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At least 1,369 records · Page 76Linked to original sources
PubMed2005

Methods to assess potential reduced exposure products.

The availability of tobacco products purported to reduce toxin exposure or potentially reduce health risks necessitates the development of methods and identification of biomarkers that can be used to assess these products. These assessments occur on multiple levels and stages, from identifying constituents in the tobacco products and smoke, to human exposure and health effects trials, to postmarketing surveillance. A conference of multidisciplinary experts was convened to present and discuss methods and biomarkers to assess these products and to consider the infrastructure necessary to facilitate the evaluation process. Although no currently available set of measures was thought to be sufficient for determining the relative health risk of potential reduced exposure products, this paper provides a blueprint for future research toward this end.

Biomarkers↗
PubMed2026

Bridging genotype, phenotype, and clinical insight: the role of multi-omics in cardiovascular disease.

INTRODUCTION: It is increasingly evident that the multifactorial nature of cardiovascular disease requires the combination of different omics approaches for improving our mechanistic understanding, identifying novel drug targets, and developing accurate diagnostic, predictive, and prognostic biomarker panels. AREAS COVERED: We review the current state and the potential of multi-omics in cardiovascular disease, with a specific focus on plasma-, spatial-, and single-cell approaches. We discuss lipidomics as a genotype‑to‑phenotype bridge, the utility of remote longitudinal monitoring via microsampling/dried blood spots, and emerging clinical‑trial integrations of multi-omics approaches. We outline critical gaps in standardization and how to overcome these, pre‑analytical challenges and constraints that are often neglected, and data‑integration methods spanning from canonical correlation analysis to modern machine learning approaches. EXPERT OPINION: Multi‑omics can shape cardiovascular care by identifying drug targets in diseased tissue and by yielding small, usable biomarker panels.

Humans↗
PubMed2026

Machine learning approaches for cancer prognosis and diagnosis via non-coding RNA: a comprehensive review.

Non-coding RNAs (ncRNAs), once considered genomic dark matter, are now established as key regulators of gene expression with widespread roles in cellular homeostasis and disease. In cancer, ncRNA expression is frequently and systematically dysregulated, and many of these molecules circulate in stable, protected form within biofluids, offering a compelling basis for non-invasive or minimally invasive diagnostic strategies. However, their clinical translation remains substantially hindered to date due to biological complexity, technical noise, and high dimensionality inherent to ncRNA expression datasets. In this context, machine learning (ML) has emerged as a powerful analytical tool to address these challenges, enabling the identification of subtle, reproducible ncRNA signatures predictive of diverse malignancies. This review critically evaluates ML-driven frameworks for cancer diagnosis and prognosis across four ncRNA subclasses, namely miRNAs, lncRNAs, circRNAs, and piRNAs, while also acknowledging the biophysical and thermodynamic models that reinforce ncRNA bioinformatics. Despite substantial methodological progress in ML-based cancer diagnosis and prognosis, key challenges persist, including tumor biological heterogeneity, limited multicenter validation, and the lack of widely adopted standardized protocols for preprocessing, normalization, and reporting workflows. Furthermore, many current ML models lack interpretability in biological or clinical context, constraining their translational utility. By synthesizing recent advances and identifying unresolved barriers, this review charts a roadmap for developing a robust, clinically actionable ncRNA biomarker platform for cancer detection. With global cancer incidence projected to exceed 35 million annual cases by 2050, validated ncRNA-ML-driven frameworks hold potential to revolutionize early-stage detection and personalized therapeutic strategies, thereby reducing the escalating socio-economic burden of cancer worldwide.

Humans↗
PubMed2025

Automating candidate gene prioritization with large language models: from naive scoring to literature-grounded validation.

