Transcriptomic and epigenomic biomarkers of antidepressant response

Abe, 2011, Altered sirtuin deacetylase gene expression in patients with a mood disorder, J. Psychiatr. Res., 45, 1106, 10.1016/j.jpsychires.2011.01.016 Allfrey, 1964, Acetylation and methylation of histones and their possible role in the regulation of rna synthesis, Proc. Natl. Acad. Sci. USA, 51, 786, 10.1073/pnas.51.5.786 Anacker, 2011, The glucocorticoid receptor: pivot of depression and of antidepressant treatment?, Psychoneuroendocrinology, 36, 415, 10.1016/j.psyneuen.2010.03.007 Bannister, 2011, Regulation of chromatin by histone modifications, Cell Res., 21, 381, 10.1038/cr.2011.22 Baylin, 2011, A decade of exploring the cancer epigenome — biological and translational implications, Nat. Rev. Cancer, 11, 726, 10.1038/nrc3130 Belzeaux, 2014, Monitoring candidate gene expression variations before, during and after a first major depressive episode in a 51-year-old man, BMC Psychiatry, 14, 73, 10.1186/1471-244X-14-73 Belzeaux, 2012, Responder and nonresponder patients exhibit different peripheral transcriptional signatures during major depressive episode, Transl. Psychiatry, 2, e185, 10.1038/tp.2012.112 Belzeaux, 2010, Clinical variations modulate patterns of gene expression and define blood biomarkers in major depression, J. Psychiatr. Res., 44, 1205, 10.1016/j.jpsychires.2010.04.011 Belzeaux, 2017, How to: measuring blood cytokines in biological psychiatry using commercially available multiplex immunoassays, Psychoneuroendocrinology, 75, 72, 10.1016/j.psyneuen.2016.10.010 Belzeaux, 2016, Predisposition to treatment response in major depressive episode: a peripheral blood gene coexpression network analysis, J. Psychiatr. Res., 81, 119, 10.1016/j.jpsychires.2016.07.009 Belzeaux, 2017, Potential use of MicroRNA for monitoring therapeutic response to antidepressants, CNS Drugs, 31, 253, 10.1007/s40263-017-0418-z Belzeaux, 2014, Longitudinal monitoring of the serotonin transporter gene expression to assess major depressive episode evolution, Neuropsychobiology, 70, 220, 10.1159/000368120 Brinkman, 2010, Whole-genome DNA methylation profiling using MethylCap-seq, Methods, 52 Brownell, 1996, Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation, Cell, 84, 843, 10.1016/S0092-8674(00)81063-6 Cattaneo, 2016, Absolute measurements of macrophage migration inhibitory factor and interleukin-1-beta mRNA levels accurately predict treatment response in depressed patients, Int. J. Neuropsychopharmacol., 19 Cattaneo, 2013, Candidate genes expression profile associated with antidepressants response in the GENDEP study: differentiating between baseline 'predictors' and longitudinal 'targets', Neuropsychopharmacology, 38, 377, 10.1038/npp.2012.191 Chen, 2011, The epigenetic effects of antidepressant treatment on human prefrontal cortex BDNF expression, Int. J. Neuropsychopharmacol., 14, 427, 10.1017/S1461145710001422 Curradi, 2002, Molecular mechanisms of gene silencing mediated by DNA methylation, Mol. Cell. Biol., 22, 3157, 10.1128/MCB.22.9.3157-3173.2002 deVos, 2009, Circulating methylated <em>SEPT9</em> DNA in plasma is a biomarker for colorectal cancer, Clin. Chem., 55, 1337, 10.1373/clinchem.2008.115808 Domschke, 2014, Serotonin transporter gene hypomethylation predicts impaired antidepressant treatment response, Int. J. Neuropsychopharmacol., 17, 1167, 10.1017/S146114571400039X Eckhardt, 2006, DNA methylation profiling of human chromosomes 6, 20 and 22, Nat. Genet., 38, 1378, 10.1038/ng1909 El-Hage, 2013, Mechanisms of antidepressant resistance, Front. Pharmacol., 4, 146, 10.3389/fphar.2013.00146 Elliott, 2010, Resilience to social stress coincides with functional DNA methylation of the