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At least 523 records · Page 29Linked to original sources
PubMed2005

Relationships between toxin gene content and genetic background in nasal carried isolates of Staphylococcus aureus from Asturias, Spain.

Staphylococcus aureus recovered from nasal carriers, producers and non-producers (43 isolates each) of classical pyrogenic toxin superantigens (PTSAgs), were screened for 17 additional PTSAg-genes by PCR. Percentages of 88.4 and 65.1 were positive for some new enterotoxin-gene, and 76.7 and 55.8 for enterotoxin-gene-clusters (egc-like), respectively. The 86 isolates belonged to 17 toxin-genotypes (all eta-, etb-, etd-, see- and sep-negative), and generated 40 SmaI-genomic profiles that in a dendrogram of similarity (S0.7) clustered into nine lineages and 11 non-clustered branches. Correlations between classical PTSAgs and SmaI-lineages were established and egc-like groupings appeared dispersed in six lineages.

Bacterial Toxins↗
PubMed2005

Clonal relationship of tumor nodules in hepatocellular carcinoma: a hierarchical clustering analysis of comparative genomic hybridization data.

Information on the clonal relationship between tumor nodules in patients diagnosed with hepatocellular carcinoma (HCC) holds prognostic significance in the prediction of recurrence and postoperative treatment. Here, we investigated the clonal relationships in 11 focal nodules from 5 patients with HCC by comparative genomic hybridization (CGH) and spectral karyotyping. CGH analysis indicated tumor nodules in 5 (100%) of 5 cases to share similar patterns of genomic imbalances, suggesting nodules to be clonally related. This clonal relationship was further substantiated in 2 cases, where spectral karyotyping analysis indicated identical structural rearrangements between focal tumors. Few studies have attempted to differentiate multicentric growth from intrahepatic dissemination in HCC using CGH analysis; however, data interpretation remained subjective. In this study, we have extended our data to include published CGH findings on 57 nodules derived from 19 HCC cases. Simulation of CGH findings by unsupervised 2-way hierarchical clustering indicated tumor nodules in 20 (83.3%) of 24 cases to cluster concordantly, signifying a high incidence of clonal similarity. In sum, bioinformatic analysis of genomic profiles may represent a reliable research tool in analyzing clonal relationships among tumor nodules.

Adult↗
PubMed2026

Co-occurrence of bronchiolar adenoma and lung adenocarcinoma: a study of nine cases revealing distinct clonal origins via integrated histologic, immunophenotypic and molecular analysis.

PURPOSE: This study sought to elucidate the possible biological association between BA and lung adenocarcinoma through an analysis of cases in which both lesions coexist within the same specimen. METHODS: In our cohort, the BA and lung cancer components of nine concurrent-type BAs were microdissected using the Millisect system and subjected to whole-exome sequencing (WES). Their histopathological, immunohistochemical, and genomic profiles were comparatively evaluated. RESULTS: Histopathologically, the BA regions of concurrent-type BAs exhibited a classic bilayered architecture, composed of continuous luminal and basal cell layers. The adjacent monolayered concurrent components were diagnosed as adenocarcinoma in situ (AIS, N = 4), minimally invasive adenocarcinoma (MIA, N = 2), and invasive adenocarcinoma (ADC, N = 3). Immunohistochemically, both luminal and basal cells in BA regions expressed thyroid transcription factor 1 (TTF1), albeit with more heterogeneous staining intensity compared to that observed in tumor components. Molecularly, EGFR mutations were the most frequently identified in either BA or tumor components, or in both (Case 9). In BA components, mutations included exon 19 p.S752F, exon 19 deletions (p.L747_T751delinsP and p.E746_T751delinsVP), and compound G719C/S768I mutations. Tumor components harbored exon 28 S1130C, exon 19 indel (p.E746_S752delins), and exon 18 p.G719C mutations. Notably, only three cases demonstrated limited overlap of mutations and copy number variations (CNVs) between the two components. Phylogenetic analysis revealed that six cases shared truncal alterations in genes including KMT2A, PIK3CA, SETD2, MITF, PBRM1, and SRSF3, one case harbored a shared canonical EGFR mutation (p.G719C), with an additional p.S768I alteration uniquely detected in the BA component. CONCLUSION: There is insufficient evidence to support BA as a premalignant lesion for lung adenocarcinoma base on morphological and molecular variables, and they may represent distinct pathological entities.

