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At least 235 records · Page 13Linked to original sources
PubMed2006

Molecular profiling of platinum resistant ovarian cancer.

The aim of this study is to discover a gene set that can predict resistance to platinum-based chemotherapy in ovarian cancer. The study was performed on 96 primary ovarian adenocarcinoma specimens from 2 hospitals all treated with platinum-based chemotherapy. In our search for genes, 24 specimens of the discovery set (5 nonresponders and 19 responders) were profiled in duplicate with 18K cDNA microarrays. Confirmation was done using quantitative RT-PCR on 72 independent specimens (9 nonresponders and 63 responders). Sixty-nine genes were differentially expressed between the nonresponders (n=5) and the responders (n=19) in the discovery phase. An algorithm was constructed to identify predictive genes in this discovery set. This resulted in 9 genes (FN1, TOP2A, LBR, ASS, COL3A1, STK6, SGPP1, ITGAE, PCNA), which were confirmed with qRT-PCR. This gene set predicted platinum resistance in an independent validation set of 72 tumours with a sensitivity of 89% (95% CI: 0.68-1.09) and a specificity of 59% (95% CI: 0.47-0.71)(OR=0.09, p=0.026). Multivariable analysis including patient and tumour characteristics demonstrated that this set of 9 genes is independent for the prediction of resistance (p<0.01). The findings of this study are the discovery of a gene signature that classifies the tumours, according to their response, and a 9-gene set that determines resistance in an independent validation set that outperforms patient and tumour characteristics. A larger independent multicentre study should further confirm whether this 9-gene set can identify the patients who will not respond to platinum-based chemotherapy and could benefit from other therapies.

Adult↗
PubMed2005

Molecular profile of catabolic versus anabolic treatment regimens of parathyroid hormone (PTH) in rat bone: an analysis by DNA microarray.

Teriparatide, human PTH (1-34), a new therapy for osteoporosis, elicits markedly different skeletal responses depending on the treatment regimen. In order to understand potential mechanisms for this dichotomy, the present investigation utilized microarrays to delineate the genes and pathways that are regulated by intermittent (subcutaneous injection of 80 microg/kg/day) and continuous (subcutaneous infusion of 40 microg/kg/day by osmotic mini pump) PTH (1-34) for 1 week in 6-month-old female rats. The effect of each PTH regimen was confirmed by histomorphometric analysis of the proximal tibial metaphysis, and mRNA from the distal femoral metaphysis was analyzed using an Affymetrix microarray. Both PTH paradigms co-regulated 22 genes including known bone formation genes (i.e., collagens, osteocalcin, decorin, and osteonectin) and also uniquely modulated additional genes. Intermittent PTH regulated 19 additional genes while continuous treatment regulated 173 additional genes. This investigation details for the first time the broad profiling of the gene and pathway changes that occur in vivo following treatment of intermittent versus continuous PTH (1-34). These results extend previous observations of gene expression changes and reveal the in vivo regulation of BMP3 and multiple neuronal genes by PTH treatment.

Animals↗
PubMed2003

Molecular profiling of the immune response in colon cancer using protein microarrays: occurrence of autoantibodies to ubiquitin C-terminal hydrolase L3.

We implemented a protein microarray approach to identify proteins that induce a humoral response in colon cancer. Solubilized proteins from the LoVo colon adenocarcinoma cell line were separated into 1760 fractions, arrayed onto nitrocellulose-coated slides, and hybridized with individual sera from 15 newly diagnosed patients with colon cancer, 15 with lung cancer, and 15 healthy subjects. 39/1760 fractions showed enhanced reactivity with sera from patients with colon cancer (p < 0.01) relative to healthy controls. A distinct pattern of reactivity was observed with sera from colon cancer relative to lung cancer. One fraction that exhibited reactivity with 9/15 colon cancer sera was subjected to mass spectrometry leading to the identification of ubiquitin C-terminal hydrolase isozyme 3 (UCH-L3) as a constituent. To validate the occurrence of autoantibodies to UCH-L3, independent analysis was done by means of Western blots. UCH-L3 antibodies were detected in 19/43 sera from patients with colon cancer, and in 0/54 sera from subjects with lung cancer (24), colon adenoma (15) or otherwise healthy (15). Our findings indicate the occurrence of an immune response to a broad set of antigens in colon cancer and the feasibility of identifying the antigenic targets using a combination of protein microarrays and mass spectrometry.

