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PubMed2004

Biology of gastrointestinal stromal tumors.

Once a poorly defined pathologic oddity, in recent years, gastrointestinal stromal tumor (GIST) has emerged as a distinct oncogenetic entity that is now center stage in clinical trials of kinase-targeted therapies. This review charts the rapid progress that has established GIST as a model for understanding the role of oncogenic kinase mutations in human tumorigenesis. Approximately 80% to 85% of GISTs harbor activating mutations of the KIT tyrosine kinase. In a series of 322 GISTs (including 140 previously published cases) studied by the authors in detail, mutations in the KIT gene occurred with decreasing frequency in exons 11 (66.1%), 9 (13%), 13 (1.2%), and 17 (0.6%). In the same series, a subset of tumors had mutations in the KIT-related kinase gene PDGF receptor alpha (PDGFRA), which occurred in either exon 18 (5.6%) or 12 (1.5%). The remainder of GISTs (12%) were wild type for both KIT and PDGFRA. Comparative studies of KIT-mutant, PDGFRA-mutant, and wild-type GISTs indicate that there are many similarities between these groups of tumors but also important differences. In particular, the responsiveness of GISTs to treatment with the kinase inhibitor imatinib varies substantially depending on the exonic location of the KIT or PDGFRA mutation. Given these differences, which have implications both for the diagnosis and treatment of GISTs, we propose a molecular-based classification of GIST. Recent studies of familial GIST, pediatric GIST, and variant forms of GIST related to Carney's triad and neurofibromatosis type 1 are discussed in relationship to this molecular classification. In addition, the role of mutation screening in KIT and PDGFRA as a diagnostic and prognostic aid is emphasized in this review.

Antineoplastic Agents↗

PubMed2001

A molecular approach to the classification of von Willebrand disease.

The marked heterogeneity of von Willebrand disease was already recognized by von Willebrand in 1926. The accumulating knowledge of the different clinical phenotypes and the pathophysiological basis of the disease was translated into a classification that differentiated between quantitative and qualitative defects by means of quantitative and functional parameters and by analysing the electrophoretic pattern of von Willebrand factor multimers. The increasing number of different von Willebrand disease phenotypes required a revision of the nomenclature at a time when only a few types of von Willebrand disease had already been analysed at the molecular level. Consequently, the molecular data played only a minor role in the revised classification. Given the pronounced, even intra-individual, variation in the manifestation of von Willebrand disease and the diagnostic difficulties caused by a non-standardized methodology, it is clear that biochemical methods alone are insufficient for a clear classification. The advent of molecular techniques provided the opportunity for genotype-phenotype studies that recently helped to elucidate or confirm not only the important functions of von Willebrand factor and the steps of its post-translational processing, but also many disease-causing defects. The reproducible correlation between certain phenotypes and particular mutations can now be used for a molecular approach towards a final classification of von Willebrand disease, equally useful for the clinician and for research requirements.

Genetic Variation↗

PubMed2003

Etiological classification of CNS malformations: integration of molecular genetic and morphological criteria.

Classification is a creative activity that helps us understand relationships. The traditional classifications of central nervous system malformations was based exclusively upon descriptive morphology, but these criteria must now be integrated with molecular genetic data to enable an etiological classification that also remains useful to the clinician, radiologist and pathologist, who rely upon imaging and tissue examination for diagnosis. Many cerebral malformations previously thought to be a single disorder are now known to be common end-results of several independent genetic mutations. Examples are holoprosencephaly and lissencephaly. Gradients of genetic expression along the axes of the neural tube, established at the time of gastrulation, may explain many varieties or anatomical and clinical manifestations of cerebral malformations, including the involvement of non-neural tissues such as in midfacial hypoplasia, that may be attributed to abnormal neural crest migration. Genes of cellular lineage and of symmetry may explain some hamartomatous malformations, such as tuberous sclerosis and hemimegalencephaly. Modern classification should be applicable to the entire CNS as well as regions; schemes that attempt to artificially isolate the cerebral cortex for a "regional classification" may be erroneous even though the genetic defect primarily affects cortical structures because genetic gradients in the neuraxis are excluded and some involve a more subtle but still important expression in subcortical structures.

