BACKGROUND: Diversity in human proteins often gives rise to pluralities of structurally similar but functionally distinct proteins. Such microheterogeneity generally escapes proteomics discovery technologies, as well as conventional immunometric assays. As an intermediate between these 2 technological approaches, targeted, full-length characterization of proteins using mass spectrometry is a suitable means of defining microheterogeneity evident in human populations.

CONTENT: We describe and explore the implications of microheterogeneity using the exemplar of human vitamin D binding protein (Gc-Globulin) as observed in cohorts of 400 individuals. Our investigations yielded: (a) population frequency data comparable to genotyping; (b) population frequency data for protein variants, with and without genotype linkage; (c) reference values for the different protein variants per cohort and genotype; and (d) associations between variant, frequency, relative abundance, and diseases.

SUMMARY: With the exception of the genotype frequency, such population data are unique and illustrate a need to more fully understand the exact full-length qualitative and quantitative idiosyncrasies of individual proteins in relation to health and disease as part of the standardized biomarker development and clinical proteomic investigation of human proteins.

BACKGROUND: The in situ proximity ligation assay (PLA) allows a protein or protein complex to be represented as an amplifiable DNA molecule. Recognition is mediated by proximity probes consisting of antibodies coupled with oligonucleotides. Upon dual binding of the proximity probes, the oligonucleotides direct the formation of a circular DNA molecule, which is then amplified by rolling-circle replication. The localized concatemeric product is then detected with fluorescent probes. The in situ PLA enables localized detection of individual native proteins or interacting protein pairs in fixed cells or tissue sections, thus providing an important tool for basic and clinical research.

METHODS: We used horseradish peroxidase (HRP)-conjugated oligonucleotides to couple in situ PLA with enzymatic visualization of the localized detection event.

RESULTS: We demonstrate the detection of protein complexes, both in cells and in tissue sections, and show that we can quantify the complexes with image-analysis software specially developed for recognizing HRP signals in bright-field microscopy images. We show that fluorescence and HRP signals produce equivalent results, both in cultured cells and in tissue samples.

CONCLUSIONS: The combination of in situ PLA with bright-field detection and automated image analysis allows the signals present to be counted in an automated fashion and thus provides a sensitive and specific method for quantification of proteins and protein complexes with bright-field microscopy. With this approach, in situ PLA can be used without the requirement for expensive fluorescence microscopes, thereby avoiding problems with nonspecific fluorescence while maintaining compatibility with conventional histologic staining.

BACKGROUND: Stroke is a devastating condition encompassing a wide range of pathophysiological entities that include thrombosis, hemorrhage, and embolism. Current diagnosis of stroke relies on physician clinical examination and is further supplemented with various neuroimaging techniques. A single set or multiple sets of blood biomarkers that could be used in an acute setting to diagnosis stroke, differentiate between stroke types, or even predict an initial/reoccurring stroke would be extremely valuable.

CONTENT: We discuss the current classification, diagnosis, and treatment of stroke, focusing on use of novel biomarkers (either solitary markers or multiple markers within a panel) that have been studied in a variety of clinical settings.

SUMMARY: The current diagnosis of stroke remains hampered and delayed due to lack of a suitable mechanism for rapid (ideally point-of-care), accurate, and analytically sensitive biomarker-based testing. There is a clear need for further development and translational research in this area. Potential biomarkers identified need to be transitioned quickly into clinical validation testing for further evaluation in an acute stroke setting; to do so would impact and improve patient outcomes and quality of life.

BACKGROUND: Hemoglobin A1c (HbA1c) point-of-care (POC) instruments are widely used to provide rapid-turnaround results in diabetic care centers. We investigated the conformance of various HbA1c POC instruments (In2it from Bio-Rad, DCA Vantage from Siemens, Afinion and Nycocard from Axis-Shield, Clover from Infopia, InnovaStar from DiaSys, A1cNow from Bayer, and Quo-Test from Quotient Diagnostics) with generally accepted performance criteria for HbA1c.

METHODS: The CLSI protocols EP-10, EP-5, and EP-9 were applied to investigate imprecision, accuracy, and bias. We assessed bias using 3 certified secondary reference measurement procedures and the mean of the 3 reference methods. Assay conformance with the National Glycohemoglobin Standardization Program (NGSP) certification criteria, as calculated from analyses with 2 different reagent lot numbers for each HbA1c method, was also evaluated.

RESULTS: Because of disappointing EP-10 results, 2 of the 8 manufacturers decided not to continue the evaluation. The total CVs from EP-5 evaluations for the different instruments with a low and high HbA1c value were: In2it 4.9% and 3.3%, DCA Vantage 1.8% and 3.7%, Clover 4.0% and 3.5%, InnovaStar 3.2% and 3.9%, Nycocard 4.8% and 5.2%, and Afinion 2.4% and 1.8%. Only the Afinion and the DCA Vantage passed the NGSP criteria with 2 different reagent lot numbers.

CONCLUSIONS: Only the Afinion and the DCA Vantage met the acceptance criteria of having a total CV <3% in the clinically relevant range. The EP-9 results and the calculations of the NGSP certification showed significant differences in analytical performance between different reagent lot numbers for all HbA1c POC instruments.

BACKGROUND: Adipocytokines may mediate the association between adiposity and lethal prostate cancer outcomes.

METHODS: In the Physicians' Health Study, we prospectively examined the association of prediagnostic plasma concentrations of adiponectin and leptin with risk of developing incident prostate cancer (654 cases diagnosed 1982–2000 and 644 age-matched controls) and, among cases, risk of dying from prostate cancer by 2007.

