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At least 1,063 records · Page 59Linked to original sources
PubMed2026

Inherited Susceptibility to Urinary Tract Infections from Kidney Papilla to Bladder.

Urinary tract infections (UTIs) are traditionally viewed as environmentally driven, yet their inherited susceptibility remains largely unexplored. We conducted a cross-biobank genome-wide association study of recurrent UTIs in 1,860,836 individuals (213,869 cases and 1,646,967 controls). We identified 36 genetic susceptibility loci and performed tissue-based multi-omic mapping to prioritize candidate causal genes. UTI risk alleles preferentially modulated epithelial gene expression in kidney and bladder, converging on urinary epithelia structure and function. PSCA, encoding a secreted epithelial surface protein, emerged as the strongest candidate under genetic control; the gene product is constitutively secreted into the urine from kidney papilla and bladder epithelia, binds uropathogenic E. coli, and inhibits bacterial growth in vitro. Our findings define the polygenic architecture of UTIs and highlight the critical role of uroepithelial surface defenses, providing a new framework for host-directed, non-antibiotic interventions.

Journal Article↗
PubMed2026

Big data analytics for CLEC5A dynamics based on single cell genomics and proteomics reveal its diverse functions in human diseases.

BACKGROUND: CLEC5A (C-type lectin domain family 5 member A) is an innate immune receptor implicated in inflammatory signaling, contributing to hyperinflammatory responses in infections and sterile inflammation. However, CLEC5A dynamics in human diseases remain to be identified. Here, we systematically characterized CLEC5A dynamics in humans across cells, tissues, and disease states, and to explore the functional significance of CLEC5A in macrophage activation based on single-cell genomics. METHODS: With multi-omics (scRNA-seq, proteomics and big data analytics), we analyzed extensive human transcriptomic datasets (>42,000 samples) to profile CLEC5A expression by cell type, tissue, and disease. Single-nucleus RNA-seq (snRNA-seq) from pediatric congenital heart disease and a virtual CLEC5A gene knockout were also performed to characterize CLEC5A dynamics in humans. RESULTS: CLEC5A is highly enriched in innate immune cells, particularly in macrophages and neutrophils. Baseline CLEC5A in most tissues is low, but it is markedly upregulated in inflammatory and infectious diseases. CLEC5A expression has sex-specific differences in certain organs. Single-cell analysis showed that CLEC5A can be considered novel marker of proinflammatory macrophages with elevated cytokine production, antigen presentation, and impaired phagocytosis. Virtual CLEC5A knockout analysis identified coordinated perturbation of immune-regulatory pathways and overlapping genes linking CLEC5A to macrophage activation networks. CONCLUSION: CLEC5A is predominantly expressed in myeloid cells and acts as a key amplifier of inflammation in human diseases. Our findings highlight CLEC5A as a potential biomarker and therapeutic target in myeloid-driven hyperinflammatory conditions, warranting further experimental and translational validation.

Humans↗
PubMed2026

Multilevel genomic, transcriptomic, and epidemiologic evidence linking diabetic retinopathy to Alzheimer disease.

BACKGROUND: Diabetic retinopathy (DR) and Alzheimer disease (AD) share metabolic and vascular dysfunctions, but the extent to which they reflect overlapping genetic susceptibility and neurovascular-metabolic regulatory pathways remains unclear. We combined multi-omics analyses with population-based data to examine the genetic convergence, cellular pathways, and longitudinal association between DR and AD. METHODS: We performed a two-sample Mendelian randomisation (MR) to estimate the association between genetically predicted DR liability and AD risk. We used Bayesian colocalisation analysis to identify shared genomic loci, and summary-data-based MR (SMR) to detect expression-mediated genes jointly associated with DR and AD. We analysed single-cell RNA sequencing data to characterise shared cellular features and related biological pathways. We also conducted an MR-based mediation analysis to explore whether lipid-related, metabolic, or inflammatory traits mediated the observed DR-AD association, and a longitudinal analysis of the UK Biobank cohort to assess the association between DR and incident AD. RESULTS: With the MR analysis, we found that genetically predicted liability to DR was associated with a modest increase in AD risk. Colocalisation analysis supported a shared genetic signal. We identified three genes with shared expression-mediated associations across DR and AD through SMR. Functional enrichment analyses revealed partially overlapping neurovascular and metabolic pathways. Using MR-based mediation analysis, we found no significant intermediary traits linking DR and AD. Findings from the UK Biobank cohort were directionally consistent with the genetic analyses. CONCLUSIONS: Genetic liability to DR is associated with an increased risk of AD and is accompanied by shared expression-mediated effects and convergent neurovascular-metabolic pathways. These findings support the possibility that DR may serve as a clinically accessible indicator of increased neurodegenerative vulnerability.