Concurrent-type bronchiolar adenoma↗
PubMed2006

Development and application of Multiple-Locus Variable number of tandem repeat Analysis (MLVA) to subtype a collection of Listeria monocytogenes.

In this study we report the development and application of a Multiple-Locus Variable number of tandem repeat Analysis (MLVA) strategy for subtyping Listeria monocytogenes. Genome profiles of a collection of forty-five food-borne L. monocytogenes isolates were compared using MLVA. These isolates were obtained as part of an active surveillance programme of foods in the south-east region of Ireland. MLVA successfully discriminated amongst the isolates. The method was easy to perform, relatively fast and could be deployed in any molecular laboratory with basic laboratory equipment. This approach is a valuable tool, which has the capability to provide comparable results when compared with other more established typing methods, including pulsed-field gel electrophoresis (PFGE).

Bacterial Typing Techniques↗
PubMed2026

Efficacy of R-GDP therapy as salvage chemotherapy for relapsed or refractory diffuse large B-cell lymphoma.

R-GDP has been established as an effective salvage treatment for Rel/Ref DLBCL. We aimed to clarify the efficacy of R-GDP therapy. We included 41 consecutive patients with Rel/Ref DLBCL, who received R-GDP therapy as salvage chemotherapy at our hospital between January 2014 and August 2024. Thirty-three patients received R-GDP therapy as a 2nd-line regimen, whereas 8 received R-GDP as a 3rd or later-line regimen. The ORR was 70.7%. 23 out of 25 relapsed patients (92%) responded to R-GDP therapy, whereas only 6 out of 16 refractory patients responded (37.5%). With regard to the duration of response, the response rates in 19 patients with late relapse (at least 12 months) and 6 with early relapse (less than 12 months) were 94.7% and 83.3% (p = 0.43). Overall, the 2-year PFS and OS rates were 48.8% and 74.2%, respectively. 18 responders underwent ASCT with a 2-year PFS after ASCT of 61.2%. Although CAR-T is recommended in patients with Rel/Ref DLBCL, R-GDP is a realistic option given the limited availability of immediate CAR-T therapy. Further studies including genomic profiles are warranted to identify factors that can predict a response to R-GDP in Rel/Ref DLBCL.

Humans↗
PubMed2026

From standardization to precision medicine: Evolution of European Leukemianet recommendations in Philadelphia-negative myeloproliferative neoplasms.

The European LeukemiaNet (ELN) recommendations have been instrumental in shaping the diagnosis, risk stratification, and management of Philadelphia-negative myeloproliferative neoplasms (MPNs), including polycythemia vera, essential thrombocythemia, and primary myelofibrosis. Over the past two decades, these recommendations have evolved from consensus-based frameworks focused on response standardization to increasingly sophisticated, evidence-based and biologically informed approaches. Early efforts primarily aimed to harmonize response criteria across clinical studies, establishing a foundation for consistent therapeutic evaluation. Subsequent updates introduced risk-adapted treatment strategies centered on thrombotic risk, reflecting the major determinants of morbidity and mortality in these disorders. However, the limitations of surrogate endpoints prompted a shift toward clinically meaningful outcomes, including symptom burden, vascular events, and disease progression. More recent advances have been driven by the integration of molecular genetics and the adoption of structured evidence-based methodologies, enabling refined diagnostic classification and more accurate prognostic assessment. Contemporary ELN frameworks increasingly incorporate dynamic clinical parameters, genomic profiling, and emerging biomarkers, supporting a transition toward individualized, risk-adapted therapeutic strategies. Beyond their role in standardizing MPN management, ELN recommendations have also influenced clinical trial design, endpoint selection, risk stratification, and therapeutic decision-making. Evidence from prospective studies and real-world cohorts supports the clinical applicability of these frameworks, although their implementation remains heterogeneous across healthcare settings. This review provides a comprehensive and critical overview of the evolution and implementation of ELN recommendations, highlighting their impact on clinical research and routine practice, current limitations, and future directions toward precision medicine in Philadelphia-negative MPNs.

