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PubMed2026

Omics in hereditary optic neuropathies: A systematic review of clinical studies with an integrated point of view.

Hereditary optic neuropathies are characterized by bilateral visual loss due to the degeneration of retinal ganglion cells, resulting in optic nerve degeneration and atrophy. Although the genetic origin of the main isolated and syndromic hereditary optic neuropathies has been characterized, the clinical phenotypes exhibit significant and poorly understood variability in both penetrance and expressivity. Additionally, the genetic and environmental factors that influence the onset of these optic neuropathies remain poorly understood, with limited biomarkers to predict disease progression or as readouts for therapeutic trials. Data-driven omics strategies allow deep phenotyping to improve our understanding of pathophysiological mechanisms and to search for new biomarkers and therapeutic targets. We explore whether the omics strategies applied to patients with hereditary optic neuropathies have provided such new insights. MEDLINE, Web of Science and EMBASE databases were screened for studies with terms relating to hereditary optic neuropathies, transcriptomics, epigenomics, proteomics, metabolomics and lipidomics in clinical studies exploring patients' samples. Out of 1244 references identified, 22 articles were included after double-masked data curation. These articles focused only on the 3 main forms of hereditary optic neuropathies, namely, OPA1-related dominant optic atrophy (n = 4), Leber hereditary optic neuropathy (n = 13), and Wolfram syndrome (n = 5). While the methodological designs and results of these studies were highly heterogeneous, they revealed molecular alterations that we have attempted to discuss at the integrated multi-omics level. This data integration highlighted several common pathophysiological mechanisms such as energetic impairment, endoplasmic reticulum stress, proteotoxic and oxidative stresses, lipid remodeling and altered amino acid and purine metabolisms, while suggesting potential new biomarkers and therapeutic targets. These findings underscore the potential of integrated multi-omics approaches to deepen our understanding of the phenotypic complexity of hereditary optic neuropathies and to support the development of innovative diagnostic and therapeutic strategies.

Humans↗
PubMed2004

Integrated methodology for forensic oil spill identification.

A new integrated methodology for forensic oil spill identification is presented. It consists of GC-MS analysis, chromatographic data processing, variable-outlier detection, multivariate data analysis, estimation of uncertainties, and statistical evaluation. The methodology was tested on four groups of diagnostic ratios composed of petroleum biomarkers and ratios within homologous PAH categories. Principal component analysis (PCA) was employed and enabled the simultaneous analysis of many diagnostic ratios. Weathering was taken into account by considering the sampling uncertainties estimated from replicate spill samples. Statistical evaluation ensured an objective matching of oil spill samples with suspected source oils as well as classification into positive match, probable match, and nonmatch. The data analysis is further refined if two or more source oils are classified as probable match by using weighted least squares fitting of the principal components, local PCA models, and additional information relevant to the spill case. The methodology correctly identified the source of two spill samples (i.e., crude oils from Oseberg East and Oseberg Field Centre) and distinguished them from closely related source oils.

Denmark↗
PubMed2026

Machine learning-guided risk stratification in elderly AML based on genomic, immunophenotypic and therapeutic profiles.

BACKGROUND: Elderly patients with acute myeloid leukemia (AML) exhibit considerable biological and clinical heterogeneity, hindering precise prognosis. Existing prognostic systems inadequately capture the complexity of elderly AML due to their reliance on data from younger cohorts and omission of key factors like immunophenotypic markers and therapeutic profiles. This study aimed to develop and internally validate a machine learning-based prognostic model specifically tailored to elderly AML patients. METHODS: A total of 156 patients were analyzed using a two-stage modeling strategy. Clinical and genomic variables were modeled first, followed by independent analysis of immunophenotypic features. Feature selection was performed using multilayer perceptron (MLP) and random forest (RF), while multivariate Cox regression was used for final model construction. Internal validation was conducted using 1000 bootstrap iterations to assess model stability and performance. RESULTS: The model demonstrated strong predictive performance, with a concordance index (C-index) of 0.702. Time-dependent area under the curve (AUC) and calibration plots confirmed accurate prediction of 1-, 3-, and 5-year overall survival. Decision curve analysis indicated favorable net benefit across a range of threshold probabilities. Key independent prognostic factors identified included TP53 mutations, high CD13 expression, and IDH2 mutations. CONCLUSION: This model provides a robust and interpretable tool for individualized risk stratification in elderly AML. By integrating genomic, immunophenotypic, and therapeutic variables, it may help optimize treatment decisions and improve outcomes for this vulnerable population. Future efforts should focus on external validation and integration of dynamic biomarkers.

