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PubMed2002

Interest of genotyping and phenotyping of drug-metabolizing enzymes for the interpretation of biological monitoring of exposure to styrene.

In the field of occupational and/or environmental toxicology, the measurement of specific metabolites in urine may serve to assess exposure to the parent compounds (biological monitoring of exposure). Styrene is one of the chemicals for which biological monitoring programs have been validated and implemented in environmental and occupational medicine. However, inter-individual differences in the urinary excretion exist both for the main end-products (mandelic acid and phenylglyoxylic acid) and for its specific mercapturic acids (phenylhydroxyethylmercapturic acids, PHEMA). This limits to a certain extent the use of these metabolites for an accurate assessment of styrene exposure. In a group of 26 volunteers selected with relevant genotypes, and exposed to styrene vapours (50 mg/m3, 8 h) in an inhalation chamber, we evaluated whether genotyping or phenotyping relevant drug-metabolizing enzymes (CYP2E1, EPHX1, GSTM1, GSTT1 and GSTP1) may help to explain the observed inter-individual variability in the urinary metabolite excretion. Peripheral blood lymphocytes were used for genotyping and as reporter cells for the phenotyping of CYP2E1 and EPHX1. The GSTM1 genotype was clearly the most significant parameter explaining the variance in urinary PHEMA excretion (6-fold lower in GSTM1 null subjects; P < 0.0001) so that systematic GSTM1 genotyping should be recommended routinely for a correct interpretation of PHEMA urinary levels. Variant alleles CYP2E1*6 (7632T>A) and His113EPHX1 were associated with a significant reduction of, respectively, the expression (P = 0.047) and activity (P = 0.022) of the enzyme in peripheral blood lymphocytes. In combination with GSTM1 genotyping, the phenotyping approach also contributed to improve the interpretation of urinary results, as illustrated by the combined effect of CYP2E1 expression and GSTM1 allelic status that explained 77% of the variance in PHEMA excretion and allows the recommendation of mercapturates as specific and reliable biomarkers of exposure to styrene.

Acetylcysteine↗
PubMed1997

Interpretation of positive results of a methacholine inhalation challenge and 1 week of inhaled bronchodilator use in diagnosing and treating cough-variant asthma.

BACKGROUND: In diagnosing cough due to asthma, methacholine chloride inhalation challenge (MIC) interpreted in a traditional fashion has been shown to have positive predictive values from 60% to 82%. OBJECTIVE: To determine whether any features of positive results of an MIC or the results of a 1-week trial of inhaled beta-agonist therapy were helpful in predicting when the cough was due to asthma. METHODS: The study design was a prospective, randomized, double-blind, placebo-controlled, crossover format performed in adult, nonsmoking subjects, who were referred for diagnosis and treatment of chronic cough. The subjects had no other respiratory complaints or medical conditions for which they were taking medications, the results of baseline spirometry and chest roentgenograms were normal, and the results of MIC were positive. After obtaining baseline data, including MICs on 2 separate days, objective cough counting, and self-assessment of cough severity using a visual analog scale, subjects were randomized to receive 2 inhalations (1.3 mg) of metaproterenol sulfate or placebo by metered dose inhaler attached to a spacer device every 4 hours while awake. At 1 week, data identical to baseline were collected, and subjects received the other metered dose inhaler for 7 days. At 1 week, data identical to baseline were collected. After completion of the protocol, subjects were followed up in the clinic to observe the final response of the cough to specific therapy. RESULTS: Based on the disappearance of the cough with specific therapy, the cough was due to asthma in 9 of 15 subjects and nonasthma in 6 of 15 subjects. Baseline data were similar between groups. With respect to MICs, there were no significant differences between groups in the cumulative dose of methacholine that provoked a 20% decrease in forced expiratory volume in 1 second from the postsaline baseline value (PD20 values), slopes of dose-response curves, and maximal-response plateaus. Cough severity significantly improved after 1 week of metaproterenol use compared with the severity of the cough at baseline (P = .03) and with placebo (P = .02) only in subjects with asthma. CONCLUSIONS: No matter how the results are analyzed, positive MIC results, without observing response to therapy, are only consistent with asthma as the cause of the cough. The results are only diagnostic of asthma when they are followed by a favorable response to asthma therapy. After 1 week of inhaled beta-agonist, only the cough due to cough-variant asthma is significantly better.

