Comparison of microarray-based mRNA profiling technologies for identification of psychiatric disease and drug signatures

Jurata, Linda W.; Bukhman, Yury V.; Charles, Vinod; Capriglione, Frank; Bullard, Jeffrey; Lemire, Andrew; Movafeghi, Ali; Pham, Quyen; Laeng, Pascal; Brockman, Jeffrey A.; Altar, C. Anthony

doi:10.1016/j.jneumeth.2004.04.002

Cited by 49 publications

(41 citation statements)

References 54 publications

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“…Fragmented labeled cRNA was then hybridized to the Agilent Human 1A oligo microarray (version 2) (Agilent Technologies) at 60˚C for 17 h (20,21). After washing and drying under nitrogen, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies) at 535 nm for Cy3 and 625 nm for Cy5.…”

Section: Methodsmentioning

confidence: 99%

A homologue of the Drosophila headcase protein is a novel tumor marker for early-stage colorectal cancer

Chien

Chang²,

Yang

et al. 2006

Oncol Rep

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Abstract. The altered expression of certain genes is frequently detected as a hallmark of malignant tumors. These differentially expressed genes have the potential to become molecular markers. We purified the fecal mRNA from patients with colorectal cancer to identify novel candidates by using oligonucleotide microarray hybridization. We identified 21 upregulated and 22 downregulated candidates with significantly altered expression in patient fecal samples that have not been previously characterized. A gene encoding a homologue of the Drosophila headcase protein (HECA) was further examined due to its high ranking and possible importance in some human cancers. A tendency towards increased expression of HECA was dependent upon the clinicopathological stage. In this report, healthy individuals expressed less HECA, either in their blood samples or feces. Moreover, we detected upregulated HECA in blood and fecal samples of patients with colorectal cancer, and its expression level was shown to be significantly correlated with disease status. Our data show that HECA may be an early-stage classifier of colorectal cancer that can discriminate between late-and early-stage disease. In conclusion, this study is the first to analyze differentially expressed genes in the feces of colorectal cancer patients using oligonucleotide microarrays. The data suggest that HECA expression levels in feces may be an effective classifier for early-stage colorectal cancer.

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Section: Methodsmentioning

confidence: 99%

A homologue of the Drosophila headcase protein is a novel tumor marker for early-stage colorectal cancer

Chien

Chang²,

Yang

et al. 2006

Oncol Rep

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“…8,12,16,17,21 The apoptosis pathway was selected as a possible connection between these pathways and prior reports of apoptotic genes related to lithium treatment. 38,39 Genes were extracted from the Top 5, 10, and 25% T ranks from each PLMfit microarray analyses in each brain region.…”

Section: Oligonucleotide Microarraysmentioning

confidence: 99%

“…Gene classifications: mitochondrial, proteasome, chaperone, apoptosis and response to reactive oxygen Five broad gene classifications were chosen a priori based upon reports of mitochondrial, proteasomal and heat-shock protein alterations of gene expression in mood disorders or schizophrenia. 8,12,16,17,21 The apoptosis pathway was selected as a possible connection between these pathways and prior reports of apoptotic genes related to lithium treatment. 38,39 Genes were extracted from the Top 5, 10, and 25% T ranks from each PLMfit microarray analyses in each brain region.…”

Section: Oligonucleotide Microarraysmentioning

confidence: 99%

“…[1][2][3] Various microarray profiles in mood disorder have been reported that use different microarray platforms, analysis methodology, regional differences, agonal factors and brain pH. [4][5][6][7][8][9][10][11][12][13][14] Presumably, a substantial heterogeneity in the pathophysiology of mood disorder coupled with small sample sizes and small fold changes contributes to the lack of consistency among the findings. 15 In five microarray studies a broad mitochondrial dysfunction was reported in neuropsychiatric disorders.…”

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confidence: 99%

“…14 Another microarray and proteomic study using a set of 105 DLPFC samples from the Stanley Array Collection found mitochondrial dysfunction in schizophrenia. 16 Not all microarray studies find a broad mitochondrial gene expression pattern in bipolar disorder 8,12 or schizophrenia. 10,[19][20][21] A few microarray studies in major depressive disorder (MDD) have not reported mitochondrial genes were differentially expressed in cortex.…”

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Mitochondrial-related gene expression changes are sensitive to agonal-pH state: implications for brain disorders

et al. 2006

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Mitochondrial defects in gene expression have been implicated in the pathophysiology of bipolar disorder and schizophrenia. We have now contrasted control brains with low pH versus high pH and showed that 28% of genes in mitochondrial-related pathways meet criteria for differential expression. A majority of genes in the mitochondrial, chaperone and proteasome pathways of nuclear DNA-encoded gene expression were decreased with decreased brain pH, whereas a majority of genes in the apoptotic and reactive oxygen stress pathways showed an increased gene expression with a decreased brain pH. There was a significant increase in mitochondrial DNA copy number and mitochondrial DNA gene expression with increased agonal duration. To minimize effects of agonal-pH state on mood disorder comparisons, two classic approaches were used, removing all subjects with low pH and agonal factors from analysis, or grouping low and high pH as a separate variable. Three groups of potential candidate genes emerged that may be mood disorder related: (a) genes that showed no sensitivity to pH but were differentially expressed in bipolar disorder or major depressive disorder; (b) genes that were altered by agonal-pH in one direction but altered in mood disorder in the opposite direction to agonal-pH and (c) genes with agonal-pH sensitivity that displayed the same direction of changes in mood disorder. Genes from these categories such as NR4A1 and HSPA2 were confirmed with Q-PCR. The interpretation of postmortem brain studies involving broad mitochondrial gene expression and related pathway alterations must be monitored against the strong effect of agonal-pH state. Genes with the least sensitivity to agonal-pH could present a starting point for candidate gene search in neuropsychiatric disorders. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author ManuscriptThe pathophysiology of depression and mania is largely unknown leaving open a question of which cellular pathway(s) to investigate. Gene expression screening is a powerful method for probing alterations in neural functions in mood disorder. Examining gene expression profiles has been extremely useful for establishing different phenotypes in cancer. [1][2][3] Various microarray profiles in mood disorder have been reported that use different microarray platforms, analysis methodology, regional differences, agonal factors and brain pH. [4][5][6][7][8][9][10][11][12][13][14] Presumably, a substantial heterogeneity in the pathophysiology of mood disorder coupled with small sample sizes and small fold changes contributes to the lack of consistency among the findings. 15 In five microarray studies a broad mitochondrial dysfunction was reported in neuropsychiatric disorders. 10,11,14,[16][17][18] One study of bipolar disorder (BPD) focused on a broad set of mitochondrial-related gene expression and found that in general, mitochondrial gene expression was predominantly decreased in BPD compared to controls in the dorsolateral pre-frontal cortex (DLPFC) when using Stanley samples...

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Genome‐wide Gene Expression Analysis: Practical Considerations and Application to the Analysis of T‐cell Subsets in Inflammatory Diseases

Rogge¹,

Bianchi²

2007

Chemical Biology

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Comparison of microarray-based mRNA profiling technologies for identification of psychiatric disease and drug signatures

Cited by 49 publications

References 54 publications

A homologue of the Drosophila headcase protein is a novel tumor marker for early-stage colorectal cancer

A homologue of the Drosophila headcase protein is a novel tumor marker for early-stage colorectal cancer

Mitochondrial-related gene expression changes are sensitive to agonal-pH state: implications for brain disorders

Genome‐wide Gene Expression Analysis: Practical Considerations and Application to the Analysis of T‐cell Subsets in Inflammatory Diseases

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