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PubMed2000

Microarray techniques in pathology: tool or toy?

Microarray technology allows the simultaneous analysis of up to thousands of different genes in histological or cytological specimens. Although microarray technology has so far mainly been applied in the research setting, its clinical application in pathology is expected in the foreseeable future. This paper presents an overview of the technical "ins and outs" of microarray technology, and discusses several putative applications in diagnostic pathology, which include tumour classification, the prediction of responses to certain chemotherapeutical or hormonal agents, the biological staging of tumours, the risk assessment of premalignant lesions, and the detection of microorganisms.

DNA Mutational Analysis↗
PubMed2006

Differential gene expression analysis reveals generation of an autocrine loop by a mutant epidermal growth factor receptor in glioma cells.

The epidermal growth factor receptor (EGFR) gene is commonly amplified and rearranged in glioblastoma multiforme leading to overexpression of wild-type and mutant EGFRs. Expression of wild-type EGFR ligands, such as transforming growth factor-alpha (TGF-alpha) or heparin-binding EGF (HB-EGF), is also often increased in gliomas resulting in an autocrine loop that contributes to the growth autonomy of glioma cells. Glioblastoma multiformes express a characteristic EGFR mutant (EGFRvIII, de 2-7) that does not bind ligand, signals constitutively, and is more tumorigenic than the wild-type receptor. However, the downstream signals that mediate this increased tumorigenicity are not well understood. We hypothesized that signals induced specifically by EGFRvIII and not the wild-type receptor are more likely to mediate its increased tumorigenic activity and examined the gene expression profiles resulting from inducible expression of comparable levels of either wild-type EGFR or EGFRvIII in a U251-MG glioma cell line. Expression of EGFRvIII resulted in specific up-regulation of a small group of genes. Remarkably, all these genes, which include TGFA, HB-EGF, EPHA2, IL8, MAP4K4, FOSL1, EMP1, and DUSP6, influence signaling pathways known to play a key role in oncogenesis and function in interconnected networks. Increased expression of EGFRvIII-induced genes was validated by real-time PCR. The mutant receptor does not bind ligand, and EGFRvIII-induced expression of TGF-alpha and HB-EGF suggests that EGFRvIII plays a role in generating an autocrine loop using the wild-type EGFR in glioma. It also raises the possibility that EGFRvIII may signal, at least in part, through the wild-type receptor. Indeed, we show that inhibiting the activity of HB-EGF, a potent mitogen, with neutralizing antibodies reduces cell proliferation induced by expression of EGFRvIII. This suggests that the EGFRvIII-HB-EGF-wild-type EGFR autocrine loop plays an important role in signal transduction by EGFRvIII in glioma cells. We also show by immunohistochemistry that HB-EGF expression correlates with the presence of EGFRvIII in glioblastoma multiforme. Thus, our study provides a new insight into oncogenic signaling by EGFRvIII and improves our understanding of how autocrine loops are generated in glioma.

Autocrine Communication↗
PubMed2005

Altered expression of TGF-beta receptors in hepatocellular carcinoma--effects of a constitutively active TGF-beta type I receptor mutant.

BACKGROUND/AIMS: Hepatocellular carcinomas (HCC) often show resistance to the effects of transforming growth factor-beta (TGF-beta). This study focuses on molecular mechanisms of this resistance to explore ways to overcome it. METHODS: Transcription and protein expression of TGF-beta type I and type II receptors (TGF-betaRI/RII) were analyzed in clinical HCCs and the human hepatoma cell lines HuH-7 and HepG2. HuH-7 cells were transiently and stably transfected with a constitutively active TGF-betaRI mutant (CA TGF-betaRI). Resulting growth kinetics, integrin expression, invasiveness, TGF-beta-mediated activation of human plasminogen activator inhibitor type-1 (PAI-1) promoter and Smad expression were determined. RESULTS: In clinical HCCs, there was less TGF-betaRII (6/10 cases) and more TGF-betaRI (8/10 cases) protein expression detectable in tumor compared to adjacent liver tissue. In HuH-7 cells, TGF-betaRII expression was likewise decreased. Cells transiently transfected with CA TGF-betaRI exhibited strong TGF-beta-related PAI-1 promoter activation. Stably transfected cells showed an attenuated response of the PAI-1 promoter, but increased Smad7 expression. Proliferation of stable clones was decreased. There was no change in integrin expression or invasiveness. CONCLUSIONS: Decreased TGF-betaRII protein expression might cause TGF-beta resistance in a subset of clinical HCCs. Stable transfection with CA TGF-betaRI reverses this in HuH-7 cells without increasing invasiveness.