Humans↗
PubMed1997

Decrease in birth weight in relation to maternal bone-lead burden.

OBJECTIVES: Birth weight predicts infant survival, growth, and development. Previous research suggests that low levels of fetal lead exposure, as estimated by umbilical cord blood-lead levels at birth, may have an adverse effect on birth weight. This report examines the relationship of lead levels in cord blood and maternal bone to birth weight. METHODS: Umbilical cord and maternal venous blood samples and anthropometric and sociodemographic data were obtained at delivery and 1-month postpartum. Blood-lead levels were analyzed by atomic absorption spectrophotometry. Maternal tibia and patella lead levels were determined at 1-month postpartum with use of a spot-source 109Cd K-X-ray fluorescence instrument. The relationship between birth weight and lead burden was evaluated by multiple regression with control of known determinants of size at birth. RESULTS: Data on all variables of interest were obtained for 272 mother-infant pairs. After adjustment for other determinants of birth weight, tibia lead was the only lead biomarker clearly related to birth weight. The decline in birth weight associated to increments in tibia lead was nonlinear and accelerated at the highest tibia lead quartile. In the upper quartile, neonates were on average, 156 grams lighter than those in the lowest quartile. Other significant birth weight predictors included maternal nutritional status, parity, education, gestational age, and smoking during pregnancy. CONCLUSIONS: Our results indicate that bone-lead burden is inversely related to birth weight. Taken together with other research indicating that lead can mobilize from bone into plasma without detectable changes in whole blood lead, these findings suggest that bone lead might be a better biomarker than blood lead. Because lead remains in bone for years to decades, mobilization of bone lead during pregnancy may pose a significant fetal exposure with health consequences, long after maternal external lead exposure has declined.

Birth Weight↗
PubMed2006

[Myeloperoxidase in the plasma of patients with acute coronary syndrome].

OBJECTIVE: To determine the diagnostic value and efficacy for risk stratification of myeloperoxidase (MPO) levels in patients with acute coronary syndrome (ACS). METHODS: One hundred and sixty-two patients were enrolled in this study. All patients underwent coronary angiography. They were divided into 3 groups: ACS group (n=54), SAP group (n=54) and control group (n=54). Blood samples were taken from the artery before angiography in all patients and the concentrations of MPO, hsCRP and cTnI were measured. Each subject was asked details of history of hypertension, hyperlipidemia, diabetes and smoking habits. The efficacy of therapy, the cardiovascular events (myocardial infarction, the need for revascularization, or death) were recorded after 6 months of follow-up. RESULTS: The plasma MPO level in ACS group (30.98 ng/mL) was significantly higher than those in the SAP group (14.67 ng/mL) and the control group(14.23 ng/mL)(P<0.01), and the plasma MPO levels in patients of the SAP group and the control group were not significantly different (P=0.74). There was no obvious correlation between the levels of plasma MPO and the serum levels of cTnI, hsCRP,the prevalence of the 4 major risk factors for CHD. Multivariate logistic regression analysis showed that plasma MPO level, free plasma glucose and sex were the significant variables. The risk for subsequent cardiovascular events was higher in the patients with elevated level of MPO. CONCLUSION: Plasma MPO may be a new risk biomarker for ACS and may predict the incidence of subsequent cardiovascular events.

Acute Coronary Syndrome↗
PubMed2005

A critical review of biomarkers used for monitoring human exposure to lead: advantages, limitations, and future needs.

