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PubMedDate not supplied

Genomic profiling in clinical oncology. The predictive value of genomic information in cancer management.

Genomic profiling is a significant addition to the clinician's armamentarium, enabling more specific diagnosis and targeted treatment of a wide range of diseases, including cancer. Although not yet widely used in a clinical setting, the new technology is providing detailed information about the particular genes expressed in malignant tissues. The predictive value of this information has been demonstrated in small clinical trials. The results of these and other groundbreaking studies are briefly reviewed.

Adult↗
PubMedDate not supplied

Ethics of genetic counseling--basic concepts and relevance to Islamic communities.

Scientific advances and technical developments in the field of laboratory diagnosis and their practical applications have raised ethical issues linked to religion, beliefs, lifestyle and traditions prevailing in different communities. Some of these are pertinent to genetic screening at various stages of life, prenatal diagnosis and the right of the genetically affected fetus to live--all aspects relevant to inbreeding marriages. Of relevance are medical and ethical principles based on professional responsibility. These ideological and social aspects encounter the challenges of science and its applications in the health field, which are linked, directly or indirectly, to scientific achievements and applications related to human genetics. Analysis of the human genome and identification of its sequence, and chemical components, and theories arising from connection of human genome components in health and disease conditions, have led to global requirements to outline legal aspects and ethical principles in relation to diagnosis, prevention and health care. This paper presents basic aspects of disseminating genetic information, guiding the individual, the couple, or the concerned family through genetically induced ill health and methods of control and prevention. The paper discusses the elements and manner and presents details of the application of genetic counseling in Islamic communities in light of scientific, religious, social and legal aspects in the Islamic arena.

Awareness↗
PubMed2003

[Genomic organization and promoter analysis of mouse apoptosis signal-regulating kinase 2 (ASK 2)].

ASK 2/MAPKKK 6 was identified as a member of the MAPKKK family, which shares 45% amino acid identity with ASK 1/MAPKKK 5. In this study, the genomic organization and promoter of mouse ASK 2 were determined. ASK 2 gene spans approximately 12 kb and is comprised of 29 exons, flanked by 5' regulatory regions. Through comparison with ASK 2 cDNA variant clones, two splice variants were identified: a transcript lacking 24 bases encoding 8 amino acids was caused by disuse of exon 3, and another frameshifted transcript due to 4 bases deletion was produced by usage of the first 4 bases of exon 17 as a part of the splicing acceptor. Reporter plasmid analysis demonstrated that a promoter existed in the immediate upstream region adjacent to exon 1. Interestingly, the 5'-flanking region of the promoter possessed a strong suppressive element. These results suggest that expression of ASK 2 is regulated by multiple mechanisms.

Animals↗
PubMed2003

Comparative studies of somatic and ongoing mutations in immunoglobulin heavy-chain variable region genes in diffuse large B-cell lymphomas of the stomach and the small intestine.

CONTEXT: Many diffuse large B-cell lymphomas (DLBCLs) of the stomach are believed to represent high-grade transformation of low-grade marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue type, which is of memory B-cell origin, displaying evidence for positive antigen selection and a low level of ongoing somatic mutation of the rearranged immunoglobulin heavy-chain variable region (V(H)) genes. The pattern of somatic mutation has been studied little in intestinal DLBCLs. OBJECTIVE: To assess evidence for antigen selection and the levels of ongoing mutation, we analyzed the ratio of replacement to silent mutations, as well as the frequency of intraclonal sequence variation in gastric and small intestinal DLBCLs that showed no concomitant low-grade component. DESIGN: Genomic DNA was extracted from formalin-fixed paraffin blocks of gastric (n = 6) and small intestinal (n = 6) DLBCLs. The complementarity-determining region 2 and framework region 3 sequences (<200 base pairs) of the rearranged immunoglobulin V(H) gene were obtained from polymerase chain reaction-amplified product, and the ratio of replacement-to-silent mutations and the frequency of intraclonal sequence variation were determined. RESULTS: Clustering of replacement mutations in complementarity-determining region 2 with a high (>2.9) ratio of replacement-to-silent mutations was observed in 5 gastric DLBCLs, whereas it was recognized in only 1 intestinal DLBCL. Intraclonal sequence variation was observed in 6 intestinal and 5 gastric DLBCLs. The frequency of ongoing mutation was much higher in the intestinal (median, 0.33%) than in the gastric DLBCLs (median, 0.13%), but the difference was not statistically significant (P =.09). CONCLUSIONS: The mutation pattern was consistent with positive antigen selection in gastric DLBCLs, but not in the intestinal tumors. Ongoing mutation was much more frequent in the intestinal than in the gastric DLBCLs. These findings suggest that positive antigen selection plays a major role in a significant proportion of gastric tumors, whereas germinal center reaction with aberrant mutation is important in small intestinal DLBCLs.

