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PubMed2006

A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies.

Over the last decade, gene expression microarrays have had a profound impact on biomedical research. The diversity of platforms and analytical methods available to researchers have made the comparison of data from multiple platforms challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and 'in-house' platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by quantitative real-time (QRT)-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent preprocessing, commercial arrays were more consistent than in-house arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms.

Chromosome Mapping↗
PubMed2000

Analysis of the expressed immunoglobulin variable region heavy chain gene products in paraproteins from Iranian patients with multiple myeloma.

The frequency of expression of immunoglobulin (Ig) variable region heavy (VH ) chain gene products was studied in 43 Iranian patients with mutiple myeloma (MM). The expressed VH gene families and associated cross-reactive idiotypes (CRI) were analysed by immunoblotting and ELISA, using peptide-induced polyclonal antibodies specific for VH 1-VH 6 gene families and monoclonal antibodies (MAb) recognising CRI linked to theVH 1, VH 3, VH 4 and VH 6 gene families. The results revealed that the VH 3 family (60. 5%) was the most predominant gene family. In contrast, no paraproteins were encoded by genes from the VH 2 gene family and only 2.3% were encoded by the VH 5 family. The panel of paraproteins tested rarely expressed the probed VH -associated CRI. Our results suggest that: 1-The Ig VH genes, may not be randomly expressed in the malignant plasma cells from Iranian patients with MM. 2- Some of the genes seem to be negatively selected or highly mutated, as evidenced by the lack of expression of the probed CRI.

Blotting, Western↗
PubMed1995

Glucocorticoid-remediable aldosteronism (GRA): diagnosis, variability of phenotype and regulation of potassium homeostasis.

Glucocorticoid-remediable aldosteronism (GRA) is a hereditary cause of human hypertension in which aldosterone secretion is regulated by adrenocorticotropin (ACTH). A genetic mutation which causes GRA has recently been identified in our laboratory, a hybrid or chimeric gene fusing nucleotide sequences of the 11 beta-hydroxylase and aldosterone synthase genes. The finding that these chimeric gene duplications are sensitive and specific markers for GRA allows for a simple, direct genetic test for this disorder. In preliminary studies, we found a wide range of blood pressure levels (including normotension) in affected GRA subjects. Studies to data indicate that this is not related to environmental factors such as sodium intake. Another possibility is that chimeric gene expression is variable, with low blood pressure subjects having reduced gene expression. However, the data have not demonstrated differences in steroid levels in subjects with severe versus mild hypertension. In fact, it is likely that the wide range in blood pressure levels in affected subjects involves interaction of other systems which control blood pressure. Preliminary data in two kindreds suggest that blood pressure levels are reciprocally related to levels of urinary kallikrein excretion, supporting the notion that GRA is a hypertension-predisposing syndrome, with the resultant blood pressure the interaction of the gene mutation with other blood pressure regulatory systems. Although GRA is a mineralocorticoid excess state, as evidenced by profoundly suppressed levels of plasma renin activity, we have observed (contrary to the reported literature) that normokalemia is a typical finding. In one large normokalemic pedigree, preliminary findings indicate that these subjects have a normal capacity to excrete potassium.(ABSTRACT TRUNCATED AT 250 WORDS)

Blood Pressure↗
PubMed2005

Expression profiling of gastric cancer samples by oligonucleotide microarray analysis reveals low degree of intra-tumor variability.

