-70. doi: 10.1111/j.1530-0277.2010.01384.x. Epub 2011 Jan 11. PubMed PMID: 21223303; PubMed Central PMCID: PMC3066294.
    Harris RA, Osterndorff-Kahanek E, Ponomarev I, Homanics GE, Blednov YA. Testing the silence of mutations: Transcriptomic and behavioral studies of GABA(A) receptor α1 and α2 subunit knock-in mice. Neurosci Lett. 2011 Jan 13;488(1):31-5. doi: 10.1016/j.neulet.2010.10.075. Epub 2010 Nov 5. PubMed PMID: 21056629; PubMed Central PMCID: PMC3033563.
    Ponomarev I, Rau V, Eger EI, Harris RA, Fanselow MS. Amygdala transcriptome and cellular mechanisms underlying stress-enhanced fear learning in a rat model of posttraumatic stress disorder. Neuropsychopharmacology. 2010 May;35(6):1402-11. doi: 10.1038/npp.2010.10. Epub 2010 Feb 10. PubMed PMID: 20147889; PubMed Central PMCID: PMC3040562.
    Mulligan MK, Ponomarev I, Boehm SL 2nd, Owen JA, Levin PS, Berman AE, Blednov YA, Crabbe JC, Williams RW, Miles MF, Bergeson SE. Alcohol trait and transcriptional genomic analysis of C57BL/6 substrains. Genes Brain Behav. 2008 Aug;7(6):677-89. doi: 10.1111/j.1601-183X.2008.00405.x. Epub 2008 Apr 7. PubMed PMID: 18397380; NIHMSID:NIHMS537404.
    Okvist A, Johansson S, Kuzmin A, Bazov I, Merino-Martinez R, Ponomarev I, Mayfield RD, Harris RA, Sheedy D, Garrick T, Harper C, Hurd YL, Terenius L, Ekström TJ, Bakalkin G, Yakovleva T. Neuroadaptations in human chronic alcoholics: dysregulation of the NF-kappaB system. PLoS One. 2007 Sep 26;2(9):e930. doi: 10.1371/journal.pone.0000930. PubMed PMID: 17895971; PubMed Central PMCID: PMC1976556.
    Maiya R, Ponomarev I, Linse KD, Harris RA, Mayfield RD. Defining the dopamine transporter proteome by convergent biochemical and in silico analyses. Genes Brain Behav. 2007 Feb;6(1):97-106. doi: 10.1111/j.1601-183X.2006.00236.x. PubMed PMID: 16643512.
    Boehm SL 2nd, Ponomarev I, Blednov YA, Harris RA. From gene to behavior and back again: new perspectives on GABAA receptor subunit selectivity of alcohol actions. Adv Pharmacol. 2006;54:171-203. doi: 10.1016/s1054-3589(06)54008-6. PubMed PMID: 17175815.
    Ponomarev I, Maiya R, Harnett MT, Schafer GL, Ryabinin AE, Blednov YA, Morikawa H, Boehm SL 2nd, Homanics GE, Berman AE, Lodowski KH, Bergeson SE, Harris RA. Transcriptional signatures of cellular plasticity in mice lacking the alpha1 subunit of GABAA receptors. J Neurosci. 2006 May 24;26(21):5673-83. doi: 10.1523/JNEUROSCI.0860-06.2006. PubMed PMID: 16723524; PubMed Central PMCID: PMC1894896.
    Crabbe JC, Metten P, Ponomarev I, Prescott CA, Wahlsten D. Effects of genetic and procedural variation on measurement of alcohol sensitivity in mouse inbred strains. Behav Genet. 2006 Jul;36(4):536-52. doi: 10.1007/s10519-006-9067-6. Epub 2006 Apr 18. PubMed PMID: 16619134.
    Mulligan MK, Ponomarev I, Hitzemann RJ, Belknap JK, Tabakoff B, Harris RA, Crabbe JC, Blednov YA, Grahame NJ, Phillips TJ, Finn DA, Hoffman PL, Iyer VR, Koob GF, Bergeson SE. Toward understanding the genetics of alcohol drinking through transcriptome meta-analysis. Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6368-73. doi: 10.1073/pnas.0510188103. Epub 2006 Apr 17. PubMed PMID: 16618939; PubMed Central PMCID: PMC1458884.
