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Impact of descriptor vector scaling on the classification of drugs and nondrugs with artificial neural networks.

The influence of preprocessing of molecular descriptor vectors for solving classification tasks was analyzed for drug/nondrug classification by artificial neural networks. Molecular properties were used to form descriptor vectors. Two types of neural networks were used, supervised multilayer neural nets trained with the back-propagation algorithm, and unsupervised self-organizing maps (Kohonen maps). Data were preprocessed by logistic scaling and histogram equalization. For both types of neural networks, the preprocessing step significantly improved classification compared to nonstandardized data. Classification accuracy was measured as prediction mean square error and Matthews correlation coefficient in the case of supervised learning, and quantization error in the case of unsupervised learning. The results demonstrate that appropriate data preprocessing is an essential step in solving classification tasks.

Algorithms↗

Molecular phylogeny as a basis for the classification of transport proteins from bacteria, archaea and eukarya.

Although enzymes catalyzing chemical reactions have long been classified according to the system developed by the Enzyme Commission (EC), no comparable system has been developed or proposed for transport proteins catalyzing transmembrane vectorial reactions. We here propose a comprehensive system, designated the Transport Commission (TC) system, based both on function and phylogeny. The TC system initially categorizes permeases according to mode of transport and energy coupling mechanism, and each category is assigned a one-component TC number (W). The secondary level of classification corresponds to the phylogenetic family (or superfamily) to which a particular permease is assigned, and each family is assigned a two-component TC number (W.X). The third level of classification refers to the phylogenetic cluster within a family (or the family within a superfamily) to which the permease belongs, and each cluster receives a three-component TC number (W.X.Y). Finally, the last level of categorization is based on substrate specificity and polarity of transport, and each entry is assigned a four component TC number (W.X.Y.Z). This system is based on the observation that mode of transport and energy coupling mechanism are fundamental properties of transport systems that very seldom transcend familial lines, but substrate specificity, being readily alterable by point mutations, is a superficial characteristic that often transcends familial lines. The proposed system has the potential to include all known permeases for which sequence data are available and has the flexibility to accommodate the multitude of permeases likely to be revealed by future genome sequencing and biochemical analysis. Major conclusions resulting from our classification efforts are described. The classification system, which will be continuously updated, is available on our World Wide Web site (http:/(/)www-biology.ucsd.edu/ approximately msaier/transport/titlepage.html).

Archaea↗

Molecular abnormalities in the major psychiatric illnesses: Classification and Regression Tree (CRT) analysis of post-mortem prefrontal markers.

Post-mortem specimens from the Stanley Foundation Neuropathology Consortium, which contains matched samples from patients with schizophrenia, bipolar disorder, non-psychotic depression and normal controls (n = 15 per group), have been distributed to many research groups around the world. This paper provides a summary of abnormal markers found in prefrontal cortical areas from this collection between 1997 and 2001. With parametric analyses of variance of 102 separate data sets, 14 markers were abnormal in at least one disease. The markers pertained to a variety of neural systems and processes including neuronal plasticity, neurotransmission, signal transduction, inhibitory interneuron function and glial cells. The data sets were also examined using the non-parametric Classification and Regression Tree (CRT) technique for the four diagnostic groups and in pair-wise combinations. In contrast to the results obtained with analyses of variance, the CRT method identified a smaller set of nine markers that contributed maximally to the diagnostic classifications. Three of the nine markers observed with CRT overlapped with the ANOVA results. Six of the nine markers observed with the CRT technique pertained to aspects of glutamatergic, GABA-ergic, and dopaminergic neurotransmission.

Adult↗

International union of pharmacology. XLV. Classification of the kinin receptor family: from molecular mechanisms to pathophysiological consequences.