RESULTS: Adiponectin concentrations were not associated with risk of overall prostate cancer. However, men with higher adiponectin concentrations had lower risk of developing high-grade or lethal cancer (metastatic or fatal disease). The relative risk (95% CI) comparing the highest quintile to the lowest (Q5 vs Q1) was 0.25 (range 0.07–0.87; P_trend = 0.02) for lethal cancer. Among all the cases, higher adiponectin concentrations predicted lower prostate cancer–specific mortality [hazard ratio (HR)_{Q5 vs Q1}= 0.39; range 0.17–0.85; P_trend = 0.02], independent of body mass index (BMI), plasma C-peptide (a marker of insulin secretion), leptin, clinical stage, and tumor grade. This inverse association was apparent mainly among men with a BMI ≥25 kg/m² (HR_{Q5 vs Q1}= 0.10; range 0.01–0.78; P_trend = 0.02), but not among men of normal weight (P_trend = 0.51). Although the correlation of leptin concentrations with BMI (r = 0.58, P < 0.001) was stronger than that of adiponectin (r = -0.17, P < 0.001), leptin was unrelated to prostate cancer risk or mortality.

CONCLUSIONS: Higher prediagnostic adiponectin (but not leptin) concentrations predispose men to a lower risk of developing high-grade prostate cancer and a lower risk of subsequently dying from the cancer, suggesting a mechanistic link between obesity and poor prostate cancer outcome.

BACKGROUND: The introduction and use of next-generation sequencing (NGS) techniques have taken genomic research into a new era; however, implementing such powerful techniques in diagnostics laboratories for applications such as resequencing of targeted disease genes requires attention to technical issues, including sequencing template enrichment, management of massive data, and high interference by homologous sequences.

METHODS: In this study, we investigated a process for enriching DNA samples that uses a customized high-density oligonucleotide microarray to enrich a targeted 280-kb region of the NF1 (neurofibromin 1) gene. The captured DNA was sequenced with the Roche/454 GS FLX system. Two NF1 samples (CN1 and CN2) with known genotypes were tested with this protocol.

RESULTS: Targeted microarray capture may also capture sequences from nontargeted regions in the genome. The capture specificity estimated for the targeted NF1 region was approximately 60%. The de novo Alu insertion was partially detected in sample CN1 by additional de novo assembly with 50% base-match stringency; the single-base deletion in sample CN2 was successfully detected by reference mapping. Interferences by pseudogene sequences were removed by means of dual-mode reference-mapping analysis, which reduced the risk of generating false-positive data. The risk of generating false-negative data was minimized with higher sequence coverage (>30x).

CONCLUSIONS: We used a clinically relevant complex genomic target to evaluate a microarray-based sample-enrichment process and an NGS instrument for clinical resequencing purposes. The results allowed us to develop a systematic data-analysis strategy and algorithm to fit potential clinical applications.

BACKGROUND: Endothelium-derived nitric oxide plays a crucial role in the regulation of vascular tone and the development of cardiovascular disease. The endogenous nitric oxide synthase inhibitor asymmetric dimethylarginine (ADMA) has emerged as a novel cardiovascular risk factor. ADMA appears to be an independent predictor for cardiovascular and overall mortality. However, the majority of studies investigating the clinical role of ADMA were performed in European study populations with few individuals of other ethnicities.

METHODS: We performed a cross-sectional study of 980 healthy, older (age 60–72 years) individuals of different ethnicities living in the San Francisco Bay area and analyzed ADMA plasma concentrations and their relationship to other cardiovascular risk factors. Plasma ADMA concentrations were measured using a recently developed, highly sensitive ELISA.

RESULTS: In our entire sample, we were able to define a reference interval for ADMA plasma concentrations of 0.47 (90% CI 0.46–0.48) µmol/L to 0.85 (0.84–0.89) µmol/L. The mean ADMA concentration was 0.63 (SD 0.11) µmol/L (median 0.61 µmol/L). Mean ADMA concentrations were significantly lower in African Americans (0.60 µmol/L; P < 0.01) and mixed non-Hispanics (0.60 µmol/L; P < 0.05) compared with whites (0.63 µmol/L). ADMA was positively correlated with cystatin-C in both men ( = 0.29) and women ( = 0.37), and median plasma ADMA concentrations increased across cystatin-C quintiles.

CONCLUSIONS: ADMA varies nearly 2-fold across a healthy sample of older men and women, correlates with age, body mass index, and renal function, and is different across ethnic groups. Additional studies in a wider age range and including larger ethnic subgroups would be useful.

BACKGROUND: Maternal plasma mRNA encoded by the PLAC4 gene (placenta-specific 4), which is transcribed from chromosome 21 in placental cells, is a potential marker for the noninvasive assessment of chromosome 21 dosage in the fetus. We evaluated the diagnostic sensitivities and specificities of 2 trisomy 21–screening approaches that use maternal plasma PLAC4 mRNA.

METHODS: We studied maternal plasma samples from 153 pregnant women carrying euploid and trisomy 21 fetuses. For the samples in which the fetuses were heterozygous for the studied PLAC4 single-nucleotide polymorphism (SNP), we measured the ratio between 2 alleles of the SNP in maternal plasma PLAC4 mRNA (RNA-SNP) by mass spectrometric (MS) and digital PCR methods. For pregnancies involving fetuses homozygous for the SNP, we quantified the total PLAC4 mRNA concentration in maternal plasma by real-time PCR and digital PCR.

RESULTS: For the RNA-SNP approach, we achieved a diagnostic sensitivity and specificity of 100% (95% CI, 40.2%–100%) and 89.7% (95% CI, 78.8%–96.1%), respectively, for both the MS and the digital PCR methods. For the mRNA-quantification approach, the areas under the ROC curves were 0.859 (95% CI, 0.741–0.903) and 0.833 (95% CI, 0.770–0.923) for plasma PLAC4 mRNA concentrations measured by the real-time PCR and the digital PCR methods, respectively.

CONCLUSIONS: For prenatal screening of trisomy 21, the quantification of the total PLAC4 mRNA concentration can be used in a synergistic manner with the RNA-SNP allelic ratio approach to increase the population coverage of cases in which diagnostic information can be obtained.