Administration, Inhalation↗
PubMed2022

Scalable approaches for functional analyses of whole-genome sequencing non-coding variants.

Non-coding genetic variants outside of protein-coding genome regions play an important role in genetic and epigenetic regulation. It has become increasingly important to understand their roles, as non-coding variants often make up the majority of top findings of genome-wide association studies (GWAS). In addition, the growing popularity of disease-specific whole-genome sequencing (WGS) efforts expands the library of and offers unique opportunities for investigating both common and rare non-coding variants, which are typically not detected in more limited GWAS approaches. However, the sheer size and breadth of WGS data introduce additional challenges to predicting functional impacts in terms of data analysis and interpretation. This review focuses on the recent approaches developed for efficient, at-scale annotation and prioritization of non-coding variants uncovered in WGS analyses. In particular, we review the latest scalable annotation tools, databases and functional genomic resources for interpreting the variant findings from WGS based on both experimental data and in silico predictive annotations. We also review machine learning-based predictive models for variant scoring and prioritization. We conclude with a discussion of future research directions which will enhance the data and tools necessary for the effective functional analyses of variants identified by WGS to improve our understanding of disease etiology.

Genome-Wide Association Study↗
PubMed1996

Normal physiological and benign pathological variants of 18-fluoro-2-deoxyglucose positron-emission tomography scanning: potential for error in interpretation.

The use of positron-emission tomography in clinical practice is increasing, particularly with the use of 18-fluoro-2-deoxyglucose (FDG) for oncological studies. As in other imaging modalities, it is important to be aware of normal variants and benign diseases that may mimic more serious pathology. Uptake of FDG in a number of sites may be variable. Uptake of FDG may be seen normally in the skeletal muscle after exercise or under tension, in the myocardium, in parts of the gastrointestinal tract, especially the stomach and cecum, and in the urinary tract. Some causes of increased physiological uptake are avoidable, and measures can be taken to minimize accumulation, thus aiding study interpretation. Inflammatory lesions may cause an increase in FDG uptake, but not usually to the same degree as malignancy. Benign disease such as Paget's disease of bone, sarcoidosis, and tuberculosis may cause uptake that occasionally mimics that of malignancy. Typical examples of a number of physiological and benign variants are described and illustrated.

Artifacts↗
PubMed1996

Genetic analysis of thermolabile methylenetetrahydrofolate reductase as a risk factor for myocardial infarction.

Hyperhomocyst(e)inemia is associated with an increased risk of coronary artery disease and myocardial infarction. Both genetic and environmental factors influence the plasma level of homocysteine. One of the metabolic pathways for homocysteine involves the enzyme methylenetetrahydrofolate reductase (MTHFR), which regulates the conversion of homocysteine to methionine. A thermolabile variant of MTHFR is associated with reduced enzyme activity and increased plasma homocysteine levels. Recently, the cause of this variant of MTFHR has been identified as a single base change altering an alanine to a valine residue in the protein. Using a PCR-based assay to distinguish the normal and thermolabile variants of MTHFR in this study, we investigated whether the thermolabile variant is a genetic risk factor for myocardial infarction. In a study of 532 subjects (310 myocardial infarction patients and 222 population-based controls), we found no difference in either MTHFR genotype distribution (p = 0.57) or allele frequencies (p = 0.68) between cases and controls. The allele frequencies of the thermolabile variant were 0.34 and 0.35 in cases and controls, respectively. The age- and sex-stratified odds ratio for risk of myocardial infarction associated with homozygosity for the thermolabile variant was 0.85 (95% CI 0.50-1.50, p = 0.57) and that with carriage of the thermolabile allele was 1.06 (95% CI 0.73-1.52, p = 0.76). The odds ratios remained non-significant when restricted to young subjects (< 60 years) or males, and were not influenced by several other risk factors for myocardial infarction considered either singly or in combination. Interestingly, in both cases and controls, there was a trend toward a higher prevalence of hypertension in subjects carrying the normal allele, although as this is a post-hoc finding it needs to be interpreted with caution. The thermolabile variant of MTHFR is not a major risk factor for myocardial infarction and is unlikely to explain a significant proportion of the reported association of hyperhomocyst(e)inemia with coronary artery disease.