Autoantibodies↗
PubMed2004

The effects of plant extracts on microbial community structure in a rumen-simulating continuous-culture system as revealed by molecular profiling.

An in vitro study in dual-flow continuous-culture fermentors was conducted with two different concentrations of monensin, cinnamaldehyde or garlic extract added to 1:1 forage-to-concentrate diet in order to determine their effects on selected rumen bacterial populations. Samples were subjected to total DNA extraction, restriction analysis of PCR amplified parts of 16S rRNA genes (ARDRA) and subsequent analysis of the restriction profiles by lab-on-chip technology with the Agilent's Bioanalyser 2100. Eub338-BacPre primer pair was used to select for the bacteria from the genera Bacteroides, Porphyromonas and Prevotella, especially the latter representing the dominant Gram-negative bacterial population in the rumen. Preliminary results of HaeIII restriction analysis show that the effects of monensin, cinnamaldehyde and garlic extract on the BacPre targeted ruminal bacteria are somewhat different in regard to targeted populations and to the nature of the effect. Garlic extract was found to trigger the most intensive changes in the structure of the BacPre targeted population. Comparison of the in silico restriction analysis of BacPre sequences deposited in different DNA databanks and of the results of performed amplified ribosomal DNA restriction analysis showed differences between the predicted and obtained HaeIII restriction profiles, and suggested the presence of novel, still unknown Prevotella populations in studied samples.

Acrolein↗
PubMed2004

Molecular profiling of prostate cancer.

The ability to distinguish between aggressive and nonaggressive tumors has not changed despite vast improvements in the detection of prostate cancer (PCA). To improve predictive accuracy, additional PCA-specific biomarkers must be identified and it is the emerging microarray technology and gene expression profiling that appear to be capable of achieving this goal. Through comparisons of a number of published microarray studies of PCA, several potential biomarkers appear on the horizon, including the serine protease Hepsin, a-methylacyl CoA racemase, and the human homologue of the Drosophila protein Enhancer of Zeste. Although these markers will move toward validation by eventual protein expression studies, another aspect of microarray expression, global signature expression patterns through multidimensional scaling, appears to be promising in distinguishing between aggressive and nonaggressive forms of PCA or in distinguishing PCA from benign prostatic hyperplasia or normal prostate tissue.

Gene Expression Profiling↗
PubMedDate not supplied

Calcium responses in human fibroblasts: a diagnostic molecular profile for Alzheimer's disease.

We have previously identified alterations of K+ channel function, IP3-mediated calcium release, and Cp20 (a memory-associated GTP binding protein) in fibroblasts from AD patients vs. controls. In the present study we introduce a scoring system based on these response alterations that integrates two or more alterations (and their degree) in AD vs. control fibroblasts. This scoring system generates an index that distinguishes AD patients from controls with both high specificity and sensitivity. We also show that low doses of bradykinin elicit intracellular calcium release almost exclusively in AD cell lines in an all or none fashion that provide a clear measurement of enhanced IP3-mediated function in AD vs. controls.

Aged↗
PubMed2004

Brain microglia and blood-derived macrophages: molecular profiles and functional roles in multiple sclerosis and animal models of autoimmune demyelinating disease.

