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At least 721 records · Page 40Linked to original sources
PubMed2003

Molecular subclassification of kidney tumors and the discovery of new diagnostic markers.

We analysed the expression profiles of 70 kidney tumors of different histological subtypes to determine if these subgroups can be distinguished by their gene expression profiles, and to gain insights into the molecular mechanisms underlying each subtype. In all, 39 clear cell renal cell carcinomas (RCC), seven primary and one metastatic papillary RCC, six granular RCC from old classification, five chromophobe RCC, five sarcomatoid RCC, two oncocytomas, three transitional cell carcinomas (TCC) of the renal pelvis and five Wilms' tumors were compared with noncancerous kidney tissues using microarrays containing 19,968 cDNAs. Based on global gene clustering of 3560 selected cDNAs, we found distinct molecular signatures in clear cell, papillary, chromophobe RCC/oncocytoma, TCC and Wilms' subtypes. The close clustering in each of these subtypes points to different tumorigenic pathways as reflected by their histological characteristics. In the clear cell RCC clustering, two subgroups emerged that correlated with clinical outcomes, confirming the potential use of gene expression signatures as a predictor of survival. In the so-called granular cell RCC (terminology for a subtype that is no longer preferred), none of the six cases clusters together, supporting the current view that they do not represent a single entity. Blinded histological re-evaluation of four cases of 'granular RCC' led to their reassignment to other existing histological subtypes, each compatible with our molecular classification. Finally, we found gene sets specific to each subtype. In order to establish the use of some of these genes as novel subtype markers, we selected four genes and performed immunohistochemical analysis on 40 cases of primary kidney tumors. The results were consistent with the gene expression microarray data: glutathione S-transferase alpha was highly expressed in clear cell RCC, alpha methylacyl racemase in papillary RCC, carbonic anhydrase II in chromophobe RCC and K19 in TCC. In conclusion, we demonstrated that molecular profiles of kidney cancers closely correlated with their histological subtypes. We have also identified in these subtypes differentially expressed genes that could have important diagnostic and therapeutic implications.

Biomarkers, Tumor↗
PubMed1989

[Classification of blood stains inside a car using molecular genetic methods].

Sex-determination of a 1-year old blood-stain was realited by Dot-blot-Hybridisierung. The bloodstains were inside of a car. It was not clear, if the origin is female or male. By using total human DNA-probe (A) and a sex-specific DNA-probe (Y), (pJA 1143), labeled with P32, as soon as the calculation of the sex-specific quotient (A/Y) you could show, the bloodstains must be descended from a man.

Accidents, Traffic↗
PubMed1998

[Classification of cell-surface receptors based on molecular structures and functions].

The majority of cell-surface receptor proteins belong to one of three main families: ionotropic receptors, G protein-coupled receptors, and enzyme-containing receptors. Additionally, recent studies have revealed the existence of receptors which couple to nonreceptor protein tyrosine kinases. These receptors could be classified as a fourth family. In this review, we summarize structural and functional characteristics of each receptor family.

Animals↗
PubMed2006

Molecular architecture of the DNA-binding region and its relationship to classification of basic helix-loop-helix proteins.

Multivariate statistical analyses are used to explore the molecular architecture of the DNA-binding and dimerization regions of basic helix-loop-helix (bHLH) proteins. Alphabetic amino acid data are transformed to biologically meaningful quantitative values using a set of 5 multivariate "indices." These multivariate indices summarize variation in a large suite of amino acid physiochemical attributes and reflect variability in polarity-accessibility-hydrophobicity, propensity for secondary structure, molecular size, codon composition, and electrostatic charge. Using these index score data, discriminant analyses describe the multidimensional aspects of physiochemical variation and clarify the structural basis of the prevailing evolutionary classification of bHLH proteins. A small number of amino acids from both the binding dimerization domains, when considered simultaneously, accurately distinguish the 5 known DNA-binding groups. The relevant sites often have well-documented structural and functional characteristics.

Animals↗
PubMed2004

Using gene expression profiling to differentiate benign versus malignant thyroid tumors.