Adult↗
PubMed1983

Osteosarcoma of extragnathic craniofacial bones.

Osteosarcomas of extragnathic craniofacial bones--those bones of the skull excepting the jaw bones--are rare lesions, constituting fewer than 2% of all osteosarcomas. In our series of 21 patients (12 male and 9 female), the ages ranged from 6 to 77 years, and 10 patients were in the third or fourth decade of life. At least six patients had predisposing conditions: Paget's disease of bone in three and prior regional irradiation in three. Most of these tumors were high-grade lesions, and most were extensive when treated. There were 11 osteoblastic, 6 fibroblastic, and 1 small cell variant; 2 lesions had features resembling malignant fibrous histiocytoma. One tumor, originally interpreted as grade 4 osteosarcoma, was unavailable for variant classification. Surgical removal, irradiation, and chemotherapy were used in treatment, alone or in combination. Only two patients survived 5 years, and one of these patients died of her disease after 65 months. Almost half of our patients died within 1 year after diagnosis. The one long-term survivor (12 years) underwent a radical surgical procedure when her tumor was small; this was the only patient in this series who had a low-grade lesion. Because of the characteristics described, osteosarcoma of extragnathic craniofacial bones must be considered a distinct disease.

Adolescent↗
PubMed1996

Association between genetic variants of mast-cell chymase and eczema.

BACKGROUND: Atopy is a common syndrome underlying asthma, rhinitis, and eczema, and is characterised by high immunoglobulin E (IgE) responses to common antigens. IgE and mast-cell chymase (MCC-a serine protease secreted by skin mast cells) have a key role in atopic or allergic inflammation of the skin. The gene for MCC is located within a cluster of genes for cellular proteases on chromosome 14q11.2. We aimed to identify variants of MCC and another gene within this complex, and assess whether there is a genetic association between variants of MCC and atopic disorders-particularly eczema. METHODS: We randomly selected 100 controls and recruited patients-100 in each group-with atopic asthma, non-atopic asthma, atopic rhinitis, and atopic eczema. PCR amplification was used to test genomic DNA for an association between allelic polymorphisms in MCC and a flanking gene (CGL1, for the cathepsin-G-like protein) on chromosome 14q11 and asthma, rhinitis, and eczema. FINDINGS: We found a significant association between a BstXI polymorphism in MCC and eczema (odds ratio 2.17 [95% CI 1.21-3.88], p = 0.009), but no association with atopic asthma, rhinitis, or non-atopic asthma. There was no association between an Mboll polymorphism in CGL1 and any of the atopic disorders. INTERPRETATION: These findings suggest that variants of MCC may be one source of genetic risk for eczema.

Adolescent↗
PubMed2026

SNP-derived CpG variation and DNA methylation linking genetic susceptibility to metabolic disease.

DNA methylation at CpG dinucleotides represents a key epigenetic mechanism linking genetic variation to gene regulation in complex human diseases. Single-nucleotide polymorphisms (SNPs) that create or disrupt CpG sites can alter local DNA methylation and transcriptional activity, thereby influencing disease susceptibility. These CpG-modifying variants provide a functional interface between inherited genetic variation and epigenetic regulation in complex metabolic disorders. This review summarizes current evidence on SNP-derived CpG variation and its role in allele-specific DNA methylation and gene regulation in metabolically relevant tissues. By integrating findings from genome-wide association studies, epigenome-wide association studies, and multi-omics research, this review provides a mechanistic framework explaining how CpG-modifying polymorphisms influence adipogenesis, pancreatic &#x3b2;-cell function, inflammation, and glucose metabolism. Special emphasis is placed on South Asian populations, who exhibit early &#x3b2;-cell dysfunction and increased visceral adiposity. Many CpG-modifying variants act as methylation quantitative trait loci (meQTLs), influencing allele-specific methylation and gene expression. Understanding SNP-CpG-methylation interactions may improve functional interpretation of disease-associated genetic variants, enhance biomarker discovery, and support precision medicine strategies for metabolic disease.