Essential thrombocythemia↗
PubMed2006

RS5444, a novel PPARgamma agonist, regulates aspects of the differentiated phenotype in nontransformed intestinal epithelial cells.

Peroxisome proliferator-activated receptor-gamma (PPARgamma) is expressed in the intestinal epithelium, yet little is known about the physiological role of PPARgamma in the small bowel or the effects of PPARgamma on small intestinal epithelial cells. The present studies investigate cellular and genomic effects of PPARgamma in nontransformed rat intestinal epithelial cells (RIE). These cells were engineered to express mouse PPARgamma1, and thereby to model the molecular phenotype that obtains upon induction of PPARgamma at the crypt/villus junction in the small intestine. In these studies, we have used a novel third generation thiazolidinedione derivative, RS5444, which activates PPARgamma with an EC50 about 1/50th that of rosiglitazone and has no effect on RIE cells that do not express PPARgamma. We used Affymetrix oligonucleotide microarrays to identify potential PPARgamma-regulated processes in RIE cells, including lipid metabolism, cell proliferation and differentiation, remodeling of the extracellular matrix, cell morphology, cell-cell adhesion, and motility. The genomic profile reflects cellular events that occur following PPARgamma activation: RS5444 inhibited culture growth and caused irreversible G1 arrest, but did not induce apoptosis. In addition, RS5444 caused dramatic changes in cellular morphology which were associated with increased motility and diminished cellular adherence, but no increase in the ability of such cells to digest and invade Matrigel. Inhibition of proliferation, cell cycle arrest, increased motility, and altered adherence are aspects of the differentiated phenotype of villus epithelial cells, which withdraw from the cell cycle at the crypt/villus interface, migrate to the villus tips, and are subsequently shed by loss of contact with the epithelium and the underlying extracellular matrix. Our results are consistent with the hypothesis that PPARgamma regulates critical aspects of differentiation in the small intestinal epithelium. Many nuclear receptors regulate differentiation. However, our results point to novel effects of PPARgamma on cell-cell and cell-matrix interactions, which are not typical of other nuclear receptors.

Animals↗
PubMed2026

MULTIPREVENT: Integrated screening for smoking-related multimorbidity using low-dose chest computed tomography.

OBJECTIVES: Tobacco consumption, combined with individual genetic predispositions, contributes to an age-dependent risk not only for lung cancer but also for other non-communicable diseases (NCDs) such as cardiovascular disease (CVD), chronic obstructive pulmonary disease (COPD), osteoporosis, and diabetes. The MULTIPREVENT project aims to validate whether low-dose computed tomography (LDCT) of the chest, combined with simple biomarkers, functional tests, and genomic profiling, can serve as an effective tool for comprehensive health assessment and risk prediction of multimorbidity in adults. STUDY DESIGN: The study is based on a prospective epidemiological design involving 3000 participants from the MOLTEST-BIS lung cancer screening cohort (2016-2018). These participants, aged 50-79 years (during MOLTEST-BIS) and with a smoking history of at least 30 pack-years, will undergo two follow-up assessments in 2025-2027 and 2030-2032. METHODS: Each follow-up includes LDCT, spirometry, standardized blood pressure measurement, anthropometric evaluation, biomarker assessment (lipid profile, lipoprotein(a), glycated haemoglobin), and health-related questionnaires. Genetic profiling will be performed using the Illumina Infinium Global Screening Arrays approach to identify inherited predispositions to major NCDs. All data, clinical, imaging (including radiomics), molecular, and genetic, will be integrated through machine learning algorithms to develop AI-based risk prediction models. RESULTS: The MULTIPREVENT study is expected to generate a wide range of scientific, clinical, and infrastructural results that will serve as a foundation for future public health initiatives in integrated prevention. CONCLUSIONS: By linking imaging and biochemical markers, genetic susceptibility, and clinical parameters within a longitudinal design, MULTIPREVENT will establish data-driven, AI-supported prevention strategies aimed at reducing morbidity and mortality among adults exposed to tobacco. The project will also serve as a model for population-based multimorbidity prevention programs.

Humans↗
PubMedDate not supplied

Thyroid hormone receptor mutations and disease: beyond thyroid hormone resistance.

