Papers by Jeanette McClintick
Progress in Molecular Biology and Translational Science, 2015
Herein, we have reviewed the role of glutamate, the major excitatory neurotransmitter in the brai... more Herein, we have reviewed the role of glutamate, the major excitatory neurotransmitter in the brain, in a number of neurochemical, -physiological, and -behavioral processes mediating the development of alcohol dependence. The findings discussed include results from both preclinical as well as neuroimaging and postmortem clinical studies. Expression levels for a number of glutamate-associated genes and/or proteins are modulated by alcohol abuse and dependence. These changes in expression include metabotropic receptors and ionotropic receptor subunits as well as different glutamate transporters. Moreover, these changes in gene expression parallel the pharmacologic manipulation of these same receptors and transporters. Some of these gene expression changes may have predated alcohol abuse and dependence because a number of glutamate-associated polymorphisms are related to a genetic predisposition to develop alcohol dependence. Other glutamate-associated polymorphisms are linked to age at the onset of alcohol-dependence and initial level of response/sensitivity to alcohol. Finally, findings of innate and/or ethanol-induced glutamate-associated gene expression differences/changes observed in a genetic animal model of alcoholism, the P rat, are summarized. Overall, the existing literature indicates that changes in glutamate receptors, transporters, enzymes, and scaffolding proteins are crucial for the development of alcohol dependence and there is a substantial genetic component to these effects. This indicates that continued research into the genetic underpinnings of these glutamate-associated effects will provide important novel molecular targets for treating alcohol abuse and dependence.
Restorative neurology and neuroscience
EGF-responsive striatal progenitor cells from rat brain have been maintained in culture in the fo... more EGF-responsive striatal progenitor cells from rat brain have been maintained in culture in the form of neurospheres for six years without exhausting their renewal capacity. The events surrounding differentiation of stem cells in the brain after a long progenitorship remain a mystery. Using DNA microarray analysis we investigated differential gene expression, comparing progenitor cells in their neurosphere state with the cells 24 hours after induction of differentiation. Eighty-one genes showed increased expression in the differentiated condition. Genes associated with cellular growth, neurite outgrowth, and synaptogenesis were activated, including both anti-apoptotic and pro-apoptotic genes. Two transmitter- related genes, acetylcholine receptor-beta and glutamate receptor-beta-unit were also elevated-, these genes not only fit the profile of early neural development, but also reflect the characteristics of striatal neurons. In addition, there are approximately 30 expressed sequence tags (ES7) increased during neural differentiation. Forty-seven genes showed decreased expression; half of them are known genes related to the cell cycle, cell adhesion, transcription, and signaling. Tbe signaling and cell cycle genes may be responsible for the life-long self-renewal. These data demonstrate for the first time that life-long quiescent stem cells retain the potential to become activated and develop into specific types of brain cells. The six-year long-term neural stem cells are an excellent model for studying developmental neurobiological processes and aging.
BioTechniques
. Example of output from BRept_Sum. NM_001043 is the reference sequence for cDNA SLC6A2 , a norad... more . Example of output from BRept_Sum. NM_001043 is the reference sequence for cDNA SLC6A2 , a noradrenalin transporter. Regions that align are sorted in sequence order along the query rather than in order of scores. This aids in the identification of exons in the cDNA. AC007602.3 is a working draft sequence containing six unordered pieces (deposited 6 April 2000). In this case, all 13 exons (spanning 2136 bp in the reference sequence) match sequences spanning 46006 bp within a 71312-bp contig.
Translational psychiatry, 2015
Adult antisocial behavior (AAB) is moderately heritable, relatively common and has adverse conseq... more Adult antisocial behavior (AAB) is moderately heritable, relatively common and has adverse consequences for individuals and society. We examined the molecular genetic basis of AAB in 1379 participants from a case-control study in which the cases met criteria for alcohol dependence. We also examined whether genes of interest were expressed in human brain. AAB was measured using a count of the number of Antisocial Personality Disorder criteria endorsed under criterion A from the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV). Participants were genotyped on the Illumina Human 1M BeadChip. In total, all single-nucleotide polymorphisms (SNPs) accounted for 25% of the variance in AAB, although this estimate was not significant (P=0.09). Enrichment tests indicated that more significantly associated genes were over-represented in seven gene sets, and most were immune related. Our most highly associated SNP (rs4728702, P=5.77 × 10(-7)) was located in the protein-...
