Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Molecular Classification”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 703 records · Page 39Linked to original sources
PubMed1994

[Criteria of genetic predisposition to hereditary non polyposis colorectal cancers].

Clinical and histological characteristics of non polypoid colorectal cancers with an hereditary predisposition are presented. The various known genetic syndromes (hereditary non polyposis colorectal cancers, Lynch syndrome type I and type II, Torre-Muir's syndrome, hereditary flat adenoma syndrome) are discussed to find a possible correlation between this nosological classification and their molecular substratum. The main problem today, is to correctly define the population of hereditary predisposed patients to colon cancer, in order to seek and identify the major responsible gene. Any physician, specialist or not, should be encouraged to give the details of the cancer familial context of his patients, in order to aid the oncologist geneticist in his task.

Adult↗
PubMed1993

Expression of oligodendrocyte-associated genes in cell lines derived from human gliomas and neuroblastomas.

Two putative human oligodendroglioma cell lines were examined for the expression of the oligodendrocyte-associated genes, 2',3'-cyclic nucleotide-3'-phosphodiesterase, myelin basic protein, myelin proteolipid proteins, and myelin-associated glycoprotein. The expression of these genes also was examined in control astrocytoma and neuroblastoma cell lines. In addition, the expression of the non-oligodendrocyte-specific genes, glial fibrillary acidic protein (GFAP), neuron-specific enolase and neurofilaments (NF) NF-L and NF-M also were examined. All the cell lines expressed 2',3'-cyclic nucleotide 3'-phosphodiesterase, neuron-specific enolase, and vimentin, and none expressed myelin-associated glycoprotein. The "oligodendrocyte-specific" myelin proteolipid protein mRNAs and the "neuron-specific" NF-L mRNA were expressed in the two astrocytoma cell lines, which also expressed GFAP. Expression of intermediate filament protein genes was more restricted. The astrocytoma, neuroblastoma, and oligodendroglioma cell lines expressed only GFAP, NF-M, and cytokeratin K7, respectively. These results: (a) provide molecular data confirming the classification of the two cell lines as oligodendrogliomal and suggest that their molecular profiles are indicative of immature oligodendrocytes; (b) demonstrate the expression of cytokeratins in oligodendrogliomal cell lines and suggest that apparent GFAP expression in oligodendrogliomas detected by immunocytochemical methods may be due to cross-reactivity with cytokeratins, with which they share common polypeptide sequence; and (c) indicate that astrocytoma cell lines can exhibit a "mixed" phenotype, expressing genes associated with fully differentiated oligodendrocytes and neurons.

Astrocytoma↗
PubMed2005

The molecular signature of normal squamous esophageal epithelium identifies the presence of a field effect and can discriminate between patients with Barrett's esophagus and patients with Barrett's-associated adenocarcinoma.

BACKGROUND AND AIM: Genetic alterations in the normal tissues surrounding various cancers have been described, but a comprehensive analysis of this carcinogenic field effect in Barrett's-associated adenocarcinoma of the esophagus disease has not been reported. The aim of this study was to analyze the gene expression profile of a panel of highly selected genes in the normal squamous esophagus epihelium of patients with Barrett's esophagus, patients with Barrett's-associated adenocarcinoma, and a healthy control group to define the existence of a carcinogenic field effect, and to investigate the clinical importance of such a field effect in the management of Barrett's disease. METHODS: Forty-nine histologic normal squamous esophageal epithelia collected from 19 patients with Barrett's esophagus, 20 patients with Barrett's-associated esophageal adenocarcinoma, and a healthy control group of 10 patients were studied. A quantitative real-time reverse transcription-PCR method (TaqMan) was used to measure the expression of a panel of genes with known associations with gastrointestinal carcinogenesis. RESULTS: A widespread carcinogenic field effect was detected for more than 50% of the genes analyzed including Bax, BFT, CDX2, COX2, DAPK, DNMT1, GSTP1, RARalpha, RARgamma, RXRalpha, RXRbeta, SPARC, TSPAN, and VEGF. Based on the expression signature of the normal appearing squamous esophagus, a linear discriminant analysis was able to distinguish between the three groups of patients with an error rate of 0%. CONCLUSION: This study provides the first comprehensive investigation of a carcinogenic field effect in Barrett's esophagus disease. Based on the gene expression signature of the normal esophagus, patients could be correctly characterized according to their pathologic classification by applying a linear discriminant analysis. Our results provide evidence that a molecular classification might have clinical importance for the diagnosis and treatment of patients with Barrett's esophagus disease.