Brain Diseases↗

PubMed2004

Immunophenotypic and molecular studies in the diagnosis and classification of malignant lymphoma.

Immunophenotypic and molecular studies play an increasingly important role in the diagnosis and classification of lymphoid neoplasms. These studies are not yet a substitute for expert histopathologic evaluation, but are a valuable adjunct to the examination of the hematoxylin and eosin-stained slide. Major applications include determination of lineage, determination of B and T cell monoclonality, detection of oncoprotein expression, and detection of oncogene rearrangements and chromosomal translocations. The recognition of the lymphomas as distinct biologic entities with specific immunophenotypic and genotypic features, as embodied in the Revised European-American Lymphoma (REAL) and World Health Organization (WHO) classifications, is a key to the future development and application of targeted biologic and molecular therapies. In the future, application of gene expression array analysis to the lymphoid neoplasms will permit classification of the lymphomas at a molecular level.

B-Lymphocytes↗

PubMed2000

Evaluation of a specific nested PCR targeting domain III of the 23S rRNA gene of "Tropheryma whippelii" and proposal of a classification system for its molecular variants.

"Tropheryma whippelii"-associated infections are usually confirmed histopathologically by using light microscopy. PCR assays targeting the 16S rRNA gene (16S rDNA) of "T. whippelii" are increasingly being applied for this purpose. Compared to microscopic analysis, PCR seems to be more sensitive, as indicated by the fact that several cases of Whipple's disease with negative histopathological findings but positive PCR results have been reported. Considering the lack of pathognomonic clinical features for this disease and the fact that "T. whippelii" DNA has repeatedly been found in patients without clinical Whipple's disease, such PCR results should be confirmed by additional tests. We have, therefore, evaluated a "T. whippelii"-specific nested PCR targeting domain III of the 23S rDNA with 41 clinical specimens known to contain "T. whippelii" 16S rDNA. All of these specimens were also positive for "T. whippelii" 23S rDNA. The specificity of the test was shown by sequencing of the amplicons and by the absence of amplicons in 38 negative controls. We consider this PCR test to be a suitable tool for confirming the presence of "T. whippelii" DNA in specimens with inconclusive histopathological findings. The information derived from sequencing of the partial "T. whippelii" 23S rDNA was then combined with our recent data of the 16S-23S rDNA spacer region of this organism. Overall, four different rDNA types are recognized in our proposed classification system for molecular variants of "T. whippelii." This preliminary scheme may provide a basis for further epidemiological and clinical studies with "T. whippelii" and associated diseases.

Actinobacteria↗

PubMed1997

The neuropathology of CAG repeat diseases: review and update of genetic and molecular features.

Classification of inherited neurodegenerative diseases is increasingly based on their genetic features, which supplement, clarify, and sometimes replace the older clinical and pathologic schemata. This change has been particularly rapid and impressive for the CAG repeat disorders. In Huntington's disease, X-linked spinobulbar muscular atrophy, dentatorubropallidoluysian atrophy, and a series of autosomal dominant cerebellar atrophies, genetic advances have resolved many nosologic issues, and opened new avenues for exploration of pathogenesis. In this review, we summarize classic and current concepts in neuropathology of these CAG repeat diseases.

Genetic Linkage↗

PubMed2002

Microarrays and molecular markers for tumor classification.

Human cancers have traditionally been classified according to their tissue of origin, histological characteristics and, to some extent, molecular markers. Clinical studies have associated different tumor classes with differences in prognosis and in response to therapy. Measurement of the expression of thousands of genes in hundreds of cancer specimens has begun to reveal novel molecularly defined subclasses of tumor; some of these classes appear to predict clinical behavior, while others may define tumor types that are ripe for directed development of therapeutics. Unfortunately, at present, differences between studies of similar tumor types can be as striking as their similarities.