Humans↗
PubMed1996

[Grounded theory as an approach to interpretive research].

Interpretative research comprehends studies on qualitative methodology and inductive research. According to Lowenberg's classification (1994), grounded theory is a type of interpretative research situated as a variant of symbolic interaction. The purpose of the present study was to discuss grounded theory as a methodological reference, presenting it and indicating its method. The following stages were presented: collection of empirical data, proceedings of data codification or analysis; open coding, axial coding or concept modification and integration and theory delimitation. The studies of CALIRI (1994) and CASSIANI (1994) exemplified the utilization of this methodological reference. Finally, authors visualized grounded theory as an useful reference of analysis, providing means and orienting, through its stages, the researcher aiming at using it.

Data Interpretation, Statistical↗
PubMedDate not supplied

CT colonography: pitfalls and interpretation.

A knowledge of normal colonic anatomy and its variants as demonstrated on CT colonography is essential to limit false positive results and ensure a high sensitivity for polyp detection. Interpretive and perceptual errors undoubtedly decrease with increasing operator experience. To provide a confident and accurate report, radiologists must be familiar with common pitfalls and pseudolesions on CT colonography.

Colon↗
PubMed1999

Micronodular thymoma with lymphoid B-cell hyperplasia: clinicopathologic and immunohistochemical study of eighteen cases of a distinctive morphologic variant of thymic epithelial neoplasm.

We describe 18 cases of a distinctive morphologic variant of primary thymic epithelial neoplasm characterized by a micronodular growth pattern associated with florid lymphoid follicular hyperplasia of the stroma. The tumors occurred in seven women and 11 men aged 41 to 76 years (mean, 58 years). All cases were asymptomatic and discovered incidentally on routine chest radiograph or during coronary artery bypass surgery. The tumors measured from 3 to 10 cm in greatest dimension and were well circumscribed and encapsulated. In seven cases, the lesions were grossly described as cystic or partially cystic masses. Histologically, they were characterized by a proliferation of small tumor nodules separated by abundant lymphoid stroma with prominent germinal centers. The nodules were composed of spindle cells containing oval nuclei devoid of atypia or mitotic activity. Immunohistochemical studies showed strong positivity of the spindle tumor cells for CAM 5.2 and broad spectrum keratin antibodies. The surrounding lymphoid cell population was strongly positive for LCA and L26 and showed a polyclonal pattern of staining for kappa and lambda. Stains for UCHL-1, CD1a, CD3, CD5, and CD99 were negative in the stromal lymphoid cell population. The tumor in one of the patients was associated with active pulmonary tuberculosis, and in another with anemia and splenomegaly of unknown etiology. None of the patients had clinical signs or history of myasthenia gravis or other autoimmune disorders. The present cases are interpreted as an unusual morphologic variant of spindle cell thymoma with prominent B-cell lymphoid hyperplasia. The possible significance of this phenomenon is discussed.

Adult↗
PubMed2026

Clinically actionable stratification of uncommon MET fusions: a precision oncology framework.

