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PubMed2026

Machine Learning-Driven Prediction of Coronary Artery Disease Risk Based on UK Biobank Plasma Proteomics.

BACKGROUND: Coronary artery disease (CAD) is a leading global cause of mortality, yet the predictive accuracy of conventional risk models is limited. Here, we integrate conventional risk factors, polygenic risk scores, and large-scale proteomics to develop a unified model for enhanced CAD risk prediction. METHODS: Using data from UK Biobank, participants with plasma proteomics and genetic risk data were included after excluding prevalent CAD. Participants from England were split into training (n=32 330) and internal validation (n=13 857) sets, and Scotland/Wales participants formed an external validation set (n=5775). Incident CAD was ascertained from linked health records. A 202-protein proteomic risk score was derived by least absolute shrinkage and selection operator Cox regression, and CatBoost models were trained using conventional risk factors alone and with incremental addition of polygenic risk scores and protein proteomic risk scores; Shapley Additive Explanations-guided forward selection identified a compact protein panel. RESULTS: Across cohorts, the median age was 58 years and ∼45% were men. Protein proteomic risk score was dose-dependently associated with CAD risk. Compared with conventional risk factors alone, integrating polygenic risk scores and protein proteomic risk scores improved discrimination, with the area under the curve increasing from 0.750 (95% CI, 0.732-0.767) to 0.789 (95% CI, 0.772-0.805) in internal validation and from 0.717 (95% CI, 0.683-0.750) to 0.762 (95% CI, 0.732-0.791) in external validation. A 9-protein panel (GDF15 [growth differentiation factor 15], MMP12 [matrix metalloproteinase 12], NPPB [natriuretic peptide B], PGF [placental growth factor], REN [renin], ADGRG2 [adhesion G-protein coupled receptor], ACE2 [angiotensin-converting enzyme 2], CDCP1 [CUB domain-containing protein 1], CXCL17 [C-X-C motif chemokine ligand 17)]) captured most proteomic predictive information. CONCLUSIONS: Our findings demonstrate that integrating conventional risk factors, polygenic risk scores, and proteomic data improves CAD risk prediction. This study highlights the utility of proteomics in precision cardiovascular medicine and simplified risk stratification tools.

Humans↗
PubMed2005

Needs and opportunities for research in hypersensitivity pneumonitis.

Hypersensitivity pneumonitis (HP) develops after inhalation of many different environmental antigens, causing variable clinical symptoms that often make diagnosis uncertain. The prevalence of HP is higher than recognized, especially its chronic form. Mechanisms of disease are still incompletely known. Strategies to improve detection and diagnosis are needed, and treatment options, principally avoidance, are limited. A workshop recommended: a population-based study to more accurately document the incidence and prevalence of HP; better classification of disease stages, including natural history; evaluation of diagnostic tests and biomarkers used to detect disease; better correlation of computerized tomography lung imaging and pathologic changes; more study of inflammatory and immune mechanisms; and improvement of animal models that are more relevant for human disease.

Adult↗
PubMed2006

Axonal damage markers in cerebrospinal fluid are increased in ALS.

OBJECTIVE: To test whether biomarkers for axonal degeneration correlated with clinical subtypes and were of use in predicting progression of ALS. METHODS: Patients with ALS (n = 69), patients with Alzheimer disease (AD; n = 73), and age-matched controls (n = 33) were included in this prospective study. CSF levels of tau protein and neurofilaments (NfHSMI35) were measured using ELISA. In 49 patients with ALS, follow-up data were available (median follow-up 7 months). RESULTS: CSF levels of NfHSMI35 were five times higher in patients with ALS (1.7 ng/mL) than in controls (0.3 ng/mL, p < 0.001) and 10 times higher than in patients with AD (0.14 ng/mL, p < 0.001). NfHSMI35 values were also higher in patients with upper motor neuron-dominant ALS than in patients with typical ALS (upper motor neuron + lower motor neuron) at p = 0.02. Values of NfHSMI35 were higher in ALS of more rapid progression. The values of NfH and tau did not correlate with CSF protein content. CONCLUSIONS: The authors propose that axonal damage markers in CSF may discriminate between subtypes of ALS and that they could be used as markers for therapeutic trials. CSF NfH was superior to tau in these discriminations.