Gene Expression Profiling↗

PubMed2003

The skeletal muscle channelopathies: distinct entities and overlapping syndromes.

PURPOSE OF REVIEW: This review outlines recent advances in clinical, genetic and molecular aspects of skeletal muscle channelopathies. RECENT FINDINGS: A new molecular genetic classification of skeletal muscle channelopathies has now emerged. This genetic classification complements previous clinical classifications. It is evident that there is considerable phenotypic diversity associated with dysfunction of a given muscle ion channel. Treatment response is likely to be related to genotype. DNA-based diagnosis is now achievable in most patients. SUMMARY: Ion channel dysfunction is now known to be the basis for familial variants of common neurological diseases such as migraine and epilepsy. Such discoveries were made possible through earlier work on the skeletal muscle channelopathies which remain the best understood example of all channelopathies. Classification of muscle channelopathies initially relied upon their specific clinical and neurophysiological features. This classification remains useful, but recent advances have led to a new system of classification based on the underlying molecular genetic defect. Recent advances have highlighted the broad phenotypic spectrum of muscle channelopathies and remarkable genetic heterogeneity is now recognized. DNA-based diagnosis is now available and should be achieved in all patients. Accurate genetic diagnosis is of major importance for accurate prognosis, for genetic counselling and has implications for therapeutics.

Animals↗

PubMed1992

Classification and staging of lymphoma by molecular genetics.

Recombinant DNA technology has provided a wealth of new observations in the study of lymphoma. Progress has been enhanced by the unique rearrangement of immune-specific genes during normal lymphocyte differentiation. Because these gene rearrangements are irreversible and are inherited in all cellular progeny, lymphoid tumors have a monoclonal genomic structure. Molecular analysis of genomic structure is a powerful new method of assessing clonality and lineage to supplement histologic examination in achieving accurate diagnosis and staging of lymphomas. Furthermore, the frequent occurrence of translocations in lymphoid neoplasms provides a second pathway for genomic analysis. In 57 B-cell lymphomas tested by Southern blot and polymerase chain reaction, the authors found evidence of bc12 gene translocation in 100% of follicular small cleaved cell lymphomas, 67% of diffuse small cleaved cell lymphomas, 33% of mixed lymphomas, 25% of diffuse large cell lymphomas, and 25% of small noncleaved lymphomas. They also describe their experience with immunoglobulin heavy chain and T-cell receptor beta chain genomic analysis as well as review the published literature on the utility of molecular genetics in the classification and staging of lymphoma. Future applications of molecular diagnostics in the clinical management of lymphoma patients are assessed.

Base Sequence↗

PubMed2000

A proposed classification of mastocytosis incorporating molecular genetics.

As an understanding of the molecular genetic causes of different forms of mastocytosis is developed, the therapy of choice may depend on the specific genetic abnormalities expressed by a patient's neoplastic mast cells. The authors propose a new classification system for mastocytosis that incorporates both molecular-genetic and clinical data. This system provides a theoretic framework for mast cell researchers and helps practicing physicians in estimating prognosis and determining therapeutic options for individual patients.

Adult↗

PubMed1982

Adrenergic receptors: classification, ligand binding and molecular properties.

The interaction of catecholamines and drugs with adrenergic receptors leads to a set of biochemical reactions which ultimately results in a physiological response. A brief review is given of the classification of adrenergic receptors into subtypes and the use of ligand binding techniques for the identification and characterization of these receptors. Recent advances in the biochemistry of adrenergic receptors are reviewed with special reference to the interaction of the beta and alpha 2-receptors with guanine nucleotide regulatory proteins and adenylate cyclase. The role of calcium and phosphoinositides in the function of the alpha 1-receptor is also discussed.

Animals↗

PubMed2005

WHO/EORTC classification of cutaneous lymphomas 2005: histological and molecular aspects.