BACKGROUND: Deleterious mutations in BRCA1 (breast cancer 1, early onset; MIM 113705) increase human breast and ovarian cancer [HB(O)C] risk; however, many variants cannot be readily classified as deleterious or neutral. Unclassified variants (UVs) pose serious problems in genetic counseling. RNA-splicing analysis is essential for the assessment of many UVs.

METHODS: Denaturing gradient gel electrophoresis was used to genotype the BRCA1 c.591C>T variant in 685 index cases of HB(O)C families, 326 sporadic breast cancer cases, and 450 healthy controls from Spain. In silico tools were used to predict the effect of the c.591C>T variant on splicing. In vitro splicing analysis was performed in 7 c.591C>T carriers and 10 noncarriers. cDNAs were PCR-amplified with primers designed to detect BRCA1 alternative splicing isoforms. The products were analyzed by capillary electrophoresis. Peak areas were used to quantify the relative abundance of each isoform. Sequencing through exonic single-nucleotide polymorphisms (SNPs) enabled us to discriminate wild-type and variant transcripts.

RESULTS: c.591C>T was detected in HB(O)C cases (1.5%), breast cancer cases (0.3%), and controls (0.9%). c.591C>T induced BRCA1 exon 9 skipping and modified the relative expression of (9,10), (9,10,11B), 11B, and full-length isoforms. The mean ratio of (9,10) to the full-length isoform increased from 0.25 in noncarriers to 1.5 in carriers. The mean (9,10,11B)/11B ratio increased from 0.2 to 4. Overall expression levels of c.591C>T and wild-type alleles were similar.

CONCLUSIONS: Our data support a nonpathogenic role for the BRCA1 c.591C>T variant. Naturally occurring alternative splicing isoforms need to be considered when assessing the role of BRCA1 UVs on splicing.

AIM: A digital PCR approach has recently been suggested to detect greater amounts of cell-free fetal DNA in maternal plasma than conventional real-time quantitative PCR (qPCR). Because the digital qPCR approach uses shorter PCR amplicons than the real-time qPCR assay, we investigated whether a real-time qPCR assay appropriately modified for such short amplicons would improve the detection of cell-free fetal DNA.

METHODS: We developed a novel universal-template (UT) real-time qPCR assay that was specific for the DYS14 sequence on Y chromosome and had a short amplicon size of 50 bp. We examined this "short" assay with 50 maternal plasma samples and compared the results with those for a conventional real-time qPCR assay of the same locus but with a longer amplicon (84 bp).

RESULTS: Qualitatively, both assays detected male cell-free fetal DNA with the same specificity and detection capability. Quantitatively, however, the new UT real-time qPCR assay for shorter amplicons detected, on average, almost 1.6-fold more cell-free fetal DNA than the conventional real-time qPCR assay with longer amplicons.

CONCLUSIONS: The use of short PCR amplicons improves the detection of cell-free fetal DNA. This feature may prove useful in attempts to detect cell-free fetal DNA under conditions in which the amount of template is low, such as in samples obtained early in pregnancy.

BACKGROUND: The clinical relevance of very highly increased high-sensitivity C-reactive protein (hsCRP) concentrations (>10 mg/L) is incompletely understood. We examined the association between very highly increased hsCRP and risk of incident cardiovascular disease (CVD) events and all-cause mortality.

METHODS: We recruited 5248 participants free from overt CVD and acute infection [mean age 53.5 (SD 12.4) years, 55.5% women] from the Scottish Health Survey, a representative sample of community-dwelling adults. hsCRP and other conventional risk factors were measured at baseline.

RESULTS: Over an average of 7 years' follow-up, there were a total of 259 incident CVD events (including myocardial infarction, coronary artery bypass, percutaneous coronary angioplasty, stroke, heart failure) and 357 all-cause deaths. Very highly increased hsCRP was associated with CVD events after adjustment for Framingham risk score (FRS), body mass index (BMI), central obesity, and hormone replacement therapy (HRT) (hazard ratio 2.40, 95% CI 1.51–3.81) and also with all-cause death (hazard ratio 3.64, 95% CI 2.57–5.15). With the addition of CRP scores to the conventional Framingham model, 7.4% of participants were reclassified into a high-risk (>20% FRS) CVD category. Very highly increased hsCRP was also associated with several modifiable risk factors, including smoking, HDL cholesterol, and central obesity.

CONCLUSIONS: hsCRP >10 mg/L was a stronger predictor of clinical events than a conventional cut point of 3 mg/L. Very highly increased hsCRP may provide clinically meaningful prognostic information.

An analysis of all US Food and Drug Administration (FDA) approvals for protein-based assays through 2008 reveals 109 unique protein targets in plasma or serum, as well as 62 additional tests for peptides, protein posttranslational modifications, protein complexes, autoantibodies against endogenous proteins and blood cell proteins. A further 96 unique protein targets are assayed in plasma by laboratory-developed tests available for clinical use in the US, yielding a total of 205 proteins that include products of approximately 211 genes (excluding immunoglobulins). These tests provide quantitative measurements for approximately 1% of the human protein gene products, defining a practical clinical plasma proteome. The rate of introduction of new protein analytes has remained essentially flat over the past 15 years, averaging 1.5 new proteins per year (median of 1 per year). This rate falls far short of that needed to support projected medical needs and indicates serious deficiencies in the protein biomarker pipeline, from which no proteomics-discovered analytes have yet emerged.

BACKGROUND: Exhaustive exercise can be associated with short-term immune suppression, but moderate exercise such as tai chi chuan (TCC) has been shown to have beneficial effects on immunity. The mechanisms for the health benefits of exercise remain to be determined, and no potential biomarkers for these beneficial health effects have been identified. This study investigated serum proteomic markers in individuals participating in TCC exercise.

METHODS: Two-dimensional fluorescence difference gel electrophoresis was used to compare proteomic markers in 3 individuals before and after 12 weeks of TCC exercise. The different protein spots were identified by mass spectrometry and validated in an additional 20 individuals by western blot analysis.