BACKGROUND: MET fusions represent emerging therapeutic targets in solid tumors; however, functional interpretation of non-canonical variants remains poorly understood, posing a major challenge for precision oncology. METHODS: We conducted a multicenter, pan-cancer study analyzing 23,299 clinical samples using DNA-based next-generation sequencing (NGS) to profile MET fusions. Transcriptional validation was performed using RNA-based NGS on available samples. Preliminary clinical outcomes were assessed in four patients with advanced malignancies harboring uncommon MET fusions who received MET tyrosine kinase inhibitor therapy. RESULTS: We identified 116&#x2009;MET fusions (incidence: 0.5%), with 55.2% (64/116) classified as uncommon fusions. These uncommon fusions were stratified into: Group A (5&#x2019;-retained, n&#x2009;=&#x2009;12), Group B (intergenic/exonic breakpoints, n&#x2009;=&#x2009;19), Group C (rare partners, n&#x2009;=&#x2009;23), and Group D (dual fusions, n&#x2009;=&#x2009;10). RNA validation revealed an overall low transcriptional consistency of 43.8% (14/32) for uncommon fusions, versus 100% for canonical fusions (PTPRZ1::MET, CAPZA2::MET). Notably, most 5&#x2019;-retained fusions were transcriptionally silent, while some intergenic fusions resolved into expressed canonical partners (e.g. PTPRZ1::MET). Therapeutically, all four MET inhibitor-treated patients achieved partial responses, including pediatric diffuse midline gliomas (DMG) (median OS: 11.2&#x2009;months) and lung adenocarcinoma (median OS: 34&#x2009;months), demonstrating preliminary clinical activity. CONCLUSIONS: uncommon MET fusions are heterogeneous at genomic and transcriptional levels. DNA-level findings often do not predict functional transcripts, underscoring the necessity of RNA-based confirmation for clinical interpretation. Despite low overall consistency, a subset retains therapeutic potential. We propose a refined diagnostic framework integrating DNA-based stratification and RNA validation to guide the management of MET-altered cancers in precision oncology workflows.

Humans↗
PubMedDate not supplied

[Chiari's network: persistence of the embryonic remnants of the valve of the sinus venosus in the right atrium. Echocardiographic and clinical analysis in a group of subjects].

As echocardiography is being used more often, its value and accuracy are becoming more fully appreciated, especially for identifying normal anatomic variants and their possible erroneous interpretation as pathologic states. We report the echocardiographic and clinical findings observed in sixteen subjects examined at our Cardiological Service in the period from January 1987 to April 1988. Mean age of these subjects is 40 +/- 27.04. Of these subjects, six are affected by other cardiac pathologies and ten are unaffected (Group A). First, we describe in all the patients M-mode and two dimensional patterns of persistence of the right venous sinus valve known as the Chiari network. This structure can present as a highly mobile, highly reflective echo target, which can be seen especially by means of the bi-dimensional technique. The Chiari network could be seen with all four standard approaches. The two most diagnostic views are, in our experience, the short axis parasternal view (62.5%), and the subcostal view (87.5%). In a great number of subjects (75%) the Chiari network could be seen in at least two approaches. Second, in Group A we make a clinical examination. Nine subjects in this group show the presence of a cardiac systolic murmur with vibratory characters from grade 1/6 to grade 3/6. 50% of the same patients presented supraventricular arrhythmias (particularly, two presented reciprocating paroxysmal supraventricular tachycardia and one paroxysmal atrial fibrillation). The significance of these findings is not clear yet. We, at least, emphasise that the Chiari network could be confused with other curvilinear highly mobile, echo targets such as right-heart vegetations, flail tricuspid leaflets, a small right-heart thrombus or even a pedunculated right heart tumor (especially right atrial myxoma). On the contrary, this structure might be considered a "normal anatomic variant".

Adult↗
PubMed2001

A novel neurodevelopmental syndrome responsive to 5-hydroxytryptophan and carbidopa.

Tryptophan hydroxylase (TPH; EC 1.14.16.4) catalyzes the first rate-limiting step of serotonin biosynthesis by converting l-tryptophan to 5-hydroxytryptophan. Serotonin controls multiple vegetative functions and modulates sensory and alpha-motor neurons at the spinal level. We report on five boys with floppiness in infancy followed by motor delay, development of a hypotonic-ataxic syndrome, learning disability, and short attention span. Cerebrospinal fluid (CSF) analysis showed a 51 to 65% reduction of the serotonin end-metabolite 5-hydroxyindoleacetic acid (5HIAA) compared to age-matched median values. In one out of five patients a low CSF 5-methyltetrahydrofolate (MTHF) was present probably due to the common C677T heterozygous mutation of the methylenetetrahydrofolate reductase (MTHFR) gene. Baseline 24-h urinary excretion showed diminished 5HIAA values, not changing after a single oral load with l-tryptophan (50-70 mg/kg), but normalizing after 5-hydroxytryptophan administration (1 mg/kg). Treatment with 5-hydroxytryptophan (4-6 mg/kg) and carbidopa (0.5-1.0 mg/kg) resulted in clinical amelioration and normalization of 5HIAA levels in CSF and urine. In the patient with additional MTHFR heterozygosity, a heterozygous missense mutation within exon 6 (G529A) of the TPH gene caused an exchange of valine by isoleucine at codon 177 (V177I). This has been interpreted as a rare DNA variant because the pedigree analysis did not provide any genotype-phenotype correlation. In the other four patients the TPH gene analysis was normal. In conclusion, this new neurodevelopmental syndrome responsive to treatment with 5-hydroxytryptophan and carbidopa might result from an overall reduced capacity of serotonin production due to a TPH gene regulatory defect, unknown factors inactivating the TPH enzyme, or selective loss of serotonergic neurons.