UNLABELLED: The new WHO/EORTC classification for cutaneous lymphomas comprises mature T-cell and natural killer (NK)-cell neoplasms, mature B-cell neoplasms, and immature hematopoietic malignancies. It reflects the unique features of lymphoproliferative diseases of the skin, and at the same time it is as compatible as possible with the concepts underlying the WHO classification for nodal lymphomas and the EORTC classification of cutaneous lymphomas. This article reviews the histological, phenotypical, and molecular genetic features of the various nosological entities included in this new classification. These findings always have to be interpreted in the context of the clinical features and biologic behavior. AIM: To review the histological, phenotypical and molecular genetic features of the various nosological entities of the new WHO/EORTC classification for cutaneous lymphomas. METHODS: Extensive review of the literature cited in Medline and own data of the authors. RESULTS: The WHO/EORTC classification of cutaneous lymphomas comprises mature T-cell and NK-cell neoplasms, mature B-cell neoplasms and immature hematopoietic malignancies. It reflects the unique features of primary cutaneous lymphoproliferative diseases. CONCLUSION: This classification is as much as possible compatible with the concept of the WHO classification for nodal lymphomas and the EORTC classification of cutaneous lymphomas. The histological, phenotypical and molecular genetic features always have to be interpreted in the context of the clinical features and biologic behavior.

Europe↗

PubMed2002

Molecular phylogeny and proposed classification of the simian picornaviruses.

The simian picornaviruses were isolated from various primate tissues during the development of general tissue culture methods in the 1950s to 1970s or from specimens derived from primates used in biomedical research. Twenty simian picornavirus serotypes are recognized, and all are presently classified within the Enterovirus genus. To determine the phylogenetic relationships among all of the simian picornaviruses and to evaluate their classification, we have determined complete VP1 sequences for 19 of the 20 serotypes. Phylogenetic analysis showed that A13, SV19, SV26, SV35, SV43, and SV46 are members of human enterovirus species A, a group that contains enterovirus 71 and 11 of the coxsackie A viruses. SA5 is a member of human enterovirus species B, which contains the echoviruses, coxsackie B viruses, coxsackievirus A9, and enterovirus 69. SV6, N125, and N203 are related to one another and, more distantly, to species A human enteroviruses, but could not be definitely assigned to a species. SV4 and SV28 are closely related to one another and to A-2 plaque virus, but distinct from other enteroviruses, suggesting that these simian viruses are members of a new enterovirus species. SV2, SV16, SV18, SV42, SV44, SV45, and SV49 are related to one another but distinct from viruses in all other picornavirus genera, suggesting that they may comprise a previously unknown genus in Picornaviridae. Several simian virus VP1 sequences (N125 and N203; SV4 and SV28; SV19, SV26, and SV35; SV18 and SV44; SV16, SV42, and SV45) are greater than 75% identical to one another (and/or greater than 85% amino acid identity), suggesting that the true number of distinct serotypes among the viruses surveyed is less than 20.

Animals↗

PubMed2004

Integrative classification of morphology and molecular genetics in central nervous system malformations.

We propose a scheme to classify central nervous system (CNS) malformations that integrates morphology and genetics by using patterns of genetic expression as its basis. The precise genetic mutations are not necessary to know in all cases. The premises of this classification are (1) genetic expression in the neural tube follows gradients in the axes that are established at the time of gastrulation: vertical (dorsoventral and ventrodorsal); rostrocaudal; mediolateral. (2) Overexpression in one of these gradients generally results in duplication or hyperplasia of structures, or ectopic segmental (i.e., neuromeric) expression. (3) Underexpression in a gradient generally results in hypoplasia, noncleavage in the midline of paired structures or segmental deletion of neuromeres. These gradients may also affect the formation and migration of neural crest tissue, affecting non-neural structures such as the face in the case of the mesencephalic neural crest, or induction of paraxial mesodermal in the posterior fossa. Additional criteria of the new classification allow for other genetic influences on developmental processes, such as cellular lineage, exemplified by tuberous sclerosis, and hemimegalencephaly. It is essential that the CNS be considered as a whole and classification not be regionalized, as to the cerebral cortex, because the limit of the rostrocaudal gradient may account for variability in clinical manifestations.