Lead concentration in whole blood (BPb) is the primary biomarker used to monitor exposure to this metallic element. The U.S. Centers for Disease Control and Prevention and the World Health Organization define a BPb of 10 microg/dL (0.48 micromol/L) as the threshold of concern in young children. However, recent studies have reported the possibility of adverse health effects, including intellectual impairment in young children, at BPb levels < 10 microg/dL, suggesting that there is no safe level of exposure. It appears impossible to differentiate between low-level chronic Pb exposure and a high-level short Pb exposure based on a single BPb measurement; therefore, serial BPb measurements offer a better estimation of possible health outcomes. The difficulty in assessing the exact nature of Pb exposure is dependent not so much on problems with current analytical methodologies, but rather on the complex toxicokinetics of Pb within various body compartments (i.e., cycling of Pb between bone, blood, and soft tissues). If we are to differentiate more effectively between Pb stored in the body for years and Pb from recent exposure, information on other biomarkers of exposure may be needed. None of the current biomarkers of internal Pb dose have yet been accepted by the scientific community as a reliable substitute for a BPb measurement. This review focuses on the limitations of biomarkers of Pb exposure and the need to improve the accuracy of their measurement. We present here only the traditional analytical protocols in current use, and we attempt to assess the influence of confounding variables on BPb levels. Finally, we discuss the interpretation of BPb data with respect to both external and endogenous Pb exposure, past or recent exposure, as well as the significance of Pb determinations in human specimens including hair, nails, saliva, bone, blood (plasma, whole blood), urine, feces, and exfoliated teeth.

Biomarkers↗
PubMed2006

Blood arsenic as a biomarker of arsenic exposure: results from a prospective study.

Exposure to arsenic (As)-contaminated drinking water affects millions of people worldwide. Arsenic exposure is associated with skin lesions, skin, lung, kidney and liver cancers, neurologic and cardiovascular effects. Past studies involving biomarkers of As exposure have typically examined urinary As (UAs) (adjusted for urinary creatinine), hair or toenail As, but not blood As (BAs) since blood concentrations are exceedingly low and are not detectable by conventional atomic absorption spectrophotometric techniques. In a case-cohort analysis of 303 newly diagnosed cases of skin lesions, and 849 subcohort members randomly selected from 8092 participants in the health effects of as longitudinal study (HEALS) in Araihazar, Bangladesh, we measured blood, urine and water As concentrations, and examined their associations with each other, and with the risk for skin lesions. BAs concentrations were highly correlated with creatinine-adjusted UAs concentrations (r=0.85) and with water As (WAs) (r=0.75). We observed consistent dose-response relationships between the risk of skin lesions and all the measures of As exposure. Rate ratios (RRs) for skin lesions by quintile of As exposure, adjusted for age and gender, revealed that the two highest quintiles were significantly related to an increased risk of skin lesions for each measure of exposure: BAs, UAs, WAs and a time-weighted water As variable. This prospective study confirms the increased risk of skin lesions in relation to As concentrations in blood, urine and water and also establishes that BAs is a useful biomarker of As exposure in this study population.

Adult↗
PubMed2005

Pathways of myocyte death: implications for development of clinical laboratory biomarkers.

The recognition that cardiac myocytes die by multiple mechanisms and thus substantially affect ventricular remodeling in diseased human hearts supports the concept of ongoing myocyte death in the progression of heart failure and constitutes the basis of this review. In addition, based on the pathophysiology of myocardial cell deaths, the present study emphasizes that currently methodologies, although with some inherent limitations, are available to recognize and measure quantitatively the contribution of myocyte cell death to the progression of the pathologic state of the heart. Our own studies show that application of such methodologies including modern microscopy techniques and the use of different molecular and immunohistochemical markers may generate the consensus that myocyte cell death is a quantifiable parameter in the normal and pathological human heart. The present study also demonstrates that myocyte cell death, apoptotic, oncotic or autophagic in nature, has to be regarded as an additional critical variable of the multifactorial events implicated in the alterations of cardiac anatomy and myocardial structure of the diseased human heart.

Biomarkers↗
PubMed2003

Assessment of seasonal variability of cytochemical responses to contaminant exposure in the blue mussel Mytilus edulis (complex).

