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Molecular diagnostic applications of DNA methylation technology.

Cancer arises due to the accumulation of DNA modifications that give cells a selective growth advantage. One common DNA modification is promoter hypermethylation associated with loss of expression of a tumor suppressor gene. The methylation status of a specific sequence or the pattern of methylation across the genome can be readily measured, and these sequences and analytical methods are being rapidly developed for molecular diagnostic applications. Detection of certain methylation events can be used for early detection of tumors, and analysis of patterns of methylation across the genome might provide information on disease subtype, aggressiveness, and treatment response. DNA methylation-based molecular diagnostic assays are particularly attractive because of the stability of the target analyte (DNA) and the potential sensitivity of the assays. As the field matures, methylation-based assays will make a major contribution to the field of molecular diagnostics, providing tools to fill unmet needs in current diagnostic and treatment plans for many types of cancer.

Biomarkers, Tumor↗

Novel G protein-coupled receptors: a gene family of putative human olfactory receptor sequences.

We have taken advantage of the sequence conservation in the G protein-coupled receptor superfamily to isolate a fragment of a novel G protein-coupled receptor sequence using polymerase chain reaction (PCR) amplification of human genomic DNA. Screening of human genomic and hippocampal cDNA libraries with this amplified receptor fragment revealed a number of related sequences. Sequence analysis of four genomic clones and one cDNA clone clearly identifies these as related members of the G protein-coupled receptor family, as the deduced amino acid sequence reveals putative transmembrane domains and conserved amino acid residues. Southern blot analysis of restriction digests of human genomic DNA indicates that these receptor subtypes are likely to belong to a family of related genes. One of the proposed receptor sequences indicates the presence of pseudogenes in this family. Based on the homology of these sequences to a family of recently described receptors expressed exclusively in rat olfactory epithelium, it is suggested that these receptors represent a family of human odorant receptors.

Amino Acid Sequence↗

Transformation of cultured mammalian cells by viable herpes simplex virus subtypes 1 and 2.

A continuous line of rodent cells carrying the genome of the Rous sarcoma virus was stably transformed by exposure to viable herpes simplex virus of either subtype 1 or 2. Transformation was accompanied by alteration of morphology, growth characteristics, acquisition of a thymidine kinase activity (EC 2.7.1.21) resembling the corresponding specific activity of the enzyme in the herpes simplex virus, and capacity to express continuously some antigens specific for herpes simplex virus.

Animals↗

Genomics in multiple myeloma: biology and clinical implications.

The advent of new techniques, such as interphase fluorescence in situ hybridization, and, more recently, global array-based gene expression profiling, has accelerated genomic research in myeloma. Distinct biologic subtypes, characterized by unique genetic abnormalities with differing clinical outcomes, have been identified. The identification of these primary genetic defects, and the deregulated oncogenes and pathways in myeloma, has allowed for the development of more targeted therapies. This has led to the discovery of an increased number of active agents in the treatment of myeloma. Genetics also have prognostic importance in myeloma. Recent studies have elucidated a genetic prognostic hierarchy, and have enabled improved definition of the prognostic significance of their interactions. The current challenges are to: improve the dissection of the genetic heterogeneity of the disease; better define progression events; improve the risk stratification of patients; more accurately select patients who will respond well to a particular treatment; and develop more rational combinations of treatment. Genomics will have an important role to play in all of these goals.

Disease Progression↗

KSHV strains: the origins and global spread of the virus.

Nucleotide sequence analysis at five distinct loci across the 140, 000 bp genomes of more than 60 KSHV samples from KS and PEL tumors from North America, Africa, the Middle East, Asia and the Pacific revealed that they cluster into four major subtypes (A, B, C and D) that have close associations with the geographic and ethnic background of the patients. In particular, the ORF-K1 protein subtypes encoded at the extreme LHS of the genome display up to 30% amino acid variability resulting from 85% non-synonymous nucleotide substitution rates. In addition, two alternative highly diverged forms of the complex spliced ORF-K15 gene (P or M) map at the extreme RHS of the genome and are essentially unlinked to the ORF-K1 genotypes. We conclude that: (1) KSHV is an ancient human virus with several major subtypes that reflect the migrationary divergence of modern human populations over the past 35,000-60,000 years; (2) the novel immunoglobulin receptor-like signal transducing protein ORF-K1 is subject to unusually strong biological selective pressures; and (3) a minority of KSHV genomes have undergone recombination events with a related virus producing two different alleles of the ORF-K15 latency membrane protein.