Carcinoma, Hepatocellular↗
PubMed2005

The effect of IL-13 and IL-13R130Q, a naturally occurring IL-13 polymorphism, on the gene expression of human airway smooth muscle cells.

BACKGROUND: Growing evidence shows that interleukin 13 (IL-13) may play an essential role in the development of airway inflammation and bronchial hyper-responsiveness (BHR), two defining features of asthma. Although the underlying mechanisms remain unknown, a number of reports have shown that IL-13 may exert its deleterious effects in asthma by directly acting on airway resident cells, including epithelial cells and airway smooth muscle cells. In this report, we hypothesize that IL-13 may participate in the pathogenesis of asthma by activating a set of "pro-asthmatic" genes in airway smooth muscle (ASM) cells. METHODS: Microarray technology was used to study the modulation of gene expression of airway smooth muscle by IL-13 and IL-13R130Q. TaqMan Real Time PCR and flow cytometry was used to validate the gene array data. RESULTS: IL-13 and the IL-13 polymorphism IL-13R130Q (Arg130Gln), recently associated with allergic asthma, seem to modulate the same set of genes, which encode many potentially interesting proteins including vascular cellular adhesion molecule (VCAM)-1, IL-13Ralpha2, Tenascin C and Histamine Receptor H1, that may be relevant for the pathogenesis of asthma. CONCLUSIONS: The data supports the hypothesis that gene modulation by IL-13 in ASM may be essential for the events leading to the development of allergic asthma.

Cells, Cultured↗
PubMed2005

SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data.

BACKGROUND: High throughput microarray-based single nucleotide polymorphism (SNP) genotyping has revolutionized the way genome-wide linkage scans and association analyses are performed. One of the key features of the array-based GeneChip Mapping 10K Array from Affymetrix is the automated SNP calling algorithm. The Affymetrix algorithm was trained on a database of ethnically diverse DNA samples to create SNP call zones that are used as static models to make genotype calls for experimental data. We describe here the implementation of clustering algorithms on large training datasets resulting in improved SNP call rates on the 10K GeneChip. RESULTS: A database of 948 individuals genotyped on the GeneChip Mapping 10K 2.0 Array was used to identify 822 SNPs that were called consistently less than 75% of the time. These SNPs represent on average 8.25% of the total SNPs on each chromosome with chromosome 19, the most gene-rich chromosome, containing the highest proportion of poor performers (18.7%). To remedy this, we created SNiPer, a new application which uses two clustering algorithms to yield increased call rates and equivalent concordance to Affymetrix called genotypes. We include a training set for these algorithms based on individual genotypes for 705 samples. SNiPer has the capability to be retrained for lab-specific training sets. SNiPer is freely available for download at http://www.tgen.org/neurogenomics/data. CONCLUSION: The correct calling of poor performing SNPs may prove to be key in future linkage studies performed on the 10K GeneChip. It would prove particularly invaluable for those diseases that map to chromosome 19, known to contain a high proportion of poorly performing SNPs. Our results illustrate that SNiPer can be used to increase call rates on the 10K GeneChip without sacrificing accuracy, thereby increasing the amount of valid data generated.

Algorithms↗
PubMed2000

Molecular profiling of breast cancer: portraits but not physiognomy.