Adult↗
PubMedDate not supplied

New possibilities for diagnosis and treatment of osteoporosis.

Postmenopausal osteoporosis is preventable and treatable. Women need not lose bone mineral density (BMD) after the menopause. Without intervention, all women lose bone after menopause, regardless of the amount of calcium, vitamin D, and exercise they undertake. Postmenopausal women need estrogen replacement, a selective estrogen receptor modulator (SERM), or a bisphosphonate to prevent bone loss. Alendronate, risedronate (bisphosphonates) and raloxifene (SERM) are approved for the prevention of bone loss. The diagnosis of at-risk postmenopausal women can best be accomplished by measuring BMD in all postmenopausal women age 65 years and older regardless of their risk profile and in all postmenopausal women under 65 years with one or more risk factors. Treatment guidelines direct physicians to treat postmenopausal women with T-scores lower than -2.0 SD regardless of their risk profile and postmenopausal women with T-scores lower than -1.5 SD with one or more risk factors. The lower the BMD, the greater the fracture risk, particularly in individuals with increased age, existing fragility fractures, or high bone turnover. The best intervention for a patient should be individually selected, based on careful clinical assessment. Although calcitonin is not approved for prevention, it is approved for treatment. The labeling of estrogens has been modified to state that they may be used to "manage" osteoporosis. The lack of efficacy of calcitonin to prevent bone loss during the first 5 years after menopause, and the lack of prospective fracture reduction data for estrogen, have resulted in these labeling restrictions. Alendronate, risedronate, and raloxifene are currently approved for the treatment of osteoporosis. Both of these compounds have been shown to increase BMD and decrease fracture risk. Monitoring of a patient's response to treatment may be accomplished using serial BMD testing and biomarkers of bone turnover.

Aged↗
PubMed2004

[Urinary cytology in the diagnosis of upper urinary tract urothelial tumor].

OBJECTIVES: To review the current usefulness of urinary cytology in the diagnosis of upper urinary tract urothelial tumor in relation to conservative endoscopic treatment. METHODS: Bibliographic review of the published articles about urinary cytology of the upper urinary tract urothelial tumor and evaluation of the diagnostic efficacy obtained in various series. Review of the cytological diagnostic criteria for urothelial tumors. RESULTS: From 1960 to 2003, 26 series collecting results of the cytological diagnosis of urothelial tumors of the ureter and renal pelvis have been published. Results have been variable with a diagnostic accuracy between 23 and 100%. Such an ample variation depends on sampling techniques, preparation techniques, type of tumor, and the urologists and pathologist's experience. The collection of the sample by direct endoscopical visualization significantly proves the diagnostic efficacy of cytology for upper urinary tract urothelial tumors. CONCLUSIONS: Urine cytology selectively obtained from the upper urinary tract with endoscopical techniques is a reliable method in the diagnosis of renal pelvis and ureter neoplasias. Urine cytology has a sensitivity close to 90% and specificity between 98-100% for carcinoma in situ and high-grade urothelial neoplasias, so that it can contribute in the therapeutic decision making process in a very effective manner. Despite its low sensitivity, it may be useful in the diagnosis of low grade urothelial neoplasias when samples are selectively obtained by catheterization, and it has not been excelled by any of the biomarkers molecular tests yet.

Cytological Techniques↗
PubMed2004

Comparative effects of curcumin and an analog of curcumin on alcohol and PUFA induced oxidative stress.