Humans↗
PubMed1999

[Benign hypertrophy of the prostate: which treatment, for whom?].

Approximately 25% of men over 40 or 50 suffer from lower urinary tract symptoms (LUTS) caused by benign prostatic hyperplasia (BPH). The bothersomeness of the symptoms varies considerably from one individual to the other and can fluctuate with time. Symptoms tend to gradually worsen as time goes on through. Surprisingly, there appears to be no particular relationship between symptoms and the overall prostate size and weight. Symptoms of BPH are divided in obstructive (voiding) and irritative (storage) symptoms, of which the irritative are the most bothersome. Until recently, surgery (open or transurethral resection) was the only treatment option. Nowadays, a range of less invasive treatments and pharmacological therapies are available to relieve BPH symptoms. Finasteride, for instance, reduces the prostate size by blocking 5-alpha-reductase, the enzyme which plays a role in the growth of the prostate. It takes however a long time before a clinically significant effect is noticed: +/- 6 to 12 months. Then, there are alpha 1-blockers. These agents result in relaxation of prostatic and bladder neck smooth muscle. alpha 1-blockers act relatively fast. Most alpha 1-blockers used in the treatment of symptomatic BPH were originally developed to treat hypertension. The adverse events most commonly associated with alpha 1-blockers, such as dizziness, headache, asthenia, tachycardia/palpitation, postural hypotension and syncope are possibly related to the blood pressure lowering effect. This stimulated the search for more selective alpha-blockers which act predominantly on the prostate and have less effect on the blood levels (afluzosin: Xatral and tamsulosin: Omic). Presently, alpha-blockers have become the first-line drugs in the medical treatment of symptomatic BPH. Surgery (open or TURP) is limited to patients with recurrent infections, large residue (> 200 ml), recurrent hematuria, bladder stones. New alternative and minimally invasive treatment such as TUNA generate necrotic lesions within the prostate through needle introduced endoscopically. This leads also to marked improvement in patients symptomatology.

5-alpha Reductase Inhibitors↗
PubMed2002

"A system biology" approach to bioinformatics and functional genomics in complex human diseases: arthritis.

Human and other annotated genome sequences have facilitated generation of vast amounts of correlative data, from human/animal genetics, normal and disease-affected tissues from complex diseases such as arthritis using gene/protein chips and SNP analysis. These data sets include genes/proteins whose functions are partially known at the cellular level or may be completely unknown (e.g. ESTs). Thus, genomic research has transformed molecular biology from "data poor" to "data rich" science, allowing further division into subpopulations of subcellular fractions, which are often given an "-omic" suffix. These disciplines have to converge at a systemic level to examine the structure and dynamics of cellular and organismal function. The challenge of characterizing ESTs linked to complex diseases is like interpreting sharp images on a blurred background and therefore requires a multidimensional screen for functional genomics ("functionomics") in tissues, mice and zebra fish model, which intertwines various approaches and readouts to study development and homeostasis of a system. In summary, the post-genomic era of functionomics will facilitate to narrow the bridge between correlative data and causative data by quaint hypothesis-driven research using a system approach integrating "intercoms" of interacting and interdependent disciplines forming a unified whole as described in this review for Arthritis.

Animals↗
PubMed2001

High-throughput interpretation of pathways and biology.

The genomics revolution is opening many diverse pathways in science. In the midst of the tidal wave of information being generated by the new "omics" disciplines, bioinformatics is meeting the challenge to decipher and organize the data mountain. The endeavor to integrate diverse biological data into a common vocabulary will be an essential part of the "biotechnological age" leading to a new understanding of complex biological systems. This potential promises to revolutionize medicine as knowledge is translated into novel therapies. The Integrated Bioinformatics meeting held in Zurich January 2426, 2001, provided an insight into the cutting edge of bioinformatics and its central role in the genomics revolution. The evolution of bioinformatics will act as a guide in 21st century biological sciences.

Journal Article↗
PubMed2003

From transcriptomics to bibliomics.