Adenocarcinoma↗
PubMed1998

The genotype-phenotype controversy in ophthalmology. Implications of heterogeneity on diagnosis, embryology and molecular function.

Genetic heterogeneity in ophthalmology adds a new dimension to differential diagnosis and prognosis. The indispensable clinical classification is refined by molecular genetic strategies. They sometimes build up new families of diseases, sometimes indicate that what was thought to be aetiologically related disorders are caused by different genetic mechanisms. Heterogeneity throws new light on embryological pathways, and the molecular genetics of the eye increases the information of the localisation of metabolically active substances and structural proteins in the eye.

Diagnosis, Differential↗
PubMed1994

Distal renal tubular acidosis: molecular and clinical aspects.

The traditionally descriptive classification of DRTA disorders is being refined as molecular defects are identified. Diagnosis of DRTA is easy: Hyperchloremic acidosis should arouse suspicion, and confirmation can be obtained by measuring urinary pH and ammonia excretion. Treatment is also relatively straightforward and readily corrects all manifestations of the acidification defect.

Acidosis, Renal Tubular↗
PubMed1993

Fish eye syndrome: a molecular defect in the lecithin-cholesterol acyltransferase (LCAT) gene associated with normal alpha-LCAT-specific activity. Implications for classification and prognosis.

We have identified the molecular defect in two siblings presenting with classical clinical and biochemical features of Fish Eye disease (FED), including corneal opacities, HDL cholesterol < 10 mg/dl, normal plasma cholesteryl esters, and elevated triglycerides. In contrast to previously reported patients with FED who are unable to esterify HDL-associated cholesterol, our patients' plasma lecithin-cholesterol acetyltransferase (alpha-LCAT)-specific activities assayed using an HDL-like proteoliposome substrate were 12.7-25.7 nmol/micrograms (19.5 +/- 1.8 in controls). In addition, significant residual cholesterol esterification was present in VLDL/LDL-depleted plasma, confirming the presence of HDL-associated alpha-LCAT activity. DNA sequence analysis of the proband's LCAT gene identified deletion of the triplet coding for leu300, which resulted in the loss of a restriction site for MlnI. Digestion of PCR-amplified DNA using MlnI established that both siblings are homozygous for this defect. Expression of LCAT300-del. in human embryonic kidney-293 cells revealed normal mRNA and intracellular LCAT concentrations. However, reduced amounts of LCAT300-del., which had a normal specific alpha-LCAT activity, were present in the media. In summary, we report the first case of FED associated with a mutant enzyme that has a normal alpha-LCAT-specific activity. The functional significance of this LCAT gene defect has been established in an in vitro expression system, which demonstrates that very small amounts of this functional LCAT mutant enzyme accumulate in the media. Characterization of LCAT300-del. established that selective alpha-LCAT deficiency is not a prerequisite for the development of FED. On the basis of our combined results, we propose that the residual amounts of total plasma LCAT activity and not its distribution on lipoproteins primarily determines the heterogeneity in phenotypic expression observed in familial LCAT deficiency syndromes.

Base Sequence↗
PubMed2001

Classification of trypanosomatids from fruits and seeds using morphological, biochemical and molecular markers revealed several genera among fruit isolates.