Kinins are proinflammatory peptides that mediate numerous vascular and pain responses to tissue injury. Two pharmacologically distinct kinin receptor subtypes have been identified and characterized for these peptides, which are named B1 and B2 and belong to the rhodopsin family of G protein-coupled receptors. The B2 receptor mediates the action of bradykinin (BK) and lysyl-bradykinin (Lys-BK), the first set of bioactive kinins formed in response to injury from kininogen precursors through the actions of plasma and tissue kallikreins, whereas the B(1) receptor mediates the action of des-Arg9-BK and Lys-des-Arg9-BK, the second set of bioactive kinins formed through the actions of carboxypeptidases on BK and Lys-BK, respectively. The B2 receptor is ubiquitous and constitutively expressed, whereas the B1 receptor is expressed at a very low level in healthy tissues but induced following injury by various proinflammatory cytokines such as interleukin-1beta. Both receptors act through G alpha(q) to stimulate phospholipase C beta followed by phosphoinositide hydrolysis and intracellular free Ca2+ mobilization and through G alpha(i) to inhibit adenylate cyclase and stimulate the mitogen-activated protein kinase pathways. The use of mice lacking each receptor gene and various specific peptidic and nonpeptidic antagonists have implicated both B1 and B2 receptors as potential therapeutic targets in several pathophysiological events related to inflammation such as pain, sepsis, allergic asthma, rhinitis, and edema, as well as diabetes and cancer. This review is a comprehensive presentation of our current understanding of these receptors in terms of molecular and cell biology, physiology, pharmacology, and involvement in human disease and drug development.

Animals↗

Two categories of synovial sarcoma defined by divergent chromosome translocation breakpoints in Xp11.2, with implications for the histologic sub-classification of synovial sarcoma.

Molecular analysis of a new series of synovial sarcomas confirms that t(X;18)(p11.2;q11.2) breakpoints occur at two distinct regions on Xp designated SS1 and SS2. Breakpoint position correlates with tumor phenotype. Monophasic tumors with no evidence of glandular components have breakpoints within the SS2 region in Xp11.21, and biphasic tumors with a focal poorly differentiated or extensive glandular structure have breakpoints within the SS1 region in Xp11.23.

Adolescent↗

The molecular analyses of hematological malignancies--lineage specific classification and its clinical implications.

Cells from 203 children with leukemia/lymphoma were analyzed by the FAB (French-American-British) system using a broad panel of markers such as immunological marker studies, Southern blot and Northern blot analyses to establish a lineage specific classification of childhood leukemia. Phenotypically, they were divided into B-lineage (62.6%), T-lineage (9.8%), non-lymphoid (14.3%) and uncertain lineage (13.3%). Two B-lineage ALL cells and two T-lineage ALL cells studied did not show immunoglobulin (Ig) or T-cell receptor (TCR) gene rearrangements, respectively. Therefore, those four cases were excluded from the final classification. The uncertain lineage leukemia, which includes undifferentiated leukemia and mixed lineage leukemia, were further subclassified at the DNA and RNA levels. The definitions of B-lineage and T-lineage cells, incidence of dual genotypes or spillover, heterogeneity of undifferentiated leukemia, and a new classification for mixed lineage leukemia were discussed.

Child↗

Genotype-phenotype correlation in hepatocellular adenoma: new classification and relationship with HCC.

Hepatocellular adenomas are benign tumors that can be difficult to diagnose. To refine their classification, we performed a comprehensive analysis of their genetic, pathological, and clinical features. A multicentric series of 96 liver tumors with a firm or possible diagnosis of hepatocellular adenoma was reviewed by liver pathologists. In all cases, the genes coding for hepatocyte nuclear factor 1alpha (HNF1alpha) and beta-catenin were sequenced. No tumors were mutated in both HNF1alpha and beta-catenin enabling tumors to be classified into 3 groups, according to genotype. Tumors with HNF1alpha mutations formed the most important group of adenomas (44 cases). They were phenotypically characterized by marked steatosis (P < 10(-4)), lack of cytological abnormalities (P < 10(-6)), and no inflammatory infiltrates (P < 10(-4)). In contrast, the group of tumors defined by beta-catenin activation included 13 lesions with frequent cytological abnormalities and pseudo-glandular formation (P < 10(-5)). The third group of tumors without mutation was divided into two subgroups based on the presence of inflammatory infiltrates. The subgroup of tumors consisting of 17 inflammatory lesions, resembled telangiectatic focal nodular hyperplasias, with frequent cytological abnormalities (P = 10(-3)), ductular reaction (P < 10(-2)), and dystrophic vessels (P = .02). In this classification, hepatocellular carcinoma associated with adenoma or borderline lesions between carcinoma and adenoma is found in 46% of the beta-catenin-mutated tumors whereas they are never observed in inflammatory lesions and are rarely found in HNF1alpha mutated tumors (P = .004). In conclusion, the molecular and pathological classification of hepatocellular adenomas permits the identification of strong genotype-phenotype correlations and suggests that adenomas with beta-catenin activation have a higher risk of malignant transformation.