RESULTS: We identified 39 protein spots for 18 proteins with a significant increase or decrease after TCC exercise. Validation of the differentially displayed proteins with 20 paired pre- and postexercise samples revealed a significant increase in complement factor H (P = 0.0034) associated with decreases in C1q esterase inhibitor (P = 0.0038) and complement factor B (P = 0.0029).

CONCLUSIONS: In this first study of proteomic biomarkers of TCC exercise, we found an increase in complement factor H associated with a decrease in complement factor B. Complement factor H is involved in protection from microangiopathy and macular degeneration and may represent a useful marker of the health effects of exercise.

BACKGROUND: Serial measurements of neurohormones have been shown to improve prognostication in the setting of acute heart failure (HF) or chronic HF without therapeutic intervention. We investigated the prognostic role of serial measurements of emerging neurohormones and BNP in a cohort of chronic HF patients undergoing increases in HF-specific therapy.

METHODS: In this prospective study we included 181 patients with chronic systolic HF after an episode of hospitalization for worsening HF. Subsequently, HF therapy was gradually increased in the outpatient setting until optimized. We measured copeptin, midregional proadrenomedullin, C-terminal endothelin-1 precursor fragment, midregional proatrial natriuretic peptide, and B-type natriuretic peptide before and after optimization of HF therapy. The primary endpoint was all-cause mortality at 24 months.

RESULTS: Angiotensin-converting enzyme/angiotensin receptor blocker and β-blockers were increased significantly during the 3-month titration period (P < 0.0001 for both). In a stepwise Cox regression analysis adjusted for age, sex, glomerular filtration rate, diabetes mellitus, and ischemic HF, baseline and follow-up neurohormone concentrations were predictors of the primary endpoint as follows (baseline hazard ratios): copeptin 1.92, 95% CI 1.233–3.007, P = 0.004; midregional proadrenomedullin 2.79, 95% CI 1.297–5.995, P = 0.009; midregional proatrial natriuretic peptide 2.05, 95% CI 1.136–3.686, P = 0.017; C-terminal endothelin-1 precursor fragment 2.24, 95% CI 1.133–4.425, P = 0.025; B-type natriuretic peptide 1.46, 95% CI 1.039–2.050, P = 0.029.

CONCLUSIONS: In pharmacologically unstable chronic HF patients, baseline values and follow-up measures of copeptin, midregional proadrenomedullin, C-terminal endothelin-1 precursor fragment, midregional proatrial natriuretic peptide, and B-type natriuretic peptide were equally predictive of all-cause mortality. Relative change of neurohormone values was noncontributory.

BACKGROUND: The use of fetal DNA in maternal plasma for noninvasive prenatal diagnosis of trisomy 21 (T21) is an actively researched area. We propose a novel method of T21 detection that combines fetal-specific epigenetic and genetic markers.

METHODS: We used combined bisulfite restriction analysis to search for fetal DNA markers on chromosome 21 that were differentially methylated in the placenta and maternal blood cells and confirmed any target locus with bisulfite sequencing. We then used methylation-sensitive restriction endonuclease digestion followed by microfluidics digital PCR analysis to investigate the identified marker. Chromosome-dosage analysis was performed by comparing the dosage of this epigenetic marker with that of the ZFY (zinc finger protein, Y-linked) gene on chromosome Y.

RESULTS: The putative promoter of the HLCS (holocarboxylase synthetase) gene was hypermethylated in the placenta and hypomethylated in maternal blood cells. A chromosome-dosage comparison of the hypermethylated HLCS and ZFY loci could distinguish samples of T21 and euploid placental DNA. Twenty-four maternal plasma samples from euploid pregnancies and 5 maternal plasma samples from T21 pregnancies were analyzed. All but 1 of the euploid samples were correctly classified.

CONCLUSIONS: The epigenetic–genetic chromosome-dosage approach is a new method for noninvasive prenatal detection of T21. The epigenetic part of the analysis can be applied to all pregnancies. Because the genetic part of the analysis uses paternally inherited, fetal-specific genetic markers that are abundant in the genome, broad population coverage should be readily achievable. This approach has the potential to become a generally usable technique for noninvasive prenatal diagnosis.

BACKGROUND: Succinylacetone (SUAC) is the primary metabolite accumulated in tyrosinemia type I—an inborn error of metabolism that, if untreated, can cause death from liver failure during the first months of life. Newborn screening laboratories measure SUAC in dried blood spot (DBS) samples to detect asymptomatic tyrosinemia type I. We used panels of SUAC-enriched DBSs to compare and evaluate the performance of these screening tests.

METHODS: We prepared sets of DBS materials enriched with predetermined SUAC concentrations and distributed samples of these materials, along with a screening practices questionnaire, to laboratories that perform SUAC tests. We compared their reported SUAC concentrations and questionnaire responses to identify screening practices that affect SUAC test outcomes.

RESULTS: Data from 2 pilot surveys showed large differences among laboratories in SUAC recoveries, reproducible within-laboratory recoveries, and stable performance of the DBS materials. Results from 257 proficiency test analyses contained a total of 6 false-negative misclassifications. Reported recoveries of added SUAC ranged from 0 to >200%. Low-biased SUAC recoveries were associated with 1 method used by 5 laboratories. All laboratories that reported SUAC recoveries ≥100% used DBS matrix calibrators.

CONCLUSIONS: The wide ranges of SUAC concentrations reported for pilot and proficiency testing specimens demonstrate a need to harmonize quantitative results among laboratories. Although DBS matrix calibrators are important for optimizing SUAC recoveries, the preparation of these calibrators is not standardized among laboratories. Certified DBS-based SUAC calibrators are needed for accuracy and harmonization.