Trypanosomatids are widespread in several plant families and although most isolates have been classified as Phytomonas, other trypanosomatid genera can also infect plants. In order to assess the natural occurrence of non-Phytomonas trypanosomatids in plants we characterized 21 new trypanosomatid cultures, 18 from fruits and three from seeds of 17 plant species. The trypanosomatids from fruit and seeds were compared in terms of morphological, growth, biochemical and molecular features. The high diversity among the isolates permitted the classification of the new flagellates into the genera Crithidia and Leptomonas as well as Phytomonas. The data showed that natural fruit infection with non-Phytomonas trypanosomatids is more common than usually thought, being detected in 43% of the fruit isolates.

Animals↗
PubMed2005

Staging and classification of lymphoma.

In 2004, new cases of non-Hodgkin's lymphoma in the United States were estimated at 54,370, representing 4% of all cancers and resulting 4% of all cancer deaths, and new cases of Hodgkin's lymphoma were estimated at 7,880. The appropriate staging and management of lymphomas greatly depend on an accurate pathological diagnosis and classification. The recently established Revised European-American Classification of Lymphoid Neoplasms (REAL) and the subsequently adopted and updated World Health Organization (WHO) classification include modern cytogenetic, molecular, and immunologic techniques and knowledge and reach an international consensus on the classification of lymphomas. This classification scheme represents an advance in our understanding of lymphomas and serves as an operative guideline for studying and diagnosing lymphomas. Imaging techniques always have served as staging and monitoring tools for the clinical management of lymphomas. The understanding and adoption of the current classification system is important in refining the role of imaging modalities in the management of specific lymphoma. To help one understand the current classification, this current review gives a brief history of lymphoma classifications and summaries the recent classification schemes, including new entities, clinical staging methods, and clinical prognostic criteria.

Animals↗
PubMed1988

Molecular systematics of higher primates: genealogical relations and classification.

We obtained 5' and 3' flanking sequences (5.4 kilobase pairs) from the psi eta-globin gene region of the rhesus macaque (Macaca mulatta) and combined them with available nucleotide data. The completed sequence, representing 10.8 kilobase pairs of contiguous noncoding DNA, was compared to the same orthologous regions available for human (Homo sapiens, as represented by five different alleles), common chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and orangutan (Pongo pygmaeus). The nucleotide sequence for Macaca mulatta provided the outgroup perspective needed to evaluate better the relationships of humans and great apes. Pairwise comparisons and parsimony analysis of these orthologues clearly demonstrated (i) that humans and great apes share a high degree of genetic similarity and (ii) that humans, chimpanzees, and gorillas form a natural monophyletic group. These conclusions strongly favor a genealogical classification for higher primates consisting of a single family (Hominidae) with two subfamilies (Homininae for Homo, Pan, and Gorilla and Ponginae for Pongo).

Animals↗
PubMedDate not supplied

Classification of inhibitors of protein tyrosine phosphatase 1B using molecular structure based descriptors.

Loss of Protein Tyrosine Phosphatase 1B (PTP 1B) activity is known to enhance insulin sensitivity and resistance to weight gain. So potent and orally active PTP1B inhibitors could be potential pharmacological agents for the treatment of Type 2 diabetes and obesity. Classification models of PTP1B inhibitors are developed using a data set containing 128 compounds. Their inhibitory concentrations ranged from -1.59 to 1.68 log units. Initially a two-class (active, inactive) problem is tackled using a number of different methods. The data set was divided into active and inactive classes on the basis of inhibitory activity of the compounds. Molecular structure-based descriptors were calculated and used in the model development. Descriptors encoding the flexibility of the molecules were investigated. Classification models were generated using k-nearest neighbors (k-NN), linear discriminant analysis (LDA), and radial basis function neural network (RBFNN). All models are tested using an external prediction set, compounds not used anywhere during the model development procedure. A five-descriptor model is developed that produces a classification rate of 85.7% for an external prediction set. Then a three-class (active, moderately active, inactive) problem was explored. This time the data set was divided into highly active, moderate, and inactive classes on the basis of inhibitory activity of the compounds. The best classification rate achieved for an external prediction set was 85%. The classification rates achieved indicate that these models could serve as a screening mechanism, to identify potentially useful PTP 1B inhibitors. In addition multiple linear regression and computational neural network models are also developed for prediction of log IC(50) values. All QSAR models are tested using the same external prediction set.