Microglia and macrophages, one a brain-resident, the other a mostly hematogenous cell type, represent two related cell types involved in the brain pathology in multiple sclerosis and its autoimmune animal model, the experimental allergic encephalomyelitis. Together, they perform a variety of different functions: they are the primary sensors of brain pathology, they are rapidly recruited to sites of infection, trauma or autoimmune inflammation in experimental allergic encephalomyelitis and multiple sclerosis and they are competent presenters of antigen and interact with T cells recruited to the inflamed CNS. They also synthesise a variety of molecules, such as cytokines (TNF, interleukins), chemokines, accessory molecules (B7, CD40), complement, cell adhesion glycoproteins (integrins, selectins), reactive oxygen radicals and neurotrophins, that could exert a damaging or a protective effect on adjacent axons, myelin and oligodendrocytes. The current review will give a detailed summary on their cellular response, describe the different classes of molecules expressed and their attribution to the blood derived or brain-resident macrophages and then discuss how these molecules contribute to the neuropathology. Recent advances using chimaeric and genetically modified mice have been particularly telling about the specific, overlapping and nonoverlapping roles of macrophages and microglia in the demyelinating disease. Interestingly, they point to a crucial role of hematogenous macrophages in initiating inflammation and myelin removal, and that of microglia in checking excessive response and in the induction and maintenance of remission.

Animals↗
PubMed2006

Clinical, immunophenotypic, and molecular profiling of trisomy 12 in chronic lymphocytic leukemia and comparison with other karyotypic subgroups defined by cytogenetic analysis.

In a cohort of 130 unselected chronic lymphocytic leukemia (CLL) patients, 73 cases had normal karyotypes, 57 cases had abnormal karyotypes, and 22/57 cases carried more than one abnormality. Trisomy 12 (+12) was the most common abnormality (26/130 cases; 20%), and 17/26 cases had isolated +12. Del(13q)/t13q/-13 was detected in 19/130 cases (14.6%), and 5/19 cases had isolated del(13)(q12q14). Deletion (11)(q23) and del(17p)/-17 were detected in 5/130 cases, respectively. CD38 expression was significantly more frequent in the +12/11q/17p versus the normal/del(13q) subgroups. A significant association was detected between +12 and FMC7 positivity. IGHV-unmutated cases were significantly more frequent in the +12/11q/17p subgroups. Patients with normal karyotype/del(13q) had a longer median time to progression versus the patients in the +12/11q/17p subgroups. According to multivariate analysis, only IGHV mutation status remained a statistically significant variable for progression-free survival (PFS). Furthermore, IGHV mutation status and clinical stage at diagnosis were the only significant prognostic factors for overall survival. Among Binet-A patients, significant parameters for shorter PFS were +12 or 11q/17p aberrations, CD38 expression, and IGHV unmutated status. In multivariate analysis, only CD38 expression and IGHV-unmutated status retained statistical significance for PFS. In conclusion, trisomy 12 in CLL is characterized by considerable heterogeneity and seems to be associated with disease progression.

Adult↗
PubMed2005

Molecular profile of hyalinizing trabecular tumours of the thyroid: high prevalence of RET/PTC rearrangements and absence of B-raf and N-ras point mutations.

Hyalinizing trabecular tumour (HTT) of the thyroid is a neoplasm of follicular derivation that shares several morphological similarities with papillary thyroid carcinoma (PTC). In this study, we investigated the prevalence of B-raf point mutations, RET/PTC rearrangements and N-ras point mutations in a large HTT series (28 samples). Twenty benign thyroid lesions and 10 PTC served as control cases. A high (47%) prevalence of RET/PTC rearrangements was found in HTT. By contrast, neither B-raf nor N-ras mutations were found in HTT. These findings suggest that, although RET/PTC, N-ras, and B-raf proteins may act along the same signalling cascade, the biological and morphological outcome of their oncogenic activation is not completely overlapping. Thus, in clinical practice, the detection of B-raf mutations in a thyroid follicular tumour may prove to be a valuable tool, supplementing histological examination, and allowing a differential diagnosis between PTC and HTT.

Adult↗
PubMed2005

Molecular profiling of polycystic ovaries for markers of cell invasion and matrix turnover.