AIM: Gene expression profiling provides an unique opportunity to gain insight into the development of different types of gastric cancer. Tumor sample heterogeneity is thought to decrease the sensitivity and tumor specificity of microarray analysis. Thus, microdissection and pre-amplification of RNA is frequently performed. However, this technique may also induce considerable changes to the expression profile. To assess the effect of gastric tumor heterogeneity on expression profiling results, we measured the variation in gene expression within the same gastric cancer sample by performing a gene chip analysis with two RNA preparations extracted from the same tumor specimen. METHODS: Tumor samples from six intestinal T2 gastric tumors were dissected under liquid nitrogen and RNA was prepared from two separate tumor fragments. Each extraction was individually processed and hybridized to an Affymetrix U133A gene chip covering approximately 18 000 human gene transcripts. Expression profiles were analyzed using Microarray Suite 5.0 (Affymetrix) and GeneSpring 6.0 (Silicon Genetics). RESULTS: All gastric cancers showed little variance in expression profiles between different regions of the same tumor sample. In this case, gene chips displayed mean pair wise correlation coefficients of 0.94+/-0.02 (mean+/-SD), compared to values of 0.61+/-0.1 for different tumor samples. Expression of the variance between the two expression profiles as a percentage of "total change" (Affymetrix) revealed a remarkably low average value of 1.18+/-0.78 for comparing fragments of the same tumor sample. In contrast, comparison of fragments from different tumors revealed a percentage of 24.4+/-4.5. CONCLUSION: Our study indicates a low degree of expression profile variability within gastric tumor samples isolated from one patient. These data suggest that tumor tissue heterogeneity is not a dominant source of error for microarray analysis of larger tumor samples, making total RNA extraction an appropriate strategy for performing gene chip expression profiling of gastric cancer.

Aged↗
PubMed2004

Housekeeping gene variability in normal and cancerous colorectal, pancreatic, esophageal, gastric and hepatic tissues.

Careful normalization is essential for the accurate quantitation of mRNA levels in biopsy-sized tissue samples. Commonly, normalization of the target gene with an endogenous standard, mainly housekeeping genes (HKGs), is applied. However, differences in the expression levels of endogenous reference genes have been reported between different tissues and pathological states. Therefore, we were challenged to identify a set of endogenous reference genes whose mRNA expression levels would not change significantly between normal and cancerous tissues. Quantitative real-time PCR (Q-RT-PCR) analysis was applied to evaluate the variability in gene expression among 21 classical housekeeping genes in colorectal, pancreatic, esophageal and gastric cancer as well as in liver metastases in comparison to the corresponding normal tissue. Our results indicated that some housekeeping genes were candidates with relatively stable gene expression in several of the investigated tissues but for most of the HKGs under investigation our data have revealed distinct differences in the extent of variability in gene expression between the different tissues and pathological states. However, for each of the five tissues investigated we found a group of genes that were expressed at a constant level thus representing a panel of candidates that we can recommend as housekeeping genes in the respective tissue types. In summary, our results can be used as guidance for other scientists studying various carcinomas for tissue-specific selection of the optimal housekeeping gene (HKG) to be used in normalizing target gene expression.

Colorectal Neoplasms↗
PubMed2003

Constitutive androstane receptor and pregnane X receptor gene expression in human liver: interindividual variability and correlation with CYP2B6 mRNA levels.

The constitutive androstane receptor (CAR) and pregnane X receptor (PXR) mediate the expression of mammalian cytochrome p450 (p450) 2B genes, including CYP2B6 in humans. Large interindividual differences exist in hepatic CYP2B6 expression, but the molecular basis for this variability is not well understood. In the present study, we developed real-time polymerase chain reaction methods to measure CYP2B6, CAR, and PXR mRNA expression and compared the levels in a panel of 12 individual human liver samples. The transcripts of CAR and CYP2B6 were present in all the samples analyzed, whereas those of PXR were detectable in all but one sample. A striking finding was the 240-fold interindividual variability in hepatic CAR mRNA levels, which was similar to the variability (278-fold) in CYP2B6 mRNA levels but greater than the 27-fold variability in PXR mRNA expression. Additional analysis revealed positive and statistically significant correlations between the mRNA levels of CAR and CYP2B6 (r(2) = 0.63, p = 0.002), PXR and CYP2B6 (r(2) = 0.75. p < 0.001), and CAR and PXR (r(2) = 0.86, p < 0.001). In summary, substantial interindividual differences exist in hepatic CAR and, to a lesser extent, PXR gene expression. The variability in the abundance of these transcription factors may contribute to the large interindividual differences in CYP2B6 gene expression in human liver.

