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Biomedical subjects

Mark A Watson

Publications and source records attributed to Mark A Watson.

At least 37 records · Page 2Linked to original sources
PubMed2004

Expression profiles provide insights into early malignant potential and skeletal abnormalities in multiple endocrine neoplasia type 2B syndrome tumors.

Identifying the molecular basis for genotype-phenotype correlations in human diseases has direct implications for understanding the disease process and hence for the identification of potential therapeutic targets. To this end, we performed microarray expression analysis on benign (pheochromocytomas) and malignant (medullary thyroid carcinomas, MTCs) tumors from patients with multiple endocrine neoplasia (MEN) type 2A or 2B, related syndromes that result from distinctive mutations in the RET receptor tyrosine kinase. Comparisons of MEN 2B and MEN 2A MTCs revealed that genes involved in the process of epithelial to mesenchymal transition, many associated with the tumor growth factor beta pathway, were up-regulated in MEN 2B MTCs. This MEN 2B MTC profile may explain the early onset of malignancy in MEN 2B compared with MEN 2A patients. Furthermore, chondromodulin-1, a known regulator of cartilage and bone growth, was expressed at high levels specifically in MEN 2B MTCs. Chondromodulin-1 mRNA and protein expression was localized to the malignant C cells, and its high expression was directly associated with the presence of skeletal abnormalities in MEN 2B patients. These findings provide molecular evidence that associate the previously unexplained skeletal abnormalities and early malignancy in MEN 2B compared with MEN 2A syndrome.

Gene Expression Profiling↗
PubMed2004

Density-functional generalized-gradient and hybrid calculations of electromagnetic properties using Slater basis sets.

In this paper we extend our density-functional theory calculations, with generalized gradient approximation and hybrid functionals, using Slater-type orbitals (STOs), to the determination of second-order molecular properties. The key to the entire methodology involves the fitting of all STO basis function products to an auxiliary STO basis, through the minimization of electron-repulsion integrals. The selected properties are (i) dipole polarizabilities, (ii) nuclear magnetic shielding constants, and (iii) nuclear spin-spin coupling constants. In all cases the one-electron integrals involving STOs were evaluated by quadrature. The implementation for (ii) involved some complexity because we used gauge-including atomic orbitals. The presence of two-electron integrals on the right-hand side of the coupled equations meant that the fitting procedure had to be implemented. For (iii) in the hybrid case, fitting procedures were again required for the exchange contributions. For each property we studied a number of small molecules. We first obtained an estimate of the basis set limit using Gaussian-type orbitals (GTOs). We then showed how it is possible to reproduce these values using a STO basis set. For (ii) a regular TZ2P quality STO basis was adequate; for (i) the addition of one set of diffuse functions (determined by Slater's rules) gave the required accuracy; for (iii) it was necessary to add a set of 1s functions, including one very tight function, to give the desired result. In summary, we show that it is possible to predict second-order molecular properties using STO basis sets with an accuracy comparable with large GTO basis sets. We did not encounter any major difficulties with either the selection of the bases or the implementation of the procedures. Although the energy code (especially in the hybrid case) may not be competitive with a regular GTO code, for properties we find that STOs are more attractive.

Journal Article↗
PubMed2004

Mammaglobin is associated with low-grade, steroid receptor-positive breast tumors from postmenopausal patients, and has independent prognostic value for relapse-free survival time.

PURPOSE: The tumor mRNA expression levels of mammaglobin, a novel breast-specific and breast cancer-associated marker, were correlated with disease outcome in 280 patients with primary breast cancer. PATIENTS AND METHODS: Mammaglobin expression levels were assessed by quantitative reverse transcriptase polymerase chain reaction in frozen tumor tissue from breast cancer patients with a median age of 60 years (range, 30 to 88 years) and a median follow-up of 85 months (range, 2 to 169 months). RESULTS: High expression levels were associated with low-grade tumors (P =.018), with positive estrogen and progesterone receptor status (P <.001), and postmenopausal status (P =.010). In the analysis of all patients, low tumor mammaglobin expression levels predicted an early relapse both in Cox univariate (hazard ratio [HR], 0.52; 95% CI, 0.34 to 0.79; P =.002) and multivariate regression analyses corrected for the traditional prognostic factors (HR, 0.55; 95% CI, 0.35 to 0.88; P =.012). The association of mammaglobin expression with the rate of relapse was particularly favorable in patients who received adjuvant tamoxifen treatment (HR, 0.35; 95% CI, 0.17 to 0.71; P =.004). CONCLUSION: These results demonstrate that the assessment of the tumor mRNA expression level of the breast-specific protein mammaglobin could be useful to stratify patients for individual adjuvant treatment strategies.