MOTIVATION: Identifying promising therapeutic targets from thousands of genes in transcriptomic studies remains a major bottleneck in biomedical research. While large language models (LLMs) show potential for gene prioritization, they suffer from hallucination and lack systematic validation against expert knowledge. RESULTS: The framework identified 609 sepsis-relevant genes with >94% filtering efficiency, demonstrating strong enrichment for inflammatory pathways including TNF-α signaling, complement activation, and interferon responses. Literature validation yielded 30 ultra-high confidence therapeutic candidates, including both established sepsis genes (IL10, TREM1, S100A9, NLRP3) and novel targets warranting investigation. Benchmark validation against expert-curated databases achieved 71.2% recall, with systematic correlation between computational confidence and evidence quality. The final candidate set balanced discovery (11 novel genes) with validation (19 known genes), maintaining biological coherence throughout the filtering process. This framework demonstrates that rigorous methodology can transform unreliable LLM outputs into systematically validated biological insights. By combining computational efficiency with literature grounding, the approach provides a practical tool for prioritizing experimental validation efforts. The modular design enables adaptation to other diseases through knowledge base substitution, offering a systematic approach to literature-guided biomarker discovery. AVAILABILITY AND IMPLEMENTATION: We developed a two-stage computational framework that combines LLM-based screening with literature validation for systematic gene prioritization. Starting with 10 824 genes from the BloodGen3 repertoire, we applied multi-criteria evaluation for sepsis relevance, followed by retrieval-augmented generation using 6346 curated sepsis publications. A novel faithfulness evaluation system verified that LLM predictions aligned with retrieved literature evidence. Source code and implementation details are available at https://github.com/taushifkhan/llm-geneprioritization-framework, vector database at https://doi.org/10.5281/zenodo.15802241, and Interactive demonstration at https://llm-geneprioritization.streamlit.app/.

Humans↗
PubMed2002

Development and molecular characterization of HCT-116 cell lines resistant to the tumor promoter and multiple stress-inducer, deoxycholate.

Evidence from live cell bioassays shows that the flat mucosa from patients with colon cancer exhibits resistance to bile salt-induced apoptosis. Three independent cell lines derived from the colonic epithelial cell line HCT-116 were selected for resistance to bile salt-induced apoptosis. These cell lines were developed as tissue culture models of apoptosis resistance. Selection was carried out for resistance to apoptosis induced by sodium deoxycholate (NaDOC), the bile salt found in highest concentrations in human fecal water. Cultures of HCT-116 cells were serially passaged in the presence of increasing concentrations of NaDOC. The resulting apoptosis resistant cells were able to grow at concentrations of NaDOC (0.5 mM) that cause apoptosis in a few hours in unselected HCT-116 cells. These cells were then analyzed for changes in gene expression. Observations from cDNA microarray, 2-D gel electrophoresis/MALDI-mass spectroscopy, and confocal microscopy of immunofluorescently stained preparations indicated underexpression or overexpression of numerous genes at either the protein or mRNA level. Genes that may play a role in apoptosis and early stage carcinogenesis have been identified as upregulated in these cell lines, including Grp78, Bcl-2, NF-kappaB(p50), NF-kappaB(p65), thioredoxin peroxidase (peroxiredoxin) 2, peroxiredoxin 4, maspin, guanylate cyclase activating protein-1, PKCzeta, EGFR, Ras family members, PKA, PI(4,5)K, TRAF2 and BIRC1 (IAP protein). Under-expressed mRNAs included BNIP3, caspase-6, caspase-3 and serine protease 11. NF-kappaB was constitutively activated in all three resistant cell lines, and was responsible, in part, for the observed apoptosis resistance, determined using antisense oligonucleotide strategies. Molecular and cellular analyses of these resistant cell lines has suggested potential mechanisms by which apoptosis resistance may develop in the colonic epithelium in response to high concentrations of hydrophobic bile acids that are associated with a Western-style diet. These analyses provide the rationale for the development of hypothesis-driven intermediate biomarkers to assess colon cancer risk on an individual basis.

Apoptosis↗
PubMed2001

Cyclin D1 protein overexpression and gene amplification in benign breast tissue and breast cancer risk.

Cyclin D1 amplification and/or protein overexpression have been observed not only in breast cancer but also in the putative early stages of breast neoplasia. In a case-control study nested within a cohort of 4888 women, we investigated whether the occurrence of cyclin D1 gene amplification and/or protein overexpression in benign breast tissue might identify women at increased risk of subsequent breast cancer development. Cases were 92 women with a histological diagnosis of benign breast disease who subsequently developed breast cancer. Five controls (women with benign breast disease who had not developed breast cancer by the date of diagnosis of the corresponding case) were selected randomly for each case from those non-cases available within strata defined by screening centre, National Breast Screening Study (NBSS) study arm, year of birth and age at diagnosis of benign breast disease. Paraffin blocks of benign tissue were suitable for immunostaining for 71 cases and 293 controls. Sufficient DNA for analysis was obtained from a total of 356 subjects (69 cases, 287 controls). The benign breast tissues and breast cancers were immunostained for cyclin D1 and also analysed for the presence of cyclin D1 gene amplification by differential polymerase chain reaction (PCR). Fifteen cases and 60 controls showed evidence of cyclin D1 immunostaining, and 12 cases and 29 controls showed cyclin DL gene amplification. There was essentially no association between cyclin D1 protein overexpression in benign breast tissue and risk of subsequent breast cancer (adjusted odds ratio (OR) 1.06; 95% confidence interval (CI) 0.56-2.02). After adjustment for potential confounding, there was a statistically non-significant 40% increase in risk of breast cancer in association with cyclin D1 gene amplification (adjusted OR 1.41; 95% CI 0.62-3.22). As multiple genetic changes are required to develop breast cancer, it may not be until the cascade of molecular alterations leading to breast cancer development is understood that identification of biomarkers of breast cancer risk will be possible.