Aryl Hydrocarbon Hydroxylases↗
PubMed2003

Variability of antioxidant-related gene expression in the airway epithelium of cigarette smokers.

Cigarette smoking is the major risk factor for developing chronic bronchitis, yet only 15-20% of smokers develop this disorder. Because oxidants are the major mechanism of smoking-induced airway damage, we hypothesized that smoking is associated with upregulation of various antioxidant-related genes in the airway epithelium, but the magnitude of the response shows high inter-individual variability. Microarray analysis was used to assess levels of expression of 44 antioxidant-related genes in four categories (catalase/superoxide dismutase family; glutathione metabolism; redox balance; and pentose phosphate cycle) in bronchoscopy-obtained airway epithelium of matched cohorts (13 current smokers, 9 nonsmokers), none of whom had lung disease. There was minimal variation in gene expression levels within the same individual (right versus left lung or over time), but significant upregulation of 16/44 antioxidant-related genes in smoker epithelium compared with nonsmokers. Subgroups of smokers were identified with clusters of expression levels of antioxidant-related genes. We propose that the antioxidant-related genes demonstrating the most variability in the level of expression in smokers may be useful genetic markers in epidemiologic studies assessing susceptibility to smoking-induced chronic bronchitis.

Adult↗
PubMed1996

Structural diversity of monoclonal CD4 antibodies and their capacity to block the HIV gp120/CD4 interaction.

A number of monoclonal antibodies have been raised against CD4, the receptor on T cells for the HIV envelope glycoprotein gp120. In the present paper we describe biological activities and sequence analysis of seven CD4 MAb. Five of these MAb preparations compete with HIV/gp120 for CD4 binding. The sequences of the variable regions for these MAb were determined in order to ascertain any correlation with selective V gene usage. A relationship was found between the expressed variable region genes and the CD4 recognition pattern. The VH genes that are used can be subdivided into two major groups expressing either a VH gene belonging to the J558 family or to the VGam family. The usage of the VL genes varies, indicating that the epitope specificity is predominantly determined by the rearranged VH genes. The distinct cross-reactivity pattern of these MAb also correlates with their capacity to block binding of recombinant gp120 to CD4 in vitro. Although five of these MAb were able to block gp120 binding none of the CDR sequences shows a relevant homology to the gp120 sequence. This indicates a steric hinderence mechanism for blocking gp120 binding and not a direct interaction with the receptor binding site on CD4. The data also confirm the failure of these MAb as a potential target for receptor mimicry.

Amino Acid Sequence↗
PubMed2004

[Cloning, ligation and expression of the variable region genes of the monoclonal antibody against human HnRNPA2/B1].

OBJECTIVE: To clone the variable region genes of the monoclonal antibody (McAb) against human heterogeneous nuclear ribonucleoprotein A2/B1 (HnRNPA2/B1), ligate them to assemble single chain Fv (ScFv) gene and express in Escherichia coli. METHODS: The specificity of the anti-HnRNPA2/B1 McAb 3E8 to synthetic HnRNPA2/B1 peptide, HnRNPA2/B1 protein in lung cancer cells were examined by dot-immunobinding assay, Western blot and immunohistochemistry. The variable region genes of heavy chain (VH) and light chain (VL) were amplified from hybridoma cell by reverse transcription-polymerase chain reaction(RT-PCR), and then were linked by a linker peptide using SOE-PCR (splicing by overlap extension-PCR) to construct recombination ScFv gene. The latter was cloned into the expression vector pET28 (a+) and expressed in E coli BL21. The expressed product was identified by SDS-PAGE and competitive ELISA inhibition test. RESULTS: It was shown that the McAb combined specifically with synthetic HnRNPA2/B1 peptide and HnRNPA2/B1 protein in three lung cancer cells. The cloned VH gene and VL gene were 345 bp and 309 bp respectively and were linked successfully to obtain ScFv gene. The ScFv protein was expressed in the form of inclusion body, with molecular weight of 28,000 and immunoreactivity to HnRNPA2/B1. CONCLUSION: VH gene, VL gene and ScFv gene of anti-HnRNPA2/B1 antibody were cloned, constructed and functionally expressed in E coli. These results provide the experimental basis for elucidating the role of HnRNPA2/B1 in lung cancer.