Pharmacology Biochemistry and Behavior, 2012
The objective of this study was to determine if there are common innate differences in gene expre... more The objective of this study was to determine if there are common innate differences in gene expression or gene pathways in the ventral tegmental area (VTA) among 5 different pairs of rat lines selectively bred for high (HEC) or low (LEC) ethanol consumption: (a) alcohol-preferring (P) vs. alcohol-non-preferring (NP) rats; (b) high-alcohol-drinking (HAD) vs. low-alcohol-drinking (LAD) rats (replicate line pairs 1 and 2); (c) ALKO alcohol (AA) vs. nonalcohol (ANA) rats; and (d) Sardinian alcohol-preferring (sP) vs. alcoholnonpreferring (sNP) rats. Microarray analysis revealed between 370 and 1340 unique named genes that significantly differed in expression between the individual line-pairs. Analysis using Gene Ontology (GO) and Ingenuity Pathways information indicated significant categories and networks in common for up to 3 linepairs, but not for all 5 line-pairs; moreover, there were few genes in common in these categories and networks. ANOVA of the combined data for the 5 line-pairs indicated 1295 significant (p b 0.01) differences in expression of named genes. Although no individual named gene was significant across all 5 line-pairs, there were 22 genes that overlapped in the same direction in 3 or 4 of the line-pairs. Overall, the findings suggest that (a) some biological categories or networks may be in common for subsets of line-pairs; and (b) regulation of different genes and/or combinations of multiple biological systems (e.g., transcription, synaptic function, intracellular signaling and protection against oxidative stress) within the VTA (possibly involving dopamine and glutamate) may be contributing to the disparate alcohol drinking behaviors of these line-pairs.
Molecular Biology of the Cell, 2013
Molecular Biology of the Cell, 2011
Disruptions of the endoplasmic reticulum (ER) that perturb protein folding cause ER stress and el... more Disruptions of the endoplasmic reticulum (ER) that perturb protein folding cause ER stress and elicit an unfolded protein response (UPR) that involves translational and transcriptional changes in gene expression aimed at expanding the ER processing capacity and alleviating cellular injury. Three ER stress sensors (PERK, ATF6, and IRE1) implement the UPR. PERK phosphorylation of the α subunit of eIF2 during ER stress represses protein synthesis, which prevents further influx of ER client proteins. Phosphorylation of eIF2α (eIF2α∼P) also induces preferential translation of ATF4, a transcription activator of the integrated stress response. In this study we show that the PERK/eIF2α∼P/ATF4 pathway is required not only for translational control, but also for activation of ATF6 and its target genes. The PERK pathway facilitates both the synthesis of ATF6 and trafficking of ATF6 from the ER to the Golgi for intramembrane proteolysis and activation of ATF6. As a consequence, liver-specific depletion of PERK significantly reduces both the translational and transcriptional phases of the UPR, leading to reduced protein chaperone expression, disruptions of lipid metabolism, and enhanced apoptosis. These findings show that the regulatory networks of the UPR are fully integrated and help explain the diverse biological defects associated with loss of PERK.