DNA microarrays allow quick and complete evaluation of a cell's transcriptional activity. Expression genomics is very powerful in that it can generate expression data for a large number of genes simultaneously across multiple samples. In cancer research, an intriguing application of expression arrays includes assessing the molecular components of the neoplastic process and utilizing the data for cancer classification (Miller LD, et al. Cancer Cell 2002;2:353-61). Classification of human cancers into distinct groups based on their molecular profile rather than their histological appearance may prove to be more relevant to specific cancer diagnoses and cancer treatment regimes. Several attempts to formulate a consensus about classification and treatment of thyroid carcinoma based on standard histopathological analysis have resulted in published guidelines for diagnosis and initial disease management (Sherman SI. Lancet 2003;361:501-11). In the past few decades, no improvement has been made in the differential diagnosis of thyroid tumors by fine needle aspiration biopsy, specifically suspicious or indeterminate thyroid lesions, suggesting that a new approach to this should be explored. Therefore, in this study, we developed a gene expression approach to diagnose benign versus malignant thyroid lesions in 73 patients with thyroid tumors. We successfully built a 10 and 6 gene model able to differentiate benign versus malignant thyroid tumors. Our results support the premise that a molecular classification system for thyroid tumors is possible, and this in turn may provide a more accurate diagnostic tool for the clinician managing patients with suspicious thyroid lesions.

Diagnosis, Differential↗
PubMed1988

[A principle of maximum topological similarity in molecular systematics].

The paper deals with the problem of phylogenetic reconstruction on the basis of comparative analysis of features. Main attention is paid to comparison and classification of the biopolymer sequences. Different approaches to this task are critically reviewed. The novel principle of construction of tree-like classification schemes permitting subsequent evolutionary analysis is proposed. It concentrates on reconstruction of the tree with a topologic structure that is most close to topologic features, imprinted in the source distance matrix. Realization of this approach was made possible by development of the special formalism, enabling evaluation and comparison of topologic features of distance matrices and trees.

Animals↗
PubMed2004

Proteomic analysis of human acute leukemia cells: insight into their classification.

PURPOSE: French-American-British (FAB) classification of acute leukemia with genetic heterogeneity is important for treatment and prognosis. However, the distinct protein profiles that contribute to the subtypes and facilitate molecular definition of acute leukemia classification are still unclear. EXPERIMENTAL DESIGN: The proteins of leukemic cells from 61 cases of acute leukemia characterized by FAB classification were separated by two-dimensional electrophoresis, and the differentially expressed protein spots were identified by both matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF-MS) and tandem electrospray ionization MS (ESI-MS/MS). RESULTS: The distinct protein profiles of acute leukemia FAB types or subtypes were successfully explored, including acute myeloid leukemia (AML), its subtypes (M2, M3, and M5) and acute lymphoid leukemia (ALL), which were homogeneous within substantial samples of the respective subgroups but clearly differed from all other subgroups. We found a group of proteins that were highly expressed in M2 and M3, rather than other subtypes. Among them, myeloid-related proteins 8 and 14 were first reported to mark AML differentiation and to differentiate AML from ALL. Heat shock 27 kDa protein 1 and other proteins that are highly expressed in ALL may play important roles in clinically distinguishing AML from ALL. Another set of proteins up-regulated was restricted to granulocytic lineage leukemia. High-level expression of NM23-H1 was found in all but the M3a subtype, with favorable prognosis. CONCLUSIONS: These data have implications in delineating the pathways of aberrant gene expression underlying the pathogenesis of acute leukemia and could facilitate molecular definition of FAB classification. The extension of the present analysis to currently less well-defined acute leukemias will identify additional subgroups.

Acute Disease↗
PubMed2006

[Cutaneous lymphomas: classification and stage-adjusted therapy].

Cutaneous lymphomas are a heterogeneous group of clonal proliferations of T and B lymphocytes with various clinical manifestations and prognosis. The new EORTC WHO classification of cutaneous T- and B-cell lymphomas provides a uniform nomenclature based on clinical, histologic, cytologic and molecular biological features. Accurate classification is a prerequisite for uniform therapeutic concepts. For office-based dermatologist, more than 50% of the therapies deal with classic forms of cutaneous T-cell lymphomas, type mycosis fungoides. In recent years the paradigm for the therapy of cutaneous T-cell lymphomas has changed. Since early aggressive treatment with cytostatic agents does not increase the response rate or overall survival, a commonly accepted stage-adapted therapy is recommended. In this review the current status of the therapy of cutaneous lymphoma is described in detail.