Benzofurans↗
PubMed2001

Feature (gene) selection in gene expression-based tumor classification.

There is increasing interest in changing the emphasis of tumor classification from morphologic to molecular. Gene expression profiles may offer more information than morphology and provide an alternative to morphology-based tumor classification systems. Gene selection involves a search for gene subsets that are able to discriminate tumor tissue from normal tissue, and may have either clear biological interpretation or some implication in the molecular mechanism of the tumorigenesis. Gene selection is a fundamental issue in gene expression-based tumor classification. In the formation of a discriminant rule, the number of genes is large relative to the number of tissue samples. Too many genes can harm the performance of the tumor classification system and increase the cost as well. In this report, we discuss criteria and illustrate techniques for reducing the number of genes and selecting an optimal (or near optimal) subset of genes from an initial set of genes for tumor classification. The practical advantages of gene selection over other methods of reducing the dimensionality (e.g., principal components), include its simplicity, future cost savings, and higher likelihood of being adopted in a clinical setting. We analyze the expression profiles of 2000 genes in 22 normal and 40 colon tumor tissues, 5776 sequences in 14 human mammary epithelial cells and 13 breast tumors, and 6817 genes in 47 acute lymphoblastic leukemia and 25 acute myeloid leukemia samples. Through these three examples, we show that using 2 or 3 genes can achieve more than 90% accuracy of classification. This result implies that after initial investigation of tumor classification using microarrays, a small number of selected genes may be used as biomarkers for tumor classification, or may have some relevance in tumor development and serve as a potential drug target. In this report we also show that stepwise Fisher's linear discriminant function is a practicable method for gene expression-based tumor classification.

Humans↗
PubMed2003

The neuronal ceroid-lipofuscinoses.

The neuronal ceroid-lipofuscinoses (NCLs) collectively constitute the most common group of neurodegenerative diseases in childhood and usually show an autosomal recessive mode of inheritance. Despite varying ages of onset and clinical course characterized in most instances by progressive mental and motor deterioration, blindness, epileptic seizures, and premature death, all forms of NCL show unifying histopathological features. There is accumulation of autofluorescent, periodic acid-Schiff-, and Sudan black B-positive granules that are resistant to lipid solvents in the cytoplasm of most nerve cells and. to a lesser degree, of many other cell types. The storage process is associated with progressive and selective neuronal loss and gliosis with secondary white matter lesions. The ultrastructure of the storage deposits varies between different forms of NCL and, along with the age of onset, has provided the basis for the traditional classification of NCLs. Recent molecular genetic findings have established that defects in at least 7 different genes underlie the various forms of NCL. The purpose of this paper is to provide an overview of the NCLs, review recent molecular genetic and biochemical findings, and discuss their impact on our views on the classification and pathogenesis of these devastating brain disorders.

Animals↗
PubMed1993

[Molecular evolutionary analysis of hepatitis B virus (HBV) and genetic classification].

HBsAg of Hepatitis B virus (HBV) has been classified into four major subtypes (adw, adr, ayw, ayr) by the serological methods. Using molecular evolutionary analysis technique, we constructed the phylogenetic tree for the partial S gene (HBsAg gene) of HBV. The tree shows that 51 strains of HBV can be classified into following four genetic subgroups: (1) strains of subtypes ayw and adyw, (2) those of adw and adr, (3) another of adw, and (4) other subgroup of adr, adw, ayr, ar and ad. We propose that these subgroups be designated gyw, gdw-1, gdw-2, and gdr, respectively, with "g" standing for genetic classification. It is important that the genetic classification of HBVs is not always compatible with conventional serological subtypes. It is possible that the conventional subtypes do not represent a classification according to the degree of genetic difference among strains of HBVs. Thus, our genetic classification is more suitable for studies of epidemiological and virological features of HBVs.