Central Nervous System↗

PubMed2025

Recent Advances in nccRCC Classification and Therapeutic Approaches.

Non-clear cell renal cell carcinoma (nccRCC) constitutes a biologically diverse category of renal malignancies. The 2022 WHO classification framework has significantly evolved to incorporate molecularly defined entities alongside traditional histologic subtypes, reflecting the growing recognition of distinct pathogenic drivers. Current therapeutic paradigms for advanced disease remain suboptimal, with treatment strategies often extrapolated from clear cell renal cell carcinoma (ccRCC). In this review, we highlight transformative multi-omics approaches to address nccRCC's profound heterogeneity, which enables molecular stratification beyond conventional pathology, identifying novel subtypes characterized by unique immune microenvironment features, metabolic profiles, and genomic instability patterns. This molecular reclassification provides a foundational framework for precision oncology, facilitating patient selection for targeted therapies and immunomodulatory strategies. Advancements in multi-omics subtyping represent a pivotal shift toward biologically guided clinical management and underscore the imperative for biomarker-driven therapeutic development in nccRCC.

Humans↗

PubMed2004

Role of molecular studies in the classification of lymphoma.

The classification of lymphomas has historically lacked both precision and accuracy, potentially compromising both optimal diagnosis and therapy. The genetic characterization of key oncogenic events and the advent of expression profiling have afforded the opportunity to understand, diagnose and treat these diseases in a much more rational and targeted manner. As exciting as these new and testable data are, it is also worth noting that molecular genetic analysis of the tumor in isolation will not be the sole arbiter of patient outcome. It is likely that we will remain reliant on traditional and sometimes subjective technologies, albeit probably to a lesser degree, with molecular studies significantly complementing, but certainly not replacing, microscopic, immunophenotypic and cytogenetic approaches. Furthermore, we will perhaps need to extend genotyping to the tumor milieu (the patient) in order to molecularly dissect drug metabolic pathways and the immune response.

Chromosome Aberrations↗

PubMedDate not supplied

Molecular descriptors for effective classification of biologically active compounds based on principal component analysis identified by a genetic algorithm.

We have evaluated combinations of 111 descriptors that were calculated from two-dimensional representations of molecules to classify 455 compounds belonging to seven biological activity classes using a method based on principal component analysis. The analysis was facilitated by application of a genetic algorithm. Using scoring functions that related the number of compounds in pure classes (i.e., compounds with the same biological activity), singletons, and mixed classes, effective descriptor sets were identified. A combination of only four molecular descriptors accounting for aromatic character, hydrogen bond acceptors, estimated polar van der Waals surface area, and a single structural key gave overall best results. At this performance level, approximately 91% of the compounds occurred in pure classes and mixed classes were absent. The results indicate that combinations of only a few critical descriptors are preferred to partition compounds according to their biological activity, at least in the test cases studied here.

Algorithms↗

PubMed2003

Molecular evidence supporting the classification of Hosta virus X as a distinct species of the genus.

Apotexvirus, Hosta virus X (HVX-Kr), causing mosaic and mottle symptoms was isolated from hosta plants ( Hosta spp.) in Korea. The 3'-terminal 2,711 nucleotides excluding the poly (A) tail were determined and shown to include the partial viral replicase, triple gene block (TGB) 1 (26 kDa), TGB2 (13 kDa), TGB3 (8 kDa), and 23 kDa coat protein (CP) and the 3'-nontranslated region (NTR), typical of potexviruses. The CP gene of the type isolate of HVX (HVX-U) was amplified by RT-PCR and its nucleotide sequence was determined. The CPs of HVX-Kr and HVX-U had 100% and 98.9% identical amino acids and nucleotides, respectively. Most of the regions of the genome HVX had over 50% nucleotide identical to other sequenced potexviruses. This is the first report of sequence information of HVX and molecular evidence supporting the virus as a distinct species of the genus Potexvirus.

3' Untranslated Regions↗