Antineoplastic Agents↗
PubMed2000

Molecular systematics of the order anaspidea based on mitochondrial DNA sequence (12S, 16S, and COI).

Fragments from three mitochondrial genes (12S, 16S, and COI) were sequenced to reconstruct a molecular phylogeny of the opisthobranch order Anaspidea. The molecular phylogeny supports the placement of the genus Akera, a taxon previously regarded by some authors as a cephalaspidean, within the Anaspidea. Incongruence between the molecular data and the classifications based on morphology suggests that some of the taxonomic characters (i.e., shell, parapodia fusion) traditionally used for the classification of sea hares must be reevaluated, since they may be homoplastic. The ancestral nature of Notarchus based on the molecular evidence suggests that homoplasy may be an explanation for the morphological resemblance of this species to the more derived sea hares with highly fused parapodia and concentrated nerve ganglia. Finally, examples are given of how comparative studies of the evolution of learning mechanisms in the anaspidean clade will benefit from the phylogenetic hypothesis presented in this paper.

Animals↗
PubMed2001

A tissue-specific marker of Ecdysozoa.

Over the past few years, molecular studies of phylogeny have challenged the traditional view of evolutionary relationships among protostomian animal phyla. Based on analysis of 18S ribosomal RNA gene sequences, it has been suggested that some traditional groups, like the articulata and the pseudocoelomata, should be completely abandoned and that instead the protostomians should be split into two major clades: the Ecdysozoa and the Lophotrochozoa. However, this new molecular phylogeny still awaits confirmation by independent methods. In this study, we present a cytological feature that supports the new classification. The carbohydrate epitope that is recognised by antisera against the plant glycoprotein horseradish peroxidase (HRP) is known to be selectively expressed by membrane proteins on the surface of neural tissue in insects. We found that the major ecdysozoan phyla show neural expression of HRP immunoreactivity, which is completely absent in the nervous tissue of lophotrochozoans, deuterostomians, and cnidarians. This suggests that the presence of anti-HRP-reactive glycoproteins in neural tissue is an ecdysozoan autapomorphy.

Animals↗
PubMed2007

SINEs of progress: Mobile element applications to molecular ecology.

Mobile elements represent a unique and under-utilized set of tools for molecular ecologists. They are essentially homoplasy-free characters with the ability to be genotyped in a simple and efficient manner. Interpretation of the data generated using mobile elements can be simple compared to other genetic markers. They exist in a wide variety of taxa and are useful over a wide selection of temporal ranges within those taxa. Furthermore, their mode of evolution instills them with another advantage over other types of multilocus genotype data: the ability to determine loci applicable to a range of time spans in the history of a taxon. In this review, I discuss the application of mobile element markers, especially short interspersed elements (SINEs), to phylogenetic and population data, with an emphasis on potential applications to molecular ecology.

Classification↗
PubMed1987

[High correlation between isoenzyme classification and kinetoplast DNA variability in Trypanosoma cruzi].

By means of 14 restriction enzymes, we have studied the kinetoplast DNA polymorphism in 21 Trypanosoma cruzi isolates previously classified into 19 different genotypes based on the analysis of 15 isozyme loci. We have found a high correlation (p less than 0.001) between the proportion of restriction bands (fragments) common to any two given isolates and the corresponding genetic identities calculated from the isozyme data. This shows that the two classifications (kDNA and isozymes) corrobate one another and strongly suggests that the two types of variability are correlated with time (molecular clocks). The phylogenic classifications so obtained can be used as rational bases for medical and epidemiological studies. Although they are correlated, the two types of analysis are complementary as they do not yield identical results. Like the isozyme genetic distances and genetic identities, the values obtained for the proportion of common restriction bands (fragments) exhibit a continuum. This seems to confirm that natural T. cruzi populations exhibit a wide range of genotypes rather than a few well-differentiated clusters of strains.

Animals↗
PubMed2000

New insights into the pathogenesis of renal tubular acidosis--from functional to molecular studies.