Adenocarcinoma↗
PubMed1993

Increased IL-6 gene expression and production in patients with common variable immunodeficiency.

We have studied IL-6 gene expression and production by in vitro stimulated peripheral blood mononuclear cells (PBMC) isolated from common variable immunodeficiency (CVI) patients. A strong hybridization signal for the IL-6 probe was observed in mRNA extracted from phytohaemagglutinin (PHA)- and PHA/phorbol myristate acetate (PMA)-stimulated PBMC from most of 12 CVI patients analysed. IL-6 production by PHA-stimulated PBMC from 28 CVI patients was evaluated in ELISA and found to be significantly (P < 0.0001) higher than in normal controls. IL-6 production, however, did not correlate with the lymphocyte populations examined, nor with the absolute number of monocytes. We have also showed that IL-6 was able to increase IgM secretion by several Epstein-Barr virus (EBV)-transformed cell lines derived from both normal donors and CVI patients, but it failed to modify substantially the amounts of IgM and IgG produced in vitro by PBMC derived from CVI patients and activated with pokeweed mitogen (PWM) or anti-IgM. Our data indicate that IL-6 gene expression and production is increased in CVI, but CVI cells do not respond to IL-6 with increased production of immunoglobulin.

Adolescent↗
PubMed1990

Control of DNA structure and gene expression.

In the usual metabolic control theory, the concentrations of enzymes are considered to be parameters rather than variables, i.e., they remain constant as the system relaxes to a new steady state. They can only be reset by interventions. This type of control analysis is useful for understanding principles of metabolic control, and for understanding metabolic changes that are too quick or in too limited a metabolic system to involve changes in gene expression. In actual living systems, metabolic changes are often accompanied by changes in gene expression. In this contribution we shall illustrate how metabolic control analysis is enriched when gene expression is variable. To discuss the new principles emerging in control analysis with variable gene expression, we shall first discuss theoretical model systems. In the first, the number of genes is fixed, but the concentrations of mRNA and enzymes are determined by the activities of RNA polymerase, RNAases, ribosomes and proteases. In a second, there is feedback repression by a metabolite at the level of translation. New coefficients quantifying the strength of regulatory loops will be defined. Also coefficients that indicate to what extent these regulatory strengths themselves are controlled by system parameters, are defined and provided with a summation theorem. The experimental model system we employ, addresses the phenomenon that in prokaryotes, transcription rates are influenced by the extent of supercoiling of the DNA. This includes the transcription of the genes encoding the two enzymes (DNA gyrase and topoisomerase I) involved in the regulation of DNA supercoiling. In vitro the activity of DNA gyrase is influenced by the hydrolytic free energy of ATP. We shall present experimental evidence that the cellular free-energy state influences DNA supercoiling. We shall also discuss experiments inspecting the effect of active transcription on active DNA supercoiling. Also this system will be analyzed in terms of the control analysis with variable gene expression; here the four hierarchical levels (DNA, RNA, enzymes, metabolites) interact, adding complexity to the control analysis.

Computer Simulation↗
PubMed2003

A novel mutation in the PSEN2 gene (T430M) associated with variable expression in a family with early-onset Alzheimer disease.