Adult↗
PubMed2004

Ganglion-specific patterns of diabetes-modulated gene expression are established in prevertebral and paravertebral sympathetic ganglia prior to the development of neuroaxonal dystrophy.

In both humans and animal models, diabetic sympathetic autonomic neuropathy is associated with the selective development of markedly enlarged distal axons and nerve terminals (neuroaxonal dystrophy, NAD). NAD occurs in the prevertebral superior mesenteric and celiac ganglia (SMG-CG), but not in the paravertebral superior cervical ganglion (SCG). To identify molecular differences between these ganglia that may explain their selective vulnerability to NAD, we have examined global gene expression patterns in control and diabetic rat sympathetic ganglia before and after the onset of structural evidence of NAD. As predicted, major differences in transcriptional profiles exist between SCG and SMG-CG in normal young adult animals including, but not limited to, known differences in neurotransmitter-related gene expression. Gene expression patterns of diabetic SMG-CG and SCG, prior to the development of NAD lesions, also differ from their age-matched non-diabetic counterparts. However, diabetes has ganglion-specific effects on gene expression; of approximately 110 transcripts that were differentially expressed between diabetic and control sympathetic ganglia, only 5 were differentially expressed as a result of diabetes in both SCG and SMG-CG. Genes involving synapse and mitochondrial structure and function, oxidative stress, and glycolysis were highly represented in the differentially expressed gene set. Differences in the number of synapse-related gene alterations in diabetic SMG-CG (18 genes) versus SCG (2 genes) prior to the onset of NAD may also well explain the selective development of NAD in the SMG-CG. These results provide support for the specificity of diabetes-modulated gene expression for selected neuronal subpopulations of sympathetic noradrenergic neurons.

Animals↗
PubMed2004

Gene expression profiling reveals unique molecular subtypes of Neurofibromatosis Type I-associated and sporadic malignant peripheral nerve sheath tumors.

Malignant peripheral nerve sheath tumors (MPNSTs) are highly aggressive Schwann cell neoplasms that are frequently associated with Type I Neurofibromatosis (NF1) and respond poorly to current therapeutic regimens. To better understand the molecular heterogeneity of these tumors, we performed gene expression profiling on 25 NF1-associated and 17 sporadic MPNSTs using oligonucleotide microarrays representing approximately 8100 unique human gene transcripts. Using several previously reported statistical approaches, we were unable to identify a molecular signature that could reliably distinguish between NF1-associated and sporadic MPNSTs in independent training and test sample sets. However, using an unsupervised clustering approach, we identified an extensive gene expression signature that distinguished 9 of the 42 tumors analyzed. This signature corresponded to relative overexpression of transcripts associated with neuroglial differentiation (NCAM, MBP, L1CAM, P1P) and relative down-regulation of proliferation and growth factor associated transcripts (IGF2, FGFR1, MDK, Ki67). All tumors with this gene expression signature lacked expression of EGFR and all but one tumor were derived from patients with NF1. However, there were no other obvious associations with histological grade, tumor site, metastasis, recurrence, age, or patient survival. We conclude that distinct molecular classes of MPNST exist and that the ability to stratify these tumors based on unique and biologically relevant gene expression profiles may be important for future targeted therapeutics.

Adolescent↗
PubMed2004

Mammaglobin-based strategies for treatment of breast cancer.