The diagnosis and classification of renal tubular acidosis (RTA) have traditionally been made on the basis of functional studies. On these grounds, RTA has been separated into three main categories: (1) proximal RTA, or type 2; (2) distal RTA, or type 1; and (3) hyperkalemic RTA, or type 4. In recent years significant advances have been made in our understanding of the subcellular mechanisms involved in renal bicarbonate (HCO3-) and H+ transport. Application of molecular biology techniques has also opened a completely new perspective to the understanding of the pathophysiology of inherited cases of RTA. Mutations in the gene SLC4A4, encoding Na+-HCO3- cotransporter (NBC-1), have been found in proximal RTA with ocular abnormalities; in the gene SLC4A1, encoding Cl(-)-HCO3- exchanger (AE1), in autosomal dominant distal RTA; in the gene ATP6B1, encoding B1 subunit of H+-ATPase, in autosomal recessive distal RTA with sensorineural deafness; and in the gene CA2, encoding carbonic anhydrase II, in autosomal recessive osteopetrosis. Syndromes of aldosterone resistance have been also characterized molecularly and mutations in the gene MLR, encoding mineralocorticoid receptor, and in the genes SNCC1A, SNCC1B, and SCNN1G, encoding subunits of the epithelial Na+ channel, have been found in dominant and recessive forms of pseudohypoaldosteronism type 1, respectively. It can be concluded that, although functional studies are still necessary, a new molecular era in the understanding of disorders of renal acidification has arrived.

Acidosis, Renal Tubular↗
PubMed2003

Predicting the genotoxicity of thiophene derivatives from molecular structure.

We report several binary classification models that directly link the genetic toxicity of a series of 140 thiophene derivatives with information derived from the compounds' molecular structure. Genetic toxicity was measured using an SOS Chromotest. IMAX (maximal SOS induction factor) values were recorded for each of the 140 compounds both in the presence and in the absence of S9 rat liver homogenate. Compounds were classified as genotoxic if IMAX >or= 1.5 in either test or nongenotoxic if IMAX < 1.5 for both tests. The molecular structures were represented by numerical descriptors that encoded the topological, geometric, electronic, and polar surface area properties of the thiophene derivatives. The classification models used were linear discriminant analysis (LDA), k-nearest neighbor classification (k-NN), and the probabilistic neural network (PNN). These were used in conjunction with either a genetic algorithm or a generalized simulated annealing to find optimal subsets of descriptors for each classifier. The quality of the resulting models was determined by the number of misclassified compounds, with preference given to models that produced fewer false negative classifications. Model sizes ranged from seven descriptors for LDA to three descriptors for k-NN and PNN. Very good classification results were obtained with all three classifiers. Classification rates for the LDA, k-NN, and PNN models were 80, 85, and 85%, respectively, for the prediction set compounds. Additionally, a consensus model was generated that incorporated all three of the basic model types. This consensus model correctly predicted the genotoxicity of 95% of the prediction set compounds.

DNA Damage↗
PubMed2007

Classification of colorectal cancer based on correlation of clinical, morphological and molecular features.

Over the last 20 years it has become clear that colorectal cancer (CRC) evolves through multiple pathways. These pathways may be defined on the basis of two molecular features: (i) DNA microsatellite instability (MSI) status stratified as MSI-high (MSI-H), MSI-low (MSI-L) and MS stable (MSS), and (ii) CpG island methylator phenotype (CIMP) stratified as CIMP-high, CIMP-low and CIMP-negative (CIMP-neg). In this review the morphological correlates of five molecular subtypes are outlined: Type 1 (CIMP-high/MSI-H/BRAF mutation), Type 2 (CIMP-high/MSI-L or MSS/BRAF mutation), Type 3 (CIMP-low/MSS or MSI-L/KRAS mutation), Type 4 (CIMP-neg/MSS) and Type 5 or Lynch syndrome (CIMP-neg/MSI-H). The molecular pathways are determined at an early evolutionary stage and are fully established within precancerous lesions. Serrated polyps are the precursors of Types 1 and 2 CRC, whereas Types 4 and 5 evolve through the adenoma-carcinoma sequence. Type 3 CRC may arise within either type of polyp. Types 1 and 4 are conceived as having few, if any, molecular overlaps with each other, whereas Types 2, 3 and 5 combine the molecular features of Types 1 and 4 in different ways. This approach to the classification of CRC should accelerate understanding of causation and will impact on clinical management in the areas of both prevention and treatment.