Adenoma, Liver Cell↗

[Genetic dystonia].

A NEW CLASSIFICATION: The advent of molecular genetics has led to a total revision of earlier classifications of primary dystonias. LOCUS DYT-1 PRIMARY DYSTONIA: Locus DYT1, situated on chromosome 9, is responsible for the most common phenotypic expression of generalized primary dystonia, Ziehen-Oppenheim disease. This autosomal dominant disease has variable penetration. It has long been recognized that some individuals in families with typical disease only have segmentary, multifocal or even focal dystonia. It has been proven by molecular genetics that the disease can be expressed simply by familial writers cramp with particularly early, and often bilateral, onset. The mutation concerns the torsine A gene, whose function remains to be elucidated. Torsine A is found in the central nervous system, particularly in the dopaminergic neurons of the locus niger. GENERALIZED PRIMARY DYSTONIA UNRELATED TO DYT-1: These dystonias are phenotypically different: younger and more variable age at onset, focal localization early in the disease course generally involving the cervical or cephalic pole, less severe course. Certain forms are linked to chromosome 8 (locus DYT 6). PRIMARY FOCAL OR SEGMENTARY DYSTONIAS: These primary dystonias cause functional or postural disorders and were long considered as sporadic despite rare familial cases suggesting a genetic factor. When searched for systematically, familial cases are found in 20 to 30% of the cases. The dystonia is transmitted by dominant autosomal heredity with reduced penetration. Phenotypically, expression is heterogeneous with a constant frequency of unrecognized or neglected forms and of postural forms. One form is known to be linked to chromosome 18 (locus DYT 7). DOPA-RESPONSIVE DYSTONIA: This class represents 5 to 10% of childhood dystonias. The phenotypic expression is polymorphous but symptoms always improve with very small doses of L-dopa. Both sporadic, and more frequently familial, cases are described. Some forms are recessive, caused by mutation of the gene coding for tyrosine hydroxylase, others are autosomal dominant, often linked to mutation of the gene coding for GTP cyclohydrolase. RAPID ONSET DYSTONIA SYNDROME-PARKINSONISM: This dominant autosomal dystonia is quite exceptional, ... and intriguing.

Adolescent↗

[Current concepts of digestion and absorption of carbohydrates].

The aim of this paper is to review recent aspects of digestion and absorption of carbohydrates that are the main source of energy in human diets. Recent researches have found that starch is not largely hydrolysed and absorbed in the small bowel but one part of it is resistant to digestion. Several food factors may be responsible for digestion and absorption velocity and totality of carbohydrates. Therefore, carbohydrate classification must be based not only on molecular size to express the real carbohydrates utilization as an energy source by humans. In agreement with molecular size of carbohydrate, its classification can be: a) monosaccharides; b) disaccharides; c) oligosaccharides; d) polysaccharides. In agreement with carbohydrate digestibility or availability, its classification can be: a) digestible carbohydrates; b) undigestable carbohydrates (NSP). Carbohydrate digestibility can be altered by several factors like: Intrinsic factors: a) physical structure; b) molecular physical distribution; c) physical state of food; d) food antinutrients. Extrinsics factors: a) chewing; b) transit time of food; c) amount of starch present; d) diet antinutrients. Under influence of this factors, process of digestion happen by enzymatic activity a long the gastrointestinal tract. Salivary and pancreatic amylase; glycosidases of the duodenal enterocyte brush border (lactase, sacarase and maltase), whose activity happen by close interaction of digestive breakdown with transport. The summarized pathways of the absorptive process: 1. movement from the bulk phase of the lumenal or mucosal fluid to enterocyte surface; 2. movement across the brush border membrane through specific transporters: a) SGLT1; b) GLUT 5; c) passive diffusion. 3. movement across the basolateral membrane by the GLUT 2.

Carbohydrate Metabolism↗

Receptors for 5-hydroxytryptamine: current perspectives on classification and nomenclature.

With the increasing number of 5-HT receptors recently identified, using molecular biology techniques, the classification of 5-HT receptors is under review. An integrated approach is proposed to include operational and transductional as well as structural criteria for definitive receptor characterization. On this basis the existence of as many as seven classes of 5-HT receptor are recognized although only the 5-HT1, 5-HT2 and 5-HT3 receptor classes are well defined.

Animals↗

Ocular adnexal lymphoid proliferations: clinical, histologic, flow cytometric, and molecular analysis of forty-three cases.