OBJECTIVE: To study gene expression profiles of connective tissue components in polycystic ovaries using complementary deoxyribonucleic acid (cDNA) array technology. DESIGN: Descriptive study of normal and polycystic human ovarian biopsy samples analyzed by cDNA array hybridizations. SETTING: Experimental laboratory research. PATIENT(S): Eight women with polycystic ovary syndrome (PCOS) and two normally cycling women treated with electrocauterization and hysterectomy, respectively. INTERVENTIONS: Ovarian biopsy samples. MAIN OUTCOME MEASURE(S): Expression levels of 588 genes involved in cellular invasion, extracellular matrix (ECM) turnover, and cell-ECM interactions in polycystic ovaries. RESULT(S): A majority of the 30 genes down-regulated in PCOS ovaries represented those related to cell adhesion and motility, as well as angiogenesis, followed by regulators of cell cycle and growth. The 14 up-regulated genes represented those regulating cell fate and development, growth factors, cytokines, chemokines, and cell-cell interactions. Of the 44 transcripts exhibiting marked changes in the cDNA array analysis, only one - proliferating cell nuclear antigen messenger ribonucleic acid (PCNA mRNA) - was systematically down-regulated; 2 transcripts, for CDC27HS protein and CD9 antigen, were down-regulated in 7 out of 8 PCOS samples. CONCLUSION(S): The present data suggest that gene expression profiling may become a useful tool to classify PCOS patients into subgroups with different etiologies. Genome-wide expression profiling using microarrays should be performed to better understand the metabolic derangement(s) in PCOS.

Adult↗
PubMed2004

Molecular profiling of microbial communities associated with seeds of Beta vulgaris subsp. Vulgaris (sugar beet).

The composition of microbial communities on and within seeds may effect their storage and field performance, whether they are indigenous or applied as biocontrol agents. In this study, we have explored the usefulness of profiling small subunit ribosomal (SSR) gene fragments for studying the microflora associated with seeds. DNA was amplified by the polymerase chain reaction (PCR) and the amplicons separated using denaturing gradient gel electrophoresis (DGGE). Primers targeting eukaryotic SSRs were used to investigate fungal communities, and primers targeting bacterial SSRs were employed to study the eubacterial microflora. As a case study, we attempted to profile the fungi and bacteria associated with seeds of Beta vulgaris (sugar beet) to permit an insight into the varying field performance of several well-characterised commercial seed lots. Serious interference with the microbial signals was observed from the plant's own nuclear 18S rRNA genes and chloroplast 16S rRNA genes using standard PCR conditions and DNA extracted from whole seeds as template. Hot-start and touchdown PCR made no appreciable improvement to these signals. Seed imbibition and dissection into operculum and fruit wall and true seed prior to DNA extraction improved signal recovery in the fruit fraction. With primer modification, bacteria and fungi were detected in an excess of plant DNA of 100:1 and 10:1, respectively. With this method, microbial communities on seeds could be profiled, however, it is likely that targeted depletion of plant rDNA targets will be a necessary extra step before this approach can be used to screen seeds routinely.

Beta vulgaris↗
PubMed2005

Molecular profiling of Bacteroides spp. in human feces by PCR-temperature gradient gel electrophoresis.

A group-specific PCR-based temperature gradient gel electrophoresis (TGGE) method was developed to study the population composition of genus Bacteroides in human gut. Highly reproducible and well-separated bands in TGGE fingerprints of ten unrelated human fecal samples showed complex and host-specific Bacteroides species composition. Dynamic monitoring over 22 months of samples from one healthy 10-year-old boy indicated a relatively stable population profile of Bacteroides. The species identity of each band in TGGE gel of this boy was also resolved via comigration analysis of sequenced inserts in a Bacteroides group-specific clone library. This work provides a rapid and effective technique for analyzing the species composition of Bacteroides in human gut.

Bacterial Typing Techniques↗
PubMed2006

Expression of simian immunodeficiency virus Nef protein in CD4+ T cells leads to a molecular profile of viral persistence and immune evasion.