Adenocarcinoma↗
PubMed1995

Karyotype findings and molecular analysis of the bcr gene rearrangement supplementing the histologic classification of chronic myeloproliferative disorders.

BACKGROUND: Histologic examination of bone marrow is important in establishing diagnoses among chronic myeloproliferative disorders (CMPD). Only a few studies, however, have compared cytogenetic or molecular genetic findings to histopathology in CMPD. Diverging results on the presence of the Ph1-translocation in patients with myelofibrosis have been reported. EXPERIMENTAL DESIGN: Cytogenetic studies and molecular analysis of the bcr gene were performed in bone marrow cells of patients with CMPD simultaneously with histopathologic examination of plastic-embedded bone marrow biopsies. RESULTS: The Ph1-chromosome was found in 120/128 (93%) cases with histopathologic diagnosis of chronic myeloid leukemia (CML), including a notable proportion of cases with an increase of megakaryocytes and/or myelofibrosis; the latter was associated with a significant increase of chromosome aberrations, in addition to Ph1. Among those additional changes in myelofibrosis of Ph1-positive CML were del (13q) and t(1;11) in one case each. A bcr gene rearrangement was detected in 92% (24/26) of the CML cases examined. All other groups of CMPD, comprising cases of myelofibrosis and unclassifiable cases, were Ph1-negative by both cytogenetics (n = 102) and molecular analysis (n = 18). Karyotype changes associated with myelofibrosis in various CMPD concerned mainly balanced translocations involving 1p36 and 11q11, deletions of 5q13-34, 3p, 11q23, 13(q12,q22), and 20q12 as well as gain of 1q and trisomy 3, 8, 19, or 21. In histologically unclassifiable CMPD, karyotyping provided additional information for the differential diagnosis. CONCLUSIONS: The correlation of cytogenetic findings and histopathologic features is helpful in confirming or supporting histopathologic diagnoses and in characterizing new marker chromosomes in CMPD.

Aged↗
PubMed2003

Basal cell carcinoma: a dermatopathological and molecular biological update.

The ideal classification of basal cell carcinoma (BCC) should be able to identify subtypes which correlate with clinical behaviour and treatment requirements. Unfortunately, however, such a classification has yet to be defined. In the interim, the currently most favoured classification is one based predominantly on histological growth pattern. This classification contributes to the useful concept of low- and high-risk histological subtypes of BCC. The latter are characterized by an increased probability of subclinical extension and/or incomplete excision and/or aggressive local invasive behaviour and/or local recurrence. The Royal College of Pathologists has published a minimum dataset for the histopathological reporting of BCC and this has been written to be compatible with the British Association of Dermatologists' management guidelines. Growth patterns to be reported include nodular, superficial, infiltrative/morphoeic and micronodular types, together with differentiation when of severely atypical or malignant squamous type (basosquamous carcinoma). Deep and peripheral excision margins will be reported to be either involved or clear. The latter will include a comment of a clearance of less than 1 mm for close margins and a measured distance in whole millimetres for other excisions. Clinical assessment and histology remain the 'gold standard' for evaluating BCC and cancers in general. However, in the postgenomic era emphasis is changing from the gathering and archiving of genomic data to its analysis and use in guiding clinical practice. In this context, a current goal is to define cancer phenotype in terms of molecular abnormalities and use this as a new gold standard. One way to assess whether this goal is being achieved for BCC is to determine whether our knowledge of its molecular pathology has any relevance to the minimum dataset for histological reporting. Knowledge of BCC molecular pathology has been fuelled by the recent discovery that deregulation of the Hedgehog (Hh) signalling pathway, a key player in embryonic patterning, appears to be fundamental to tumour growth. But despite accrual of a large amount of data concerning Hh pathway molecular alterations in neoplasia, little is known about the functional consequences of these changes in BCC, how they lead to tumour development, or how they relate to non-Hh pathway alterations such as TP53 mutation. Recent work suggests that the cellular localization of beta-catenin gives a degree of credence to the growth pattern classification of BCC. Furthermore, it is possible that beta-catenin may have a pathogenetic role in the invasive behaviour of BCC. This review draws on current evidence to discuss these issues and assess whether they are relevant to the minimum dataset.

Basal Cell Carcinoma↗