Breast cancers differ in response to treatment and may have a divergent clinical course despite having a similar histopathological appearance. New technology using DNA microarrays provides a systematic method to identify key markers for prognosis and treatment response by profiling thousands of genes expressed in a single cancer. Microarray profiling of 38 invasive breast cancers now confirms striking molecular differences between ductal carcinoma specimens and suggests a new classification for oestrogen-receptor negative breast cancer. Future approaches will need to include methods for high-throughput clinical validation and the ability to analyze microscopic samples.

Breast Neoplasms↗
PubMed2005

The BLADE ON PETIOLE genes act redundantly to control the growth and development of lateral organs.

Developmental processes in multicellular organisms involve an intricate balance between mechanisms that promote cell division activity and growth, and others that promote cell differentiation. Leaf development in Arabidopsis thaliana is controlled by genes like BLADE ON PETIOLE1 (BOP1), which prevent the development of ectopic meristematic activity that leads to the formation of new organs, and JAGGED (JAG), which control the proximodistal development of the leaf by regulating cell-division activity. We have isolated and characterized the BOP1 gene together with a functionally redundant close homolog that we name BOP2. The BOP genes are members of a gene family containing ankyrin repeats and a BTB/POZ domain, suggesting a role in protein-protein interaction. We show that the BOP genes are expressed in the proximal parts of plant lateral organs where they repress the transcription not only of class 1 knox genes but also of JAG. We also show that the BOP genes are acting together with the flower meristem identity gene LEAFY in the suppression of bract formation. These findings show that the BOP genes are important regulators of the growth and development of lateral organs.

Amino Acid Sequence↗
PubMed2003

Molecular profile and clinical-pathologic features of the follicular variant of papillary thyroid carcinoma. An unusually high prevalence of ras mutations.

The follicular variant (FV) of papillary thyroid carcinoma is characterized by a follicular growth pattern and cytologic features of papillary carcinoma. ret/PTC rearrangements are common in classic papillary thyroid carcinoma (PTC) and PAX8-PPAR gamma and ras mutations in follicular thyroid carcinoma. Their prevalence in FV has not been established. We studied these genetic alterations and clinical-pathologic features in 30 FV cases and compared those with 46 non-FV papillary carcinomas. FV cases revealed 1 ret/PTC rearrangement (3%) and 13 ras mutations (43%). Non-FV cases harbored 13 ret/PTC (28%) (P = .006) and no ras mutations (P = .0002). No PAX8-PPAR gamma was found in either group. FV cases demonstrated a significantly higher prevalence of tumor encapsulation, angiovascular invasion, and poorly differentiated areas and a lower rate of lymph node metastases. These data indicate that the FV of papillary carcinoma has a distinct set of molecular alterations and is characterized by a high frequency of ras point mutations.

Adult↗
PubMed2004

MALDI-TOF mass spectrometry: a versatile tool for high-performance DNA analysis.

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has developed during the past decade into a versatile tool for biopolymer analysis. The aim of this review is to summarize this development and outline the applications, which have been enabled for routine use in the field of nucleic acid analysis. These include the analysis of mutations, the resequencing of amplicons with a known reference sequence, and the quantitative analysis of gene expression and allelic frequencies in complex DNA mixtures.

Animals↗
PubMed2005

Mechanistic basis of adverse drug reactions: the perils of inappropriate dose schedules.