Adult↗
PubMed2005

Correlation of HR-MAS spectroscopy derived metabolite concentrations with collagen and proteoglycan levels and Thompson grade in the degenerative disc.

STUDY DESIGN: A quantitative high-resolution magic angle spinning (HR-MAS) NMR study of human lumbar discs was conducted to determine biomarkers of disc degeneration. OBJECTIVES: To correlate HR-MAS quantification of compounds relevant to human lumbar disc degeneration to conventional methods of disc grading such as Thompson grading and biochemical analysis. SUMMARY OF BACKGROUND DATA: It has been shown that there is poor correlation between MRI and CT morphologic findings, spinal biomechanics, and patient symptoms in degenerative disc disease and low back pain. There is a need for an objective, quantitative measurement of biochemical status, morphology, and function. METHODS: A total of 17 cadaveric human lumbar intervertebral discs were harvested from patients ranging from 20 to 85 years of age. Quantitative HR-MAS data were acquired, and proteoglycan and collagen biochemical analyses were conducted on 3-mm biopsy punches taken from the anulus fibrosus and nucleus pulposus of each sample. HR-MAS data were fitted and analyzed for hydroxyproline (3.42 ppm), glycine (3.56 ppm), and the N-acetyl peak (2.04 ppm) associated with proteoglycans in comparison with an internal standard. These concentrations were then compared directly to biochemical analyses and Thompson grade. RESULTS: HR-MAS data correlated well with Thompson grade (P < 0.001). An increase was seen in the levels of unbound hydroxyproline and glycine in annular tissue, which is directly associated to collagen breakdown. This trend also correlates with the changes of total collagen measured by a collagen biochemical assay. HR-MAS also detected a decrease in concentration of nucleus pulposus proteoglycans with degeneration. This proteoglycan decrease was verified by a standard proteoglycan biochemical assay. CONCLUSIONS: Changes in disc chemical composition can be accurately quantified using quantitative HR-MAS NMR spectroscopy ex vivo. This noninvasive method of qualitatively and quantitatively assessing disc degeneration supports the utility of these biomarkers and underlines the need for developing in vivo magnetic resonance spectroscopic imaging (MRSI) for characterizing intervertebral disc degeneration.

Adult↗
PubMed1993

Developmental differences in neural damage following trimethyl-tin as demonstrated with GFAP immunohistochemistry.

Long-Evans rat pups received intraperitoneal (i.p.) injections of trimethyl-tin (TMT) 6 mg/kg hydroxide or saline on postnatal day (PND) 10 or PND 18 and were sacrificed for immunohistochemical staining for glial fibrillary acidic protein (GFAP) on PND 12, 18, 20, or 25. After dosing with TMT on PND 10 there was a transient increase in GFAP immunoreactivity (IR) in the amygdala, piriform, and entorhinal cortex 2 days post-dosing (PND 12) and a persistent increase in GFAP IR in the hippocampus and cingulate cortex up to two weeks post-dosing. Following dosing with TMT on PND 18 there was a delayed (PND 25) increase in GFAP IR in the amygdala, hippocampus, cingulate, piriform, and entorhinal cortex. In addition, increases in GFAP IR were observed in the neocortex 7 days post-dosing, which was not observed following earlier postnatal dosing. The regions in which gliosis and loss of Nissl-staining were consistent for the different time points of TMT treatment were the amygdala, hippocampus, cingulate, piriform, and entorhinal cortex. The present findings indicate the GFAP immunohistochemistry can be used to reveal regional effects of developmental neurotoxicant exposure during early stages of development.