Journal of Biological Chemistry, 2010
Two important nutrient-sensing and regulatory pathways, the general amino acid control (GAAC) and... more Two important nutrient-sensing and regulatory pathways, the general amino acid control (GAAC) and the target of rapamycin (TOR), participate in the control of yeast growth and metabolism during changes in nutrient availability. Amino acid starvation activates the GAAC through Gcn2p phosphorylation of translation factor eIF2 and preferential translation of GCN4, a transcription activator. TOR senses nitrogen availability and regulates transcription factors such as Gln3p. We used microarray analyses to address the integration of the GAAC and TOR pathways in directing the yeast transcriptome during amino acid starvation and rapamycin treatment. We found that GAAC is a major effector of the TOR pathway, with Gcn4p and Gln3p each inducing a similar number of genes during rapamycin treatment. Although Gcn4p activates a common core of 57 genes, the GAAC directs significant variations in the transcriptome during different stresses. In addition to inducing amino acid biosynthetic genes, Gcn4p in conjunction with Gln3p activates genes required for the assimilation of secondary nitrogen sources such as ␥-aminobutyric acid (GABA). Gcn2p activation upon shifting to secondary nitrogen sources is suggested to occur by means of a dual mechanism. First, Gcn2p is induced by the release of TOR repression through a mechanism involving Sit4p protein phosphatase. Second, this eIF2 kinase is activated by select uncharged tRNAs, which were shown to accumulate during the shift to the GABA medium. This study highlights the mechanisms by which the GAAC and TOR pathways are integrated to recognize changing nitrogen availability and direct the transcriptome for optimal growth adaptation.
Pharmacology Biochemistry and Behavior, 2009
The objective of this study was to determine the effects of binge-like alcohol drinking on gene e... more The objective of this study was to determine the effects of binge-like alcohol drinking on gene expression changes in the nucleus accumbens (ACB) of alcohol-preferring (P) rats. Adult male P rats were given ethanol under multiple scheduled access (MSA; three 1-hr dark-cycle sessions/day) conditions for 8 weeks. For comparison purposes, a second ethanol drinking group was given continuous/daily alcohol access (CA; 24 hr/day). A third group was ethanol-naïve (W group). Average ethanol intakes for the CA and MSA groups were approximately 9.5 and 6.5 g/kg/day, respectively. Fifteen hr after the last drinking episode, rats were euthanized, the brains extracted, and the ACB dissected. RNA was extracted and purified for microarray analysis. The only significant differences were between the CA and W groups (p < 0.01; Storey false discovery rate = 0.15); there were 374 differences in named genes between these 2 groups. There were 20 significant Gene Ontology (GO) categories, which included negative regulation of protein kinase activity, antiapoptosis, and regulation of G-protein-coupled receptor signaling. Ingenuity® analysis indicated a network of transcription factors, involving oncogenes (Fos, Jun, Junb had higher expression in the ACB of the CA group), suggesting increased neuronal activity. There were 43 genes located within rat QTLs for alcohol consumption and preference; 4 of these genes (Tgfa, Hspa5, Mtus1 and Creb3l2) are involved in anti-apoptosis and increased transcription, suggesting that they may be contributing to cellular protection and maintaining high alcohol intakes. Overall, these findings suggest that chronic CA drinking results in genomic changes that can be observed during the early acute phase of ethanol withdrawal. Conversely, chronic MSA drinking, with its associated protracted withdrawal periods, results in genomic changes that may be masked by tight regulation of these genes following repeated experiences of ethanol withdrawal.
PLOS ONE, 2015
Pachymic acid (PA) is a purified triterpene extracted from medicinal fungus Poria cocos. In this ... more Pachymic acid (PA) is a purified triterpene extracted from medicinal fungus Poria cocos. In this paper, we investigated the anticancer effect of PA on human chemotherapy resistant pancreatic cancer. PA triggered apoptosis in gemcitabine-resistant pancreatic cancer cells PANC-1 and MIA PaCa-2. Comparative gene expression array analysis demonstrated that endoplasmic reticulum (ER) stress was induced by PA through activation of heat shock response and unfolded protein response related genes. Induced ER stress was confirmed by increasing expression of XBP-1s, ATF4, Hsp70, CHOP and phospho-eIF2α. Moreover, ER stress inhibitor tauroursodeoxycholic acid (TUDCA) blocked PA induced apoptosis. In addition, 25 mg kg -1 of PA significantly suppressed MIA PaCa-2 tumor growth in vivo without toxicity, which correlated with induction of apoptosis and expression of ER stress related proteins in tumor tissues. Taken together, growth inhibition and induction of apoptosis by PA in gemcitabine-resistant pancreatic cancer cells were associated with ER stress activation both in vitro and in vivo. PA may be potentially exploited for the use in treatment of chemotherapy resistant pancreatic cancer.
