Microarray Characterization of Gene Expression Changes in Blood During Acute Ethanol Exposure

Overview

Journal BMC Med Genomics

Publisher Biomed Central

Specialty Genetics

Date 2013 Jul 26

PMID 23883607

Citations 11

Authors

Doris M Kupfer

Vicky L White

David L Strayer

Dennis J Crouch

Dennis Burian

Affiliations

Soon will be listed here.

Abstract

Background: As part of the civil aviation safety program to define the adverse effects of ethanol on flying performance, we performed a DNA microarray analysis of human whole blood samples from a five-time point study of subjects administered ethanol orally, followed by breathalyzer analysis, to monitor blood alcohol concentration (BAC) to discover significant gene expression changes in response to the ethanol exposure.

Methods: Subjects were administered either orange juice or orange juice with ethanol. Blood samples were taken based on BAC and total RNA was isolated from PaxGene™ blood tubes. The amplified cDNA was used in microarray and quantitative real-time polymerase chain reaction (RT-qPCR) analyses to evaluate differential gene expression. Microarray data was analyzed in a pipeline fashion to summarize and normalize and the results evaluated for relative expression across time points with multiple methods. Candidate genes showing distinctive expression patterns in response to ethanol were clustered by pattern and further analyzed for related function, pathway membership and common transcription factor binding within and across clusters. RT-qPCR was used with representative genes to confirm relative transcript levels across time to those detected in microarrays.

Results: Microarray analysis of samples representing 0%, 0.04%, 0.08%, return to 0.04%, and 0.02% wt/vol BAC showed that changes in gene expression could be detected across the time course. The expression changes were verified by qRT-PCR.The candidate genes of interest (GOI) identified from the microarray analysis and clustered by expression pattern across the five BAC points showed seven coordinately expressed groups. Analysis showed function-based networks, shared transcription factor binding sites and signaling pathways for members of the clusters. These include hematological functions, innate immunity and inflammation functions, metabolic functions expected of ethanol metabolism, and pancreatic and hepatic function. Five of the seven clusters showed links to the p38 MAPK pathway.

Conclusions: The results of this study provide a first look at changing gene expression patterns in human blood during an acute rise in blood ethanol concentration and its depletion because of metabolism and excretion, and demonstrate that it is possible to detect changes in gene expression using total RNA isolated from whole blood. The analysis approach for this study serves as a workflow to investigate the biology linked to expression changes across a time course and from these changes, to identify target genes that could serve as biomarkers linked to pilot performance.

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References

Wang H, Bloom O, Zhang M, Vishnubhakat J, Ombrellino M, Che J . HMG-1 as a late mediator of endotoxin lethality in mice. Science. 1999; 285(5425):248-51. DOI: 10.1126/science.285.5425.248. View

Ame J, Spenlehauer C, de Murcia G . The PARP superfamily. Bioessays. 2004; 26(8):882-93. DOI: 10.1002/bies.20085. View

Ikonomov O, Sbrissa D, Mlak K, Shisheva A . Requirement for PIKfyve enzymatic activity in acute and long-term insulin cellular effects. Endocrinology. 2002; 143(12):4742-54. DOI: 10.1210/en.2002-220615. View

Jain N, Thatte J, Braciale T, Ley K, OConnell M, Lee J . Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays. Bioinformatics. 2003; 19(15):1945-51. DOI: 10.1093/bioinformatics/btg264. View

Carnegie G, Sleeman J, Morrice N, Hastie C, Peggie M, Philp A . Protein phosphatase 4 interacts with the Survival of Motor Neurons complex and enhances the temporal localisation of snRNPs. J Cell Sci. 2003; 116(Pt 10):1905-13. DOI: 10.1242/jcs.00409. View

Donato R . S100: a multigenic family of calcium-modulated proteins of the EF-hand type with intracellular and extracellular functional roles. Int J Biochem Cell Biol. 2001; 33(7):637-68. DOI: 10.1016/s1357-2725(01)00046-2. View

Matthews S, Dayalu R, Thompson L, Scharenberg A . Regulation of protein kinase Cnu by the B-cell antigen receptor. J Biol Chem. 2002; 278(11):9086-91. DOI: 10.1074/jbc.M211295200. View

Chiu Y, Sun Q, Chen Z . E1-L2 activates both ubiquitin and FAT10. Mol Cell. 2007; 27(6):1014-23. DOI: 10.1016/j.molcel.2007.08.020. View

McFadden K . DWI convictions linked to a higher risk of alcohol-related aircraft accidents. Hum Factors. 2003; 44(4):522-9. DOI: 10.1518/0018720024496962. View

10.

McMonagle J, FELIG P . Effects of ethanol ingestion on glucose tolerance and insulin secretion in normal and diabetic subjects. Metabolism. 1975; 24(5):625-32. DOI: 10.1016/0026-0495(75)90142-0. View

11.

Keiver K, Duggal S, Simpson M . Ethanol administration results in a prolonged decrease in blood ionized calcium levels in the rat. Alcohol. 2006; 37(3):173-8. DOI: 10.1016/j.alcohol.2005.07.008. View

12.

Andersen C, Jensen J, Orntoft T . Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 2004; 64(15):5245-50. DOI: 10.1158/0008-5472.CAN-04-0496. View

13.

Pfaffl M, Horgan G, Dempfle L . Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res. 2002; 30(9):e36. PMC: 113859. DOI: 10.1093/nar/30.9.e36. View

14.

Gunster M, Satijn D, Hamer K, den Blaauwen J, de Bruijn D, Alkema M . Identification and characterization of interactions between the vertebrate polycomb-group protein BMI1 and human homologs of polyhomeotic. Mol Cell Biol. 1997; 17(4):2326-35. PMC: 232081. DOI: 10.1128/MCB.17.4.2326. View

15.

Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A . Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002; 3(7):RESEARCH0034. PMC: 126239. DOI: 10.1186/gb-2002-3-7-research0034. View

16.

Norkina O, Dolganiuc A, Shapiro T, Kodys K, Mandrekar P, Szabo G . Acute alcohol activates STAT3, AP-1, and Sp-1 transcription factors via the family of Src kinases to promote IL-10 production in human monocytes. J Leukoc Biol. 2007; 82(3):752-62. DOI: 10.1189/jlb.0207099. View

17.

Fenner B, Scannell M, Prehn J . Identification of polyubiquitin binding proteins involved in NF-kappaB signaling using protein arrays. Biochim Biophys Acta. 2009; 1794(7):1010-6. DOI: 10.1016/j.bbapap.2009.02.013. View

18.

Zhao Y, Zhou L, Liu B, Deng Y, Wang Y, Wang Y . ZNF325, a novel human zinc finger protein with a RBaK-like RB-binding domain, inhibits AP-1- and SRE-mediated transcriptional activity. Biochem Biophys Res Commun. 2006; 346(4):1191-9. DOI: 10.1016/j.bbrc.2006.06.031. View

19.

Futschik M, Carlisle B . Noise-robust soft clustering of gene expression time-course data. J Bioinform Comput Biol. 2005; 3(4):965-88. DOI: 10.1142/s0219720005001375. View

20.

Lignitto L, Carlucci A, Sepe M, Stefan E, Cuomo O, Nistico R . Control of PKA stability and signalling by the RING ligase praja2. Nat Cell Biol. 2011; 13(4):412-22. DOI: 10.1038/ncb2209. View