Alleles↗

Molecular characterization of a full genome Turkish hepatitis C virus 1b isolate (HCV-TR1): a predominant viral form in Turkey.

Based on direct sequencing information from 5'UTR and NS5B regions, we identified subtype lb as a predominant hepatitis C virus genome in Turkey, which affected more than 91% of 79 patients studied. Next, the full genome sequence of a Turkish lb isolate was obtained by the cloning of polypeptide-encoding region into 7 overlapping fragments. Turkish 1b isolate, which was named HCV-TR1, comprises 9361 nucleotides, including 306 nucleotides of 5'UTR, a single long open reading frame of 9033 nucleotides, and 22 nucleotides of 3'UTR. When compared to HCV lb polypeptide sequences available at GenBank, the predicted polypeptide displayed a total of 36 amino acid substitutions, of which 16 was specific for HCV-TR1 isolate. Despite these changes, major structural and functional motifs of HCV proteins were maintained in HCV-TR1. In contrast, HCV-TR1 displayed amino acid substitutions in 6 out of 9 major cytotoxic T-cell epitopes. These data suggest that HCV-TR1 encodes functionally intact viral proteins, but it also encodes altered viral epitopes, which may affect host immune-response.

Amino Acid Sequence↗

Feasibility, reliability, and clinical value of genomic assay on pre-therapeutic biopsy for endocrine receptor-positive HER2-negative early breast cancer.

Endocrine receptor-positive (ER+) and HER2-negative breast cancer (BC) represents approximately 80% of all BCs. Most patients are treated with upfront surgery; however, 15%-30% will develop late recurrences. Genomic assay indication is usually based on postoperative pathological data including histology subtype, tumor size, lymph node status, SBR grade, and Ki67. Performing genomic testing on core needle biopsy specimens prior to surgery may offer several advantages. In this manuscript, we assess the feasibility, reliability, utility, and potential benefits of such genomic analyses performed on core needle biopsies. Several factors may lead to proposing genomic assay analysis on biopsy: (1) optimization of the patient pathway by reducing time to therapeutic decision-making, (2) predicting response to neoadjuvant chemotherapy (NAC) or neoadjuvant endocrine therapy (NET), and (3) refining prognostic assessment to guide adjuvant chemotherapy decisions in patients for whom axillary surgery is not planned. Given the feasibility and reliability of genomic assay on core needle biopsies, it can be suggested that this practice may become more common in the near future. Knowledge of the evolutive risk determined by the result of genomic assay, as well as clinicopathological characteristics, allows more precise personalization of the therapeutic strategy, including the choice between upfront surgery and neoadjuvant therapy, the selection of systemic treatments, and decision-making in the absence of axillary staging.

breast cancer↗

Multiple genomic alterations including N-myc amplification in a primary large cell medulloblastoma.

The large cell (LC) subtype is a recently described histologic variant of medulloblastoma (Mb) associated with a rapid and aggressive clinical course. We describe the genomic profile of a LC-Mb tumor obtained from a patient who developed recurrent and fulminant disease despite 'good-risk' features at diagnosis and state- of-the-art multidisciplinary therapy. The tumor sample was analyzed using comparative genomic hybridization (CGH) and complementary molecular approaches. CGH revealed amplicons at chromosome bands 2p24-25, 2q12-22, and 17p11; losses of chromosomes 11q and 18; and low-level gains of 3q, 11p, 13q and 14q. Southern blot analysis confirmed N-myc amplification. No evidence of p53 mutation was detected. The genomic profile of this LC-Mb tumor sample revealed a distinctive pattern of genetic alterations including amplification of N-myc and anonymous oncogenes at chromosome bands 2q12-22 and 17p11. These genomic abnormalities are uncommon in other subtypes of Mb.

Blotting, Southern↗

The major dopamine D2 receptor: molecular analysis of the human D2A subtype.

The structural diversity of the human D2 dopamine receptor was examined at the nucleic acid level. Sequence analysis of receptor cDNA clones isolated from human brain and pituitary libraries and polymerase chain reaction (PCR) analysis of rat brain RNA and human genomic DNA demonstrate the presence of a predominant D2 subtype, D2A. The D2A subtype differs from the D2B subtype, previously described in rat brain RNA, in that an additional 29 amino acids are present in the putative third cytoplasmic domain, a region thought to be important for coupling to different G-proteins. The demonstration of intron sequences flanking the DNA encoding the 29-amino-acid insertion suggests that the generation of two distinct D2 dopamine receptor subtypes may arise from alternative splicing of a common genomic sequence.