Animals↗
PubMed1995

Is an elevated circulating maternal homocysteine concentration a risk factor for neural tube defects?

The mechanism by which folic acid supplementation reduces neural tube defect (NTD) incidence is unknown. Recent evidence suggests that mothers with NTD neonates have higher circulating homocysteine concentrations compared with controls. This presumably indicates impaired homocysteine remethylation, resulting in a possible methionine shortage at a crucial stage of fetal development.

Biomarkers↗
PubMed2005

Biomarkers in paediatric research and practice.

Children's health is, to a large extent, a function of their environment. Infectious agents remain the leading cause of death and disability in the world. In contrast, many of the new morbidities--asthma, intellectual impairments, behavioural problems, and cancer--are linked with industrial pollutants or other environmental influences. Our understanding of the risk factors for many diseases is incomplete, but it is widely recognised that disability and death result largely from interactions of environmental factors, broadly defined, and host susceptibility.

Biomarkers↗
PubMed2006

Noninvasive magnetic resonance spectroscopic pharmacodynamic markers of the choline kinase inhibitor MN58b in human carcinoma models.

MN58b is a novel anticancer drug that inhibits choline kinase, resulting in inhibition of phosphocholine synthesis. The aim of this work was to develop a noninvasive and robust pharmacodynamic biomarker for target inhibition and, potentially, tumor response following MN58b treatment. Human HT29 (colon) and MDA-MB-231 (breast) carcinoma cells were examined by proton (1H) and phosphorus (31P) magnetic resonance spectroscopy (MRS) before and after treatment with MN58b both in culture and in xenografts. An in vitro time course study of MN58b treatment was also carried out in MDA-MB-231 cells. In addition, enzymatic assays of choline kinase activity in cells were done. A decrease in phosphocholine and total choline levels (P < 0.05) was observed in vitro in both cell lines after MN58b treatment, whereas the inactive analogue ACG20b had no effect. In MDA-MB-231 cells, phosphocholine fell significantly as early as 4 hours following MN58b treatment, whereas a drop in cell number was observed at 48 hours. Significant correlation was also found between phosphocholine levels (measured by MRS) and choline kinase activities (r2 = 0.95, P = 0.0008) following MN58b treatment. Phosphomonoesters also decreased significantly (P < 0.05) in both HT29 and MDA-MB-231 xenografts with no significant changes in controls. 31P-MRS and 1H-MRS of tumor extracts showed a significant decrease in phosphocholine (P < or = 0.05). Inhibition of choline kinase by MN58b resulted in altered phospholipid metabolism both in cultured tumor cells and in vivo. Phosphocholine levels were found to correlate with choline kinase activities. The decrease in phosphocholine, total choline, and phosphomonoesters may have potential as noninvasive pharmacodynamic biomarkers for determining tumor response following treatment with choline kinase inhibitors.

Animals↗
PubMed2006

Does "clock" matter in prostate cancer?

The ancient adaptation of a 24-hour circadian clock has profound effect on our daily biochemical, physiologic, and behavioral processes, including the monitoring of sex hormone levels. Although the disruption of the circadian cycle has been implicated in the etiology of hormone-related female breast cancer, few studies have been undertaken to determine if a link exists in the development of the most common cancer type among men whose etiology remains largely unknown: hormone-related prostate cancer. Here, we hypothesize that both altered-lighted environments and genetic variations in genes responsible for maintaining circadian rhythms may result in deregulation of clock-associated biological processes, such as androgen expression, and consequently influence an individual's risk of prostate cancer. There is also a potential for the interaction of genetic variants and exposures, such as evening shift work. Confirmation of this hypothesis will add to our understanding of the role of the circadian clock in prostate tumorigenesis and further facilitate the development of novel risk and prognostic biomarkers for prostate cancer.

Androgens↗
PubMed2004

Molecularly targeted approaches to the chemoprevention of lung cancer.