BACKGROUND: Autosomal dominant early-onset Alzheimer disease is a heterogeneous condition that has been associated with mutations in 3 different genes: the amyloid precursor protein (APP), presenilin 1 (PSEN1), and presenilin 2 (PSEN2) genes. Most cases are due to mutations in the PSEN1 gene, whereas mutations in the APP and PSEN2 genes are rare. OBJECTIVE: To describe a novel mutation in the PSEN2 gene associated with early-onset autosomal dominant Alzheimer disease. PATIENTS AND METHODS: The proband was a 49-year-old individual who displayed progressive dementia beginning at age 45 years. One of the parents and one of the grandparents had developed dementia at ages 64 years and 60 years, respectively, and 1 sibling had mild cognitive impairment. Some family members also had Tourette syndrome. Mutation analysis of the APP, PSEN1, PSEN2, and tau (TAU) genes was performed. Apolipoprotein E (APOE) was also genotyped. RESULTS: We found a missense mutation at codon 430 of the PSEN2 gene that predicts a threonine-to-methionine substitution. This mutation was detected in the affected individuals and in 1 cognitively healthy sibling. The mutation was absent in 260 control chromosomes. The normal amino acid was conserved in the human and mouse PSEN1 and mouse PSEN2 homologues. No influence of the APOE genotype was observed. CONCLUSIONS: We have found a novel mutation in the PSEN2 gene in a family with early-onset Alzheimer disease. The variation in the age at onset confirms that PSEN2 mutations are associated with variable clinical expression.

Age of Onset↗
PubMed2005

Robustness of gene expression profiling in glioma specimen samplings and derived cell lines.

One of the most promising applications of microarrays is class distinction through gene expression profiling as a diagnostic tool. However, as there is apparent spatial heterogeneity in the morphology of cancer cells within a tumor, it is unclear if tumor sampling can be applied and yield consistent signals. In this report, we examined six brain tumors, four glioblastoma, and two oligodendroglioma biopsies. The six brain tumor tissues from two distinct different classes were dissected in four distinct areas and gene expression was profiled using microarrays. We used hierarchical clustering to compare the variability of gene expression profiles between spatially distinct biopsies of the same tumor as compared to the variability between tumors of the same histologic group. We conclude that, in general, repeat spatially distinct samples are not needed for microarray experiments and the gene expression signatures are robust across the tumor. Predominantly, variation was much greater between samples from different patients than from the multiple samplings of given tumor. Further, we compared biopsy expression profiles to the cell lines derived from those tissues. In general, the tumor cell lines vary greatly from the parental tissues and cluster more strongly with each other than the parental tissue. We select and examine the set of genes altered in expression to allow adaptation to cell culture.

Brain Neoplasms↗
PubMed1990

Variable expression of the uteroglobin gene following the administration of norethisterone and its A-ring reduced metabolites.

Enzyme-mediated A-ring reduction of norethisterone (NET) results in the transformation of a molecule with potent intrinsic progestational activity into neutral derivatives with estrogen-like effects. To ascertain whether these structural modifications of NET are able to modify the uteroglobin (U) gene (G) expression, a series of experiments assessing the UG products after the administration of NET and its reduced A-ring metabolites were conducted in prepubertal female rabbits. Synthesis of endometrial uteroglobin and its specific mRNA were studied in animals following the administration of NET, 5 alpha-dihydro NET,3 beta,5 alpha-tetrahydro NET and progesterone. Animals treated with either estradiol or vehicle alone served as controls. The uteroglobin content in uterine flushings and cytosols was determined by immunodiffusion and polyacrilamide gel electrophoresis techniques and by a specific double-antibody radioimmunoassay, while the U mRNA synthesis was assessed by its molecular hybridization to [alpha 32P]d-ATP uteroglobin cDNA. NET induced a significant increase of the uterine content of uteroglobin similar to that observed with progesterone with a simultaneous increase on U mRNA synthesis. On the contrary, 5 alpha-NET and 3 beta,5 alpha-NET induced very little, if any uteroglobin synthesis with a concomitantly low U mRNA production as compared with NET; thus exhibiting a similar effect to that observed in estradiol-treated animals. The overall results were interpreted as demonstrating that the enzyme mediated structural changes of NET which occur at the target organs induce variable expression of the uteroglobin gene. The data indicate that the rabbit uteroglobin gene products are suitable molecular markers to evaluate the hormonal potency of contraceptive synthetic progestins and their derivatives.

Animals↗
PubMed2004

The use of real time rtPCR to quantify inflammatory mediator expression in leukocytes from patients with severe sepsis.