Proceedings of the 2003 ACM symposium on Applied computing - SAC '03, 2003
Page 1. La6rat L1M5: An Exten5161e Framew0rk f0r Deve10p1n9 La60rat0ry 1nf0rmat10n Mana9ement, An... more Page 1. La6rat L1M5: An Exten5161e Framew0rk f0r Deve10p1n9 La60rat0ry 1nf0rmat10n Mana9ement, Ana1y515, and 8101nf0rmat1c5 501ut10n5 f0r M1cr0array5 Marcu5 R. 8ree5e ~ Matthew J. 5tephen5 ~ Jeanette N. McC11nt1ck Y ...
BMC proceedings, 2007
To explore the mapping of factors regulating gene expression, we have carried out linkage studies... more To explore the mapping of factors regulating gene expression, we have carried out linkage studies using expression data from individual transcripts (from Affymetrix microarrays; Genetic Analysis Workshop 15 Problem 1) and composite data on correlated groups of transcripts. Quality measures for the arrays were used to remove outliers, and arrays with sex mismatches were also removed. Data likely to represent noise were removed by setting a minimum threshold of present calls among the non-redundant set of 190 arrays. SOLAR was used for genetic analysis, with MAS5 signal as the measure of expression. Probe sets with larger CVs generated more linkages (LOD > 2.0). While trans linkages predominated, linkages with the largest LOD scores (>4) were mostly cis. Hierarchical clustering was used to generate correlated groups of genes. We tested four composite measures of expression for the clusters. The average signal, average normalized signal, and the first principal component of the d...
BMC bioinformatics, 2006
Affymetrix GeneChips are widely used for expression profiling of tens of thousands of genes. The ... more Affymetrix GeneChips are widely used for expression profiling of tens of thousands of genes. The large number of comparisons can lead to false positives. Various methods have been used to reduce false positives, but they have rarely been compared or quantitatively evaluated. Here we describe and evaluate a simple method that uses the detection (Present/Absent) call generated by the Affymetrix microarray suite version 5 software (MAS5) to remove data that is not reliably detected before further analysis, and compare this with filtering by expression level. We explore the effects of various thresholds for removing data in experiments of different size (from 3 to 10 arrays per treatment), as well as their relative power to detect significant differences in expression. Our approach sets a threshold for the fraction of arrays called Present in at least one treatment group. This method removes a large percentage of probe sets called Absent before carrying out the comparisons, while retain...
BMC genomics, 2003
Low RNA yields from small tissue samples can limit the use of oligonucleotide microarrays (Affyme... more Low RNA yields from small tissue samples can limit the use of oligonucleotide microarrays (Affymetrix GeneChips). Methods using less cRNA for hybridization or amplifying the cRNA have been reported to reduce the number of transcripts detected, but the effect on realistic experiments designed to detect biological differences has not been analyzed. We systematically explore the effects of using different starting amounts of RNA on the ability to detect differential gene expression. The standard Affymetrix protocol can be used starting with only 2 micrograms of total RNA, with results equivalent to the recommended 10 micrograms. Biological variability is much greater than the technical variability introduced by this change. A simple amplification protocol described here can be used for samples as small as 0.1 micrograms of total RNA. This amplification protocol allows detection of a substantial fraction of the significant differences found using the standard protocol, despite an increa...
Alcohol (Fayetteville, N.Y.), 2013
The chronic high-level alcohol consumption seen in alcoholism leads to dramatic effects on the hi... more The chronic high-level alcohol consumption seen in alcoholism leads to dramatic effects on the hippocampus, including decreased white matter, loss of oligodendrocytes and other glial cells, and inhibition of neurogenesis. Examining gene expression in post mortem hippocampal tissue from 20 alcoholics and 19 controls allowed us to detect differentially expressed genes that may play a role in the risk for alcoholism or whose expression is modified by chronic consumption of alcohol. We identified 639 named genes whose expression significantly differed between alcoholics and controls at a False Discovery Rate (FDR) ≤ 0.20; 52% of these genes differed by at least 1.2-fold. Differentially expressed genes included the glucocorticoid receptor and the related gene FK506 binding protein 5 (FKBP5), UDP glycosyltransferase 8 (UGT8), urea transporter (SLC14A1), zinc transporter (SLC39A10), Interleukin 1 receptor type 1 (IL1R1), thioredoxin interacting protein (TXNIP), and many metallothioneins. P...
