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PubMed2003

Gene expression profiling of melanocytic lesions.

DNA microarrays, microscopic grids of DNA, can be used to assess gene expression within a particular cell or cell population. Since DNA from thousands of genes can be hybridized and analyzed in one experiment, researchers can globally characterize genes expressed in normal and various pathologic states. To accurately assess the differences between normal and pathologic states, one derives cDNA from control and diseased tissue specimens for genes expression profiling. For these reasons, microarray technology may be of particular interest to dermatopathologists and dermatologists interested in understanding cutaneous disease because these physicians have access to tissue specimens. In addition, microarray technology is an efficient way of identifying molecules expressed in a cell population; therefore, it can be used to search for unique immunohistologic markers. To this end, we have used microarray technology to define differences in the gene expression profile of nevi and melanomas. In this manuscript, we discuss the results of our study, which confirm previously known differences in gene expression between melanoma and nevi. While a few genes appear slightly overexpressed in nevi, a number of genes involved in regulating cell proliferation were upregulated in melanoma, such as cyclin D1, cdc2-related protein kinase, c-Myc binding protein, early growth response protein 1, and pleiotrophin. "Housekeeping" genes such as glyceraldehyde 3-phosphate dehydrogenase were expressed at similar levels in melanoma and nevi. Surprisingly, a majority of genes were expressed at similar levels in both nevi and melanoma. Based on this study, DNA microarray technology appears to be a valuable tool for identifying genes that may be specifically expressed in cutaneous lesions.

Biomarkers, Tumor↗

PubMed2003

Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients.

MOTIVATIONS AND RESULTS: For classifying gene expression profiles or other types of medical data, simple rules are preferable to non-linear distance or kernel functions. This is because rules may help us understand more about the application in addition to performing an accurate classification. In this paper, we discover novel rules that describe the gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients. We also introduce a new classifier, named PCL, to make effective use of the rules. PCL is accurate and can handle multiple parallel classifications. We evaluate this method by classifying 327 heterogeneous ALL samples. Our test error rate is competitive to that of support vector machines, and it is 71% better than C4.5, 50% better than Naive Bayes, and 43% better than k-nearest neighbour. Experimental results on another independent data sets are also presented to show the strength of our method. AVAILABILITY: Under http://sdmc.lit.org.sg/GEDatasets/, click on Supplementary Information.

Algorithms↗

PubMed2003

Predicting survival in patients with metastatic kidney cancer by gene-expression profiling in the primary tumor.

To identify potential molecular determinants of tumor biology and possible clinical outcomes, global gene-expression patterns were analyzed in the primary tumors of patients with metastatic renal cell cancer by using cDNA microarrays. We used grossly dissected tumor masses that included tumor, blood vessels, connective tissue, and infiltrating immune cells to obtain a gene-expression "profile" from each primary tumor. Two patterns of gene expression were found within this uniformly staged patient population, which correlated with a significant difference in overall survival between the two patient groups. Subsets of genes most significantly associated with survival were defined, and vascular cell adhesion molecule-1 (VCAM-1) was the gene most predictive for survival. Therefore, despite the complex biological nature of metastatic cancer, basic clinical behavior as defined by survival may be determined by the gene-expression patterns expressed within the compilation of primary gross tumor cells. We conclude that survival in patients with metastatic renal cell cancer can be correlated with the expression of various genes based solely on the expression profile in the primary kidney tumor.

Adult↗

PubMed2001

Expression profiling in knockout mice: lymphotoxin versus tumor necrosis factor in the maintenance of splenic microarchitecture.

Expression profiling provides a powerful approach to define the underlying molecular mechanisms in disease. Several techniques referred collectively to as gene profiling may be also helpful in the analysis of the phenotype of mice with targeted mutations, especially if applied to distinct histological compartments, to specific cell types or to evaluate the effect of specific challenges, such as infection. Here we review several of the existing techniques applicable to genetic knockout studies, and share our experience from the study of mice with tumor necrosis factor (TNF) and lymphotoxin (LT) deficiencies, with specific emphasis on the distinction between TNF- and LT-mediated signalling pathways in vivo. Gene expression profiling analysis of TNF/LT-deficient mice supports the notion that TNF and LT, originally discovered as distinct biological activities, manifest both distinct and redundant functions in vivo.

Animals↗

PubMed2002

Single-cell RT-PCR detects shifts in mRNA expression profiles of basal forebrain neurons during aging.