Amino Acid Sequence↗

Widespread adaptive evolution in the human immunodeficiency virus type 1 genome.

We investigated variable selective pressures among amino acid sites in HIV-1 genes. Selective pressure at the amino acid level was measured by using the nonsynonymous/synonymous substitution rate ratio (omega = dN/dS). To identify amino acid sites under positive selection with omega > 1, we applied maximum likelihood models that allow variable omega ratios among sites to analyze genomic sequences of 26 HIV-1 lineages including subtypes A, B, and C. Likelihood ratio tests detected sites under positive selection in each of the major genes in the genome: env, gag, pol, vif, and vpr. Positive selection was also detected in nef, tat, and vpu, although those genes are very small. The majority of positive selection sites is located in gp160. Positive selection was not detected if omega was estimated as an average across all sites, indicating the lack of power of the averaging approach. Candidate positive selection sites were mapped onto the available protein tertiary structures and immunogenic epitopes. We measured the physiochemical properties of amino acids and found that those at positive selection sites were more diverse than those at variable sites. Furthermore, amino acid residues at exposed positive selection sites were more physiochemically diverse than at buried positive selection sites. Our results demonstrate genomewide diversifying selection acting on the HIV-1.

Amino Acid Sequence↗

Standard tea intake is causally associated with a reduced risk of wet age-related macular degeneration: a Mendelian randomization study.

Researchers have posited that increased consumption of tea and coffee may be associated with more favorable treatment outcomes in patients with age-related macular degeneration (AMD). However, there is no clear evidence regarding the causal associations. To delve deeper into this potential connection, scientists used a rigorous method known as Mendelian randomization (MR). This technique was used to explore the causal impact of tea and coffee consumption on the development or progression of AMD. With the aim of investigating the cause-and-effect relationship between 16 tea- and coffee-consuming subtypes and 3 AMD, we designed a two-sample MR study using comprehensive data from genome-wide association studies (GWAS). The major approach adopted was inverse variance weighting (IVW). Furthermore, we implemented complementary methods like the weighted median (WM), weighted mode, and MR-Egger to strengthen our findings. Sensitivity analyses, including MR-Egger, MR-PRESSO, leave-one-out, and Cochran's Q tests, were used to validate results, explore heterogeneity and pleiotropy, and pinpoint potential biases. Two hundred and sixty-eight instrumental variables were selected for MR analysis. The results showed that standard tea intake may be a protective factor for wet AMD [odds ratio (OR) = 0.7076, 95% confidence interval (CI) = 0.5776-0.8668, P = 8 × 10-4, PFDR = 0.0402]. Sensitivity analysis suggests that the results are robust. Our findings provide genetic evidence that standard tea intake is a protective factor against wet AMD, providing new insights into early risk stratification and prevention strategies for the disease.NEW & NOTEWORTHY This study investigates the potential causal relationship between tea and coffee consumption and age-related macular degeneration (AMD) using Mendelian randomization. Analyzing data from genome-wide association studies, we focused on 16 beverage subtypes and 3 AMD conditions. Our findings suggest that standard tea consumption may protect against wet AMD, with robust evidence supporting this link. The results offer new insights into risk stratification and prevention strategies for AMD, highlighting the importance of dietary factors in eye health.

Mendelian Randomization Analysis↗

Automated Classification of Lymphoma Subtypes From Histopathological Images Using a U-Net Deep Learning Model: Comparative Evaluation Study.