Adult↗
PubMed2026

Ovarian Carcinoma Presenting Mucoepidermoid Carcinoma-Like Features in Association With Seromucinous Borderline Tumor: A Real Seromucinous Carcinoma?

Ovarian seromucinous carcinoma is generally classified within the spectrum of endometrioid carcinoma. We report a rare ovarian carcinoma with mucoepidermoid carcinoma-like features arising in direct association with a seromucinous borderline tumor. A 56-year-old postmenopausal female presented with a 10-cm pelvic multilocular cystic tumor and markedly elevated carbohydrate antigen 19-9. Histopathological examination showed a seromucinous borderline tumor with transition to invasive carcinoma composed of mucinous epithelial cells and p40-positive intermediate-like cells. The tumor was diffusely positive for PAX8 and negative for cytokeratin 20, supporting Mullerian differentiation. The p40-positive cell population persisted in the borderline, invasive, and para-aortic lymph node metastatic components. Comprehensive genomic profiling identified KRAS p.G12D without CTNNB1, PTEN, or ARID1A mutations. The patient developed platinum-resistant recurrence and died 11 months after diagnosis. This case is compatible with a potential endometriosis-independent pathway from seromucinous borderline tumor to an aggressive mucoepidermoid-like carcinoma.

mucoepidermoid carcinoma↗
PubMed1999

How does replication-associated mutational pressure influence amino acid composition of proteins?

We have performed detrended DNA walks on whole prokaryotic genomes, on noncoding sequences and, separately, on each position in codons of coding sequences. Our method enables us to distinguish between the mutational pressure associated with replication and the mutational pressure associated with transcription and other mechanisms that introduce asymmetry into prokaryotic chromosomes. In many prokaryotic genomes, each component of mutational pressure affects coding sequences not only in silent positions but also in positions in which changes cause amino acid substitutions in coded proteins. Asymmetry in the silent positions of codons differentiates the rate of translation of mRNA produced from leading and lagging strands. Asymmetry in the amino acid composition of proteins resulting from replication-associated mutational pressure also corresponds to leading and lagging roles of DNA strands, whereas asymmetry connected with transcription and coding function corresponds to the distance of genes from the origin or terminus of chromosome replication.

Amino Acid Sequence↗
PubMed2003

Karyotypic complexity of the NCI-60 drug-screening panel.

We used spectral karyotyping to provide a detailed analysis of karyotypic aberrations in the diverse group of cancer cell lines established by the National Cancer Institute for the purpose of anticancer drug discovery. Along with the karyotypic description of these cell lines we defined and studied karyotypic complexity and heterogeneity (metaphase-to-metaphase variations) based on three separate components of genomic anatomy: (a) ploidy; (b) numerical changes; and (c) structural rearrangements. A wide variation in these parameters was evident in these cell lines, and different association patterns between them were revealed. Analysis of the breakpoints and other specific features of chromosomal changes across the entire set of cell lines or within particular lineages pointed to a striking lability of centromeric regions that distinguishes the epithelial tumor cell lines. We have also found that balanced translocations are as frequent in absolute number within the cell lines derived from solid as from hematopoietic tumors. Important similarities were noticed between karyotypic changes in cancer cell lines and that seen in primary tumors. This dataset offers insights into the causes and consequences of the destabilizing events and chromosomal instability that may occur during tumor development and progression. It also provides a foundation for investigating associations between structural genome anatomy and cancer molecular markers and targets, gene expression, gene dosage, and resistance or sensitivity to tens of thousands of molecular compounds.

Cell Line, Tumor↗
PubMed2004

[Active oxygen forms and genome damage by environmental factors].