Large, randomized trials have been conducted in the primary prevention of lung cancer using micronutrients or derivative agents for which epidemiological data suggested a potential role in lung cancer prevention. The disappointing primary prevention trials of beta-carotene, alpha-tocopherol, and retinyl palmitate have led to the development of a more compact, biomarker-driven series of translational trials of lung cancer prevention that target reversal of premalignancy as the primary end point. Serial trials of 13-cis-retinoic acid (isotretinoin) and other retinoids have failed to show a difference in reversal of premalignancy in active smokers or in second primary tumor prevention. However, a trial of 9-cis-retinoic acid, a pan retinoid/rexinoid agonist, showed up-regulation of retinoic acid receptor beta (RAR-beta), a potentially important intermediate marker of response in lung cancer premalignancy. Other planned or ongoing trials currently target important molecular markers of lung carcinogenesis and progression including cyclooxygenase-2, the ras-signaling pathway through farnesyl transferase inhibitors, and the tyrosine kinase/epidermal growth factor receptor pathway (gefitinib, erlotinib). Early results of bioadjuvant trials in head and neck cancer suggest that combination chemoprevention will ultimately be an important option.

Biomarkers, Tumor↗
PubMed2000

Bone loss. Epidemiology of bone loss.

Bone loss occurs when the cellular events of bone formation are quantitatively larger than bone formation. This manuscript discusses the measurement of bone loss, occurrence in the population, risk factors and consequences of bone loss. Recent developments in bone mass measurement and biomarkers have improved our ability to assess bone loss. This process is a normal concomitant of ageing. There are a number of other risk factors, including sex hormone deficiency, physical inactivity, calcium/vitamin D deficiency, inflammatory arthritis, corticosteroids, smoking and alcohol. The major consequence of bone loss in our ageing society is fracture.

Humans↗
PubMed2005

Gene expression profiling of sporadic Parkinson's disease substantia nigra pars compacta reveals impairment of ubiquitin-proteasome subunits, SKP1A, aldehyde dehydrogenase, and chaperone HSC-70.

Sporadic Parkinson's disease (PD) constitutes 99% of the disorder, while the remaining 1% of the cases is of familial (genetic) origin. The mutations reported to be associated with familial PD indicate impairment in protein processing and misfolding, as is handled by the ubiquitin-proteasome system (UPS), and in mitochondrial function. For these reasons, we have recently applied, for the first time, Affymetrix oligonucleotide microarray technique in the substantia nigra pars compacta of sporadic parkinsonian patients for studying global gene expression analysis and comparison to the alterations identified in inherited PD. This study identified decreased expression of 68 genes and elevation of 69 genes. Classification into functional groups revealed that the downregulated genes are related to signal transduction, protein degradation (e.g., ubiquitin-proteasome subunits), dopaminergic transmission/metabolism, iron transport, protein modification/phosphorylation, and energy pathways/glycolysis functional classes. A major finding is the decreased expressions of 5 subunits of the UPS, SKP1A, a member of the SCF (E3) ubiquitin ligase complex, and chaperone HSC-70, which can lead to a wide impairment in the function of an entire repertoire of proteins. The upregulated genes are clustered in cell adhesion/cytoskeleton, extracellular matrix components, cell cycle, protein modification/phosphorylation, protein metabolism and transcription, and inflammation/hypoxia (e.g., key iron and oxygen sensor EGLN1) classes. The study shows, for the first time, a convergence in the pathogenic processes that are observed in hereditary (familial) and sporadic PD, where abnormal iron metabolism, oxidative stress, and aggregation of proteins occur. An additional breakthrough in this research is the identification of a number of previously unsuspected crucial gene players that are also involved in the process of neurodegeneration, which can serve as specific biomarkers for PD and novel drug development.

Aldehyde Dehydrogenase↗
PubMed2003

Cervical cancer screening: from the Papanicolaou smear to the vaccine era.

In the next 20 years, cervical cancer screening will have evolved through four phases. The first was traditional screening, which has been associated with a two-thirds reduction in cancer incidence and death rates in the last 50 years and currently is ending. We are entering a second phase, human papillomavirus (HPV) testing, for managing cytologic abnormalities and possibly for primary screening. A third phase, new in development, proposes the use of host biomarkers (or combinations thereof) as either surrogates of HPV infection or, potentially, indicators to assess cancer risk and concentrate available resources on a subset of women. The fourth and, likely, final phase will be screening in an era of vaccines. If HPV vaccines are successful, the pool of at-risk individuals and the prevalence of papillomaviruses that place them at risk will gradually shrink. In this climate, screening strategies that target HPVs alone (as opposed to cytologic testing) may become more economical. If so, previous strategies may become obsolete as the balance of cervical cancer prevention shifts from traditional screening to primary prevention coupled with HPV testing.

Biomarkers, Tumor↗