Thyroid hormone receptors (TRs) are ligand-dependent transcription factors that mediate the biological activities of thyroid hormone (T3). Two THR genes (A and B), located on different chromosomes, yield four T3-binding isoforms with highly conserved sequences in the DNA- and ligand-binding domains. Mutations of THRB cause a human genetic disease, thyroid hormone resistance syndrome (RTH). Comprehensive genomic profiling unveiled the contribution of novel change-of-function mutations of TRbeta to the pathogenesis of RTH. In addition, abnormalities associated with mutations of the THRA gene have been uncovered recently. The phenotypic manifestations of mutated THRB and THRA genes are distinct, indicating isoform-dependent actions of TR mutants in vivo. Therefore, mutant TRs provide a new paradigm to understand the molecular basis of receptor disease.

Animals↗
PubMed2006

Adjuvant therapy for patients who have node-positive breast cancer.

The treatment of node-positive breast cancer has improved dramatically in the last 3 decades. Adjuvant therapies have evolved from single-agent chemotherapy to anthracycline- and taxane-based polychemotherapeutics to target-specific trastuzumab, with or without endocrine manipulation and with or without PMRT. Almost 85% of patients who have node-positive disease can now enjoy a 5-year DFS. This progress has come from incremental improvements made over the years. In spite of these advances, lingering questions remain. Is it possible to reduce treatment-associated toxicity? Can patient selection be improved based on tumor genomic profiling? Given the high cost of many of these therapies (37,000 dollars with the newer agents versus $391 for the classic six cycles of intravenous CMF), is it possible to achieve equivalent efficacy and yet reduce the economic cost per patient? Only continued clinical trials and cooperative effort among researchers, clinicians, and patients can answer these questions and improve care for breast cancer.

Adult↗
PubMed2003

Identification of new phages to type Staphylococcus aureus strains and comparison with a genotypic method.

The aim of this study was to optimize the epidemiological monitoring of strains of Staphylococcus aureus, a major cause of hospital-acquired infections. From September to December 1998 47 S. aureus strains isolated from swabs taken from orthopaedic and trauma patients were in studied. Thirty-five isolates were sensitive to methicillin (MSSA) and 12 were methicillin-resistant (MRSA). Ten of the 47 isolates could not be phage-typed using the international set of typing phages: five of these isolates were MSSA and five were MRSA. These MRSA isolates, which were also not typeable by the phages currently recommended for phage-typing MRSA, were lysed by locally isolated experimental phages 584 and 1814. Phage 1814 lysed the gentamicin-resistant MRSA and phage 584 acted on the gentamicin-sensitive MRSA. Both new phages were inactive against the methicillin-sensitive isolates. Cloning of certain isolates was confirmed by macrorestriction genomic profiles obtained by pulsed-field gel electrophoresis analysis (PFGE). The results showed good discriminatory ability of antibiotic-resistance pattern phenotyping and phage-typing when the phages used were adapted to epidemic-associated MRSA strains.

Bacteriophage Typing↗
PubMed2001

Characterisation and clonal relationships of Shiga-toxigenic Escherichia coli (STEC) isolated from Australian dairy cattle.

A total of 136 Shiga toxin-producing Escherichia coli (STEC) isolated during a longitudinal survey of three Australian dairy farms were examined to determine their virulence factors, serotype and genomic relationships. This study aimed to assess the potential of these STEC to cause disease in humans and to analyse the on-farm ecology of STEC. Virulence factors (stx, eae, ehxA) were used as determinants of potential to be enterohaemorrhagic E. coli (EHEC) and were examined using polymerase chain reaction (PCR). Among the cattle groups tested, calves, both before and during weaning, shed the most putative EHEC and were the main source of serotypes commonly associated with human disease. E. coli O157:H7 and E. coli O26:H11 represented 9.4 and 7.8% of cattle STEC isolates respectively, with other putative EHEC serotypes reported for the first time from cattle. Based on serotype and virulence factors, 20% of STEC were putative EHEC. Pulsed-field gel electrophoresis (PFGE) was used to compare the genomic profiles of STEC from dairy farms. Isolates common to cattle and the farm environment were identified. Multiple strains of STEC with high clonal turnover were detected in the faeces of cattle, and isolates appeared to be specific to individual farms. To fully assess the pre-slaughter EHEC risk factors on-farm, examination of STEC virulence is as important as determination of STEC prevalence.