The role played by active oxygen forms in damaging the human genome by environmental factors as well as the application of antioxidants to keep the oncology statistics among the hazardous-area residents low are under discussion. According to the independent results, there are essential differences between mechanisms of inflicting a genetic lesion to healthy subjects and to individuals of the risk categories due to that the latter have contacts with high concentrations of chemical compounds and with clinical patients with developed free-radical pathologies.

Environmental Exposure↗
PubMed2006

[Non-LTR retrotransposons: LINEs and SINEs in plant genome].

Retrotransposons are one of the drivers of genome evolution. They include LTR (long terminal repeat) retrotransposons, which widespread in Eukaryotagenomes, show structural similarity to retroviruses. Non-LTR retrotransposons were first discovered in animal genomes and then identified as ubiquitous components of nuclear genomes in many species across the plant kingdom. They constitute a large fraction of the repetitive DNA. Non-LTR retrotransposons are divided into LINEs (long interspersed nuclear elements) and SINEs (short interspersed nuclear elements). Transposition of non-LTR retrotransposons is rarely observed in plants indicating that most of them are inactive and/or under regulation of the host genome. Transposition is poorly understood, but experimental evidence from other genetic systems shows that LINEs are able to transpose autonomously while non-autonomous SINEs depend on the reverse transcription machinery of other retrotransposons. Phylogenic analysis shows LINEs are probably the most ancient class of retrotransposons in plant genomes, while the origin of SINEs is unknown. This review sums up the above data and wants to show readers a clear picture of non-LTR retrotransposons.

Genome, Plant↗
PubMed1990

A malaria sporozoite surface antigen distinct from the circumsporozoite protein.

Monoclonal antibody NYS4 recognizes a single 140 kDa antigen on the surface of Plasmodium yoelii sporozoites, an antigen which is distinct from the extensively characterized circumsporozoite (CS) protein. To more thoroughly characterize this additional surface component, a genomic expression library was screened with NYS4 and an immunoreactive clone (M4) was obtained which expressed part of the antigen gene. The deduced amino acid sequence of the M4 peptide included two unique repetitive sequences of amino acids and a conserved sequence motif which is found in several proteins including the CS protein (region II). The cloned DNA hybridized to a PCR (polymerase chain reaction) amplified sporozoite mRNA demonstrating the sporozoite-stage expression of this gene. A synthetic peptide of one of the repeats, (Asn-Pro-Asn-Glu-Pro-Ser), was recognized by NYS4 and mice immunized with (Asn-Pro-Asn-Glu-Pro-Ser)3 conjugated to KLH (keyhole limpet haemocyanin) produced high levels of antibodies that reacted with the surface of sporozoites and specifically to the 140 kDa antigen. Thus, at least two different proteins are on the surface of the P. yoelii sporozoite indicating that the immunoreactive exterior of the infective stage of malaria parasites is more antigenically complex than previously thought.

Animals↗
PubMed1995

Evaluation of retroviral vectors based on the gibbon ape leukemia virus.

The gibbon ape leukemia viruses (GaLVs) are primate-derived C-type retroviruses with a broad host range. Using an infectious, full-length clone of the GaLV SEATO strain, we have determined that this virus replicates efficiently in 13 of 17 human cell lines tested. In fact, the SB lymphoblast cell line, while resistant to infection by wild-type amphotropic mouse leukemia virus (A-MLV), was infected by GaLV-SEATO. We constructed vectors containing GaLV components and compared the performance of genomes containing an enhancer and promoter derived either from the SEATO or SF strains of GaLV. The GaLV vector genomes were packaged in a Moloney (Mo)MLV core with either an A-MLV or GaLV SEATO envelope. We found that, in some cases, the vector genome appeared to be critical in obtaining optimal infection. For example, vectors with a GaLV SF-based genome infected the human HL60 cell line, whereas vectors with a GaLV SEATO-based genome did not. We also found that most, but not all, of the human cell lines tested were more susceptible to vectors packaged with the GaLV SEATO than A-MLV envelope. The source of the viral core was also important, in that some human cells appeared susceptible to infection only with GaLV genomes packaged in particles composed of a GaLV core and envelope. Our results show that GaLV-based packageable genomes can be expressed in target cells not efficiently infected by vectors containing MoMLV-based genomes. These results suggest that judicious combinations of retroviral genomes and structural components can significantly improve gene transfer into human cells.