    Ponomarev I, Schafer GL, Blednov YA, Williams RW, Iyer VR, Harris RA. Convergent analysis of cDNA and short oligomer microarrays, mouse null mutants and bioinformatics resources to study complex traits. Genes Brain Behav. 2004 Dec;3(6):360-8. doi: 10.1111/j.1601-183x.2004.00088.x. PubMed PMID: 15544578.
    Boehm SL 2nd, Ponomarev I, Jennings AW, Whiting PJ, Rosahl TW, Garrett EM, Blednov YA, Harris RA. gamma-Aminobutyric acid A receptor subunit mutant mice: new perspectives on alcohol actions. Biochem Pharmacol. 2004 Oct 15;68(8):1581-602. doi: 10.1016/j.bcp.2004.07.023. Review. PubMed PMID: 15451402.
    Ponomarev I, Crabbe JC. Characterization of acute functional tolerance to the hypnotic effects of ethanol in mice. Alcohol Clin Exp Res. 2004 Jul;28(7):991-7. doi: 10.1097/01.alc.0000131978.79857.5e. PubMed PMID: 15252284.
    Ponomarev I, Crabbe JC. A novel method to assess initial sensitivity and acute functional tolerance to hypnotic effects of ethanol. J Pharmacol Exp Ther. 2002 Jul;302(1):257-63. doi: 10.1124/jpet.302.1.257. PubMed PMID: 12065725.
    Ponomarev I, Crabbe JC. Ethanol-induced activation and rapid development of tolerance may have some underlying genes in common. Genes Brain Behav. 2002 May;1(2):82-7. doi: 10.1034/j.1601-183x.2002.10203.x. PubMed PMID: 12884978.
    Lê AD, Kiianmaa K, Cunningham CL, Engel JA, Ericson M, Söderpalm B, Koob GF, Roberts AJ, Weiss F, Hyytiä P, Janhunen S, Mikkola J, Bäckström P, Ponomarev I, Crabbe JC. Neurobiological processes in alcohol addiction. Alcohol Clin Exp Res. 2001 May;25(5 Suppl ISBRA):144S-151S. doi: 10.1111/j.1530-0277.2001.tb02389.x. Review. PubMed PMID: 11391064.
    Ponomarev I, Crabbe JC. Genetic association between chronic ethanol withdrawal severity and acoustic startle parameters WSP and WSR mice. Alcohol Clin Exp Res. 1999 Nov;23(11):1730-5. PubMed PMID: 10591588.
    Cowan N, Nugent LD, Elliott EM, Ponomarev I, Saults JS. The role of attention in the development of short-term memory: age differences in the verbal span of apprehension. Child Dev. 1999 Sep-Oct;70(5):1082-97. doi: 10.1111/1467-8624.00080. PubMed PMID: 10546336.
    Kolpakov VG, Barykina NN, Alekhina TA, Ponomarev IY. Some Genetic Animal Models for Comparative Psychology and Biological Psychiatry Novosibirsk, Siberian Branch of the Russian Academy of Science: Institute of Cytology and Genetics; 1996.
    Kolpakov VG, Barykina NN, Ponomarev IIu, Gevorgian MM. [A comparison of the frequency of the Straub tail elevation reaction as a measure of the activity of the endogenous opiate system in rats of different strains]. Zh Vyssh Nerv Deiat Im I P Pavlova. 1996 Mar-Apr;46(2):342-7. PubMed PMID: 8726568.

  • NIH, R03AA028370 - Effects of chronic alcohol consumption on the synaptic translatome 
    NIH, R01AA027096- The Neuroimmune model of excessive alcohol consumption: Transition to Alcohol Use Disorder

Leadership

Igor Yurievich Ponomarev

Associate Professor

Meet Our Team

    • Isabel Castro-Piedras – Senior Research Associate
    • Brent Kisby – Ph.D. Student
    • Luke Wagner – Medical Research Tech