Diabetes, 2015
Intrauterine exposure to gestational diabetes mellitus (GDM) is linked to development of 38 hyper... more Intrauterine exposure to gestational diabetes mellitus (GDM) is linked to development of 38 hypertension, obesity, and type 2 diabetes in children. Our previous studies determined that 39 endothelial colony forming cells (ECFCs) from neonates exposed to GDM exhibit impaired 40 function. The current goals were to identify aberrantly expressed genes that contribute to 41 impaired function of GDM-exposed ECFCs and to evaluate for evidence of altered epigenetic 42 regulation of gene expression. Genome-wide mRNA expression analysis was conducted on 43 ECFCs from control and GDM pregnancies. Candidate genes were validated by qRT-PCR and 44 western blotting. Bisulfite sequencing evaluated DNA methylation of PLAC8. Proliferation and 45 senescence assays of ECFCs transfected with siRNA to knockdown PLAC8 were performed to 46 determine functional impact. Thirty-eight genes were differentially expressed between control 47 and GDM-exposed ECFCs. PLAC8 was highly expressed in GDM-exposed ECFCs, and PLAC8 48 expression correlated with maternal hyperglycemia. Methylation status of 17 CpG sites in 49 PLAC8 negatively correlated with mRNA expression. Knockdown of PLAC8 in GDM-exposed 50 ECFCs improved proliferation and senescence defects. This study provides strong evidence in 51 neonatal endothelial progenitor cells that GDM exposure in utero leads to altered gene 52 expression and DNA methylation, suggesting the possibility of altered epigenetic regulation. 53 54 Page 2 of 42 Diabetes The Barker hypothesis postulates that alterations in the intrauterine environment and in fetal and 55 infant nutrition correlate with development of adult diseases (1). This concept of a 56 developmental origin of adult disease was based upon a landmark study linking low birth weight 57 with increased risk of death from ischemic heart disease (2). Several subsequent studies have 58 confirmed that infants born small at birth are at increased risk of developing hypertension, 59 stroke, type 2 diabetes, and obesity (1). Collectively, these observations infer that permanent 60 changes occur during fetal development allowing adaptation and survival in a suboptimal 61 intrauterine environment and that in a postnatal setting these developmental adaptations 62 mechanistically contribute to the pathogenesis of multiple chronic diseases. Similarly, infants 63 born to women with pre-gestational diabetes mellitus (PGDM) and gestational diabetes mellitus 64 (GDM) have an increased risk for developing chronic diseases including hypertension, type 2 65 diabetes, and obesity (3-7). Numerous animal studies show long-term, harmful effects of fetal 66 overnutrition (8,9). Thus, fetal intrauterine exposure to either undernourishment or diabetes 67 increases disease risk later in life. 68 69 Because of the long-lasting nature of an individual's response to adverse intrauterine 70 environment exposure, dysfunctional stem and progenitor cells are hypothesized to participate in 71 disease pathogenesis. Our previous work evaluating the function of endothelial progenitor cells 72 supports this supposition. Using cord blood endothelial colony forming cells (ECFCs), a highly 73 proliferative and self-renewing endothelial progenitor population, we identified numerous 74 functional deficits of ECFCs exposed to GDM in utero (10). Importantly, fetal GDM exposure 75 resulted in increased proliferation, reduced vasculogenesis, and resistance to hyperglycemia-76 induced senescence of ECFCs (10).