PURPOSE: To describe the clinical features, histologic findings, flow cytometric immunophenotypes, and molecular profiles of ocular adnexal lymphoid proliferations. STUDY DESIGN: Prospective noncomparative case series. PARTICIPANTS: Forty-three patients suspected of having ocular adnexal lymphoid proliferations were biopsied and prospectively evaluated. METHODS: Provisional diagnoses were made on the basis of routine histology and immunohistochemistry for B and T cells. Results of flow cytometric immunophenotyping (FCI) and molecular assessment using polymerase chain reaction for immunoglobulin heavy chain (IgH) and TCR gamma chain gene rearrangement and bcl-2/IgH translocation were then incorporated into a final diagnosis. Demographic and clinical outcome data were collected. MAIN OUTCOME MEASURES: Final diagnosis based on histology, flow cytometry, and polymerase chain reaction. RESULTS: Forty-three cases were studied. Final diagnoses included 17 lymphomas, 18 chronic inflammations, 4 reactive lymphoid hyperplasias, and 4 atypical lymphoid infiltrates. Preliminary evaluation accurately categorized all 43 cases as either lymphoma or nonlymphoma. FCI permitted more precise subclassification of the lymphomas according to the Revised European American Lymphoma (REAL) system of nomenclature as follows: eight marginal zone B cell (mucosa-associated lymphoid tissue type), three mantle cell, two follicular, three large cell, and one lymphoplasmacytoid lymphoma. FCI showed a clonal B cell proliferation in 94% (16 of 17) of the lymphomas; FCI identified a clonal B cell population in 4% (1 of 25) of cases of nonlymphomas. Molecular evidence of clonality was identified in 88% (15 of 17) of lymphomas, 39% (7 of 18) of chronic inflammations, and 50% (4 of 8) of reactive lymphoid hyperplasias and atypical lymphoid infiltrates. CONCLUSIONS: The histologic diagnosis of ocular adnexal lymphoid lesions is highly accurate when determined by an experienced pathologist. FCI refines the histologic diagnosis and classification. Results of molecular studies should be interpreted in conjunction with clinical, histologic, and immunophenotyping findings.

Adolescent↗

Autoradiography of adrenoceptors in rat and human brain: alpha-adrenoceptor and idazoxan binding sites.

This chapter reviews the current classification of adrenoceptors, and notes the difficulties of combining the molecular biological and pharmacological classifications of adrenoceptors. Possibilities for mapping the distribution of the proposed subtypes of adrenoceptors using currently available ligands are discussed, and the autoradiographic visualisation of the broad subtypes of alpha 1-, alpha 2-, beta 1-, and beta 2-adrenoceptors in the rat, monkey and human brain described and illustrated. The non-selectivity of ligands currently being used to label alpha-adrenoceptors is shown; we compare the distribution of [3H]idazoxan binding sites with the distribution of alpha 2-adrenoceptors visualised using other ligands. Resolution limitations of current autoradiographic approaches are considered and we shown how in situ hybridisation can complement data from receptor labelling studies used to localise receptors to pre- or postsynaptic sites.

Animals↗

Is promiscuity of G protein interaction an issue in the classification of receptors?

It is clear that the details of binding of different classes of agonist ligands to the same receptor may be distinct. This could result in subtle differences in the profile of G protein activation by individual ligands at the same receptor due to agonist-induced selection of conformational states of the receptor which favor interaction and ternary-complex formation with different G proteins. This can result in differences in the details of receptor pharmacology when measured at the level of effector output. Such differences are also likely to be dependent upon both the levels of expression of the receptor and the relevant G proteins and the G protein and effector enzyme isoform expression profile of a particular tissue. It would be foolish, however, to use such differences, in isolation, as a means to expand the classification of G protein-coupled receptors particularly when more molecular approaches to receptor classification are readily available.

Animals↗

Integration of multi-omics data uncovers novel germline susceptibility candidates in early-onset colorectal cancer.