BACKGROUND: Current biological investigations tend to operate with genomes, instead of genes as during the last century. It is possible to compare entire genomes, transcriptomes or proteomes, using alphanumeric data corresponding to the differential expression levels of thousands of genes. What remains difficult is to link array results to factual or bibliographical data and retrieve information that is highly structured and - in Shannon's sense - rare. MATERIAL/METHODS: We have developed a tool, Documentation and Information LIBrary (DILIB), that enables us to retrieve, organize and analyze huge amounts of data available on the Internet and related to microarray experiments. DILIB can link hundreds of differentially expressed genes - through their Single Identifier or GenBank accession number - to hundreds of Medline records, and can retrieve, analyze, and compare automatically thousands of non-trivial descriptors related to gene clusters. RESULTS: As exemplified with frequency comparison of MEdical Subject Headings and Registry Number descriptors, we reanalyzed the involvement of 'integrin', 'interleukin' and 'CD Antigens' in mesotheliomas. Thus, DILIB allowed us to: (i). associate literature to expressed genes, (ii). link functional transcriptomes in various experiments, (iii). associate specific descriptors to experiments, (iv). define new research areas, and eventually (v). find new functions for co-expressed genes. CONCLUSIONS: We propose a new concept, 'bibliomics', representing a subset of high quality and rare information, retrieved and organized by systematic literature-searching tools from existing databases, and related to a subset of genes functioning together in '-omic' sciences.

Databases, Genetic↗
PubMed2004

Lipomic profiling in drug discovery, development and clinical trial evaluation.

Dysregulation of lipid metabolism plays a crucial role in the progression of many diseases and in adverse drug response. Changes in lipid metabolism leading to disease are often not detected using biomarker analyses because these changes are defined by a subtle, long-term shift in the concentrations of many metabolites simultaneously. The application of the principals of 'omics to the study of lipids, which include the development of comprehensive, high-throughput assays and centralized reference databases, is beginning to produce an integrated and actionable knowledge of lipids and their relationship to pathology. These analytical tools and the assembled knowledge will enable the discovery, development and testing of drugs to be conducted with a deeper knowledge of their effects on lipid metabolism.

Animals↗
PubMed2004

Trends in early drug safety.

Successful introduction of a new drug to the market is not only an extremely costly and complicated process, but also fraught with a substantial risk of failure. The number of new drugs launched each year from 1990 to 2000 has stayed relatively constant, while the cost of pharmaceutical research and development has risen by almost 2.5-fold over the same period. What is not revealed by these figures is that the chance of success for a drug candidate passing through the various hurdles in pharmaceutical development is at best 1 in 10 and has barely changed despite advancing technology in other areas of research and development. While we expect high failure rates in drug discovery, it is of substantial concern that most candidates in development on which large investments have already been made are probably not going to make any return. A major stumbling block is the absorption, distribution, metabolism, excretion and toxicology profile of drug candidates. These issues were discussed at the Society for Medicines Research symposium held September 18, 2003, in London, United Kingdom. Recent SMR symposia have focused on the ADME and pharmacokinetic aspects of drug discovery and development. Indeed, it is now uncommon for drug discovery projects not to address these issues early in their lifetimes. Although it is less common to address drug safety early in a project, it is being utilized more frequently to help select the best clinical candidates for further development. This meeting report summarizes some of the key aspects of early drug safety issues facing the drug discoverer today. Classical approaches to toxicology, p450-mediated safety, cardiovascular safety, "omics" approaches and their impact upon clinical safety will be discussed.

Animals↗
PubMed2005

Large-scale integrated databases supporting drug discovery.

Over the past 15 years, genomics, combinatorial chemistry and high-throughput automation have transformed the setting for drug discovery, from an information-poor to a data-rich environment. The next challenge for informatics scientists is to convert the large amount of disparate data produced into useful, integrated information. Consolidation of the different types of information related to drug discovery requires a good working knowledge of database technology, the existence of accepted data standards for achieving uniformity and a complete understanding of the different data systems that are already available. Chemogenomic databases represent the first example of truly integrated systems that make 'omic' technologies directly relevant to small-molecule drug discovery. Researchers within drug discovery programs now have an opportunity to take advantage of new information domains, through the advance and adoption of integrated chemogenomic databases.

Animals↗
PubMed2005

Integrating data from biological experiments into metabolic networks with the DBE information system.