BACKGROUND: The phospholipase A₂ (PLA2) family comprises multiple isoenzymes that vary in their physicochemical properties, cellular localizations, calcium sensitivities, and substrate specificities. Despite these differences, PLA2s share the ability to catalyze the synthesis of the precursors of the proinflammatory mediators. To investigate the potential of PLA2 as a biomarker in screening neuroinflammatory disorders in both clinical and research settings, we developed a PLA2 assay and determined the predominant types of PLA2 activity in cerebrospinal fluid (CSF).

METHODS: We used liposomes composed of a fluorescent probe (bis-Bodipy® FL C11-PC [1,2-bis-(4,4- difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-undecanoyl)-sn-glycero-3-phosphocholine]) and 1,2-dioleoyl-l--phosphatidylcholine as a substrate to measure CSF PLA2 activity in a 96-well microtiter plate format. We established the type of CSF PLA2 activity using type-specific inhibitors of PLA2.

RESULTS: Using 5 µL CSF per assay, our PLA2 activity assay was reproducible with CVs <15% in 2 CSF samples and for recombinant secretory Ca²⁺-dependent PLA2 (sPLA2) in concentrations ranging from 0.25 to 1 µmol/L. This PLA2 assay allowed identification of sPLA2 activity in lumbar CSF from healthy individuals 20–77 years old that did not depend on either sex or age. Additionally, CSF sPLA2 activity was found to be increased (P = 0.0008) in patients with Alzheimer disease.

CONCLUSIONS: Adult human CSF has sPLA2 activity that can be measured reliably with the assay described. This enzyme activity in the CSF is independent of both sex and age and might serve as a valuable biomarker of neuroinflammation, as we demonstrated in Alzheimer disease.

BACKGROUND: Stearoyl-coenzyme A desaturase 1 (SCD1) catalyzes the limiting step of monounsaturated fatty acid synthesis in humans and is an important player in triglyceride generation. SCD1 has been repeatedly implicated in the pathogenesis of metabolic and inflammatory diseases. Therefore it is of great importance to determine SCD1 activity in human samples. In this study we aimed to evaluate a hepatic SCD1 activity index derived from plasma VLDL triglyceride composition as a tool to estimate hepatic SCD1 expression in humans. Additionally, we further evaluated commonly used fatty acid ratios [elongase, de novo lipogenesis, and 5 and 6 desaturase] in plasma VLDL and hepatic lipid fractions.

DESIGN AND METHODS: Liver biopsies and plasma samples were simultaneously collected from 15 individuals. Plasma VLDL was obtained by ultracentrifugation. Hepatic and plasma VLDL lipids were fractionated by thin-layer chromatography, and the fatty acid composition of each fraction was analyzed by gas chromatography. Hepatic SCD1 expression was determined by real-time PCR.

RESULTS: Hepatic SCD1 mRNA expression was associated with the product/precursor ratios (16:1/16:0 and 18:1/18:0) of hepatic lipid fractions. The 16:1/16:0 ratio in hepatic and VLDL triglycerides as well as the 18:1/18:0 ratio in plasma VLDL were closely associated with hepatic SCD1 expression. The hepatic de novo lipogenesis index from triglycerides was associated with expression of lipogenic genes expression [fatty acid synthase (FASN), acetyl-Coenzyme A carboxylase alpha (ACACA), and sterol regulatory element binding transcription factor 1 (SREBP-1)] and is closely reflected by the de novo lipogenesis index in VLDL triglycerides.

CONCLUSION: We demonstrated for the first time that hepatic SCD1 expression can be estimated noninvasively from routine blood samples by measuring the SCD1 activity index in fasting plasma VLDL.

BACKGROUND: We hypothesized that liver-derived mRNA, such as ALB (albumin) mRNA, would be released into human plasma with liver cell death.

METHODS: We genotyped ALB mRNA molecules in samples of plasma and whole blood from liver and bone marrow transplant recipients by RNA single-nucleotide polymorphism analysis. Plasma and whole blood ALB mRNA genotypes were compared with the DNA genotypes of the recipients and donors. A reverse-transcription quantitative real-time PCR assay was used to measure plasma ALB mRNA concentrations in 107 patients [hepatocellular carcinoma (HCC), cirrhosis, or chronic hepatitis B (CHB)] and 207 healthy controls.

RESULTS: The RNA genotype data revealed ALB mRNA in plasma to be liver derived, whereas tissue compartments other than the liver also contributed to the ALB mRNA detected in whole blood. Statistically significant increases in plasma ALB mRNA concentrations were observed for HCC, cirrhosis, and active CHB, compared with controls. A cutoff of 835 copies/mL of plasma ALB mRNA identified by ROC curve analysis showed 85.5% diagnostic sensitivity and 92.8% diagnostic specificity for the detection of liver pathologies. Only 21.5% of patients with liver pathologies had increased alanine aminotransferase (ALT) activities, whereas 73.8% had increased plasma ALB mRNA concentrations. Only 49% of the HCC patients had increased serum -fetoprotein concentrations, whereas 91.4% had increased plasma ALB mRNA concentrations.

CONCLUSIONS: ALB mRNA is liver specific in plasma, but not in whole blood. Plasma ALB mRNA is increased in some liver pathologies and may be more diagnostically sensitive than -fetoprotein and ALT.

BACKGROUND: The large number of CFTR [cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)] mutations and the existence of variants of unclear significance complicate the prenatal diagnosis of cystic fibrosis (CF). The aim of this study was to determine whether the pattern of amniotic fluid digestive enzymes (AF-DEs) could be correlated with the severity of CFTR mutations.

METHODS: The AF-DE pattern (-glutamyltranspeptidase, aminopeptidase M, and the intestinal isoform of alkaline phosphatase) was retrospectively analyzed in 43 AF samples. All fetuses presented 2 CFTR mutations, which were classified according to the severity of the disease: CF/CF (n = 38); CF/CFTR-related disorders (n = 1); and CF/unknown variant (n = 4). The relationships between clinical CF status, CFTR mutations, and AF-DE pattern were studied.