The medial septum and nucleus of the diagonal band (MS/nDB) contain cholinergic and GABAergic neuronal populations that have been identified based on immunohistochemical staining and/or electrophysiological properties. We explored the molecular diversity of MS/nDB neurons using single-cell reverse transcription-polymerase chain reaction (scRT-PCR) to assess gene expression profiles during aging in individual neurons acutely isolated from young (2-4 months) and aged (26-27 months) F344 rats. Neuronal gene expression profiles were characterized by detection of mRNAs for choline acetyltransferase (ChAT, cholinergic) and glutamate decarboxylase (GAD67, GABAergic), as well as mRNAs for calcium binding proteins (CaBPs) calbindin-D28k, calretinin and parvalbumin. Four major neuronal populations were identified: ChAT-positive (ChAT+) cells, GAD-positive (GAD+) cells, ChAT+/GAD+ cells and ChAT negative/GAD negative (ChAT-/GAD-) cells. With age, the percentage of cells expressing ChAT mRNA decreased from 53% in young to 40%, and the expression of GAD67 mRNA was reduced from 56 to 35% of the cells tested. The percentage of cells with detectable levels of both ChAT and GAD67 mRNA was reduced from 24% in young to 9% in aged. Concomitantly, the percentage of ChAT-/GAD- cells increased from 15 to 34% with age. Of the CaBPs, calretinin expression was observed most frequently in this study, and its detection decreased from 33 to 22% of the cells with age. Observations concerning the CaBPs were confirmed using in situ hybridization. These results suggest a shift in the mRNA expression profiles of MS/nDB neuronal populations during aging and exemplify the molecular diversity of cholinergic and GABAergic cells.

Aging↗

PubMed1998

Expression profile of active genes in granulocytes.

A number of genes active in granulocytes have been intensively studied as to the function of their products and their expression controls. However, the intensities and relative order of these gene activities have not been studied. This report describes an expression profile of 748 different species of active genes in human peripheral granulocytes obtained by analyzing a 3'-directed cDNA library that faithfully represents the mRNA population in the source cells. A significant fraction (20.3% of the total) of the expressed genes in granulocytes consisted of nuclear proteins such as DNA binding proteins, of secretory proteins such as cytokines, and of membrane proteins such as major histocompatibility complex (MHC) proteins and receptors. By comparing this expression profile with 11 profiles similarly obtained with unrelated human cells/tissues, we discovered 10 novel genes that are likely to act specifically in granulocytes. Comparison of this expression profile with that obtained with granulocytoids widely used as a granulocyte model by inducing a cultured promyelocytic leukemia cell line HL60 showed similarities and dissimilarities of gene expressions.

Adult↗

PubMed2002

Expression profiles of craniosynostosis-derived fibroblasts.

BACKGROUND: Craniosynostosis syndromes, a group of connective disorders characterized by abnormalities in vault osteogenesis and premature fusion of bone sutures, are associated with point mutations in FGF receptor family members. The cellular phenotype is characterized by abnormal extracellular matrix turnover. MATERIAL AND METHODS: We used primary cultures of periosteal fibroblasts derived from two different craniosynostosis syndromes, the Apert and Crouzon syndromes. The FGFR2 third immunoglobulin-like domain and its flanking linker regions were analyzed for mutation. DNA microarrays containing 19,200 cDNAs were used to study the gene expression profiles of Apert and Crouzon fibroblasts. The pathologic cells were compared to wild-type human periosteal fibroblasts. RESULTS: The P253R missense mutation and the G338R mutation were observed in Apert and Crouzon fibroblasts, respectively. The genetic profiles, as evaluated by DNA microarrays, yielded different clusters of expressed sequence tag (ESTs) expression within the experiment. Expression profiles from craniosynostosis-derived fibroblasts differ from those of wild-type fibroblasts (288 human ESTs, p< 0.01, pFDR = 0.12). Furthermore, two ESTs clusters discriminate the Crouzon from Apert fibroblasts. The differentially expressed genes cover a broad range of functional activities, including (1) bone differentiation, (2) cell-cycle regulation, (3) apoptotic stimulation, and (4) signaling transduction, cytoskeleton, and vesicular transport. CONCLUSIONS: The transcriptional program of craniosynostosis fibroblasts differs from that of wild-type fibroblasts. Expression profiles of Crouzon and Apert fibroblasts can also be distinguished by two EST expression clusters, thus hinting at a different genetic background.

Acrocephalosyndactylia↗

PubMed2003

Comparison of gene expression profiles between frozen original meningiomas and primary cultures of the meningiomas by GeneChip.

