Substance-Specific and Shared Transcription and Epigenetic Changes in the Human Hippocampus Chronically Exposed to Cocaine and A
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Substance-specific and shared transcription and epigenetic changes in the human hippocampus chronically exposed to cocaine and alcohol Zhifeng Zhoua, Qiaoping Yuana, Deborah C. Mashb, and David Goldmana,1 aLaboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD 20849; and bDepartment of Neurology, University of Miami School of Medicine, Miami, FL 33146 Edited by Leslie Lars Iversen, University of Oxford, Oxford, United Kingdom, and approved March 5, 2011 (received for review December 20, 2010) The hippocampus is a key brain region involved in both short- and to the nucleus accumbens in the mesolimbic system and can also long-term memory processes and may play critical roles in drug- activate dopaminergic neurons of the ventral tegmental area, associated learning and addiction. Using whole genome sequencing explaining its involvement in cue-conditioned dopamine release. of mRNA transcripts (RNA-Seq) and immunoprecipitation-enriched Cocaine modulates hippocampal functions such as long-term genomic DNA (ChIP-Seq) coupled with histone H3 lysine 4 trime- potentiation (LTP) (6), raising the possibility that long-term drug thylation (H3K4me3), we found extensive hippocampal gene ex- exposure may impair adaptive plasticity relevant to learning. pression changes common to both cocaine-addicted and alcoholic By using a massively parallel sequencing approach, which individuals that may reflect neuronal adaptations common to both enables whole genome views of RNA transcription and epige- netic state, we surveyed genome-wide changes in gene expression addictions. However, we also observed functional changes that fi were related only to long-term cocaine exposure, particularly the and histone methylation modi cation in postmortem hippo- inhibition of mitochondrial inner membrane functions related to campal tissue from individuals chronically exposed to cocaine or oxidative phosphorylation and energy metabolism, which has also alcohol, and from carefully matched drug-free controls. Based been observed previously in neurodegenerative diseases. Cocaine- on their mechanisms of action, and, to some extent, published literature, we hypothesized that this approach would reveal and alcohol-related histone H3K4me3 changes highly overlapped, changes that were substance-specific and other changes that were but greater effects were detected under cocaine exposure. There common to general processes of addiction. was no direct correlation, however, between either cocaine- or alcohol- related histone H3k4me3 and gene expression changes at Results an individual gene level, indicating that transcriptional regulation Global Change in mRNA Expression in Chronic Cocaine and Alcohol as well as drug-related gene expression changes are outcomes of Exposure. The hippocampal mRNA transcriptome was sequenced a complex gene-regulatory process that includes multifaceted fi in 24 age-, ethnicity-, and postmortem interval-matched men: histone modi cations. eight chronic cocaine addicts, eight alcoholics, and eight drug- free control subjects (SI Appendix, Table S1). RNA expression drug addiction | histone methylation was detected for 16,008 RefSeq genes by using the sequencing reads pooled from all individuals. The expression of each gene nowledge of the cellular and molecular adaptations un- was thereby quantified for each individual within a consistent Kderlying addiction to cocaine and alcohol has primarily been physical framework, defined by pooled analysis of expression sig- gained from animal models of acute and chronic drug exposure, nals and by National Center for Biotechnology Information gene from which specific molecular pathways to addiction have been annotations that allowed signals from multiple exons to be com- identified (1, 2). Studies on human postmortem brain (3) have bined into a measure of average sequencing read counts for each yielded data that are complementary and tend to validate animal gene. Gene expression was highly correlated among individual models of exposure. Addiction-associated molecular alterations samples (SI Appendix, Fig. S1A), indicating reproducibility and observed in animal and human studies are diverse. Clearly, cel- quality of RNA-Seq results. The signal distribution (SI Appendix, lular and molecular responses to addictive drugs depend on the Fig. S1B) of all expressed transcripts was also consistent with type and timing of exposure, the timing of observations within previous studies of gene expression in the brain (7). However, the progression to addiction, and the brain regions and cells in the depth of sequencing coverage enabled the detection, and which observations are