PURPOSE: Alcoholic liver disease is a major medical complication of alcohol abuse and a common liver disease in western countries. Increasing evidence demonstrates that oxidative stress plays an important etiologic role in the development of alcoholic liver disease. Alcohol alone or in combination with high fat is known to cause oxidative injury. The present study therefore aims at evaluating the protective role of curcumin, an active principle of turmeric and a synthetic analog of curcumin (CA) on alcohol and thermally oxidised sunflower oil (DeltaPUFA) induced oxidative stress. METHODS: Male albino Wistar rats were used for the experimental study. The liver marker enzymes: gamma-glutamyl transferase (GGT), alkaline phosphatase (ALP), the lipid peroxidative indices: thiobarbituric acid reactive substances (TBARS) and hydroperoxides (HP) and antioxidants such as vitamin C, vitamin E, reduced glutathione (GSH), superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) were used as biomarkers for testing the antioxidant potential of the drugs. RESULTS: The liver marker enzymes and lipid peroxidative indices were increased significantly in alcohol, DeltaPUFA and alcohol + DeltaPUFA groups. Administration of curcumin and CA abrograted this effect. The antioxidant status which was decreased in alcohol, DeltaPUFA and alcohol + DeltaPUFA groups was effectively modulated by both curcumin and CA treatment. However, the reduction in oxidative stress was more pronounced in CA treatment groups compared to curcumin. CONCLUSION: In conclusion, these observations show that CA exerts its protective effect by decreasing the lipid peroxidation and improving antioxidant status, thus proving itself as an effective antioxidant.

Alkaline Phosphatase↗
PubMed1989

[State of the art in immuno-allergology: histamine-releasing factors (HRF)].

The present concepts on histamina releasing factors are discussed, their cellular origins, their effect on the target cells and its importance in asthma immunopathology. Personal results on the production of HRF by alveolar macrophages stimulated by allergen and its action on non atopic basophils are presented. Alveolar macrophages from atopic asthmatics release HRF in presence of allergen. Macrophage from non atopic do not. HRF has been tested in a Human Basophil Degranulation Test (HBDT) preparation, a significant degranulation induced by HRF from atopic patient being only observed when atopic basofils are used in HBDT. These results confirm that allergen could induce HRF production from alveolar macrophages and that this HRF could degranulate basophils in atopic and induce mediators release.

Basophil Degranulation Test↗
PubMed1989

[The state of the art in immuno-allergology: histamine releasing factors (HRF)].

The present concepts on histamine releasing factors are discussed, their cellular origins, their effect on the target cells and its importance in asthma immunopathology. Personal results on the production of HRF by alveolar macrophages stimulated by allergen and its action on non atopic basophils are presented. Alveolar macrophages from atopic asthmatics release HRF in presence of allergen. Macrophage from non atopic do not. HRF has been tested in a Human Basophil Degranulation Test (HBDT) preparation, a significant degranulation induced by HRF from atopic patient being only observed when atopic basophils are used in HBDT. These results confirm that allergen could induce HRF production from alveolar macrophages and that this HRF could degranulate basophils in atopic and induce mediators release.

Basophil Degranulation Test↗
PubMed2006

Strategies for plasma proteomic profiling of cancers.

Despite a voluminous literature on potential protein biomarkers and a compelling need for diagnostic tests based on biomarkers to detect cancers at much earlier, more treatable stages, progress has been limited. New methods and new instruments for analysis of differences in gene expression, gene methylation, and proteomics are being employed to try to accelerate the discovery phase. Given the heterogeneity of tumor mechanisms and the limitations of analytical methods, it is likely that a variety of strategies will be needed and will be complementary. That is the basis of this review of proteomic approaches. This article adopts a systems biology view, starting with mRNA transcripts in tumors and cultured tumor cells to detect mRNA overexpression, some of which will be correlated with protein overexpression. Some of those proteins may be secreted or released into proximal biofluids and plasma. Detection of low-abundance tumor proteins in the complex and dynamic mixture that is plasma requires combinations of increasingly powerful technologies. The biological amplification of protein signals through the immune system offers autoantibodies as potential biomarkers. Higher abundance proteins, including acute-phase reactants, may have practical value, especially if the proteins are modified as part of the cancer processes. Low molecular weight proteins, fragments, and peptides may offer complementary biomarkers. Promising biomarker candidates must be confirmed in independent studies. Then they must be submitted to higher-throughput methods practical for large-scale validation studies and, hopefully, for clinical and epidemiological applications. Standardized operating procedures for specimen handling, design and use of various reference standards, care to avoid bias and confounding, and guidelines for reporting findings and contributing datasets should enhance the prospects for predictive proteomic profiling of people at risk for cancers.

Biomarkers, Tumor↗
PubMed2004

Environmental metabonomics: applying combination biomarker analysis in earthworms at a metal contaminated site.