RESULTS: Of 38 severely affected CF fetuses, an "obstructive" AF-DE pattern was observed in 15 of 15 samples collected before 22 weeks, irrespective of the CFTR mutation (diagnostic sensitivity, 100%; diagnostic specificity, 99.8%). In the 23 fetuses evaluated after 22 weeks, the AF-DE pattern was abnormal in 7 cases and noncontributive in 16 (diagnostic sensitivity, 30.4%; diagnostic specificity, 99.8%). Of the 5 questionable cases (F508del/N1224K, F508del/L73F, 3849+10kbC>T/G1127E, F508del/S1235R, F508del/G622D), all were CF symptom free at 2–4 years of follow-up. The AF-DE pattern (<22 weeks) was typical in 3 cases but abnormal in the last 2 cases.

CONCLUSIONS: AF-DE analysis is of value for prenatal CF diagnosis in classic forms of CF and could be helpful in nonclassic CF.

BACKGROUND: To improve ante mortem diagnostic accuracy of Alzheimer disease (AD), measurement of the biomarkers amyloid-β(1–42) (Aβ42), total (Tau), and phosphorylated at threonine₁₈₁ (pTau) in cerebrospinal fluid (CSF) has been proposed. We have used these markers and evaluated their performance.

METHODS: From January 2001 to January 2007, we assessed Aβ42, Tau, and pTau by commercial ELISAs in CSF from 248 consecutive AD patients and 131 patients with subjective memory complaints attending our outpatient memory clinic. Diagnoses were made blind to the results of the biomarker assays. We assessed sensitivity and specificity and analyzed trends over time.

RESULTS: Interassay CVs from analysis of pools of surplus CSF specimens were mean 11.3% (SD 4.9%) for Aβ42; 9.3% (1.5%) for Tau, and 9.4% (2.5%) for pTau, respectively (n = 7–18). To achieve 85% sensitivity, cutoff values were 550 (95% CI 531–570) ng/L for Aβ42; 375 (325–405) ng/L for Tau, and 52 (48–56) ng/L for pTau. Corresponding specificities were 83% (95% CI 76%–89%) for Aβ42, 78% (70%–85%) for Tau, and 68% (60%–77%) for pTau. Logistic regression to investigate the simultaneous impact of the 3 CSF biomarkers on the diagnosis yielded a sensitivity of 93.5% and specificity of 82.7%, at a discrimination line of Aβ42 = 373 + 0.82 x Tau. The area under the ROC curves of Tau and pTau showed significant fluctuation over time.

CONCLUSIONS: CSF biomarkers Aβ42 and Tau can be used as a diagnostic aid in AD. pTau did not have additional value over these 2 markers. Cutoff values, sensitivities, specificities, and discrimination lines depend on the patient groups studied and laboratory experience.

BACKGROUND: Methylmalonic acid (MMA) in plasma or serum is widely used for assessment of vitamin B₁₂ status. However, data are sparse regarding factors, besides renal function, that may influence MMA concentrations. We searched for important determinants of plasma MMA in the general population.

METHODS: In 6946 middle-aged (47–49 years) and elderly (71–74 years) individuals from the Hordaland Homocysteine Study in Norway, we collected anthropometric measurements, lifestyle data, and plasma MMA, vitamin B₁₂, and creatinine measurements. For 5820 individuals, we also collected dietary data.

RESULTS: Age and plasma creatinine were positively associated with plasma MMA, whereas plasma vitamin B₁₂ was negatively associated. These variables together with sex were the strongest determinants of plasma MMA, accounting for 16% of the variation (R² = 0.16). Addition of anthropometric measures and lifestyle and dietary factors only gave slight improvement (total R² = 0.167). Increased plasma MMA was seen when plasma vitamin B₁₂ was <400 pmol/L. In individuals with vitamin B₁₂ ≥400 µmol/L (vitamin B₁₂–replete), the 2.5th–97.5th reference limits for MMA were 0.10–0.28 µmol/L (middle-aged) and 0.10–0.36 µmol/L (elderly). When plotted against creatinine (nomograms), the 97.5th percentile of MMA was similar in men and women but approximately 0.15 µmol/L higher in elderly than middle-aged individuals. Vitamin B₁₂–replete participants had MMA upper limits approximately 0.1 µmol/L (elderly) and 0.04 µmol/L (middle-aged) below those of the unselected population at all creatinine concentrations.

CONCLUSIONS: Identified determinants accounted for <17% of the overall variation in plasma MMA. The difference in MMA between middle-aged and elderly individuals is only partly explained by creatinine and vitamin B₁₂ concentrations.

BACKGROUND: ⁹-Tetrahydrocannabinol (THC) is the primary psychoactive constituent of cannabis and an active cannabinoid pharmacotherapy component. No plasma pharmacokinetic data after repeated oral THC administration are available.

METHODS: Six adult male daily cannabis smokers resided on a closed clinical research unit. Oral THC capsules (20 mg) were administered every 4–8 h in escalating total daily doses (40–120 mg) for 7 days. Free and glucuronidated plasma THC, 11-hydroxy-THC (11-OH-THC), and 11-nor-9-carboxy-THC (THCCOOH) were quantified by 2-dimensional GC-MS during and after dosing.

RESULTS: Free plasma THC, 11-OH-THC, and THCCOOH concentrations 19.5 h after admission (before controlled oral THC dosing) were mean 4.3 (SE 1.1), 1.3 (0.5), and 34.0 (8.4) µg/L, respectively. During oral dosing, free 11-OH-THC and THCCOOH increased steadily, whereas THC did not. Mean peak plasma free THC, 11-OH-THC, and THCCOOH concentrations were 3.8 (0.5), 3.0 (0.7), and 196.9 (39.9) µg/L, respectively, 22.5 h after the last dose. Escherichia coli β-glucuronidase hydrolysis of 264 cannabinoid specimens yielded statistically significant increases in THC, 11-OH-THC, and THCCOOH concentrations (P < 0.001), but conjugated concentrations were underestimated owing to incomplete enzymatic hydrolysis.