Modern 'omics'-technologies result in huge amounts of data about life processes. For analysis and data mining purposes this data has to be considered in the context of the underlying biological networks. This work presents an approach for integrating data from biological experiments into metabolic networks by mapping the data onto network elements and visualising the data enriched networks automatically. This methodology is implemented in DBE, an information system that supports the analysis and visualisation of experimental data in the context of metabolic networks. It consists of five parts: (1) the DBE-Database for consistent data storage, (2) the Excel-Importer application for the data import, (3) the DBE-Website as the interface for the system, (4) the DBE-Pictures application for the up- and download of binary (e. g. image) files, and (5) DBE-Gravisto, a network analysis and graph visualisation system. The usability of this approach is demonstrated in two examples.

Computational Biology↗
PubMed2005

Selected topics in probiotics and prebiotics: meeting report for the 2004 international scientific association for probiotics and prebiotics.

On August 29-31, 2004, 84 academic and industry scientists from 16 countries gathered in Copper Mountain, Colorado USA to discuss certain issues at the forefront of the science of probiotics and prebiotics. The format for this invitation only meeting included six featured lectures: engineering human vaginal lactobacilli to express HIV-inhibitory molecules (Peter Lee, Stanford University), programming the gut for health (Thaddeus Stappenbeck, Washington University School of Medicine), immune modulation by intestinal helminthes (Joel Weinstock, University of Iowa Hospitals and Clinics), hygiene as a cause of autoimmune disorders (G. A. Rook, University College London), prebiotics and bone health (Connie Weaver, Purdue University) and prebiotics and colorectal cancer risk (Ian Rowland, Northern Ireland Centre for Food and Health). In addition, all participants were included in one of eight discussion groups on the topics of engineered probiotics, host-commensal bacteria communication, 'omics' technologies, hygiene and immune regulation, biomarkers for healthy people, prebiotic and probiotic applications to companion animals, development of a probiotic dossier, and physiological relevance of prebiotic activity. Brief conclusions from these discussion groups are summarized in this paper.

Animals↗
PubMed2005

[Achieving pathogenesis understanding of ocular diseases by deciphering the underlying molecular pathways].

The field of ophthalmology research has experienced a revolution since the 1970's, when molecular biology techniques were gradually and widely adopted. Many of the developments generated impact that went far beyond the field of ophthalmology. A classic case was the identification and characterization of the Retinoblastoma susceptibility gene (Rb), whose impact went far beyond the rare and obscure disease, as it provides key evidence for the concept of tumor suppressor gene and the "two hit" theory of tumor formation. The identification of scores of genes involved in retinitis pigmentosum (pigmentosa), on the other hand, show cases the complexity of multi-factorial diseases. Ophthalmology researchers in China have been quick in integrating these novel tools into their research. However, the field still lags behind in the effective use of these technologies to carry out in-depth inquiries into key disease mechanisms. The advent of "omics" technologies heralded a new era in biomedical research that allows for the global and rapid survey of genetic and biochemical profiles. Effective integration of these novel technologies into ophthalmology research will have far-reaching impact for the whole field.

Biotechnology↗
PubMed2006

Integration of genomic and metabonomic data in systems biology--are we 'there' yet?

The measurement of genes, proteins and metabolites has gained increasing acceptance as a means by which to study the response of an organism to stimuli, whether they are environmental, genetic, pharmacological, toxicological, etc. Typically referred to as genomics, proteomics, and metabonomics or metabolomics, respectively, these methods as independent entities have undoubtedly provided new biological insight that was not attainable a decade ago. Not surprisingly, scientists continue to push the boundaries to extract knowledge from data, and it is currently recognized that the full realization of these technologies is limited by a lack of tools to enable data integration. Integration of these 'omic datasets, or integromics, is desirable as it links the individual biological elements together to provide a more complete understanding of dynamic biological processes. Accordingly, in addition to developing new data analysis methods to extract further details from each of the high-content datasets individually, effort is also being expended to create or improve statistical methods, databases, annotations and pathway mapping to maximize our learning. There are several recent examples, in both mammalian and non-mammalian systems, in which genes, proteins and/or metabolites have been integrated using either biology- or data-driven strategies. Herein, key findings are reviewed, gaps in our current tools and technologies are identified and illustrated, and perspective is provided on the potential of integromics in biological research.