OBJECTIVE: In vitro experiments are performed on a daily basis to study the molecular biology of tumors. For some benign tumors, however, established cell lines are not always available, or it may not be feasible to establish new ones. In such cases, primary cultures are used to perform in vitro experiments. Gene expression profiles in vitro differ from those in vivo, but information as to which genes have significantly altered levels is limited. In this study, gene expression profiles of meningiomas in primary cultures and frozen tumors were compared. METHODS: Affymetrix U95A chips were applied to three sets of meningiomas. For each tumor, the gene expression profiles in frozen specimens (Fr) and primary cultures from the same tumor at Pass 5 (P5) and Pass 10 (P10) were compared. A paired t test (P < 0.025) was applied between Fr and P5, and then between Fr and P10. Genes that demonstrated significantly different expression levels in both comparisons were then identified. The expression levels for a subset of these genes were confirmed by quantitative real-time reverse transcription-polymerase chain reaction. RESULTS: Among 12,000 genes examined, up-regulation of 51 genes by fivefold or more and down-regulation of 19 genes by twofold or more was found in primary cultures (P5 and P10) compared with the corresponding Fr. Up-regulation of genes encoding for extracellular matrix, cytoskeleton, and cell surface receptors was particularly notable. CONCLUSION: Gene expression of tissue-cultured meningiomas and in situ meningiomas is significantly different for a large number of genes. Therefore, gene expression and therapeutic studies on cultured meningiomas need to be interpreted with caution.

Cryopreservation↗

PubMed2002

Expression profile and genome location of cDNA clones from an infant human trabecular meshwork cell library.

PURPOSE: To delineate the profile of genes expressed in infant human trabecular meshwork and identify candidate genes for glaucoma. METHODS: Human trabecular meshwork cell cultures were established from six young donors. A cDNA library was made from the combined trabecular meshwork mRNA. The end-sequence of random clones was determined by direct sequencing. These sequences were then analyzed by a National Center for Biotechnology Information (NCBI, Bethesda, MD) database search. Nucleotide searches were performed using the BLASTN (ver. 2.1.3; against the nonredundant nucleic acid sequence) and dbEST databases (both provided by NCBI in the public domain at www.ncbi.nlm.nih.gov). RESULTS: Sequences from 1118 clones from this nonamplified trabecular meshwork cDNA library were categorized. Of these, 877 expressed sequence tags (ESTs) (78.7%) were known genes. One hundred thirty-nine ESTs (12.5%) showed close identity to EST sequences reported in the public domain database (dbEST). Thirteen ESTs (1.2%) showed no significant similarity to known genes or ESTs in the public databases and were thus defined as novel ESTs. The most abundant genes expressed by the human trabecular meshwork included ferritin H, eukaryotic translation elongation factor 1-alpha, ferritin L, fibronectin, and TIMP-1. Ferritin H was the most abundant transcript, making up more than 4% of the genes expressed by the human trabecular meshwork. Extracellular matrix proteins were also highly expressed. The chromosome location of the trabecular meshwork ESTs is reported. CONCLUSIONS: A profile of genes expressed by human trabecular meshwork is presented. Thirteen novel ESTs were identified. The combined information obtained from expression analysis and chromosomal localization of trabecular meshwork cDNAs should be valuable in identifying candidate genes for glaucoma.

Cells, Cultured↗

PubMed2003

Molecular classification of synovial sarcomas, leiomyosarcomas and malignant fibrous histiocytomas by gene expression profiling.

In this study, we have used genome-wide expression profiling to categorise synovial sarcomas, leiomyosarcomas and malignant fibrous histiocytomas (MFHs). Following hierarchical clustering analysis of the expression data, the best match between tumour clusters and conventional diagnosis was observed for synovial sarcomas. Eight of nine synovial sarcomas examined formed a cluster that was characterised by higher expression of a set of 48 genes. In contrast, sarcomas conventionally classified as leiomyosarcomas and MFHs did not match the clusters defined by hierarchical clustering analysis. One major cluster contained a mixture of both leiomyosarcomas and MFHs and was defined by the lower expression of a set of 202 genes. A cluster containing a subgroup of MFHs was also detected. These results may have implications for the classification of soft tissue sarcomas, and are consistent with the view that sarcomas conventionally defined as MFHs do not represent a separate diagnostic category.

Cluster Analysis↗

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↗

PubMed2001

Gene expression profile changes in initiation and progression of squamous cell carcinoma of esophagus.