Pharmacology Biochemistry and Behavior, 2009
The objective of this study was to determine the effects of binge-like alcohol drinking on gene e... more The objective of this study was to determine the effects of binge-like alcohol drinking on gene expression changes in the nucleus accumbens (ACB) of alcohol-preferring (P) rats. Adult male P rats were given ethanol under multiple scheduled access (MSA; three 1-hr dark-cycle sessions/day) conditions for 8 weeks. For comparison purposes, a second ethanol drinking group was given continuous/daily alcohol access (CA; 24 hr/day). A third group was ethanol-naïve (W group). Average ethanol intakes for the CA and MSA groups were approximately 9.5 and 6.5 g/kg/day, respectively. Fifteen hr after the last drinking episode, rats were euthanized, the brains extracted, and the ACB dissected. RNA was extracted and purified for microarray analysis. The only significant differences were between the CA and W groups (p < 0.01; Storey false discovery rate = 0.15); there were 374 differences in named genes between these 2 groups. There were 20 significant Gene Ontology (GO) categories, which included negative regulation of protein kinase activity, antiapoptosis, and regulation of G-protein-coupled receptor signaling. Ingenuity® analysis indicated a network of transcription factors, involving oncogenes (Fos, Jun, Junb had higher expression in the ACB of the CA group), suggesting increased neuronal activity. There were 43 genes located within rat QTLs for alcohol consumption and preference; 4 of these genes (Tgfa, Hspa5, Mtus1 and Creb3l2) are involved in anti-apoptosis and increased transcription, suggesting that they may be contributing to cellular protection and maintaining high alcohol intakes. Overall, these findings suggest that chronic CA drinking results in genomic changes that can be observed during the early acute phase of ethanol withdrawal. Conversely, chronic MSA drinking, with its associated protracted withdrawal periods, results in genomic changes that may be masked by tight regulation of these genes following repeated experiences of ethanol withdrawal.
Genome Biology, 2010
Background: Selectively bred alcohol-preferring (P) and alcohol-nonpreferring (NP) rats differ gr... more Background: Selectively bred alcohol-preferring (P) and alcohol-nonpreferring (NP) rats differ greatly in alcohol preference, in part due to a highly significant quantitative trait locus (QTL) on chromosome 4. Alcohol consumption scores of reciprocal chromosome 4 congenic strains NP.P and P.NP correlated with the introgressed interval. The goal of this study was to identify candidate genes that may influence alcohol consumption by comparing gene expression in five brain regions of alcohol-naïve inbred alcohol-preferring and P.NP congenic rats: amygdala, nucleus accumbens, hippocampus, caudate putamen, and frontal cortex. Results: Within the QTL region, 104 cis-regulated probe sets were differentially expressed in more than one region, and an additional 53 were differentially expressed in a single region. Fewer trans-regulated probe sets were detected, and most differed in only one region. Analysis of the average expression values across the 5 brain regions yielded 141 differentially expressed cis-regulated probe sets and 206 trans-regulated probe sets. Comparing the present results from inbred alcohol-preferring vs. congenic P.NP rats to earlier results from the reciprocal congenic NP.P vs. inbred alcohol-nonpreferring rats demonstrated that 74 cis-regulated probe sets were differentially expressed in the same direction and with a consistent magnitude of difference in at least one brain region.
Blood, Jan 15, 2005
Embryonic stem (ES) cells homozygous for a Shp-2 mutation (Shp-2(Delta46-110)) demonstrate leukem... more Embryonic stem (ES) cells homozygous for a Shp-2 mutation (Shp-2(Delta46-110)) demonstrate leukemia inhibitory factor (LIF) hypersensitivity and increased LIF-stimulated phosphorylation of signal transducer and activator of transcription (STAT3). We hypothesized that LIF-responsive genes in Shp-2(Delta46-110) cells would represent potential candidates for molecules vital for ES cell self-renewal. Using microarray analysis, we detected 41 genes whose expression was modified by LIF in Shp-2(Delta46-110) ES cells. Induction of 2 significantly up-regulated genes, suppressor of cytokine signaling-3 (SOCS-3) and Kruppel-like factor 4 (Klf4), was verified using Northern blotting. ES cells overexpressing SOCS-3 had an increased capacity to differentiate to hematopoietic progenitors, rather than to self-renew. In contrast, ES cells overexpressing Klf4 had a greater capacity to self-renew based on secondary embryoid body (EB) formation. Klf4-transduced d6 EBs expressed higher levels of Oct-4,...
Uploads
Papers by Jeanette McClintick