made. Specific changes in signal trans- quantification of more transcripts of low-abundance compared duction pathways, including in the transcription factor ΔFosB and with microarray-based analysis. the cAMP-response element binding protein (CREB), are likely Among the 16,008 hippocampal expressed genes, at an un- to be more prominent in early stages of drug-induced neuro- corrected P value lower than 0.05, a total of 1,994 were differen- adaptation (4). Longstanding adaptations may be marked by tially expressed in chronic cocaine-exposed individuals, and 1,275 changes in expression of genes involved in the regulation of cel- were differentially expressed in the chronic alcohol-exposed lular functions including ion transport, chromosome remodeling, individuals. However, to compensate for multiple testing leading stress and immune response, cell adhesion, cell cycle, apoptosis, to false-positive findings at any significance threshold, we calcu- protein and lipid metabolism, and mitochondrial functions (3). Later changes may be more closely relevant to addictive behav- iors and long-lasting vulnerability to relapse. Author contributions: Z.Z., Q.Y., D.C.M., and D.G. designed research; Z.Z., Q.Y., D.C.M., The hippocampus is also a brain region critically involved in and D.G. performed research; Z.Z., Q.Y., and D.C.M. contributed new reagents/analytic addiction. Most studies have focused on the mesolimbic system, tools; Z.Z., Q.Y., and D.G. analyzed data; and Z.Z. and D.G. wrote the paper. in which medium-sized spiny neurons in the dorsal striatum and The authors declare no conflict of interest. nucleus accumbens mediate dopaminergic, glutamatergic, and This article is a PNAS Direct Submission. GABAergic neurotransmission (5) and are key in drug-reward Data deposition: The sequences reported in this paper have been deposited in the and drug-seeking behavior. However, hippocampal functions GenBank database (accession nos. SRA029279 and SRA029275). related to short- and long-term memory processes and involving 1To whom correspondence should be addressed. E-mail: [email protected]. synaptic plasticity are necessary for drug-associated learning and This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. memory. The hippocampus directly projects excitatory efferents 1073/pnas.1018514108/-/DCSupplemental. 6626–6631 | PNAS | April 19, 2011 | vol. 108 | no. 16 www.pnas.org/cgi/doi/10.1073/pnas.1018514108 Downloaded by guest on September 30, 2021 lated a false discovery rate (FDR; Benjamini–Hochberg) q value results. The scatterplots of relative expression levels (average for each gene and applied it for genome-wide corrections. As seen normalized sequencing read counts), degree (fold) of change, and in Fig. 1A, by using a relatively stringent FDR cutoff of less than P values (both uncorrected and FDR cutoffs) of all 16,008 ex- 0.2, which includes the genes with the maximum probability of pressed genes in both cocaine and alcohol groups are also shown false discovery of less than 20% (P < 0.005 in cocaine group and in Fig. 2. P < 0.0007 in alcohol group) and many of those with a lower FDR probability, there were a total of 394 differentially expressed genes Genes Affected by both Cocaine and Alcohol Exposure. Although it is in the cocaine-addicted subjects and 48 in the alcoholic subjects apparent that long-term cocaine exposure resulted in wider and (Fig. 1B and SI Appendix, Tables S2 and S3). The use of an FDR more severe effects on gene expression in the hippocampus (Fig. fi < × −7 lower than 0.05 identified 80 genes in the cocaine addicts and 11 in 1), we also observed a signi cant overlap (P 4.04 10 )of the alcoholics (Fig. 1B). The numbers of genes that are either up- differentially expressed genes between cocaine addiction and regulated or down-regulated in the cocaine addicts and alcoholics alcoholism. Under a FDR lower than 0.2, a total of 29 genes are summarized in Fig. 1B. Gene expression changes detected by showed expression changes in both the cocaine-exposed and RNA-Seq were also validated by quantitative RT-PCR for 11 alcohol-exposed hippocampus (Fig. 1 A and B). Furthermore, in each case, the change was in the same direction [nominal like- transcripts in eight control and eight cocaine-addicted individual lihood, (1/2)29]. The details of these 29 genes are listed in Table R2 samples. There was a strong correlation ( = 0.90) between the 1. Examining the 11 genes whose expression in alcoholics was RNA-Seq and quantitative RT-PCR measurement (Fig. 1C and altered with a FDR lower than 0.05, nine were also common SI Appendix, Fig. S2), indicating overall reliability of the RNA-Seq in the cocaine group. These convergent alterations in gene expression indicate sharing of processes in cocaine- and alcohol- related hippocampal neural adaptation. However, it is