Crf gene in adult mice, Nat. Neurosci., 13, 1351, 10.1038/nn.2642 Eyre, 2016, Modulatory effects of antidepressant classes on the innate and adaptive immune system in depression, Pharmacopsychiatry, 49, 85, 10.1055/s-0042-103159 Fabbri, 2013, Pharmacogenetics of antidepressant drugs: an update after almost 20 years of research, Am. J. Med. Genet. B Neuropsychiatr. Genet., 162B, 487, 10.1002/ajmg.b.32184 Falaleeva, 2015, SNORD116 and SNORD115 change expression of multiple genes and modify each other's activity, Gene, 572, 266, 10.1016/j.gene.2015.07.023 Fiori, 2016, Investigating epigenetic consequences of early-life adversity: some methodological considerations, Eur. J. Psychotraumatol., 7, 31593, 10.3402/ejpt.v7.31593 Foster, 2013, Gut-brain axis: how the microbiome influences anxiety and depression, Trends Neurosci., 36, 305, 10.1016/j.tins.2013.01.005 Freedman, 2016, Diverse human extracellular RNAs are widely detected in human plasma, Nat. Commun., 7, 11106, 10.1038/ncomms11106 Gadad, 2017, Peripheral biomarkers of major depression and antidepressant treatment response: current knowledge and future outlooks, J. Affect Disord. Gaiteri, 2014, Beyond modules and hubs: the potential of gene coexpression networks for investigating molecular mechanisms of complex brain disorders, Genes Brain Behav., 13, 13, 10.1111/gbb.12106 Gassen, 2015, Chaperoning epigenetics: FKBP51 decreases the activity of DNMT1 and mediates epigenetic effects of the antidepressant paroxetine, Sci. Signal, 8, ra119, 10.1126/scisignal.aac7695 Gladkevich, 2004, Lymphocytes as a neural probe: potential for studying psychiatric disorders, Prog. Neuropsychopharmacol. Biol. Psychiatry, 28, 559, 10.1016/j.pnpbp.2004.01.009 Gross, 2015, Characterizing 5-hydroxymethylcytosine in human prefrontal cortex at single base resolution, BMC Genom., 16, 672, 10.1186/s12864-015-1875-8 Group, F.-.N.B.W., 2016. BEST (Biomarkers, EndpointS, and other Tools) Resource, In: (US), S.S.M.F.a.D.A. (Ed.). Guilloux, 2015, Testing the predictive value of peripheral gene expression for nonremission following citalopram treatment for major depression, Neuropsychopharmacology, 40, 701, 10.1038/npp.2014.226 Ha, 2014, Regulation of microRNA biogenesis, Nat. Rev. Mol. Cell Biol., 15, 509, 10.1038/nrm3838 Hennings, 2015, RNA expression profiling in depressed patients suggests retinoid-related orphan receptor alpha as a biomarker for antidepressant response, Transl. Psychiatry, 5, e538, 10.1038/tp.2015.9 Himmerich, 2010, Regulatory T cells increased while IL-1beta decreased during antidepressant therapy, J. Psychiatr. Res., 44, 1052, 10.1016/j.jpsychires.2010.03.005 Hobara, 2010, Altered gene expression of histone deacetylases in mood disorder patients, J. Psychiatr. Res., 44, 263, 10.1016/j.jpsychires.2009.08.015 Hodgson, 2016, Transcriptomics and the mechanisms of antidepressant efficacy, Eur. Neuropsychopharmacol., 26, 105, 10.1016/j.euroneuro.2015.10.009 Iga, 2005, Serotonin transporter mRNA expression in peripheral leukocytes of patients with major depression before and after treatment with paroxetine, Neurosci. Lett., 389, 12, 10.1016/j.neulet.2005.06.048 Iga, 2007, Altered HDAC5 and CREB mRNA expressions in the peripheral leukocytes of major depression, Prog. Neuro-Psychopharmacol. Biol. Psychiatry, 31, 628, 10.1016/j.pnpbp.2006.12.014 Issler, 2015, Determining the role of microRNAs in psychiatric disorders, Nat. Rev. Neurosci., 16, 201, 10.1038/nrn3879 Iwasaki, 2015, PIWI-interacting RNA: its biogenesis and functions, Annu Rev. Biochem, 84, 405, 10.1146/annurev-biochem-060614-034258 Jenuwein, 2001, Translating the histone code, Science, 293, 1074, 10.1126/science.1063127 Kang, 2013, Association of SLC6A4 