Colorectal cancer (CRC) is increasingly diagnosed in individuals under 50 years of age, yet the underlying genetic predisposition remains largely unexplained, particularly in mismatch repair (MMR)-proficient cases. This study aimed to identify novel hereditary CRC susceptibility genes by integrating germline and tumour whole-exome sequencing (WES) with transcriptomic profiling across a cohort of early-onset CRC (EOCRC) patients. Tumours were categorised using Consensus Molecular Subtypes (CMS) classification and analysed for mutational signature and burden. We used a novel 'All vs One' multi-omic integration approach to identify loss-of-function rare germline variants with concordant gene expression alterations in tumour tissue. Five candidate genes (ADCY4, NOXO1, CDHR2, ARHGAP10, EEF2K) were prioritised based on this approach and potential biological relevance in CRC. These findings highlight the molecular heterogeneity of EOCRC and demonstrate the utility of multi-omic approaches in refining germline variant interpretation. Integrating tumour transcriptomics enhances gene discovery efforts and supports a more comprehensive understanding of CRC heritability in younger individuals.

Humans↗

Personalised medicine for cancer: from drug development into clinical practice.

Personalised management of cancer means the prescription of specific therapeutics that are best suited for an individual patient and the type of tumour. Molecular diagnostics influences cancer management in several ways that aid personalisation. These technologies are enabling the classification of cancer, using molecular profiles, as a basis for more effective personalised therapies. Using microarrays, classification of a cancer based on the gene expression profile is important for personalising cancer therapy. Molecular imaging, such as by positron emission tomography, enables determination of tumour response to drug action at the molecular level. The combination of diagnostics with therapeutics--an important feature of personalised cancer therapy--is facilitated by the use of monoclonal antibodies and nanobiotechnology. Development of drug resistance--an important problem in cancer management--varies according to the anticancer agent, type of tumour and individual patient. There are no universal strategies to overcome drug resistance in cancer. Various efforts to deal with this problem should be tailored to each patient, and examples are given in this review. A better understanding of cancer biology will facilitate rational drug discovery for cancer, by linking the various pathways involved to targeted therapies. Oncoproteomics will play an important role in the development of personalised cancer therapy. Use of pharmacogenomic technologies in early clinical trials is enabling rapid assessment of the efficacy of anticancer agents, and reducing the time of drug development. Application of pharmacogenetics will reduce the adverse effect of anticancer drugs. Cell/gene therapies, cancer vaccines and RNA interference will facilitate the development of personalised cancer therapy.

Animals↗

Molecular characterization of acute myeloblastic leukemia according to the new WHO classification: a different distribution in Central-West Spain.

BACKGROUND AND OBJECTIVES: Molecular analysis has contributed to the identification of several non-random chromosomal translocations, such as t(15;17), t(8:21), inv(16)/t(16;16) and 11q23 abnormalities, typically associated with acute myeloid leukemia (AML). The identification of these chromosomal abnormalities helps not only to define different AML subtypes with distinct prognoses and treatments but also to monitor the disappearance of malignant cells after treatment. Recent reports suggest that the frequency of these alterations may differ according to geographic distribution. However, most of these reports focus on just one or two genetic alterations, which may lead to some selection bias. Appropriate epidemiological studies should be based on unselected consecutive series of patients in which all relevant genes are simultaneously analyzed. The aim of the present study was to explore whether or not the incidence of genetic lesions in Spanish AML patients differs from that reported in other countries. DESIGN AND METHODS: In a series of 145 consecutive un-selected adult patients with AML we simultaneously analyzed the presence of 4 genetic abnormalities, PML/RARalpha for t(15;17), AML1/ETO for t(8;21), CBFbeta/MYH11 for inv(16)/t(16;16) and rearrangements of the MLL gene for 11q23 abnormalities. AML were classified using the new World Health Organization (WHO) classification for hematologic malignancies. The techniques used were standardized according to the recommendations of the European BIOMED-1 Concerted Action. RESULTS: The PML/RARalpha transcript was present in 34 patients (23.4%) (23 were bcr1, 2 bcr2 and 9 bcr3). The AML1/ETO fusion transcript was detected in only 2 cases (1.4%) both with M2 morphology, but 29 other cases with M2 morphology were negative. CBFbeta/MYH11 transcript was present in 9 cases (6.2%) eight of them displaying M4Eo morphology. Finally, 5 cases (3.5%) showed rearrangements of theMLL gene. Our results differ from those reported from the United States and North/Central Europe, particularly regarding the incidence of t(15;17) and t(8;21) translocations. In Spain the frequency of t(15;17) is higher while that of t(8;21) is lower. INTERPRETATION AND CONCLUSIONS: These data add epidemiological information about geographic heterogeneity of such chromosome aberrations in AML and would contribute to the design of specific screening strategies adapted to the incidence in each country.

Adolescent↗