Mammaglobin is a gene that is expressed almost exclusively in the normal breast epithelium and human breast cancer. It is a member of the secretoglobin gene family and forms a heterodimer with lipophilin B. We have focused on the tissue-specificity of mammaglobin as a potential mechanism for the specific killing of breast cancer cells. By elucidating the promoter region of mammaglobin, we hope to utilize this site as a method for turning on the apoptosis inducer gene, Bax, in breast cancer cells. The Bax gene will only be expressed at levels necessary to induce apoptosis in mammaglobin positive cells. This would include > 80% of all breast cancers and some normal breast epithelium. This type of targeted killing could be conceptualized as a biochemical mastectomy, that is, genetic ablation of breast tumor cells and perhaps non-malignant breast epithelium while preserving the adipose and stromal components of the breast. Work is also being done to address the binding specificity of the secreted mamaglobin protein. There is early evidence that the mammaglobin heterodimer may in fact bind to breast and breast cancer cells. If this finding is validated, this creates the possibility that mammaglobin can be tagged with radioisotope or toxin, so that binding of the tagged-mammaglobin complex results in the specific killing of that breast cancer cell. Finally, mammaglobin is being explored as a target for immune-based interventions. In vitro studies have demonstrated that T cell-mediated immune responses can be induced against mammaglobin-derived peptides expressed by MHC molecules on tumor cells and antigen-presenting cells.

Animals↗
PubMed2003

Murine cytomegalovirus paralyzes macrophages by blocking IFN gamma-induced promoter assembly.

Macrophages (M phi) are activated by IFN gamma and are important cellular targets for infection by human and murine cytomegalovirus (MCMV), making it advantageous for CMVs to block IFN gamma-induced M phi differentiation. We found that MCMV infection inhibited IFN gamma regulation of many genes in M phi. MCMV infection blocked IFN gamma responses at the level of transcription without blocking Janus kinase/signal transducer and activator of transcription pathway activation and targeted IFN response factor 1- and class II transactivator-dependent and independent promoters. MCMV did not alter basal transcription from IFN gamma-responsive promoters and left the majority of cellular transcripts unchanged even after 48 h of infection. The effects of MCMV infection were specific to chromosomal rather than transiently transfected promoters. Characterization of the IFN gamma-responsive chromosomal class II transactivator promoter revealed that MCMV infection blocked IFN gamma-induced promoter assembly, allowing the virus to transcriptionally paralyze infected M phi responses while allowing basal transcription to proceed.

Animals↗
PubMed2003

Plasminogen activator inhibitor-1 gene polymorphism and colorectal cancer risk and prognosis.

Plasminogen activator inhibitor-1 (PAI-1) is a factor in urokinase-type plasminogen activator proteolytic system, which is important for tumour invasion and metastasis. Elevated PAI-1 levels in tumours are associated with poor prognosis. An insertion/deletion (4G/5G) promoter polymorphism in the PAI-1 gene affects activity of its product, the 4G/4G genotype being related to higher transcription levels. We assessed the association between the polymorphism and colorectal cancer risk in 206 cancer patients and 355 healthy controls. The results indicated that the PAI-1 gene polymorphism did not affect colorectal cancer risk. Nevertheless, within the case group, the 4G/4G genotype was associated with more advanced tumours (Dukes' C&D), whereas the 5G/5G homozygocity was associated with the Dukes' A&B tumours. The association with the 4G/4G presence was stronger in patients with proximal colon cancers (odds ratio= 6.02, 95% confidence interval, 1.15-31.54). Our results suggest that PAI-1 genotype may be a useful prognostic marker for colorectal cancer, however further specifically designed studies are needed to assess its value in this respect.

Adenocarcinoma↗
PubMed2003

Accurate and reproducible gene expression profiles from laser capture microdissection, transcript amplification, and high density oligonucleotide microarray analysis.

Gene expression profiling using high density oligonucleotide arrays is a powerful method to generate an unbiased survey of a cell's transcriptional landscape. Increasingly complex biological questions require that this approach be applicable to the small numbers of cells that are obtained from sources such as laser capture microdissection (LCM) of solid tissues. In this report, we demonstrate that two rounds of transcript amplification can generate accurate and reproducible gene expression profiles using high density oligonucleotide microarrays, starting with as little as 10 ng of total RNA. Biased amplification of the 3' end of transcripts does not have a major impact on the overall transcript profile due to the 3' bias of probe sets incorporated in the array design. Furthermore, greater than 95% of all genes detected demonstrate less than a twofold difference in expression when independent tissue dissections of identical cell populations are compared. The accuracy and technical reproducibility of the method suggests that expression profiling using transcript amplification and high density oligonucleotide microarrays can be used on a routine basis.

