This page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.

MicroArray data on GRM7

A key finding in the original study linking GRM7 to alcoholism was that mice homozygous for an allele causing lowered expression of Grm7  (the mouse ortholog of human GRM7), exhibited increased levels of alcohol consumption (see the Popular Press and Scientific Article reviews on this website) (Vadasz, et al.,2007). While the role of GRM7 in alcoholism in humans has not yet been directly explored, the findings of this original study suggest that, if GRM7 does contribute to human alcoholism, differences in susceptibility to alcoholism are likely to be caused by genetic variations that alter GRM7 expression (Vadasz, et al.,2007). Therefore, MicroArray data on GRM7, which can be used to compare expression patterns of the gene across different samples, may provide especially useful insight into the role GRM7 plays in alcoholism.

To learn more about how MicroArrays work, check out this slideshow video: http://www.dnalc.org/ddnalc/resources/dnaarray.html

To find MicroArray experiments in which differences in GRM7 expression levels were observed, “GRM7” was queried on the Gene Expression Omnibus (GEO) website (Barrett, et al., 2006; Edgar, et al., 2002). GEO returned a number of experiments; however, two stuck out as particularly pertinent to the role GRM7 might have in human alcoholism (Barrett, et al., 2006; Edgar, et al., 2002). The first noteworthy experiment returned showed that, in postmortem samples from the hypothalamus of humans averaging 70 years of age, men had, on average, lower GRM7 expression levels than women (See Figure 1) (Rinn, et al., 2004). This experiment is particularly interesting because men have been shown to have higher rates of alcohol dependence than women, and like the mice that had increased levels of alcohol consumption in the Vadasz et al. study, they have lower GRM7 expression levels (2007; MFMER, 2008; Rinn, et al., 2004). Perhaps, not only could lowered expression of GRM7 in and of itself contribute to a risk for alcoholism, but lowered expression of this gene in males, as compared to females, might also contribute the differences that have been observed between the sexes in the prevalence of alcoholism (MFMER, 2008; Rinn, et al., 2004). Such a difference in GRM7 expression between the sexes could be possible if, for example, a trans-acting regulator of GRM7 transcription functioned differently in males than in females (Rinn, et al., 2004).


Figure 1. Sex specific transcription of GRM7 in hypothalamus of postmortem individuals averaging 70 years of age. The chart above represents the abundance profile for GRM7 expression in the hypothalamus of postmortem males and females averaging 70 years of age (Barrett, et al., 2006; Rinn et al., 2004; Edgar, et al., 2002). As indicated by the green bars across the bottom of the chart, samples from males are on the left, while samples from females are on the right (Barrett, et al., 2006; Rinn et al., 2004; Edgar, et al., 2002). All individuals used in this experiment, except the first female, were sampled twice: starting with the two samples on the far left, pairs of samples from the same individual are found next to one another (Barrett, et al., 2006; Rinn et al., 2004; Edgar, et al., 2002). The height of the red bars reflects the level of abundance of GRM7 in the samples (values are presented as arbitrary units), while the blue squares represent rank order and give an indication of where the expression of GRM7 falls with respect to all other genes on the array from which this data was taken (Barrett, et al., 2006; Rinn et al., 2004; Edgar, et al., 2002). Pink bars and light blue squares correspond to samples for which the Affymetrix 'Detection call' was categorized as absent (Barrett, et al., 2006; Edgar, et al., 2002). This may happen if expression is not detected or if stray cross-hybridization signals are detected (Barrett, et al., 2006; Edgar, et al., 2002). Expression of GRM7 is, on average, lower in males than in females (Rinn et al., 2004).


Using the data generated by Rinn et al. (2004) in their study of gene expression in the hypothalamus of postmortem samples from the hypothalamus of humans averaging 70 years of age, a cluster analysis was conducted to see what genes GRM7 was most similar to in expression levels (Barrett, et al., 2006; Edgar, et al., 2002). Comparison of GRM7 to the expression profiles of the 13,095 genes characterized by Rinn et al. (2004) showed that it was most similar to PCGF3 and FGF7 (Figure 2) (Barrett, et al., 2006; Edgar, et al., 2002). The relationship between GRM7 and FGF7 likely arose by chance, as FGF7 is an epithelial cell-specific fibroblast growth factor, while GRM7 is expressed primarily in the brain (Entrez Gene, 2009). It is unclear what relationship GRM7 and PCGF3 have, as this gene is, as of yet, uncharacterized (Entrez Gene, 2009). It is interesting to speculate that maybe this gene is also involved in neurotransmission and is regulated by the same transciption factors as GRM7. Other genes showing expression profiles like that of GRM7, such as USP33 and MYST4, are also relatively uncharacterized, and do not provide any clear insight into how they and GRM7 might be related (Entrez Gene, 2009).


Figure 2. MicroArray cluster analysis of GRM7. The expression profiles of the 13, 095 genes examined by Rinn et al. (2004) in their study of sex specific transcription in the human hypothalamus were used to conduct conduct a cluster analysis to see what genes were expressed similarly to GRM7. Using uncentered correlation as the distance setting and UPGMA as the hierarchical setting, GEO returned the above clustering for GRM7. GRM7 and the genes which show similar expression profiles to it are listed on the far right of the figure. The colored bar just to the left of each gene shows its expression in each of the samples, which are listed across the top (samples are the same as in Figure 1). As shown by the bars in the upper left, magenta color corresponds to high expression levels and green corresponds to low expression levels. The tree to the left of the colored bars represents the clustering of the individual genes: genes with more similar expression profiles lie on branches that are closer together. GRM7, which is fourth from the bottom, is most similar to  PCGF3 and FGF7. (Barrett, et al., 2006; Rinn et al., 2004; Edgar, et al., 2002).