A selected suite of cytochemical parameters in Mytilus edulis are altered in response to field and laboratory exposure to chemical contaminants. These biomarkers include lysosomal stability, nicotinamide adenine dinucleotide phosphate (NADPH)-ferrihemoprotein reductase activity, liposfuscin deposition, and accumulation of lysosomal and cytoplasmic unsaturated neutral lipid. Normal variations in physiological processes (influenced by exogenous seasonal changes in temperature, salinity, food availability, etc.) may alter the sensitivity of these biomarkers to contaminant exposure. To address this issue, M. edulis (complex) were sampled monthly from a reference nonurban site (Coupeville, Penn Cove) and a polluted urban site (Seacrest, Elliott Bay) in Puget Sound, WA, for a period of 15 months. Physiological measurements including total length, total weight, somatic and mantle weights (an indication of gonadal development and reproductive status), condition index, and the presence or absence of hemic neoplasia (HN, or leukemia) were recorded. Significant differences in lysosomal stability, lysosomal and cytoplasmic unsaturated neutral lipids, lipofuscin deposition, and NADPH-ferrihemoprotein reductase activity in cells of the digestive gland or digestive tubules were generally found in mussels taken throughout the year from Seacrest compared to mussels sampled from Coupeville, consistent with exposure to chemical contaminants. No seasonally influenced suppression of the entire suite of parameters as measures of contaminant exposure was evident. Therefore these biomarkers can be used to evaluate contaminant exposure in mussels throughout the entire year.

Adaptation, Physiological↗
PubMed2002

Brainstem neural conduction biomarkers in lead-exposed children of Andean lead-glaze workers.

Pediatric lead (Pb) intoxication remains a major medical challenge in some developing countries where Pb is used in glazing industries. Pb exposure is reported to induce neurophysiological and neurocognitive impairment in children. However, the threshold and level of Pb intoxication necessary to induce neuropathology have not been established. Brainstem auditory evoked responses (BAERs) have been used widely as a sensitive biomarker for Pb-induced neurotoxicity. In this field study, BAER neural conduction time was used as a biomarker for central nervous system impairment in Andean children living in areas of high Pb contamination from Pb-glazing cottage industries. The mean Pb level in blood (PbB) for 112 Pb-exposed children was 49.25 microg/dL (SD, 270 microg/dL range, 4.4-119.1 microg/dL). Although BAERs in some children showed prolongations in neural conduction times, regression analyses revealed no significant correlation between PbB levels and BAER interpeak conduction times for 112 replicate recordings (I-III, r = 0.008, P = 0.93; II-V, r = 0.13, P = 0.16; I-V, r = 0.09, P = 0.35; and I-VI, r = 0.14, P = 0.27). A subgroup of 69 children in the study area with PbB levels in the United States Centers for Disease Control and Prevention (CDC) medical intervention-emergency classifications (CDC IV and V; mean, 67.0 microg/dL, SD, 15.8 microg/dL; range, 45.1-119.1 microg/dL) showed no significant correlation between PbB and BAER interpeak interval and no significant differences in BAER than a normal subgroup (t test, P > 0.05). The results demonstrate some evidence of abnormal possibly Pb-induced neural conduction delays in some individual children but a remarkable overall neurobiological functioning in severe, chronic pediatric Pb intoxication without measurable impairment of brainstem auditory nuclei and tracts, as evidenced by neurophysiological conduction times. The findings also demonstrate the variability in the threshold level and duration of Pb exposure necessary to induce brainstem neuropathology.

Adolescent↗
PubMed2006

Screening of toxicity biomarkers for methionine excess in rats.

Although many animal studies have reported that dietary excess of methionine causes toxic changes including growth suppression and hemolytic anemia, the biochemical mechanism and biomarkers for methionine toxicity have not been well elucidated. The present study aimed to identify toxicity biomarkers from plasma metabolites in rats fed excessive methionine. Young growing rats were fed graded doses of additional methionine for 2 wk. Cluster analysis of multivariate correlations was performed on the physiological and toxicity variables with plasma metabolites detected by GC/MS, amino acid analyzer, and thiol-specific analysis. Indicative variables for hemolysis such as splenic nonheme iron content and plasma bilirubin were grouped in the same cluster as many methionine metabolites. Homocysteine and some undefined metabolites in this cluster were found to be strong discriminators between nontoxic and toxic levels of methionine intake. Product-to-precursor ratios of each methionine metabolite demonstrated that excessive methionine intake caused a marked decrease only in the ratio of cystathionine to homocysteine, suggesting that metabolism from homocysteine to cystathionine would be rate limiting in the disposal of excessive methionine. Collectively from these results, homocysteine appeared to be the most plausible biomarker to assess methionine excess as a surrogate marker both for toxicity and for setting a metabolic upper limit.