Adhesins, Bacterial↗
PubMed2000

Epidemiology and molecular characterization of nosocomially transmitted multidrug-resistant Klebsiella pneumoniae.

OBJECTIVES: To describe the epidemiology, antimicrobial susceptibility, genomic profiles, and control of a nosocomial outbreak of multidrug-resistant Klebsiella pneumoniae (MRKP) that occurred in the pediatric oncology unit of the University of Malaya Medical Centre in Kuala Lumpur. MATERIALS AND METHODS: A prospective epidemiologic and microbiologic study was conducted of MRKP isolated from the blood and wound of a boy with necrotizing fasciitis after a 7-day course of ceftazidime and amikacin. In the following 2 weeks, phenotypically similar MRKP were isolated from the blood cultures of four other patients and rectal swabs of another three patients and two liquid soap samples located in the same ward. RESULTS: Antimicrobial profiles demonstrated that all the isolates were resistant to ceftazidime, sensitive to imipenem and ciprofloxacin, and confirmed to be extended-spectrum beta-lactamase producers. Plasmids of varying molecular weights were present in all isolates. In eight of these isolates, which included four from blood, there were common large molecular weight plasmids ranging from 80 kb to 100 kb. Pulsed-field gel electrophoresis analysis using XbaI demonstrated six different DNA profiles, A to F. Profile A was shared by two blood culture isolates and were related by 91%. Profile B was found in one rectal swab isolate and one isolate from liquid soap and were related by 94%. Profile C was shared by one blood isolate and one liquid soap isolate and showed 100% relatedness. Profiles D, E, and F each were demonstrated by one blood isolate and two rectal swab isolates, respectively. These showed only 65% relatedness. CONCLUSIONS: The MRKP strains in this outbreak were not clonal in origin. The decline of the outbreak after 4 weeks was attributed to the reemphasis of standard infection control procedures and the implementation of a program that addressed sites of environmental contamination.

Anti-Bacterial Agents↗
PubMed2000

The prevalence and clonal diversity of penicillin-resistant Streptococcus pneumoniae in Kuwait.

Penicillin-resistant Streptococcus pneumoniae (PRSP) is widespread all over the world, including countries previously free of PRSP. This study was undertaken to determine the prevalence, the common serotypes and the clonality of PRSP isolated over a period of 1 year, from various clinical samples from three major hospitals in Kuwait. Strains were identified by standard methods and their antibiotic susceptibility was determined by the agar dilution method. The clonality of the isolates was determined by repetitive extragenic palindromic sequence polymerase chain reaction (REP-PCR) genomic profiling and pulsed field gel electrophoresis (PFGE). Serotyping was done by Quellung reaction using specific antisera. We found that 55% of the S. pnuemoniae were resistant to penicillin (46% and 9% exhibited intermediate and full resistance, respectively). Nearly 41% were resistant to sulfamethoxazole-trimethoprim, 9% to cefotaxime and ceftriaxone, 15% to amoxycillin-clavulanate, 17% to cefuroxime, 77 % to cefaclor, and 14% to clindamycin. The commonest serotypes among the PRSPs were 6A, 6B, 14, 19F, 23F and nontypable. PFGE and REP-PCR patterns showed a large diversity of genetic clones of the PRSP. Serotypes 6B, 14, 19F and 23F were more clonally related than the others. Our data showed that the prevalence of PRSP was high, the serotypes were diversified and different genetic clones make up the population of circulating PRSP in Kuwait.

DNA, Bacterial↗
PubMed1998

Evaluation of pulsed-field gel electrophoresis of genomic restriction fragments in the discrimination of Yersinia enterocolitica O:3.