Another noteworthy experiment returned by GEO showed that GRM7 expression differs in the small airway epithelial cells of (human) smokers as compared to non-smokers (Figure 3) (Tilley, et al., 2009; Harvey, et al., 2007; Barrett, et al., 2006; Edgar, et al., 2002). Like alcoholism, cigarette smoking is caused by an addictive behavior, and therefore, it might be expected that GRM7 contributes to smoking in a similar matter to the way it contributes to alcoholism. However, unlike the mice from the Vadasz, et al. study, for which decreased GRM7 expression led to increased alcohol consumption, smokers have increased GRM7 expression levels (see Figure 3) (2007; Tilley, et al., 2009; Harvey, et al., 2007).  This difference may be due to different roles for GRM7 in the related, but different, addictive behaviors leading to alcoholism and smoking. The difference also might be due to where the samples were taken from: the samples for the mouse expression data were taken from the brain, while the samples for the smoking expression data were from the airway epithelium (Tilley, et al., 2009; Harvey, et al., 2007; Rinn, et al, 2004). While these two MicroArray experiments offer some insight, more expression data on brain samples from alcoholics vs. non-alcoholics will clearly be needed to more fully understand how levels of GRM7 expression may contribute to alcoholism in humans.


Figure 3. Transcription of GRM7 in small airway epithelial cells of phenotypically normal smokers vs. non-smokers. The chart above represents the abundance profile for GRM7 expression in the small airway epithelial cells of phenotypically normal cigarette smokers and non-smokers(Tilley, et al., 2007; Harvey, et al., 2007; Barrett, et al., 2006;Edgar, et al., 2002). As indicated by the green bars across the bottom of the chart, samples from non-smokers are on the left, while samples from smokers are on the right (Tilley, et al., 2007; Harvey, et al., 2007; Barrett, et al., 2006;Edgar, et al., 2002). The height of the red bars reflects the level of abundance of GRM7 in the samples (values are presented as arbitrary units), while the blue squares represent rank order and give an indication of where the expression of GRM7 falls with respect to all other genes on the array from which this data was taken (Barrett, et al., 2006; Rinn et al., 2004; Edgar, et al., 2002). Pink bars and light blue squares correspond to samples for which the Affymetrix 'Detection call' was categorized as absent (Barrett, et al., 2006; Edgar, et al., 2002). This may happen if expression is not detected or if stray cross-hybridization signals are detected (Barrett, et al., 2006; Edgar, et al., 2002). Expression of GRM7 is, on average, lower in smokers than in non-smokers (Tilley, et al., 2007; Harvey, et al., 2007).


References

References

 

Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R. (2006). NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res., 35(Database issue):D760. doi:10.1093/nar/gkl887

Edgar, R., Domrachev, M., Lash, A.E. (2002). Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30(1):207.

Entrez Gene. (2009). FGF7 fibroblast growth factor 7 (keratinocyte growth factor) [Homo sapiens]. Retrieved May 11, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=retrieve&dopt=full_report&list_uids=2252&log$=databasead&logdbfrom=nuccore.

Entrez Gene. (2009). MYST4 MYST histone acetyltransferase (monocytic leukemia) 4 [Homo sapiens]. Retrieved May 11, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=23522&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum.

Entrez Gene. (2009). PCGF3 polycomb group ring finger 3 [Homo sapiens]. Retrieved May 11, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=retrieve&dopt=full_report&list_uids=10336&log$=databasead&logdbfrom=nuccore.

Entrez Gene. (2009). USP33 ubiquitin specific peptidase 33 [Homo sapiens]. Retrieved May 11, 2009, from, http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=retrieve&dopt=full_report&list_uids=23032&log$=databasead&logdbfrom=nuccore.

Harvey, B.G., Heguy, A., Leopold, P.L., Carolan, B.J., Ferris, B., Crystal, R.G. (2007). Modification of gene expression of the small airway epithelium in response to cigarette smoking. J Mol Med, 85(1):39. doi: 10.1007/s00109-006-0103-z

Mayo Foundation for Medical Education and Research (MFMER). (2008, May 8). Alcoholism. Retrieved February 2, 2009, from http://www.mayoclinic.com/print/alcoholism/DS00340/METHOD=print&DSECTION=all

Rinn, J.L., Rozowsky, J.S., Laurenzi, I.J., Petersen, P., Zon, K., Zhong, W., Gerstein, M., Snyder, M.P. (2004). Sex Specific Transcription in Human Hypothalamus. Retrieved April 22, 2009 from http://www.ncbi.nlm.nih.gov/geo/gds/profileGraph.cgi?&dataset=595j46FBzmACVZ2lmXkl28-&dataset=dfcjbcRKmkHM7-ajk8jjbff$&gmin=24.600000&gmax=750.500000&absc=19194p2p1p1p1p3p1p3p3p3&gds=564&idref=207548_at&annot=GRM7.

Tilley, A.E., Harvey, B.G., Heguy, A., Hackett, N.R., Wang, R. , O’Conner, T.P., Crystal, R.G. (2009). Down-regulation of the notch pathway in human airway epithelium in association with smoking and chronic obstructive pulmonary disease. Am J Respir Crit Care Med, 179(6):457. doi:10.1164/rccm.200705-795OC

Vadasz, C., Saito, M., Gyetvai, B. M., Oros, M., Szakall, I., Kovacs, K. M., Prasad, V. V. T. S., Toth, R. (2007). Glutamate receptor metabotropic 7 is cis-regulated in the mouse brain and modulates alcohol drinking. Genomics, 90(6):690. doi:10.1016/j.ygeno.2007.08.006

 


Jennifer Wagner
wagner4@wisc.edu
Updated May 11, 2009
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