5-Hydroxytryptophan↗
PubMed1978

Variant chromosome 3 (inv3) in normal newborns and their parents, and in children with mental retardation.

The chromosomes of 102 normal newborn babies (51 boys and 51 girls) born at term, their parents, and 45 nonrelated children with mental retardation at the level of imbecility were investigated by fluorescence microscopy using propyl quinacrine mustard. In each of the 11 families, one of the parents had a variant chromosome 3 that was interpreted as resulting from a pericentric inversion of the brilliant band (or C band) only (inv3). In four cases inv3 was transmitted to the child. The frequency of inv3 in newborn boys and girls was 2 and 6% respectively, and in adult men and women 5 and 6% respectively. In children with mental retardation of unknown etiology the inv3 was detected in five cases (11.1%). This difference from normal persons was not significant.

Child↗
PubMed1978

A microprobe analysis of Gomori-positive glial cells in the rat arcuate nucleus.

Astrocytes and microglial cells in the arcuate nucleus of the rat hypothalamus contain lipofuscin-like granules which react with chrome alum gallocyanin and exhibit endogenous peroxidase activity. These granules were assessed with energy dispersive X-ray microanalysis and compared to neuronal dense bodies and glial cytoplasm. The granules are distinguished by a consistent content of sulphur and a frequent presence of calcium. The localization of other elements such as iron, copper, potassium and chlorine is impaired by methodical difficulties. The sulphur content as well as the endogenous peroxidase activity is interpreted as indicating a special variant of lipofuscin. The presence of calcium is discussed with respect to recent concepts of glia as a regulator of the ionic environment of the CNS.

Animals↗
PubMed1997

Malignant mesothelioma of the pleura. The reproducibility of the immunohistological diagnosis.

The reproducibility of the histopathological diagnosis of pleural malignant mesothelioma (MM), after supplementing routine H&E stain by immunohistochemistry (IH) in 77 cases of original diagnoses of MM, was assessed by examining interobserver variation between five pathologists. A battery of commercial antibodies (cytokeratins, vimentin, HMFG-2, anti Leu-M1 [CD15], BerEP4, B72.3 [TAG-72], carcinoembyonic antigen), considered to be useful in enhancing diagnostic accuracy, was used. The number of definitively classified tumors (accepted MM plus rejected MM) increased from 57 on H&E stain to 60 after IH, with 59 (76.6%) cases being accepted as true MM. Based on IH, the chance-adjusted interobserver agreement was poor (kappa w = 0.29) and lower than that observed on previous H&E alone. The intraobserver agreement for four of the five pathologists was rather good (kappa w = 0.54-0.56). The inter- and intraobserver concordance was higher in accepting than excluding the cases as MM. A larger number of cases were classified by all reviewers as mixed or sarcomatous variants after IH. In the interpretation of each immunostain, kappa values ranged from 0.19 for B72.3 to 0.62 for HMFG-2, which were respectively the least and the most consistently interpreted immunostains. The information additionally contributed by IH did not seem to change the pathologists' diagnoses very much in comparison with those made by routine H&E stain. Until highly specific and sensitive probes for the positive identification of MM become available, a careful scrutiny of routinely stained preparations still remains the most rewarding component of the diagnostic pathway.

Clinical Laboratory Techniques↗