Adverse drug reactions (ADRs) have long been recognised as a significant cause of morbidity and mortality. They account for a substantial number of clinical consultations, hospital admissions and extended duration of in-patient stay as well as mortality. By far the most common ADRs are the concentration-dependent pharmacological reactions, the majority of which ought to be preventable. As a result of high concentrations of the parent drug and/or its metabolite(s), there is an augmentation of primary pharmacological activity and/or appearance of new and undesirable secondary pharmacological activity. Typically, these high concentrations result from administration of high doses in an attempt to maximise efficacy and/or modulation of the pharmacokinetics of a drug by either genetic or non-genetic factors. High plasma concentrations of parent drug may result from inherited impairment or drug-induced inhibition of its pharmacokinetic disposition. Conversely, inherited overcapacity or drug-induced induction of the metabolism of a drug may result in low concentrations of parent drug and frequently, rapid accumulation of its metabolites. Environmental, dietary and phytochemical factors may also influence the activity of drug metabolising enzymes. As with inherited polymorphisms of acetylation and cytochrome P450-based drug metabolising enzymes, polymorphisms of other conjugation reactions, such as glucuronidation, increasingly appear to be associated with drug toxicity. Diseases of organs involved in elimination of a drug also alter its pharmacokinetics, plasma concentration and, therefore, the profile of its concentration-dependent ADRs. Inherited mutations, concurrently administered drugs or presence of certain diseases may also alter the sensitivity of some pharmacological targets, accounting for a substantial number of ADRs and interactions. When there is enhanced pharmacodynamic sensitivity, plasma drug concentrations that are apparently within the normal 'non-toxic' range give rise to ADRs. Recent advances have also provided important insights into the wider scope of drug-drug interactions. Interactions that occur at P-glycoproteins, drug transporters and efflux pumps, at various transmembrane interfaces such as the gastrointestinal wall, renal tubules, hepatobiliary border and blood-brain barrier, are beginning to explain many non-metabolic interactions. These alter the systemic exposure to drugs and have so far, begun to explain unexpected neurotoxicity and hepatotoxicity. The function of these transporters is also genetically modulated. These advances, together with continued increased awareness and education of prescribers and pharmacists, offer great opportunities for substantially minimising concentration-related ADRs.

Cisapride↗
PubMed2004

Prediction of clonal chromosome aberration frequency in human blood lymphocytes.

We recently conducted a large-scale screening for clonal aberrations among atomic bomb survivors and proposed a model for the gross clonal composition of blood lymphocytes. Here we show an application of the model indicating that the number, m,of clones detectable by cytogenetic methods in an individual is predictable by the equation m= (1.8 + 6.4FG) x FP x n/500, where FG represents the estimated translocation frequency in the 46 chromosome set, FP is the observed translocation frequency with FISH or other methods, and nis the number of cells examined. Application of the equation to the results of seven other reports gave close agreement between the observed and calculated numbers of clones. Since the model assumes that clonal expansion is ubiquitous, and any translocation can be the constituent of a clone detectable by cytogenetic means, the vast majority of observed clonal expansions of these somatic cells are likely the result of random-hit events that are not detrimental to human health. Furthermore, since our model can predict the majority of clonal aberrations among Chernobyl workers who were examined 5-6 years after irradiation, clonal expansion seems to occur primarily within a few years after exposure to radiation, most likely being coupled with the process of recovery from radiation-induced injury in the lymphoid and hematopoietic systems.

Chromosome Aberrations↗
PubMed2006

Elucidation of the molecular signatures of renal cell carcinoma by gene expression profiling.

Renal cell carcinoma (RCC) is the 10th most common cancer in United States. It is a heterogeneous disease with various histologic types. Since high-throughput technologies such as microarrays have been introduced, molecular confirmation of previously known findings in RCC has been made and new molecular findings have emerged. We review the accumulating advances in this field and their clinical implications. The published data so far have proved to be significant and promising, and numerous microarray studies with larger number of cases are currently ongoing or being planned. Although various clinical parameters are being refined for diagnosis and prognosis, these data obtained by microarray studies will undoubtedly contribute to both and eventually impacts the treatment of RCC.

Carcinoma, Renal Cell↗
PubMed2003

Epothilone B and its analogs - a new family of anticancer agents.