Earthworms were taken across an environmental gradient of metal contamination for ecotoxicology assessment. Both indigenous (Lumbricus rubellus and L. terrestris) and introduced earthworms (Eisenia andrei, exposed in mesh bags) were studied. Changes in the levels of small molecule metabolites in earthworm tissue extracts were analysed by 1H NMR spectroscopy as a means of identifying combination biomarker compounds. Principal components analysis of the NMR spectral data revealed that biochemical changes were induced across the metal contamination gradient. Native worms (L. rubellus) from the most polluted sites were associated with an increase in the relative concentration of maltose; a decrease was also seen in the concentration of an as yet unidentified biomarker compound. Introduced worms (E. andrei) did not show differences to the same extent. Direct integration of the resonances from histidine and 1-methylhistidine showed that relative histidine concentrations were elevated slightly for L. rubellus, confirming the results of earlier mesocosm studies. Conversely, the relative concentrations of both histidine and 1-methylhistidine were greatly reduced by metal contamination in L. terrestris. This study demonstrates the utility of NMR spectroscopy in detecting previously unknown potential biomarkers for ecotoxicity testing and identified maltose as a potential biomarker compound deserving of further study.

Animals↗
PubMed2004

BRCAPAP: feasibility of clinical BRCA testing on liquid-based cervical cytology: implications for biomarker development.

OBJECTIVE: The study was designed to test the feasibility that lower genital tract cytology is a compatible medium for robust germ line genetic analyses. METHOD: BRCA1 and/or BRCA2 gene mutational analysis was done on DNA isolated from liquid-based cervical or vaginal cytology taken from 17 consenting women (age 29-65 years) who previously had genetic counseling followed by BRACAnalysis (Myriad Genetics, Salt Lake City, UT) blood analyses. Eleven women had known mutations in either BRCA1 or BRCA2 (cases) and six had no identified mutations (controls) on entry into the study. Anonymized cytology samples were sent to Myriad Genetics with a request for testing that was limited to the degree of genomic testing previously done on the blood samples. RESULTS: One cervicovaginal specimen from a test-positive woman had inadequate cellular content that precluded gene sequencing and therefore was excluded from this analysis. For the 16 women with adequate cytologic specimens, there was 100% concordance for BRCA mutation test results between blood and genital tract cytology (kappa = 1.0; 95% confidence interval, 0.51-1.0). CONCLUSION: We have shown the feasibility of using liquid-based genital tract cytology as an alternative biospecimen to blood for germ line genetic analysis using a clinical approved assay. It needs to be emphasized that any type of testing for BRCA1 or BRCA2 mutation genotype should only be done in the setting of pretest and posttest counseling.

Adult↗
PubMed2005

Comparison of several toxicity tests applied to complex wastewaters and mussel biomarkers in receiving waters.

In this study, the complex wastewaters/effluents discharged to coastal regions of Turkey and Greece were sampled, and various toxicity tests were applied. The bioassays used included the assessment of the luminescence inhibition of the bacterium Vibrio fisheri, the photosynthesis inhibition (14C uptake rate) and growth inhibition of the algal species Phaeodactylum tricornutum, and the mortality of the crustacean Artemia franciscana and rotifer Brachionus plicatilis. Additionally, "neutral red retention" and "filtration rate" sublethal biomarker techniques were performed by utilizing the mussel species Mytilus galloproviancialis, inhabiting the points of discharges in Turkey. All discharges tested were found to be acutely toxic to P. tricornutum and slightly toxic to V. fisheri, A. franciscana, and B. plicatilis. Test results showed that the 14C uptake rate toxicity test was the most sensitive one among the other bioassays. The biomarker results showed that the health status of mussels in the coastal areas decreased significantly, indicating the pollution of the receiving waters in Turkey. The conclusions drawn highlight the necessity for an intesive ecotoxicological monitoring scheme that will incorporate the most suitable bioassays and biomarkers to adequately contribute to the upgrading and maintenance of the ecological quality of the coastal waters in Greece and in Turkey.

Aliivibrio fischeri↗
PubMed2025

Development and validation of blood-based diagnostic biomarkers for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) using EpiSwitch&#xae; 3-dimensional genomic regulatory immuno-genetic profiling.