Tumorigenesis is a complex process involving multiple genes. As a step toward understanding the complicated changes between normal and malignant cells, this report focused on gene expression profile variations among normal and abnormal esophageal epithelium tissues. The cDNA microarray approach was used to investigate gene expression profiles of 5 different stages during initiation and progression of esophageal cancer. According to pathological characteristics, these 5 stages were normal, dysplasia I (mild dysplasia), dysplasia II (moderate dysplasia), carcinoma in situ (CIS) and squamous cell carcinoma of esophagus (SCC). Comparing and analyzing those gene expression profiles, we observed that the expression levels of many genes changed in dysplasia I and some known tumor-related genes were over-expressed or under-expressed in all 4 abnormal stages. Using principle component analysis we identified a set of genes that may play an important role in tumor development. Hybridization data were confirmed by semi-quantitative reverse transcription-polymerase chain reaction and immunohistochemistry. These results suggest that cDNA microarray technology is a useful tool to discover genes frequently involved in esophageal neoplasia and provides novel clues to diagnosis, early detection and intervention of SCC.

Carcinoma in Situ↗

PubMed2002

Altered gene expression profiles of rat lung in response to an emission particulate and its metal constituents.

Comprehensive and systematic approaches are needed to understand the molecular basis for the health effects of particulate matter (PM) reported in epidemiological studies. Due to the complex nature of the pollutant and the altered physiological conditions of predisposed populations, it has been difficult to establish a direct cause and effect relationship. A high-throughput technology such as gene expression profiling may be useful in identifying molecular networks implicated in the health effects of PM and its causative constituents. Differential gene expression profiles derived for rat lungs exposed to PM and its constituent metals using a custom rat cardiopulmonary cDNA array are presented here. This array consists of 84 cardiopulmonary-related genes representing various biological functions such as lung injury/inflammation, repair/remodeling, structural and matrix alterations, and vascular contractility, as well as six expressed sequence tags (ESTs). The cDNA array was hybridized with (32)P-labeled cDNA generated from rat lung RNA. Total lung RNA was isolated from male Sprague-Dawley rats at 3 and 24 h following intratracheal instillation of either saline, residual oil fly ash (ROFA; 3.3 mg/kg), or its most toxic metallic constituents, nickel (NiSO(4); 3.3 mmol/kg) and vanadium (VSO(4); 5.7 mmol/kg). Metal concentrations reflected the levels present in one ROFA instillate. Densitometric scans of the array blots indicated ROFA- and metal-specific increased expression (1.5 to 3-fold) of stress response, inflammatory, and repair-related genes, and also genes involved in vascular contractility and thrombogenic activity. Expression of multiple cytokines in ROFA exposed rat lung compared to Ni and V suggest the role and importance of understanding constituent interactions in PM toxicity. Expression profiling using genomic approaches will aid in our understanding of toxicant-specific altered molecular pathways in lung injury and pathogenesis.

Air Pollutants↗

PubMed2003

Going global: protein expression profiling using shotgun mass spectrometry.

Protein expression profiling, the science of monitoring global sets of proteins produced by any given cell type, tissue or organism, has been invigorated by the introduction of proteomic technologies capable of characterizing large numbers of proteins. This review summarizes recent advances in mass spectrometry-based techniques for high-throughput protein identification and quantitation that are fueling rapid growth in the field. Key publications applying state-of-the-art 'shotgun' methods for investigating the entire protein complement of whole organelles, cells and tissues are highlighted. An overview of current proteomic challenges, particularly in the area of data analysis, and the long-term prospects of protein profiling strategies in basic biomedical research, therapeutics development and clinical discovery is also provided.

Animals↗

PubMed2001

[Gene apoptosis expression profiles in liver cancer and their comparison to normal peri-cancerous liver tissues].

OBJECTIVE: To describe a few gene expression profiles related to apoptosis and to demonstrate their difference between the liver cancer and its adjacent normal tissues. METHODS: cDNA, labeled as a-32P dATP was synthesized from the total RNA of cancer and adjacent normal tissues and, then, hybridized individually with two identical array membranes of Atlas human cancer dDNA expression containing 588 known genes. The method involving gene-specific semi-quantitative reverse transcription in the polymerase chain reaction (RT-PCR) was used to confirm the expression pattern of three known genes. RESULTS: Autoradiographic results were analyzed by specific AtlasImage (version 1.01a) software. Among 69 genes that were found to be related to apoptosis, 4 were up-related, including Aktl, and 19 were down-related, including BAK, Caspase-3, etc., all being related to cancer. The RT-PCR results showed that the expression pattern of all genes was in agreement with the results of Atlas expression array. CONCLUSION: The result obtained from Atlas microarray provides a liver cancer-specific expression profile related to apoptosis. The discovery about the apoptosis related genes may yield some clues on the oncogenetic mechanism of liver cancer in the future. The differential hybridization technique of cDNA expression array involving the Atlas human cancer can become a useful method in the understanding of the development and progression of human cancer.