methylation with early adversity, characteristics and outcomes in depression, Prog. Neuro-Psychopharmacol. Biol. Psychiatry, 44, 23, 10.1016/j.pnpbp.2013.01.006 Kennedy, 2016, Canadian Network for Mood and Anxiety Treatments (CANMAT) 2016 clinical guidelines for the management of adults with major depressive disorder: section 3. Pharmacological treatments, Can. J. Psychiatry, 10.1177/0706743716659417 Kishore, 2006, The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C, Science, 311, 230, 10.1126/science.1118265 Kohli, 2013, TET enzymes, TDG and the dynamics of DNA demethylation, Nature, 502, 472, 10.1038/nature12750 Kornberg, 1999, Twenty-FIVE YEARS OF THE NUCLEOSOME, FUNDAMENTAL PARTICLE OF THE EUKARYOTE CHROmosome, Cell, 98, 285, 10.1016/S0092-8674(00)81958-3 Laird, 2003, The power and the promise of DNA methylation markers, Nat. Rev. Cancer, 3, 253, 10.1038/nrc1045 Lam, 2016, Discovering biomarkers for antidepressant response: protocol from the Canadian biomarker integration network in depression (CAN-BIND) and clinical characteristics of the first patient cohort, BMC Psychiatry, 16, 105, 10.1186/s12888-016-0785-x Langfelder, 2008, WGCNA: an R package for weighted correlation network analysis, BMC Bioinform., 9, 559, 10.1186/1471-2105-9-559 Langie, 2016, Salivary DNA methylation profiling: aspects to consider for biomarker identification, Basic Clin. Pharmacol. Toxicol. Lee, 2011, Identification of piRNAs in the central nervous system, RNA, 17, 1090, 10.1261/rna.2565011 Leuchter, 2010, Biomarkers to predict antidepressant response, Curr. Psychiatry Rep., 12, 553, 10.1007/s11920-010-0160-4 Levenson, 2010, DNA methylation as a universal biomarker, Expert Rev. Mol. Diagn., 10, 481, 10.1586/erm.10.17 Li, 2002, Chromatin modification and epigenetic reprogramming in mammalian development, Nat. Rev. Genet., 3, 662, 10.1038/nrg887 Li, 2013, Circadian patterns of gene expression in the human brain and disruption in major depressive disorder, Proc. Natl. Acad. Sci. USA, 110, 9950, 10.1073/pnas.1305814110 Li, 2012, DNA Methylation in Peripheral Blood: a Potential Biomarker for Cancer Molecular Epidemiology, J. Epidemiol., 22, 384, 10.2188/jea.JE20120003 Lima, 2005, Allelic isoforms and decrease in serotonin transporter mRNA in lymphocytes of patients with major depression, Neuroimmunomodulation, 12, 299, 10.1159/000087108 Lopez, 2017, MicroRNAs 146a/b-5 and 425-3p and 24-3p are markers of antidepressant response and regulate MAPK/Wnt-system genes, Nat. Commun., 8, 15497, 10.1038/ncomms15497 Lopez, 2013, Epigenetic regulation of BDNF expression according to antidepressant response, Mol. Psychiatry, 18, 398, 10.1038/mp.2012.38 Lui, 2013, Small nucleolar RNAs and RNA-guided post-transcriptional modification, Essays Biochem, 54, 53, 10.1042/bse0540053 Lutz, 2014, DNA methylation and childhood maltreatment: from animal models to human studies, Neuroscience, 264, 142, 10.1016/j.neuroscience.2013.07.069 Mamdani, 2011, Gene expression biomarkers of response to citalopram treatment in major depressive disorder, Transl. Psychiatry, 1, e13, 10.1038/tp.2011.12 Mamdani, 2014, Pharmacogenomic predictors of citalopram treatment outcome in major depressive disorder, World J. Biol. Psychiatry, 15, 135, 10.3109/15622975.2013.766762 Mamrut, 2013, DNA Methylation of Specific CpG Sites in the Promoter Region Regulates the Transcription of the Mouse Oxytocin Receptor, PLOS ONE, 8, e56869, 10.1371/journal.pone.0056869 Maunakea, 2010, Epigenome mapping in normal and disease States, Circ. Res., 107, 327, 10.1161/CIRCRESAHA.110.222463 Maunakea, 2010, Conserved role of intragenic DNA methylation in regulating alternative promoters, Nature, 466, 253, 10.1038/nature09165 Nanni, 