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating, multifactorial disorder characterised by profound fatigue, post-exertional malaise, cognitive impairments, and autonomic dysfunction. Despite its significant impact on quality of life, ME/CFS lacks definitive diagnostic biomarkers, complicating diagnosis and management. Recent evidence highlights potential blood tests for ME/CFS biomarkers in immunological, genetic, metabolic, and bioenergetic domains. Chromosome conformations (CCs) are potent epigenetic regulators of gene expression and cross-tissue exosome signalling. We have previously developed an epigenetic assay, EpiSwitch&#xae;, that employs an algorithm-based CCs analysis. Using EpiSwitch&#xae; technology, we have shown the presence of disease-specific CCs in peripheral blood mononuclear cells (PBMCs) of patients with amyotrophic lateral sclerosis (ALS), rheumatoid arthritis (RA), prostate and colorectal cancers, diffuse Large B-cell lymphoma and severe COVID-19. In a recent paper, we have identified a profile of systemic chromosome conformations in cancer patients reflective of the predisposition to respond to immune checkpoint inhibitors, PD-1/PD-L1 antagonists, with 85% accuracy. In this Retrospective case/control study (EPI-ME, Epigenetic Profiling Investigation in Myalgic Encephalomyelitis), we used whole blood samples retrospectively collected from n&#x2009;=&#x2009;47 patients with severe ME/CFS and n&#x2009;=&#x2009;61 age-matched healthy control patients to perform whole-genome 3D DNA screening for CCs correlating to ME/CFS diagnosis. We identified a 200-marker model for ME/CFS diagnosis (Episwitch&#xae;CFS test). First testing on the retrospective independent validation cohort demonstrated a strong systemic ME/CFS signal with a sensitivity of 92% and a specificity of 98%.Pathways analysis revealed several likely contributors to the pathology of ME/CFS, including interleukins, TNF&#x3b1;, neuroinflammatory pathways, toll-like receptor signalling and JAK/STAT. Comparison with pathways involved in the action of Rituximab and glatiramer acetate (Copaxone) (therapies with potential in ME/CFS treatment) identified IL2 as a shared pathway with clear patient clustering, indicating a possibility of a potential responder group for targeted treatment.

Humans↗
PubMed1997

Application of biomarkers in cancer epidemiology. Workshop report.

In epidemiology, a biological marker (commonly abbreviated, for convenience, to biomarker) is any substance, structure or process that can be measured in the human body or its products and may influence or predict the incidence or outcome of disease. Biomarkers can be broadly classified into markers of exposure, effect and susceptibility. Biomarkers may include the following: xenobiotic agents and their metabolites in tissues or body products; normally occurring body constituents whether in physiological or pathological amounts; endogenous compounds that are not present under normal conditions; and inherited and acquired abnormalities of body chemistry, structure or function, including pathological manifestations of precursors to disease. Biomarkers should be distinguished from biomarker assays, specific laboratory tests aimed at measuring particular biomarkers, and biomarker measurements, the amounts of particular biomarkers present in specified units of tissues or body products as measured by biomarker assays.

Biomarkers, Tumor↗
PubMed2006

Combined dexamethasone/corticotropin releasing hormone test predicts treatment response in major depression - a potential biomarker?

BACKGROUND: Exaggerated corticotropin (ACTH) and cortisol response to the combined dexamethasone (DEX)/corticotropin releasing hormone (CRH) test, indicating impaired regulation of the hypothalamus-pituitary-adrenocortical (HPA) system, is frequently observed in depression. In the present study, we examined whether change in HPA system function during the first weeks of hospitalization predicts response to antidepressant treatment in major depression and thus constitutes a potential biomarker. METHODS: We conducted the DEX/CRH test in 50 inpatients suffering from severe major depression, once after study inclusion and a second time 2 to 3 weeks later while under continuous antidepressant treatment. RESULTS: We found increased ACTH and cortisol responses to the first DEX/CRH test compared with healthy control subjects. In the second DEX/CRH test 2 to 3 weeks later, 36 of the 50 patients showed an attenuated cortisol response, while 14 patients did not display improvement or exhibited even aggravation of the altered HPA system function. Improved HPA system regulation in the second DEX/CRH test was associated with beneficial treatment response after 5 weeks and a higher remission rate at the end of hospitalization. CONCLUSIONS: The results suggest that change in HPA system regulation assessed with repeated DEX/CRH tests is a potential biomarker that may predict clinical outcome at follow-up. There is consensus that the drug development process could be improved, once reliable biomarkers become available that help to allow a judgement regarding the efficacy of a novel drug candidate. The combined DEX/CRH test seems to be a promising candidate for such a biomarker.