Amino Acid Sequence↗
PubMed2007

Genetic analysis to complement histopathological diagnosis of brain tumors.

Gliomas, the most frequent tumors originating in the human nervous system, are divided into various subtypes. Currently, microscopic examination alone is insufficient for classification and grading so that genetic profiles are increasingly being emphasized in recognition of the emerging role of molecular diagnostic approaches to glioma classification. Glioblastomas (WHO grade IV) may develop de novo (primary glioblastomas) or through progression from lower-grade astrocytomas (secondary glioblastomas), while both glioblastomas show similar histological features. In contrast, they do constitute distinct disease entities that evolve through different genetic pathways, and are likely to differ in prognosis and response to therapy. Oligodendrogliomas (WHO grade II) account for 2.7% of brain tumors and 5-18% of all gliomas. Since this tumor is recognized as a particular subtype of glioma that shows remarkable responses to chemotherapy, a correct diagnosis is of prime importance. The difficulty is that histological differentiation of oligodendrogliomas from diffuse astrocytomas is highly subjective in cases without typical morphological features and there is a lack of reliable immunohistochemical markers. While histological distinction of low-grade gliomas from reactive astrocytes is also often difficult, reactive astrocytes usually lack genetic alterations. More biological and molecular approaches to glioma classification thus appear warranted to provide improved means to achieve correct diagnoses.

Astrocytoma↗
PubMed2002

Molecular evolution of hepatitis A virus: a new classification based on the complete VP1 protein.

Hepatitis A virus (HAV) is a positive-stranded RNA virus in the genus Hepatovirus in the family Picornaviridae So far, analysis of the genetic variability of HAV has been based on two discrete regions, the VP1/2A junction and the VP1 N terminus. In this report, we determined the nucleotide and deduced amino acid sequences of the complete VP1 gene of 81 strains from France, Kosovo, Mexico, Argentina, Chile, and Uruguay and compared them with the sequences of seven strains of HAV isolated elsewhere. Overall strain variation in the complete VP1 gene was found to be as high as 23.7% at the nucleotide level and 10.5% at the amino acid level. Different phylogenetic methods revealed that HAV sequences form five distinct and well-supported genetic lineages. Within these lineages, HAV sequences clustered by geographical origin only for European strains. The analysis of the complete VP1 gene allowed insight into the mode of evolution of HAV and revealed the emergence of a novel variant with a 15-amino-acid deletion located on the VP1 region where neutralization escape mutations were found. This could be the first antigenic variant of HAV so far identified.

Amino Acid Sequence↗
PubMedDate not supplied

The evolving concept of renal neoplasia: impact of emerging molecular and electron microscopic studies.

The classification of renal tumors has evolved from one that initially encompassed only 2 types of tumors, i.e., clear and granular cell carcinomas, to the markedly expanded recent classification that incorporates new entities, some of which are primarily defined by specific molecular abnormalities. Despite these advances, a single tumor category, clear cell carcinoma, still incorporates the majority (approximately 70%) of renal tumors. It is, however, postulated that this single category is likely to encompass several different tumor types that are, at present, undifferentiated. Electron microscopic studies have been pivotal in defining the spectrum of oncocytoma-chromophobe renal cell carcinoma. Cytoplasmic eosinophilia found in some renal cell carcinomas currently classified as clear cell type is under intense study. Tumors that have recently emerged from this group include tumors with translocations involving chromosome Xp11.2, carcinomas associated with neuroblastoma and epithelioid angiomyolipoma. The spectrum of renal tumors seen in younger patients is wider than among older patients, with rare and unusual tumors being more likely seen in younger patients. The author concludes that although the routine application of electron microscopy to kidney tumor diagnosis may not be practical, systematic ultrastructural studies of these tumors may aid in the definition of new entities.

Chromosome Aberrations↗
PubMed2006

Towards the classification of subpopulations of layer V pyramidal projection neurons.