2012, Childhood maltreatment predicts unfavorable course of illness and treatment outcome in depression: a meta-analysis, Am. J. Psychiatry, 169, 141, 10.1176/appi.ajp.2011.11020335 Nemeroff, 2016, Paradise lost: the neurobiological and clinical consequences of child abuse and neglect, Neuron, 89, 892, 10.1016/j.neuron.2016.01.019 Pérez, 2012, Impact of methylation on the physical properties of DNA, Biophys. J., 102, 2140, 10.1016/j.bpj.2012.03.056 Pettai, 2016, Whole-genome expression analysis reveals genes associated with treatment response to escitalopram in major depression, Eur. Neuropsychopharmacol., 26, 1475, 10.1016/j.euroneuro.2016.06.007 Powell, 2013, Tumor necrosis factor and its targets in the inflammatory cytokine pathway are identified as putative transcriptomic biomarkers for escitalopram response, Eur. Neuropsychopharmacol., 23, 1105, 10.1016/j.euroneuro.2012.09.009 Powell, 2013, DNA methylation in interleukin-11 predicts clinical response to antidepressants in GENDEP, Transl. Psychiatry, 3, e300, 10.1038/tp.2013.73 Quek, 2017, Defining the purity of exosomes required for diagnostic profiling of small RNA suitable for biomarker discovery, RNA Biol., 14, 245, 10.1080/15476286.2016.1270005 Raison, 2006, Cytokines sing the blues: inflammation and the pathogenesis of depression, Trends Immunol., 27, 24, 10.1016/j.it.2005.11.006 Rajasethupathy, 2012, A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity, Cell, 149, 693, 10.1016/j.cell.2012.02.057 Robertson, 2000, DNA methylation in health and disease, Nat. Rev. Genet, 1, 11, 10.1038/35049533 Rothbart, 2014, Interpreting thelanguage of histone and DNA modifications, Biochim. Et. Biophys. Acta, 1839, 627, 10.1016/j.bbagrm.2014.03.001 Rush, 2006, Acute and longer-term outcomes in depressed outpatients requiring one or several treatment steps: a STAR*D report, Am. J. Psychiatry, 163, 1905, 10.1176/ajp.2006.163.11.1905 Sullivan, 2006, Evaluating the comparability of gene expression in blood and brain, Am. J. Med Genet B Neuropsychiatr. Genet., 141B, 261, 10.1002/ajmg.b.30272 Tadic, 2014, Methylation of the promoter of brain-derived neurotrophic factor exon IV and antidepressant response in major depression, Mol. Psychiatry, 19, 281, 10.1038/mp.2013.58 Taunton, 1996, A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p, Science, 272, 408, 10.1126/science.272.5260.408 The, B.c, 2016, Quantitative comparison of DNA methylation assays for biomarker development and clinical applications, Nat. Biotechnol., 34, 726, 10.1038/nbt.3605 Trivedi, 2016, Establishing moderators and biosignatures of antidepressant response in clinical care (EMBARC): rationale and design, J. Psychiatr. Res., 78, 11, 10.1016/j.jpsychires.2016.03.001 Tsankova, 2006, Sustained hippocampal chromatin regulation in a mouse model of depression and antidepressant action, Nat. Neurosci., 9, 519, 10.1038/nn1659 Tsao, 2006, Cytokines and serotonin transporter in patients with major depression, Prog. Neuropsychopharmacol. Biol. Psychiatry, 30, 899, 10.1016/j.pnpbp.2006.01.029 Turecki, 2014, The molecular bases of the suicidal brain, Nat. Rev. Neurosci., 15, 802, 10.1038/nrn3839 Valadi, 2007, Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells, Nat. Cell Biol., 9, 654, 10.1038/ncb1596 Verbelen, 2017, Cost-effectiveness of pharmacogenetic-guided treatment: are we there yet?, Pharmacogenom. J., 10.1038/tpj.2017.21 Vinson, 2012, CG methylation, Epigenomics, 4, 655, 10.2217/epi.12.55 Wahid, 2010, MicroRNAs: synthesis, mechanism, function, and recent clinical trials, Biochim. Biophys. Acta, 1803, 1231, 10.1016/j.bbamcr.2010.06.013 Weber, 2007, Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome, Nat. Genet., 39, 457, 10.1038/ng1990