Animals↗
PubMed2000

Virus-specific adaptations for the production of a pseudorecombinant virus formed by two distinct bipartite geminiviruses from Central America.

Most whitefly-transmitted geminiviruses possess bipartite genomes comprising DNAs A and B. The production of viable pseudorecombinants by reassortment of infectious cloned components is generally limited to isolates/strains of a particular virus. Following exchange of cloned genomic components of Sida golden mosaic virus from Costa Rica (SiGMV/Co) and Sida golden mosaic virus from Honduras (SiGMV/Ho(yv)), the pseudorecombinant viruses were infectious in various plant species. Three DNA B components (B(1), B(2), B(3)), different in a few nucleotides, were isolated from Sida rhombifolia naturally infected with SiGMV/Ho(yv). Only SiGMV/Ho(yv) DNA B(2) was able to form a viable pseudorecombinant with SiGMV/Co DNA A. In protoplasts, as well as in inoculated leaves, SiGMV/Co DNA A trans-replicated the heterogenomic SiGMV/Ho(yv) DNA B(1) component, indicating that impaired movement is involved in the deficiency of SiGMV/Ho(yv) DNA B(1) to form a pseudorecombinant virus with SiGMV/Co DNA A. Even after extensive mutation analysis of SiGMV/Ho(yv) DNA B(1) and B(2), we were unable to pinpoint differences in SiGMV/Ho(yv) DNA B(2) that allowed the formation of a pseudorecombinant virus with SiGMV/Co DNA A. We observed a gradual increase of infectivity from noninfectious SiGMV/Co DNA A/SiGMV/Ho(yv) DNA B(1) and B(3) pseudorecombinant virus to pseudorecombinant viruses showing normal systemic spread of both genomic components associated with symptomatic plants.

Adaptation, Physiological↗
PubMed2003

Compatibility of rhizobial genotypes within natural populations of Rhizobium leguminosarum biovar viciae for nodulation of host legumes.

Populations of Rhizobium leguminosarum biovar viciae were sampled from two bulk soils, rhizosphere, and nodules of host legumes, fava bean (Vicia faba) and pea (Pisum sativum) grown in the same soils. Additional populations nodulating peas, fava beans, and vetches (Vicia sativa) grown in other soils and fava bean-nodulating strains from various geographic sites were also analyzed. The rhizobia were characterized by repetitive extragenomic palindromic-PCR fingerprinting and/or PCR-restriction fragment length polymorphism (RFLP) of 16S-23S ribosomal DNA intergenic spacers as markers of the genomic background and PCR-RFLP of a nodulation gene region, nodD, as a marker of the symbiotic component of the genome. Pairwise comparisons showed differences among the genetic structures of the bulk soil, rhizosphere, and nodule populations and in the degree of host specificity within the Vicieae cross-inoculation group. With fava bean, the symbiotic genotype appeared to be the preponderant determinant of the success in nodule occupancy of rhizobial genotypes independently of the associated genomic background, the plant genotype, and the soil sampled. The interaction between one particular rhizobial symbiotic genotype and fava bean seems to be highly specific for nodulation and linked to the efficiency of nitrogen fixation. By contrast with bulk soil and fava bean-nodulating populations, the analysis of pea-nodulating populations showed preferential associations between genomic backgrounds and symbiotic genotypes. Both components of the rhizobial genome may influence competitiveness for nodulation of pea, and rhizosphere colonization may be a decisive step in competition for nodule occupancy.

Bacterial Proteins↗
PubMed2005

Chompy: an infestation of MITE-like repetitive elements in the crocodilian genome.

Interspersed repeats are a major component of most eukaryotic genomes and have an impact on genome size and stability, but the repetitive element landscape of crocodilian genomes has not yet been fully investigated. In this report, we provide the first detailed characterization of an interspersed repeat element in any crocodilian genome. Chompy is a putative miniature inverted-repeat transposable element (MITE) family initially recovered from the genome of Alligator mississippiensis (American alligator) but also present in the genomes of Crocodylus moreletii (Morelet's crocodile) and Gavialis gangeticus (Indian gharial). The element has all of the hallmarks of MITEs including terminal inverted repeats, possible target site duplications, and a tendency to form secondary structures. We estimate the copy number in the alligator genome to be approximately 46,000 copies. As a result of their size and unique properties, Chompy elements may provide a useful source of genomic variation for crocodilian comparative genomics.