BACKGROUND: Accurate classification and grading of lymphoma subtypes are essential for treatment planning. Traditional diagnostic methods face challenges of subjectivity and inefficiency, highlighting the need for automated solutions based on deep learning techniques. OBJECTIVE: This study aimed to investigate the application of deep learning technology, specifically the U-Net model, in classifying and grading lymphoma subtypes to enhance diagnostic precision and efficiency. METHODS: In this study, the U-Net model was used as the primary tool for image segmentation integrated with attention mechanisms and residual networks for feature extraction and classification. A total of 620 high-quality histopathological images representing 3 major lymphoma subtypes were collected from The Cancer Genome Atlas and the Cancer Imaging Archive. All images underwent standardized preprocessing, including Gaussian filtering for noise reduction, histogram equalization, and normalization. Data augmentation techniques such as rotation, flipping, and scaling were applied to improve the model's generalization capability. The dataset was divided into training (70%), validation (15%), and test (15%) subsets. Five-fold cross-validation was used to assess model robustness. Performance was benchmarked against mainstream convolutional neural network architectures, including fully convolutional network, SegNet, and DeepLabv3+. RESULTS: The U-Net model achieved high segmentation accuracy, effectively delineating lesion regions and improving the quality of input for classification and grading. The incorporation of attention mechanisms further improved the model's ability to extract key features, whereas the residual structure of the residual network enhanced classification accuracy for complex images. In the test set (N=1250), the proposed fusion model achieved an accuracy of 92% (1150/1250), a sensitivity of 91.04% (1138/1250), a specificity of 89.04% (1113/1250), and an F1-score of 90% (1125/1250) for the classification of the 3 lymphoma subtypes, with an area under the receiver operating characteristic curve of 0.95 (95% CI 0.93-0.97). The high sensitivity and specificity of the model indicate strong clinical applicability, particularly as an assistive diagnostic tool. CONCLUSIONS: Deep learning techniques based on the U-Net architecture offer considerable advantages in the automated classification and grading of lymphoma subtypes. The proposed model significantly improved diagnostic accuracy and accelerated pathological evaluation, providing efficient and precise support for clinical decision-making. Future work may focus on enhancing model robustness through integration with advanced algorithms and validating performance across multicenter clinical datasets. The model also holds promise for deployment in digital pathology platforms and artificial intelligence-assisted diagnostic workflows, improving screening efficiency and promoting consistency in pathological classification.

Humans↗

Environmental genomics: a key to understanding biology, pathophysiology and disease.

Recent advances in human and molecular genetics provide an unparalleled opportunity to understand how genes and genetic changes interact with environmental stimuli to either preserve health or cause disease. The fields of environmental genetics and environmental genomics has enormous potential to affect our ability to accurately assess the risk of developing disease, identify and understand basic pathogenic mechanisms that are critical to disease progression, and to more precisely phenotype disease subtypes. However, the application of genetics and genomics to problems in environmental health is only the beginning yet, by itself, represents a potentially effective strategy to substantially impact morbidity and mortality. Collaborative approaches that team together environmental scientists with molecular biologists, geneticists, physiologists and physician scientists are critical to the investigation of environmental aspects of human health. Moreover, exploiting eukaryotic model systems (yeast, Caenorhabditis elegans, zebrafish, Drosophila and rodents) will accelerate our understanding of environmental exposures on human health.

Biology↗

A mutation specific polymerase chain reaction for detecting hepatitis B virus genome mutations at nt551.

AIM: The hepatitis B surface antigen (HBsAg) is considered to be one of the best markers for the diagnosis of acute and chronic HBV infection. But in some patients, this antigen cannot be detected by routine serological assays despite the presence of virus. One of the most important explanations for the lack of detectable HBsAg is that mutations which occur within the "a" determinant of HBV S gene can alter expression of HBsAg and lead to changes of antigenicity and immunogenicity of HBsAg accordingly. As a result, these mutants cannot be detected by diagnosis assays. Thus, it is essential to find out specific and sensitive methods to test the new mutants and further investigate their distribution. This study is to establish a method to investigate the distribution of the HBsAg mutant at nt551. METHODS: A mutation specific polymerase chain reaction (msPCR) was established for amplifying HBV DNA with a mutation at nt551. Four sets of primer pairs, P551A-PPS, P551G-PPS, P551C-PPS and P551T-PPS, with the same sequences except for one base at 3' terminus were designed and synthesized according to the known HBV genome sequences and the popular HBV subtypes, adr and adw, in China. At the basis of regular PCR method, we explored the specific conditions for amplifying HBV DNAs with a mutation at nt551 by regulating annealing temperature and the concentration of these primers. 126 serum samples from patients of hepatitis B were collected, among which 16 were positive for HBV S DNA in the nested PCR amplification. These 16 HBV S DNAs were detected by using the msPCR method. RESULTS: When the annealing temperature was raised to 71 degrees, nt551A and nt551G were amplified specifically by P551A-PPS and P551G-PPS; At 72 degrees and 5 pmole of the primers (each) in reaction of 25 microl volume, nt551C and nt551T were amplified specifically by P551C-PPS and P551T-PPS. 16 of HBV S gene fragments were characterized by using this method. 14 of them were positive for nt551A, one was positive for nt551G, and the other one was positive for nt551T. The results were confirmed by nucleotide sequencing. CONCLUSION: The mutation specific polymerase chain reaction is a specific and sensitive method for detecting the mutations of HBV genome at nt551.