The nature of cerebral cortical circuitry has been increasingly clarified by markers for the identification of precise cell types with specific morphology, connectivity and distinct physiological properties. Molecular markers are not only helpful in dissecting cortical circuitry, but also give insight into the mechanisms of cortical neuronal specification and differentiation. The two principal neuronal types of the cerebral cortex are the pyramidal and GABAergic cells. Pyramidal cells are excitatory and project to distant targets, while GABAergic neurons are mostly inhibitory non-pyramidal interneurons. Reliable markers for specific subtypes of interneurons are available and have been employed in the classification and functional analysis of cortical circuitry. Until recently, cortical pyramidal neurons have been considered a homogeneous class of cells. This concept is now changing as the powerful tools of molecular biology and genetics identify molecular tags for subtypes of pyramidal cells such as: Otx-1 [Frantz, G.D., Bohner, A.P., Akers, R.M., McConnell, S.K., 1994. Regulation of the POU domain gene SCIP during cerebral cortical development. J. Neurosci. 14, 472-485; Weimann, J.M., Zhang, Y.A., Levin, M.E., Devine, W.P., Brulet, P., McConnell, S.K., 1999. Cortical neurons require Otx1 for the refinement of exuberant axonal projections to subcortical targets. Neuron 24, 819-831]; SMI-32, N200 and FNP-7 [Voelker, C.C., Garin, N., Taylor, J.S., Gahwiler, B.H., Hornung, J.P., Molnár, Z., 2004. Selective neurofilament (SMI-32, FNP-7 and N200) expression in subpopulations of layer V pyramidal neurons in vivo and in vitro. Cereb. Cortex 14, 1276-1286]; ER81 [Hevner, R.F., Daza, R.A., Rubenstein, J.L., Stunnenberg, H., Olavarria, J.F., Englund, C., 2003. Beyond laminar fate: toward a molecular classification of cortical projection/pyramidal neurons. Dev. Neurosci. 25 (2-4), 139-151; Yoneshima, H., Yamasaki, S., Voelker, C., Molnár, Z., Christophe, E., Audinat, E., Takemoto, M., Tsuji, S., Fujita, I., Yamamoto, N., 2006. ER81 is expressed in a subpopulation of layer 5 projection neurons in rodent cerebral cortices. Neuroscience, 137, 401-412]; Lmo4 [Bulchand, S., Subramanian, L., Tole, S., 2003. Dynamic spatiotemporal expression of LIM genes and cofactors in the embryonic and postnatal cerebral cortex. Dev. Dyn. 226, 460-469; Arlotta, P., Molyneaux, B.J., Chen, J., Inoue, J., Kominami, R., Macklis, J.D., 2005. Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo. Neuron 45 (2), 207-221]; CTIP2 [Arlotta, P., Molyneaux, B.J., Chen, J., Inoue, J., Kominami, R., Macklis, J.D., 2005. Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo. Neuron 45 (2), 207-221]; Fez1 [Molyneaux, B.J., Arlotta, P., Hirata, T., Hibi, M., Macklis, J.D., 2005. Fez1 is required for the birth and specification of corticospinal motor neurons. Neuron 47 (6), 817-831; Chen, B., Schaevitz, L.R., McConnell, S.K., 2005. Fez1 regulates the differentiation and axon targeting of layer 5 subcortical projection neurons in cerebral cortex. Proc. Natl. Acad. Sci. U.S.A. 102 (47), 17184-17189]. These genes outline the numerous subtypes of pyramidal cells and are increasingly refining our previous classifications. They also indicate specific developmental programs operate in cell fate decisions. This review will describe the progress made on the correlation of these markers to each other within a specific subtype of layer V neurons with identified, stereotypic projections. Further work is needed to link these data with observations on somatodendritic morphology and physiological properties. The integrated molecular, anatomical and physiological characterisation of pyramidal neurons will lead to a much better appreciation of functional cortical circuits.

Animals↗