Acetaminophen↗
PubMed2006

Where to in the next ten years of health informatics education?

OBJECTIVES: To explore whether education in health/medical informatics should continue to evolve along the lines pursued since the early seventies, or whether a change is advisable. METHODS: Roots and key resulting characteristics for European and US American approaches HI education are identified. In Europe holistic approaches based on a synthesis of medicine and informatics (= computer science) with programs ranging from vocational training through university programs to doctoral and postdoctoral programs were characteristic. The US American approaches emphasized the higher levels of education and a diverse selection of specialized subjects. Changes in health and health informatics are summarized. RESULTS: Two types of changes are identified: high-tech applications arising at the interface of imaging, robotics, and the -omics (genomics, proteomics, metabolomics), and invasive applications centering on consumer health informatics and a move from curative to prospective health care. CONCLUSIONS: It is proposed that curative medicine is adequately served by current educational approaches, but that the move towards prospective health care requires a move towards education and change management for health professionals and health informatics professionals.

Delivery of Health Care↗
PubMedDate not supplied

Guidance values for the biomonitoring of occupational exposure. State of the art.

Biomonitoring was developed for the assessment of the health risks from exposure to chemicals at work, and the approaches and concepts of biomonitoring are derived from such exposures. At present, biomonitoring is increasingly used also to assess exposure from the environment. Biomonitoring and assessment of external exposure are complementing activities, where the exposure assessments are much more widely applied, especially when the number of chemicals concerned is considered; environmental analysis also offers the distinct advantage of speciation analysis--which is very poorly developed for biomonitoring. Biomonitoring on the other hand provides information on exposure from all sources, and via all absorption routes, and considers also accumulation of the chemical in the body. Bio monitoring using exposure biomarkers thus consider interindividual differences in the absorption, while use of effec biomarkers ideally also considers interindividual differences in sensitivity. Few effect biomarkers, however, have been validated. The major challenges of biomonitoring are the development of monitoring methods, which are inexpensive enough to be applied at a frequency that makes possible meaningful biomonitoring of chemicals with a short half-time; development of exposure biomarker guidance values specific to individual species of different metals; ex pansion of the repertoire of validated effect biomarkers; and validation and application to effect monitoring of the omic technologies. Another major challenge is a reconsideration of the basis of biomonitoring action limits to reflec the change in the work place: Biomonitoring should be adapted to assist in the generation of a healthy workplace which is capable of attracting workers, and assist them to perform their work effectively--rather than just to guarantee absence of serious health effects.

Air Pollutants, Occupational↗
PubMed2006

[Re-utilization of clinical laboratory patient-derived samples].

Our hospital has traditionally placed a portion of Clinical Laboratories patient-derived samples into temporary storage for purposes of re-examination. Occasionally, following a brief review, a part of these samples were provided not only for research but also for quality control. However, recent trends to protect confidential personal information have made it difficult to offer patient-derived samples to those who perform research and quality control even after a strict and complicated review of their requests. Because of recent progresses in the various "-omics" such as genomics, proteomics, and/or metabolomics, a strong need of patient-derived samples for research exists. Therefore, we have developed and, since 2002, provided a "Bio Sample Bank" to smoothly and efficiently expedite provision of patient-derived samples for research and quality control purposes. So far we have collected more than 130,000 samples. We wish to disclose our experiences concerning this bank and to develop interest in the importance of our system and its significant benefits to clinical procedures and patients.

Biological Specimen Banks↗
PubMed2006

Reflections on biomedical informatics: from cybernetics to genomic medicine and nanomedicine.

Expanding on our previous analysis of Biomedical Informatics (BMI), the present perspective ranges from cybernetics to nanomedicine, based on its scientific, historical, philosophical, theoretical, experimental, and technological aspects as they affect systems developments, simulation and modelling, education, and the impact on healthcare. We then suggest that BMI is still searching for strong basic scientific principles around which it can crystallize. As -omic biological knowledge increasingly impacts the future of medicine, ubiquitous computing and informatics become even more essential, not only for the technological infrastructure, but as a part of the scientific enterprise itself. The Virtual Physiological Human and investigations into nanomedicine will surely produce yet more unpredictable opportunities, leading to significant changes in biomedical research and practice. As a discipline involved in making such advances possible, BMI is likely to need to re-define itself and extend its research horizons to meet the new challenges.

Cybernetics↗