The Nef protein of human immunodeficiency virus and simian immunodeficiency virus is expressed early in infection and plays an important role in disease progression in vivo. In addition, Nef has been shown to modulate cellular functions. To decipher Nef-mediated changes in gene expression, we utilized DNA microarray analysis to elucidate changes in gene expression in a Jurkat CD4+ T-cell line stably expressing SIV-Nef protein under the control of an inducible promoter. Our results showed that genes associated with antigen presentation including members of the T-cell receptor and major histocompatibility class 1 complex were consistently down-regulated at the transcript level in SIV-Nef-expressing cells. In addition, Nef induced a transcriptional profile of cell-cycle-related genes that support the survival of Nef-expressing cells. Furthermore, Nef enhanced the transcription of genes encoding enzymes and factors that catalyze the biosynthesis of membrane glycolipids and phospholipids. In conclusion, gene expression profiling showed that SIV-Nef induces a transcriptional profile in CD4+ T cells that promotes immune evasion and cell survival, thus facilitating viral persistence.

Antigen Presentation↗
PubMed2005

Molecular profiling of endometrial cancers from African-American and Caucasian women.

OBJECTIVE: It is widely recognized that racial disparity in survival exists between African-American and Caucasian women with endometrial cancer (EC). Differential mutation frequencies in select genes have been postulated to explain these survival differences. The purpose of this study was to test the hypothesis that African-American women with EC have a distinct gene expression profile compared to Caucasian women with EC. METHODS: Microarray-based expression profiling using the Affymetrix U133A oligonucleotide array was performed on a series of ECs from African-American (n = 14) and Caucasian (n = 25). The two groups were matched for possible confounding variables including stage, histologic grade, and subtype. A model-based class comparison analysis was performed to generate a list of differentially expressed genes using a P value of <0.001. RESULTS: The class comparison analysis of genes differentially expressed by tumors from the two groups revealed 16 genes differentially expressed at P < 0.001, which was not statistically significant (P = 0.68). In addition, hierarchical clustering analysis did not segregate these tumors into two distinct groups based on race. CONCLUSION: These data indicate that there is no discernible difference in global gene expression profiles of ECs from African-American and Caucasian women. Thus, racial disparities in clinical outcomes are unlikely to reflect differences in gene expression and may instead be attributable to other epidemiologic, clinical, or pathologic factors.

Black or African American↗
PubMed2002

Molecular profiling of angiogenesis markers.

The goal of this study was to develop a sensitive, simple, and widely applicable assay to measure copy numbers of specific mRNAs using real-time quantitative reverse transcriptase-polymerase chain reaction (RT-PCR), and identify a profile of gene expression closely associated with angiogenesis. We measured a panel of nine potential angiogenesis markers from a mouse transgenic model of prostate adenocarcinoma (TRAMP) and a mouse skin model of vascular endothelial growth factor (VEGF)-driven angiogenesis. In both models, expression of VEGF correlated with expression of mRNAs encoding other angiogenic cytokines (angiopoietin-1 and angiopoietin-2), endothelial cell receptor tyrosine kinases (Flt-1, KDR, Tie-1), and endothelial cell adhesion molecules (VE-cadherin, PECAM-1). Relative to control, in dermis highly stimulated by VEGF, the Ang-2 mRNA transcript numbers increased 35-fold, PECAM-1 and VE-cadherin increased 10-fold, Tie-1 increased 8-fold, KDR and Flt-1 each increased 4-fold, and Ang-1 increased 2-fold. All transcript numbers were correspondingly reduced in skin with less VEGF expression, indicating a relationship of each of these seven markers with VEGF. Thus, this study identifies a highly efficient method for precise quantification of a panel of seven specific mRNAs that correlate with VEGF expression and VEGF-induced neovascularization, and it provides evidence that real-time quantitative RT-PCR offers a highly sensitive strategy for monitoring angiogenesis.

Adenocarcinoma↗