CONCLUSIONS: Plasma THC concentrations remained >1 µg/L for at least 1 day after daily cannabis smoking and also after cessation of multiple oral THC doses. We report for the first time free plasma THC concentrations after multiple high-dose oral THC throughout the day and night, and after Escherichia coli β-glucuronidase hydrolysis. These data will aid in the interpretation of plasma THC concentrations after multiple oral doses.

BACKGROUND: Human embryonic stem cells (hESCs) require expression of transcription factor genes POU5F1 (POU class 5 homeobox 1), NANOG (Nanog homeobox), and SOX2 [SRY (sex determining region Y)-box 2] to maintain their capacity for self-renewal and pluripotency. Because of the heterogeneous nature of cell populations, it is desirable to study the gene regulation in single cells. Large and potentially important fluctuations in a few cells cannot be detected at the population scale with microarrays or sequencing technologies. We used single-cell gene expression profiling to study cell heterogeneity in hESCs.

METHODS: We collected 47 single hESCs from cell line SA121 manually by glass capillaries and 57 single hESCs from cell line HUES3 by flow cytometry. Single hESCs were lysed and reverse-transcribed. Reverse-transcription quantitative PCR was then used to measure the expression POU5F1, NANOG, SOX2, and the inhibitor of DNA binding genes ID1, ID2, and ID3. A quantitative noise model was used to remove measurement noise when pairwise correlations were estimated.

RESULTS: The numbers of transcripts per cell varied >100-fold between cells and showed lognormal features. POU5F1 expression positively correlated with ID1 and ID3 expression (P < 0.05) but not with NANOG or SOX2 expression. When we accounted for measurement noise, SOX2 expression was also correlated with ID1, ID2, and NANOG expression (P < 0.05).

CONCLUSIONS: We demonstrate an accurate method for transcription profiling of individual hESCs. Cell-to-cell variability is large and is at least partly nonrandom because we observed correlations between core transcription factors. High fluctuations in gene expression may explain why individual cells in a seemingly undifferentiated cell population have different susceptibilities for inductive cues.

BACKGROUND: Analysis of clinical samples often necessitates identification of low-level somatic mutations within wild-type DNA; however, the selectivity and sensitivity of the methods are often limiting. COLD-PCR (coamplification at lower denaturation temperature–PCR) is a new form of PCR that enriches mutation-containing amplicons to concentrations sufficient for direct sequencing; nevertheless, sequencing itself remains an expensive mutation-screening approach. Conversely, high-resolution melting (HRM) is a rapid, inexpensive scanning method, but it cannot specifically identify the detected mutation. To enable enrichment, quick scanning, and identification of low-level unknown mutations, we combined COLD-PCR with HRM mutation scanning, followed by sequencing of positive samples.

METHODS: Mutation-containing cell-line DNA serially diluted into wild-type DNA and DNA samples from human lung adenocarcinomas containing low-level mutations were amplified via COLD-PCR and via conventional PCR for TP53 (tumor protein p53) exons 6–8, and the 2 approaches were compared. HRM analysis was used to screen amplicons for mutations; mutation-positive amplicons were sequenced.

RESULTS: Dilution experiments indicated an approximate 6- to 20-fold improvement in selectivity with COLD-PCR/HRM. Conventional PCR/HRM exhibited mutation-detection limits of 2%–10% mutant in mixtures with wild-type DNA, whereas COLD-PCR/HRM exhibited detection limits of 0.1%–1%. After HRM analysis of lung adenocarcinoma samples, we detected 7 mutations by both PCR methods in exon 7; however, in exon 8 we detected 9 mutations in COLD-PCR amplicons, compared with only 6 mutations in conventional-PCR amplicons. Furthermore, 94% of the HRM-detected mutations were successfully sequenced with COLD-PCR amplicons, compared with 50% with conventional-PCR amplicons.

CONCLUSIONS: COLD-PCR/HRM improves the mutation-scanning capabilities of HRM and combines high selectivity, convenience, and low cost with the ability to sequence unknown low-level mutations in clinical samples.

BACKGROUND: Although cardiac troponin (cTn) is a cornerstone marker in the assessment and management of patients with acute coronary syndrome (ACS) and heart failure (HF), cTn is not diagnostically specific for any single myocardial disease process. This narrative review discusses increases in cTn that result from acute and chronic diseases, iatrogenic causes, and myocardial injury other than ACS and HF.

CONTENT: Increased cTn concentrations have been reported in cardiac, vascular, and respiratory disease and in association with infectious processes. In cases involving acute aortic dissection, cerebrovascular accident, treatment in an intensive care unit, and upper gastrointestinal bleeding, increased cTn predicts delayed treatment, increased length of hospital stay, and increased mortality. cTn increases are diagnostically and prognostically useful in patients with cardiac inflammatory diseases and in patients with respiratory disease; in respiratory disease cTn can help identify patients who would benefit from aggressive management. In chronic renal failure patients the diagnostic sensitivity of cTn for ACS is decreased, but cTn is prognostic for the development of cardiovascular disease. cTn also provides useful information when increases are attributable to various iatrogenic causes and blunt chest trauma.

SUMMARY: Information on the diagnostic and prognostic uses of cTn in conditions other than ACS and heart failure is accumulating. Although increased cTn in settings other than ACS or heart failure is frequently considered a clinical confounder, the astute physician must be able to interpret cTn as a dynamic marker of myocardial damage, using clinical acumen to determine the source and significance of any reported cTn increase.

BACKGROUND: Epidemiologic studies require identification or typing of microbial strains. Macrorestriction DNA mapping analyzed by pulsed-field gel electrophoresis (PFGE) is considered the current gold standard of genomic typing. This technique, however, is difficult to implement because it is labor-intensive and difficult to automate, it requires a long time to obtain results, and results often vary between laboratories.