Epothilones are naturally occurring 16-membered macrolides with the ability to promote tubulin polymerization in vitro and to stabilize preformed microtubules against Ca(2+)- or cold-induced depolymerization. In contrast to paclitaxel (Taxol((R))) epothilones are also active in vitro against multidrug-resistant cancer cell lines as well as cell lines whose paclitaxel-resistance is derived from specific beta-tubulin mutations. Based on their attractive in vitro biological profile epothilones have turned into important lead structures in anticancer drug discovery and hundreds of analogs and derivatives of epothilone A and B have been prepared and biologically characterized over the past four years. A number of compounds, including natural epothilone B, deoxyepothilone B, and epothilone B lactam (BMS-247550) have also been reported to exhibit profound in vivo antitumor activity in animal models. Apart from providing a brief summary of the SAR that has emerged from the above in vitro studies, this minireview will largely focus on the biology and chemistry of those analogs for which in vivo antitumor activity has been reported in the literature. Two of these compounds, natural epothilone B and epothilone B lactam (BMS-247550) have advanced to clinical studies in humans.

Antineoplastic Agents↗
PubMed2006

Vascular endothelial growth factor (VEGF) is suppressed in WT1-transfected LNCaP cells.

The Wilms' tumor suppressor gene product (WT1) regulates expression of growth control genes. Microarray analysis of gene expression profiles of hormone-treated LNCaP prostate cancer cell lines transfected with either wild-type WT1 or a zinc finger mutant form, DDS (R394W), revealed significantly altered patterns of expression. Validation studies using quantitative real-time PCR confirmed the differential expression of the tumor progression gene, vascular endothelial growth factor (VEGF). WT1-LNCaP cells had significantly reduced levels of VEGF mRNA when compared to vector control cells; in contrast, DDS-LNCaP cells showed elevated levels of VEGF transcripts. To address a functional role for WT1 overexpression, we investigated whether induction of VEGF expression, by the synthetic androgen R1881, would be disrupted in wild-type or mutant WT1-transfected LNCaP cells. Hormone treatment failed to elevate VEGF transcript levels above uninduced baseline levels in WT1-LNCaP cells, despite 48 h of treatment with 5 nM R1881. Consistent with our quantitative real-time PCR analysis, immunofluorescent staining of VEGF protein was reduced in WT1-LNCaP cells in both the presence and absence of R1881 treatment. Conversely, VEGF levels increased in vector control and DDS-LNCaP cells treated with 5 nM R1881. Not only do these studies point out the regulatory potential of WT1 for VEGF, but they also indicate an altered function for the mutant DDS isoform. Because VEGF is associated with neovascularization and promotion of metastasis in a variety of solid tumors including prostate cancer, a better understanding of the regulation of VEGF expression by transcription factors, such as WT1, is important for halting disease progression.

Gene Expression↗
PubMed1998

Qinghaosu in combinations.

Antimalarial combinations make therapeutic sense. As we have few antimalarial drugs and even fewer in development, and as the malaria parasite shows a remarkable ability to develop resistance, all possible measures should be taken to protect those drugs that we do have available. Although in experimental animals combinations have been shown unequivocally to delay the onset of resistance, this has not yet been proved formally in human malaria. Yet formal proof is extremely difficult to obtain. However, there is sufficient circumstantial evidence to suggest that resistance can be delayed. As there are no counter arguments and the stakes are high, it seems reasonable that an artemisinin derivative should be combined with all slow acting antimalarial drugs. Those drugs with a particularly vulnerable profile, in which a single or double point mutation confers high level resistance, should not be deployed alone and should always be combined with an artemisinin derivative.

Antimalarials↗
PubMed2002

[Structural mechanism studies of hTNF alpha mutants in position 30 and 42 amino acid].

OBJECTIVE: To study the relationship between the structure and functional activity of hTNF alpha. METHODS: Four hTNF alpha mutants were constructed, different binding structures and gene responses related with these mutants were studied by the methods of immunoprecipitation and mRNA differential display. RESULTS: The specific activities and LD50 of the different hTNF alpha mutants indicated their different bioactivities. It was shown that the hTNF alpha mutants had the relative binding affinities to the wild types. The mRNA differential display assay proved that the hTNF alpha mutants stimulated different gene responses. CONCLUSION: These results suggest that the specific anti-tumor activities of hTNF alpha mutants are accomplished by inducing different or same gene response at different quantities after its binding to specific receptor.

Amino Acid Motifs↗