Amino Acids↗
PubMed2005

Early prediction of acute renal injury using urinary proteomics.

AIMS: The lack of early biomarkers for acute renal failure (ARF) has crippled our ability to launch potentially effective therapeutic measures. We tested the hypothesis that urinary proteomics could identify novel early biomarker patterns for ischemic renal injury. METHODS: Sixty patients undergoing cardiopulmonary bypass (CPB) were enrolled. Urine samples obtained at 2 and 6 h post CPB were analyzed by Surface-Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (SELDI-TOF-MS). The primary outcome variable was ARF, defined as a 50% or greater increase in serum creatinine. RESULTS: Fifteen patients (25%) developed ARF 2-3 days after CPB. SELDI-TOF-MS analysis of urine from the ARF group at baseline versus at 2 and 6 h post-CPB consistently showed a marked and statistically significant enhancement of protein biomarkers with m/z of 6.4, 28.5, 43 and 66 kDa. The same biomarkers were enhanced when comparing control versus ARF groups at 2 and 6 h post-CPB. The sensitivity and specificity of the 28.5-, 43- and 66-kDa biomarkers for the prediction of ARF at 2 h following CPB was 100%. The receiver operating characteristic curves revealed an area under the curve of 0.98. CONCLUSION: SELDI-TOF-MS is a novel, non-invasive, sensitive, highly predictive, reproducible, rapid method for the prediction of acute renal injury following CPB.

Acute Kidney Injury↗
PubMed2005

Functional expression of single-chain variable fragment antibody against c-Met in the cytoplasm of Escherichia coli.

c-Met, a high affinity receptor for hepatocyte growth factor/scatter factor, shown to be overexpressed in a variety of malignant cells, is a potential biomarker as well as a therapeutic target. Thus, single-chain antibody fragment (scFv) specific for c-Met is expected to be efficiently employed in the clinical treatment or imaging of many cancer cells. Here, we constructed the expression system for anti-c-Met scFv fused with T7 tag at its N-terminus using pET vector and investigated the expression conditions to achieve a functional and soluble expression of the scFv in the cytoplasm of recombinant Escherichia coli. The redox potential of E. coli cytoplasm was the most critical factor for the functional expression of anti-c-Met scFv. The employment of a host with oxidizing cytoplasm, E. coli trxB/gor double mutant, improved the productivity of functional anti-c-Met scFv by approximately 10-fold compared to the production of anti-c-Met scFv in the reducing cytoplasm of wild type E. coli. Productivity of functional anti-c-Met scFv could be further enhanced by co-expressing molecular chaperones such as GroELS, trigger factor, and DsbC with the scFv. Coexpression of DsbC increased the yield of functional anti-c-Met scFv about 2.5-fold in the cytoplasm of E. coli trxB/gor mutant compared to the production of scFv without DsbC coexpression. Lowering the IPTG concentration from 1 to 0.05 mM led to the slight enhancement, approximately 1.6-fold, of productivity of functional scFv. Although the use of low temperature for anti-c-Met scFv expression increased the ratio of soluble scFv fraction to insoluble fraction, productivity of soluble scFv decreased owing to the significant reduction of expression rate. The addition of 0.5 M sucrose in the medium inhibited the formation of intracellular insoluble anti-c-Met scFv. To purify the anti-c-Met scFv simply, we fused hexahistidine at the C-terminus of scFv and purified the scFv showing 98% of purity through the interaction between Ni2+ and histidine.

Antibodies↗
PubMed2002

Isolation of small-subunit rRNA for stable isotopic characterization.

Small-subunit ribosomal RNA (SSU rRNA) has several characteristics making it a good candidate biomarker compound: it is found in bacteria, archaea and eukaryotes; it is quickly degraded extracellularly, hence SSU rRNA extracted from a sample probably derives from the currently active population; it includes both conserved and variable regions, allowing the design of capture probes at various levels of phylogenetic discrimination; and rRNA sequences from uncultured species can be classified by comparison with the large and growing public database. Here we present a method for isolation of specific classes of rRNAs from mixtures of total RNA, employing biotin-labelled oligonucleotide probes and streptavidin-coated paramagnetic beads. We also show that the stable carbon isotope composition of Escherichia coli total RNA and SSU rRNA reflects that of the growth substrate for cells grown on LB, M9 glucose and M9 acetate media. SSU rRNA is therefore a promising biomarker for following the flow of carbon, and potentially nitrogen, in natural microbial populations. Some possible applications are discussed.