Breast Neoplasms↗
PubMed2003

Apolipoprotein E gene polymorphism and colorectal cancer: gender-specific modulation of risk and prognosis.

Apolipoprotein E ( ApoE ) gene polymorphism is a major factor in lipid metabolism. It has been suggested that this polymorphism can modulate colorectal tumour risk. We tested this hypothesis for colorectal cancer (CRC). ApoE genotype was determined in 206 patients with CRC and 353 healthy controls from the East Anglia region of the U.K. Compared with individuals possessing the most common epsilon 3/epsilon 3 genotype, those with the epsilon 2/epsilon 3 genotype had an increased risk of colon cancer [odds ratio (OR) = 1.91; 95% confidence interval 1.05-3.45]. However, this association was strongly affected by gender. Separate analysis of male and female subjects revealed a highly significant association in men (OR = 2.71; 95% confidence interval 1.30-5.65), but no association in women (OR = 1.01; 95% confidence interval 0.37-2.77). Likewise, the proportion of male patients with more advanced tumours (Dukes' C&D) was significantly increased among those with the ApoE epsilon 2/epsilon 3 genotype (OR = 4.16; 95% confidence interval 1.36-12.75). No significant effect of the presence of the epsilon 4 allele on CRC risk was found; however, there were no epsilon 4/epsilon 4 homozygotes among patients with proximal colon cancers. The ApoE epsilon 3/epsilon 3 majority genotype appeared to be associated with the lowest risk of CRC. These results suggest that ApoE genotype can influence both CRC risk and prognosis of the existing disease in a gender-dependent manner.

Aged↗
PubMed2002

A variable fold change threshold determines significance for expression microarrays.

The use of expression microarrays to determine bona fide changes in gene expression between experimental paradigms is confounded by noise due to variability in measurement. To assess the variability associated with transcript hybridization to commercial oligonucleotide-based microarrays, we generated a data set consisting of five replicate hybridizations of a single labeled cRNA target from three distinct experimental paradigms, using the Affymetrix human U95 GeneChip set. We found that the variability of expression level in our data set is intensity-specific. We quantified the observed variability in our data set in order to determine significant changes in gene expression. LOESS fitting to a plot of the standard deviation of replicates assigned a variability associated with a specific intensity. This allowed for the calculation of a "variable fold-change" threshold for any absolute intensity at any level of statistical confidence. Testing of this method indicates that it removes intensity-specific bias and results in a 5- to 10-fold reduction in the number of false-positive changes. We suggest that this approach can be widely used to improve prediction of significant changes in gene expression for oligonucleotide-based microarray experiments and reduce false leads, even in the absence of replicates.

Gene Expression Profiling↗
PubMed2002

Comparative gene expression profile analysis of neurofibromatosis 1-associated and sporadic pilocytic astrocytomas.

Pilocytic astrocytomas (PAs) are WHO grade I brain tumors that do not typically progress to more malignant grades of astrocytoma. Whereas there have been significant advances in the molecular genetics of high-grade astrocytomas, relatively little is known about the genetic changes associated with PA formation. In an effort to better characterize these low-grade neoplasms, we compared the gene expression profiles of six sporadic and two neurofibromatosis 1-associated PAs with other tissues and cell lines of both astrocytic and oligodendroglial origin. Hierarchical cluster analysis of gene expression data clearly delineated PAs from low-grade oligodendrogliomas and normal white matter. The two NF1-associated tumors and one of the sporadic PAs displayed expression profiles that were more closely related to those of cultured normal human fetal astrocytes. However, PAs also expressed individual genes typically associated with oligodendroglial lineage (e.g., proteolipid protein and PMP-22). The expression patterns of specific genes (e.g., ApoD) were unique to PA tumors, whereas genetic changes characteristic of high-grade astrocytomas were not encountered. Differential expression of two transcripts, neural cellular adhesion molecule and connexin-43, was confirmed at the protein level, suggesting that these cell adhesion molecules might be particularly important in the molecular pathogenesis of these tumors. We conclude that PAs are genetically unique gliomas with gene expression profiles that resemble those of fetal astrocytes and, to a lesser extent, oligodendroglial precursors.

Astrocytoma↗
PubMed2002

Mouse glioma gene expression profiling identifies novel human glioma-associated genes.