Real-time reverse transcriptase polymerase chain reaction (RT rtPCR) was used to quantify the pattern of inflammatory mediator mRNA expression in circulating leukocytes from adult patients diagnosed with severe sepsis. We analysed 29 blood samples from 26 severely septic patients with different septic sources and eight samples from eight healthy adult volunteers. RT rtPCR was used to quantify mRNA expression of 21 different inflammatory mediators in peripheral leukocytes. The median variability in gene expression in the sepsis patients was 10.5 times greater than the variability of the healthy comparison group. We found a significant change in the regulation for the following genes: C5aR (20-fold, P < 0.001), IL-8 (29-fold, P < 0.001), MMP9 (72-fold, P < 0.001), HSP70 (2.4-fold, P = 0.02), and RIP2 (1.8-fold, P < 0.04) were up-regulated. Conversely the median expression of IFNgamma, and IL-6 were zero (P < 0.001), and mtHSP (0.4-fold, P = 0.02) was significantly down-regulated. Using linear discriminant analysis, IFNgamma, IL-12, and TLR4 were correlated to a negative outcome. Different septic sources (peritonitis, burn, pneumonia and musculo-skeletal infections) resulted in significantly different mRNA patterns. The RT rtPCR is a useful tool to monitor the immune response in septic patients. We found a very high variability in inflammatory mediator expression among septic patients compared to healthy volunteers. This suggests that any future immune-modulatory therapy may need to be individualized to the patient's requirements as monitored by RT rtPCR. Different sources of sepsis may result in markedly different activation patterns.

Adult↗
PubMed1986

T cell-specific gamma genes in C57BL/10 mice. Sequence and expression of new constant and variable region genes.

The T cell-specific gamma genes in C57BL/10 (B10) mice have been analyzed. Based on the cDNA sequences of these genes from antigen-specific MHC-restricted cytotoxic T cells, we found that the repertoire of these genes is not as limited as previously postulated (8). T cells from the B10 mice express an identical copy of V gamma J gamma C gamma (V gamma 10.8A-JC gamma 10.5) transcript previously found in T cells of BALB/c mice. In addition, a potentially functional mRNA using V gamma 10.8B and newly identified J gamma and C gamma gene segments were found. The new J gamma C gamma (JC gamma 10.8) is located 5' to the inverted V gamma 10.8B in the germline DNA of both B10 and BALB/c mice. This new C gamma is only 77 and 66% homologous to the C gamma 10.5 at the nucleotide and deduced protein sequences, respectively, thus making it a potential isotype of the C gamma genes reported previously. The V gamma 5.7, J gamma 2.3 gene segments and pseudogene C gamma 7.5 found in the germline DNA of BALB/c mice are absent in B10 mice. The loss of this gamma chain pseudogene in the B10 mouse strain, and the retention of all potentially functional V gamma, J gamma, and C gamma genes with highly conserved coding sequences supports the importance of these genes.

Amino Acid Sequence↗
PubMed2000

Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations.

We present statistical methods for analyzing replicated cDNA microarray expression data and report the results of a controlled experiment. The study was conducted to investigate inherent variability in gene expression data and the extent to which replication in an experiment produces more consistent and reliable findings. We introduce a statistical model to describe the probability that mRNA is contained in the target sample tissue, converted to probe, and ultimately detected on the slide. We also introduce a method to analyze the combined data from all replicates. Of the 288 genes considered in this controlled experiment, 32 would be expected to produce strong hybridization signals because of the known presence of repetitive sequences within them. Results based on individual replicates, however, show that there are 55, 36, and 58 highly expressed genes in replicates 1, 2, and 3, respectively. On the other hand, an analysis by using the combined data from all 3 replicates reveals that only 2 of the 288 genes are incorrectly classified as expressed. Our experiment shows that any single microarray output is subject to substantial variability. By pooling data from replicates, we can provide a more reliable analysis of gene expression data. Therefore, we conclude that designing experiments with replications will greatly reduce misclassification rates. We recommend that at least three replicates be used in designing experiments by using cDNA microarrays, particularly when gene expression data from single specimens are being analyzed.

DNA, Complementary↗