Carbon Isotopes↗
PubMed1996

A clinicopathological and immunohistochemical study of the calcifying epithelial odontogenic tumour (Pindborg tumour) in Malaysians.

We reviewed the clinicopathological characteristics of 13 cases of calcifying epithelial odontogenic tumour (CEOT) (Pindborg tumour) diagnosed in the Division on Stomatology, Institute for Medical Research, Kuala Lumpur, over a 29-year period. There were eight female and five male patients. These consisted of eight (61.5 per cent) Malays, three (23.1 per cent) Chinese, one (7.7 per cent) Indian and one (7.7 per cent) Melanau. Their ages at presentation ranged from 19-61 years (mean age, 31.8 years). There were 12 central and one peripheral CEOT. Of these, 76.9 per cent of cases were located in the maxilla, the remaining in the mandible. The commonest clinical diagnosis was a dentigerous cyst (66.7 per cent). Enucleation was the main mode of treatment. Histologically, sheets and strands of polyhedral epithelial cells containing eosinophilic, homogeneous globules with Liesegang rings were observed. One case also showed extensive calcification and clear cell differentiation. Immunohistochemistry revealed a variable keratin staining of the CEOT epithelium, confirming its heterogeneity.

Adult↗
PubMed2001

Plasma N-terminal pro-atrial natriuretic peptide predicts death after premature myocardial infarction, but not as well as radionuclide ejection fraction. A ten-year follow-up study.

OBJECTIVE: To assess N-terminal pro-atrial peptide (N-ANP) as a predictor of total and cardiac death in patients with previous premature myocardial infarction (MI). DESIGN: In this prospective cohort study, we measured plasma N-ANP by ELIZA assays and ejection fraction (EF) by radionuclide ventriculography in a cohort of 247 patients (193 men and 54 women) who had had MI at a relatively young age (males: first MI at age < or =55; females <60). RESULTS: After 10 years 44 patients had died, 36 from cardiac causes. After using a stepwise procedure to adjust for other prognostic factors (i.e. plasma total homocysteine (tHcy), C-reactive protein and age), the relative risk (RR) was 2.00 (95% confidence interval (CI) 1.05-3.80) (p = 0.03) for death of all causes and 2.32 (95% CI 1.19-4.55) (p=0.01) for cardiac death when the top quartile was compared to the three lower quartiles of N-ANP. When radionuclide EF entered the Cox model, N-ANP became insignificant as a predictor of mortality. CONCLUSION: N-ANP was a significant predictor of total death and cardiac death in young survivors of MI, but radionuclide EF was a more independent prognostic variable.

Adult↗
PubMed2001

IgH, TCR-gamma, and TCR-beta gene rearrangement in 80 B- and T-cell non-Hodgkin's lymphomas: study of the association between proliferation and the so-called "aberrant" patterns.

The current study analyzes the rearrangement pattern of immunoglobulin H (IgH), T-cell receptor (TCR)-gamma, and TCR-beta genes in a group of 80 non-Hodgkin's lymphomas (NHL) of different histologic subtypes (43 B-cell and 37 T-cell types). The sensitivity and specificity provided by polymerase chain reaction amplification of these loci are evaluated. The association between the proliferation index and the presence of the so-called "aberrant" or "dual" rearrangements is also considered. Ninety-one percent of B-cell NHL showed IgH gene monoclonality, and 21% also exhibited a monoclonal pattern in one of the TCR genes. Among T-cell NHL, the sensitivity of the study was 65% for the TCR-gamma gene and 46% for the TCR-beta gene. The total sensitivity was 76%, amplifying both loci. IgH gene aberrant rearrangements were observed in 16% of T-cell neoplasms. A substantial percentage of dual rearrangements were detected in precursor and mature B- and T-cell NHL. B-cell NHL showed a tendency toward higher values of proliferation when aberrant rearrangements were present; however, this trend was not significant. Furthermore, in the case of T-cell NHL there was a significant negative association between these two variables.

Antigens, Nuclear↗