One hundred and six Yersinia enterocolitica serogroup O:3, biotype 4 isolated from human and porcine samples in 1984 and in the years 1993 5 were examined by pulsed-field gel electrophoresis (PFGE). The genomic profiles produced by the enzymes NotI and XbaI were studied. Sixteen (A-P) and 8 (1-8) different pulsotypes were obtained, respectively. By combining the pulsotypes produced by both NotI and XbaI 24 different types were distinguished. The two major types, designated as A1 and B1, comprised 36% of all strains tested. The proportions of pulsotypes A1 and B1 were, 35.9 and 25.6%, respectively, among strains isolated in 1984. The corresponding figures among the strains isolated in 1993-5 were 35.8 and 41.8%. Nine pulsotypes were found only in 1984 and nine only in 1993-5. The proportions of the major pulsotypes, A1 and B1, in human isolates were 42.9 and 35.7% and in porcine isolates 22.2 and 36.1% respectively. Six types were found among both human and porcine isolates, 8 only among human strains and 10 only among porcine strains.

Animals↗
PubMed2003

Investigation in Central Italy of the possible association between Cryptococcus neoformans var. Gattii and Eucalyptus camaldulensis.

The authors present a worldwide review of isolations of Cryptococcus neoformans, var. neoformans and C. neoformans var. gattii from animals and vegetation, referring in particular to the already well-known association of the former variety with Eucalyptus camaldulensis. They then review the Italian situation relative to this association and their studies carried out in Central Italy: in Latina (Lazio), Pisa, Viareggio and Lake Massaciuccoli (Tuscany). From the 256 E. camaldulensis trees examined C. neoformans var. gattii was not isolated. An E. camaldulensis tree situated in the nature reserve on Lake Massaciuccoli proved to be positive for C. neoformans var. neoformans. This variety was isolated from the leaves, flowers, bark and the debris at the foot of the tree, suggesting that it had colonized the entire tree and that it was capable of developing not only on its usual habitat (bird guano, soil rich with guano) but also on Eucalyptus trees. The identity of the isolates was confirmed by their genomic profiles obtained by random amplification polymorphic DNA (RAPD) with the primer (GACA)4. The presence of a single genotype indicates a sole source of contamination, perhaps brought by a bird coming from a contaminated environment.

Cryptococcosis↗
PubMed2006

Mechanisms of disease: Genetic mechanisms of atrial fibrillation.

Atrial fibrillation is the most common cardiac arrhythmia, and it increases in prevalence with advancing age to about 6% in people older than 65 years. The chance of developing atrial fibrillation at age 40 years or older is about 25% in men and women. This arrhythmia accounts for about one-third of all strokes, and 30% of all patients with atrial fibrillation have a family history of the disease. In 1997, Brugada et al. identified the first locus for familial atrial fibrillation on chromosome 10q22-24 in three different Spanish families. Since that time, seven further loci have been mapped and four relevant genes identified. All these genes encode potassium-channel subunits. The mechanism of action by which all four genes induce atrial fibrillation is via shortening of the action potential duration and atrial effective refractory period. The consistency of the mechanism of action beckons the development of therapy specifically targeted to prevent these molecular events. In addition to monogenic diseases, patients with structural heart disease are predisposed to atrial fibrillation by inherited DNA polymorphisms. The development of chips with hundreds of thousands of single-nucleotide polymorphisms to perform genome-wide scans will elucidate over the next few years the single-nucleotide polymorphisms that predispose to atrial fibrillation. Within the next decade, most of the genes responsible for atrial fibrillation and the single-nucleotide polymorphisms that confer predisposition will probably be identified, and therapies will be developed on the basis of individuals' genomic profiles. In this review I provide an overview of the understanding of the relevant genetic mutations that have been identified so far, and briefly discuss what implications this information might have for practice.

Atrial Fibrillation↗
PubMed2003

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.

DNA microarrays can be used to identify gene expression changes characteristic of human disease. This is challenging, however, when relevant differences are subtle at the level of individual genes. We introduce an analytical strategy, Gene Set Enrichment Analysis, designed to detect modest but coordinate changes in the expression of groups of functionally related genes. Using this approach, we identify a set of genes involved in oxidative phosphorylation whose expression is coordinately decreased in human diabetic muscle. Expression of these genes is high at sites of insulin-mediated glucose disposal, activated by PGC-1alpha and correlated with total-body aerobic capacity. Our results associate this gene set with clinically important variation in human metabolism and illustrate the value of pathway relationships in the analysis of genomic profiling experiments.

Animals↗