Alligators and Crocodiles↗
PubMed1994

Herpes simplex virus replicative concatemers contain L components in inverted orientation.

The structure of herpes simplex virus (HSV-1) replicative DNA was studied employing pulse-field gel electrophoresis to allow separation and direct visualization of large size virus DNA fragments. Accumulation of HSV-1 DNA that fails to enter the gel was detected from 6 hr postinfection. This corresponds, at least in part, to high molecular weight replicative intermediates. Analysis of this DNA employing restriction enzymes SpeI and AseI, which cut only once and twice respectively in the HSV-1 genome, revealed that these intermediates are concatemeric and contain adjacent genomes with L components in different orientations. Adjacent genomes with L components in the same orientation or with L components in inverted orientations were found in similar amounts, suggesting that inversions occur frequently. Our results suggest that inversions of L components are generated by a quite efficient mechanism, perhaps during replication. Observations made in this work could be explained by rolling circle-based models of replication of HSV-1 genomes, with replication starting at the different origins and/or combined with strand transfer at inverted repeats.

DNA, Viral↗
PubMed1997

Compilation of all genes encoding two-component phosphotransfer signal transducers in the genome of Escherichia coli.

Bacteria have devised sophisticated His-Asp phosphorelay signaling systems for eliciting a variety of adaptive responses to their environment, which are generally referred to as the "two-component regulatory system." The widespread occurrence of the His-Asp phosphorelay signaling in both prokaryotes and eukaryotes implies that it is a powerful device for a wide variety of adaptive responses of cells to their environment. The two-component signal transducers contain one or more of three common and characteristic phosphotransfer signaling domains, named the "transmitter, receiver, and histidine-containing phosphotransfer (HPt) domains." The recently determined entire genomic sequence of Escherichia coli allowed us to compile systematically a complete list of genes encoding such two-component signal transduction proteins. The results of such an effort, made in this study, revealed that at least 62 open reading frames (ORFs) were identified as putative members of the two-component signal transducers in this single species. Among them, 32 were identified as response regulator and 23 were identified as orthodox sensory kinases. In addition, E. coli has five hybrid sensory kinases. The precise location of each ORF was mapped on a physical map of the entire E. coli genome. All of these ORFs were then compiled and annotated extensively.

Amino Acid Sequence↗
PubMed1978

A protein linked to the 5' termini of both RNA components of the cowpea mosaic virus genome.

Evidence is presented for the presence of a protein covalently bound to the 5' termini of both M and B RNA components of CPMV. The protein is found to be linked in both cases to the 5' phosphate of the dinucleotide pUpAp, derived by ribonuclease digestion of the RNA. The intact protein is not required for infectivity or for in vitro translation of the RNA in cell-free extracts.

Mosaic Viruses↗
PubMed2001

Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions.

BACKGROUND: It has recently been shown that the detection of gene fusion events across genomes can be used for predicting functional associations of proteins, including physical interaction or complex formation. To obtain such predictions we have made an exhaustive search for gene fusion events within 24 available completely sequenced genomes. RESULTS: Each genome was used as a query against the remaining 23 complete genomes to detect gene fusion events. Using an improved, fully automatic protocol, a total of 7,224 single-domain proteins that are components of gene fusions in other genomes were detected, many of which were identified for the first time. The total number of predicted pairwise functional associations is 39,730 for all genomes. Component pairs were identified by virtue of their similarity to 2,365 multidomain composite proteins. We also show for the first time that gene fusion is a complex evolutionary process with a number of contributory factors, including paralogy, genome size and phylogenetic distance. On average, 9% of genes in a given genome appear to code for single-domain, component proteins predicted to be functionally associated. These proteins are detected by an additional 4% of genes that code for fused, composite proteins. CONCLUSIONS: These results provide an exhaustive set of functionally associated genes and also delineate the power of fusion analysis for the prediction of protein interactions.

Algorithms↗