Apoptosis↗

PubMed2002

DNA microarray analysis reveals novel gene expression profiles in collagen-induced arthritis.

Global gene expression was analyzed in early and late collagen-induced arthritis (CIA). Of 8734 cDNAs analyzed, 330 were induced and 55 downregulated greater than twofold in early or late disease. Hierarchical clustering of these 385 cDNAs demonstrated five distinct expression patterns differentiating early from late disease and correlating with histopathologic changes in the paw. Of the 385 cDNAs, 185 are known, characterized genes, the majority of which are not described as playing a role in arthritis. However, several of these genes are involved in pathological processes relating to arthritis, including apoptosis, inflammation, and cellular proliferation. One interesting gene, follistatin-like gene, is highly expressed along the margin of contact between inflammatory synovial pannus and eroding bone, suggesting a role in joint destruction. These results demonstrate that global gene expression profiles distinguish early and late CIA and reveal several genes novel to arthritis the further characterization of which will advance our understanding of arthritis.

Animals↗

PubMed2002

Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors.

Changes in mRNA and protein expression profiles of Shewanella oneidenesis MR-1 during switch from aerobic to fumarate-, Fe(III)-, or nitrate-reducing conditions were examined using DNA microarrays and two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). In response to changes in growth conditions, 121 of the 691 arrayed genes displayed at least a two-fold difference in transcript abundance as determined by microarray analysis. Genes involved in aerobic respiration encoding cytochrome c and d oxidases and TCA cycle enzymes were repressed under anaerobic conditions. Genes induced during anaerobic respiration included those involved in cofactor biosynthesis and assembly (moaACE, ccmHF, nosD, cysG), substrate transport (cysUP, cysTWA, dcuB), and anaerobic energy metabolism (dmsAB, psrC, pshA, hyaABC, hydA). Transcription of genes encoding a periplasmic nitrate reductase (napBHGA), cytochrome c552, and prismane was elevated 8- to 56-fold in response to the presence of nitrate, while cymA, ifcA, and frdA were specifically induced three- to eightfold under fumarate-reducing conditions. The mRNA levels for two oxidoreductase-like genes of unknown function and several cell envelope genes involved in multidrug resistance increased two- to fivefold specifically under Fe(III)-reducing conditions. Analysis of protein expression profiles under aerobic and anaerobic conditions revealed 14 protein spots that showed significant differences in abundance on 2-D gels. Protein identification by mass spectrometry indicated that the expression of prismane, dihydrolipoamide succinyltransferase, and alcaligin siderophore biosynthesis protein correlated with the microarray data.

Bacterial Proteins↗

PubMed2001

Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles.

Microarray technology, which allows one to quantitate the expression of thousands of genes simultaneously, has begun to have a major impact on many different areas of drug discovery and development. The question remains of whether microarray analysis and gene expression signature profiles can be applied to the field of toxicology. To date, there are very few published studies showing the use of microarrays in toxicology and important questions remain regarding the predictability and accuracy of applying gene expression profiles to toxicology. To begin to address these questions, we have treated rats with 15 different known hepatotoxins, including allyl alcohol, amiodarone, Aroclor 1254, arsenic, carbamazepine, carbon tetrachloride, diethylnitrosamine, dimethylformamide, diquat, etoposide, indomethacin, methapyrilene, methotrexate, monocrotaline, and 3-methylcholanthrene. These agents cause a variety of hepatocellular injuries including necrosis, DNA damage, cirrhosis, hypertrophy, and hepatic carcinoma. Gene expression analysis was done on RNA from the livers of treated rats and was compared against vehicle-treated controls. The gene expression results were clustered and compared to the histopathology findings and clinical chemistry values. Our results show strong correlation between the histopathology, clinical chemistry, and gene expression profiles induced by the agents. In addition, genes were identified whose regulation correlated strongly with effects on clinical chemistry parameters. Overall, the results suggest that microarray assays may prove to be a highly sensitive technique for safety screening of drug candidates and for the classification of environmental toxins.

Amiodarone↗