Base Sequence↗

Comparative genomic hybridization detects an increased number of chromosomal alterations in large cell/anaplastic medulloblastomas.

We correlate chromosomal changes in medulloblastomas with histologic subtype, reporting the analysis of 33 medulloblastoma specimens by comparative genomic hybridization, and a subset by fluorescence in situ hybridization. Of the 33 tumors, 5 were desmoplastic/nodular, 10 were histologically classic, and 18 were large cell/anaplastic. Chromosomal gains and losses were more common in anaplastic medulloblastomas than in non-anaplastic ones. We identified 4 medulloblastomas with c-myc amplification and 5 medulloblastomas with N-myc amplification; all 9 were of the large cell/anaplastic subtype. Additional regions with high level gains included 2q14-22, 3p23, 5p14-pter, 8q24, 9p22-23, 10p12-pter, 12q24, 12p11-12, 17p11-12, and Xp11. The majority of these high level gains occurred in anaplastic cases. We also found loss of chromosome 17p in 7 large cell/anaplastic cases but no nonanaplastic medulloblastomas. Finally, we detected a significantly increased overall number of chromosomal alterations in large cell/anaplastic medulloblastomas (6.8/case) compared to non-anaplastic ones (3.3/case). These findings support an association between myc oncogene amplification, 17p loss, and large cell/anaplastic histology.

Adolescent↗

Recent advances in the molecular pharmacology of the alpha 1-adrenergic receptors.

This review is intended to discuss recent developments in the molecular pharmacology of the alpha 1-adrenergic receptor (alpha 1-AR) subtypes. After a brief historical development, we will focus on the more contemporary issues having to do with this receptor family. Emphasis will be put on recent data regarding the cloning, nomenclature, signalling mechanisms, and genomic organization of the alpha 1-AR subtypes. We will also highlight recent mutational studies that identify key amino acid residues involved in ligand binding, as well as the role of the alpha 1-AR subtypes in regulating physiologic processes.

Aging↗

Genotypes of hepatitis C virus isolates from different parts of the world.

Hepatitis C virus (HCV) causes most cases of posttransfusion non-A, non-B hepatitis. HCV isolates were classified by their genetic relatedness into at least six genotypes and a series of subtypes. Methods for typing included amplification of certain genomic regions using universal or type/subtype specific primers, restriction fragment length polymorphism analysis, differential hybridization, nucleotide sequencing, and serologic genotyping. HCV genotypes and their subtypes coexist in various geographic locations but show different prevalences. The identification of genotypes/subtypes is useful for studies on the molecular epidemiology and pathogenesis of HCV infection.

DNA Primers↗

Genomic expression profiling of human inflammatory cardiomyopathy (DCMi) suggests novel therapeutic targets.

The clinical phenotype of human dilated cardiomyopathy (DCM) encompasses a broad spectrum of etiologically distinct disorders. As targeting of etiology-related pathogenic pathways may be more efficient than current standard heart failure treatment, we obtained the genomic expression profile of a DCM subtype characterized by cardiac inflammation to identify possible new therapeutic targets in humans. In this inflammatory cardiomyopathy (DCMi), a distinctive cardiac expression pattern not described in any previous study of cardiac disorders was observed. Two significantly altered gene networks of particular interest and possible interdependence centered around the cysteine-rich angiogenic inducer 61 (CYR61) and adiponectin (APN) gene. CYR61 overexpression, as in human DCMi hearts in situ, was similarly induced by inflammatory cytokines in vascular endothelial cells in vitro. APN was strongly downregulated in DCMi hearts and completely abolished cytokine-dependent CYR61 induction in vitro. Dysbalance between the CYR61 and APN networks may play a pathogenic role in DCMi and contain novel therapeutic targets. Multiple immune cell-associated genes were also deregulated (e.g., chemokine ligand 14, interleukin-17D, nuclear factors of activated T cells). In contrast to previous investigations in patients with advanced or end-stage DCM where etiology-related pathomechanisms are overwhelmed by unspecific processes, the deregulations detected in this study occurred at a far less severe and most probably fully reversible disease stage.

Adiponectin↗