Based on previous studies demonstrating increased RAS activity in human astrocytomas, we developed a transgenic mouse model (B8) that targets an activated RAS molecule to astrocytes. Within 3 to 4 months after birth, these mice develop high-grade astrocytomas that are histologically identical to human astrocytomas. To characterize genetic events associated with B8 mouse astrocytoma formation, we employed comparative gene expression profiling of wild-type cultured mouse astrocytes, non-neoplastic B8 astrocytes, B8 astrocytoma cultures, and two other astrocytoma cultures from independently derived RAS transgenic mouse lines. We identified several classes of gene expression changes, including those associated with the non-neoplastic state in the B8 transgenic mouse, those associated with astrocytoma formation, and those specifically associated with only one of the three independently derived transgenic mouse astrocytomas. Differential expression of several unique genes was confirmed at the protein level in both the RAS transgenic mouse astrocytomas and two human glioblastoma multiforme cell lines. Furthermore, reexpression of one of these downregulated astrocytoma-associated proteins, GAP43, resulted in C6 glioma cell growth suppression. The use of this transgenic mouse model to identify novel genetic changes that might underlie the pathogenesis of human high-grade astrocytomas provides a unique opportunity to discover future targets for brain tumor therapy.

Animals↗
PubMed2002

Mantel statistics to correlate gene expression levels from microarrays with clinical covariates.

Mantel statistics provide an additional step to standard approaches in the analysis of gene expression and covariate data, allow the calculation of standard statistics such as correlation, partial correlation, and regression coefficients, and, with permutation tests, provide P values for these statistics to relate the sample covariates to the expression levels. In this article we describe the Mantel statistics and illustrate their use and interpretation with data from a study of seven human oligodendrogliomas (brain tumors) where expression levels of 1013 genes and five covariates were previously analyzed using standard approaches. In the previous analysis of these data, qualitative relationships were found between gene expressions and two of the clinical covariates. We show in this article how the Mantel statistics are able to formally quantify and provide P values to determine statistical significance of these relationships. We also show how the Mantel statistics can be used to rank subsets of genes, found using standard clustering methods, in terms of differential expression across samples.

Adult↗
PubMed2002

Molecular characterization of human meningiomas by gene expression profiling using high-density oligonucleotide microarrays.

Meningiomas are common central nervous system neoplasms that exhibit remarkably diverse histopathology and biological behavior. Compared to astrocytomas, the most common central nervous system tumor, little is known about the molecular pathways critical for meningioma tumor formation and malignant progression. As an initial step toward characterizing the genetic basis of meningioma pathogenesis, we assessed cancer-related gene expression profiles of nonneoplastic leptomeningeal specimens and human meningiomas of varying World Health Organization (WHO) grade using high-density oligonucleotide microarrays. Although expression profile differences between nonneoplastic and meningioma specimens were readily discernible, the expression profile of a subset of genes could also distinguish WHO grade I from WHO grades II and III tumors. Altered expression levels of several genes identified in this study have been previously noted in meningiomas (eg, growth hormone receptor, IGFBP-7, endothelin receptor A, IGF2). However, we also identified a number of novel genes whose expression was associated with WHO grade and was confirmed by reverse transcriptase-polymerase chain reaction in a larger, independent set of meningeal tumors (n = 47). This report represents the first gene expression profiling studies of meningiomas and identifies some initial candidate genes that may provide further insights into the genetic basis for meningioma pathogenesis.

Carrier Proteins↗
PubMed2002

The Mu three-site synapse: a strained assembly platform in which delivery of the L1 transposase binding site triggers catalytic commitment.

The Mu DNA transposition reaction proceeds through a three-site synaptic complex (LER), including the two Mu ends and the transpositional enhancer. We show that the LER contains highly stressed DNA regions in the enhancer and in the L1 transposase binding site. We propose that the L1 site acts as the keystone for assembly of a catalytically competent transpososome. Delivery of L1 through HU-mediated bending completes LER assembly, provides the trigger for necessary conformational transitions in transpososome formation, and allows target capture to occur. Relief of the stress at L1 and the enhancer may help drive Mu A tetramerization and engagement of the Mu ends by the transposase active site.

Bacteriophage mu↗