Adrenocorticotropic Hormone↗
PubMed2004

Development of a gas chromatographic test for the quantification of the biomarker 3-bromopropionic acid in human urine.

An accurate and precise method was developed for the detection and quantification of 3-bromopropionic acid (3-BPA), a metabolite and biomarker for exposure to 1-bromopropane (1-BP). 1-BP is used as an industrial solvent and exposure is a health concern for industrial workers due to its toxicity. It has been associated with neurological disorders in both animals and humans. Urine sample preparation for the determination of 3-BPA consisted of liquid-liquid extraction (LLE) with ethyl acetate and silylation with N-methyl-N-[tert-butyldimethylsilyl]trifluoroacetamide (MTBSTFA). Quantification was by means of a gas chromatograph (GC) equipped with a mass selective detector (MSD) using a dimethylpolysiloxane (HP-1) capillary column and 3-chloropropionic acid was used as an internal standard in the procedure. Demonstrated accuracy and precision during this method's validation was good; recovery varied between 93 and 98% with relative standard deviations (R.D.S.) of 5.7% or less. The limit of detection (LOD) for the procedure was approximately 0.01microg/ml 3-BPA in urine. These data and other factors of the development and validation of this test method will be discussed.

Biomarkers↗
PubMed2006

Screening and testing for endocrine disruption in fish-biomarkers as "signposts," not "traffic lights," in risk assessment.

Biomarkers are currently best used as mechanistic "signposts" rather than as "traffic lights" in the environmental risk assessment of endocrine-disrupting chemicals (EDCs). In field studies, biomarkers of exposure [e.g., vitellogenin (VTG) induction in male fish] are powerful tools for tracking single substances and mixtures of concern. Biomarkers also provide linkage between field and laboratory data, thereby playing an important role in directing the need for and design of fish chronic tests for EDCs. It is the adverse effect end points (e.g., altered development, growth, and/or reproduction) from such tests that are most valuable for calculating adverseNOEC (no observed effect concentration) or adverseEC10 (effective concentration for a 10% response) and subsequently deriving predicted no effect concentrations (PNECs). With current uncertainties, biomarkerNOEC or biomarkerEC10 data should not be used in isolation to derive PNECs. In the future, however, there may be scope to increasingly use biomarker data in environmental decision making, if plausible linkages can be made across levels of organization such that adverse outcomes might be envisaged relative to biomarker responses. For biomarkers to fulfil their potential, they should be mechanistically relevant and reproducible (as measured by interlaboratory comparisons of the same protocol). VTG is a good example of such a biomarker in that it provides an insight to the mode of action (estrogenicity) that is vital to fish reproductive health. Interlaboratory reproducibility data for VTG are also encouraging; recent comparisons (using the same immunoassay protocol) have provided coefficients of variation (CVs) of 38-55% (comparable to published CVs of 19-58% for fish survival and growth end points used in regulatory test guidelines). While concern over environmental xenoestrogens has led to the evaluation of reproductive biomarkers in fish, it must be remembered that many substances act via diverse mechanisms of action such that the environmental risk assessment for EDCs is a broad and complex issue. Also, biomarkers such as secondary sexual characteristics, gonadosomatic indices, plasma steroids, and gonadal histology have significant potential for guiding interspecies assessments of EDCs and designing fish chronic tests. To strengthen the utility of EDC biomarkers in fish, we need to establish a historical control database (also considering natural variability) to help differentiate between statistically detectable versus biologically significant responses. In conclusion, as research continues to develop a range of useful EDC biomarkers, environmental decision-making needs to move forward, and it is proposed that the "biomarkers as signposts" approach is a pragmatic way forward in the current risk assessment of EDCs.

Algorithms↗