METHODS: We used direct linear analysis (DLA), which uses a single reagent set and long fragments of microbial genomic DNA to identify various microbes. In this technique, an automated system extracts fragments exceeding 100 kb from restriction enzyme digests of genomic DNA from microbial isolates and hybridizes them with a sequence-dependent fluorescent tag. These fragments are then stretched in a microfluidics chip, and the patterns of the distribution of the tags are discerned with fluorescence confocal microscopy. The tag pattern on each DNA fragment is compared with a database of known microbial DNA sequences or with measured patterns of other microbial DNAs.

RESULTS: We used DLA to type 71 Staphylococcus aureus strains. Of these, 9 had been sequenced, 10 were representative of the major pulsed-field types present in the US, and 52 were isolated recently in a hospital in Cambridge, MA. Matching DNA fragments were identified in different samples by a clustering algorithm and were used to quantify the similarities of the strains.

CONCLUSIONS: DLA-based strain typing is a powerful technique with a resolution comparable to macrorestriction mapping with PFGE, but DLA is faster, more automated, and more reproducible.

BACKGROUND: The emergence of a novel pandemic human strain of influenza A (H1N1/09) has clearly demonstrated the need for flexible tools enabling the rapid development of new diagnostic methods.

METHODS: We designed a set of reverse-transcription quantitative real-time PCR (RT-qPCR) assays based on the Universal ProbeLibrary (UPL)—a collection of 165 presynthesized, fluorescence-labeled locked nucleic acid (LNA) hydrolysis probes—specifically to detect the novel influenza A virus. We evaluated candidate primer/UPL-probe pairs with 28 novel influenza A/H1N1/09 patient samples of European and Mexican origin.

RESULTS: Of 14 assays in the hemagglutinin (HA) and neuraminidase (NA) genes, 12 detected viral nucleic acids from diluted patient samples without need for further optimization. We characterized the diagnostic specificity of the 2 best-performing assays with a set of samples comprising various influenza virus strains of human and animal origin that showed no cross-reactivity. The diagnostic sensitivity of these 2 primer/probe combinations was in the range of 100–1000 genomic copies/mL. In comparison to a reference assay recommended by the German health authorities, the analytical sensitivities and specificities of the assays were equivalent.

CONCLUSIONS: Facing the emergence of novel influenza A/H1N1/09, we were able to develop, within 2 days, a set of sensitive and specific RT-qPCR assays for the laboratory diagnosis of suspected cases. H1N1/09 served as a model to show the feasibility of the UPL approach for the expedited development of new diagnostic assays to detect emerging pathogens.

BACKGROUND: We measured plasma PCSK9 concentrations in healthy men with a PCSK9 (proprotein convertase subtilisin/kexin type 9) loss-of-function variant (p.R46L), in statin-treated patients with a clinical diagnosis of familial hypercholesterolemia (FH) and carrying a PCSK9 gain-of-function mutation (p.D374Y), and in statin-treated patients with FH due to different genetic causes.

METHODS: PCSK9 was measured with a previously described ELISA.

RESULTS: In 81 healthy middle-aged Caucasian men, the PCSK9 concentration was significantly associated with the concentrations of total cholesterol (r = 0.42; P < 0.0001), LDL cholesterol (r = 0.34; P = 0.01), and triglycerides (r = 0.25; P = 0.02). In p.R46L carriers, mean (SD) concentrations of PCSK9 were 15% lower than in RR individuals [65.5 µg/L (21.6 µg/L) vs 77.5 µg/L (18.2 µg/L); P = 0.03]. In patients with the p.D374Y variant (n = 7), the mean PCSK9 concentration was significantly lower than in the combined group of patients with an LDLR (low density lipoprotein receptor) mutation (n = 25), an APOB [apolipoprotein B (including Ag(x) antigen)] variant encoding p.R3527Q (n = 6), or no detectable mutation (n = 14) [96.4 µg/L (42.5 µg/L) vs 151.6 µg/L (69.6 µg/L); P = 0.02]. Two of the 14 patients with no mutation had PCSK9 concentrations below the mean for p.D374Y carriers; sequencing of the PCSK9 gene and promoter revealed no mutations. Among 409 FH patients, we identified 6 carriers of the promoter variant -287G>A (1.5%), a frequency similar to that (1.0%) previously reported for 2772 healthy men in the UK. In neither group was the -287G>A variant associated with differences in lipid traits.

CONCLUSIONS: The loss-of-function p.R46L variant is associated with the expected lower concentrations of circulating PCSK9; the gain-of-function p.D374Y mutation is also associated with lower concentrations, presumably because of the higher affinity of this variant for the LDL receptor and its more rapid clearance. In treated FH patients, a low plasma PCSK9 concentration does not appear to be a useful screening tool for identifying novel PCSK9 mutations.

BACKGROUND: Urine myoglobin continues to be used as a marker of rhabdomyolysis, particularly to assess risk of developing acute renal failure and evaluate treatment success. We sought to determine the predictive validity of urine myoglobin (uMb) for acute renal failure (ARF) in patients with suspected rhabdomyolysis.

METHODS: We performed a broad systemic review of the literature from January 1980 to December 2006 using the search terms myoglobin$ AND (renal OR ARF OR kidney). Only primary studies published in English where uMb measurement was related to ARF were included.

RESULTS: Of 1602 studies screened, 52 met all selection criteria. The studies covered a wide spectrum of etiologies for rhabdomyolysis, dissimilar diagnostic criteria for ARF and rhabdomyolysis, and various methods of uMb measurement and were mostly case series (n = 32). There was poor reporting on the uMb method, and 17 studies failed to provide any information about the method. The reporting of clinical criteria for ARF with respect to timing, description, performance, and interpretation also lacked adequate detail for replication. Eight studies (total 295 patients) had data for 2-by-2 tables. Sensitivity of the uMb test was 100% in 5 of the 8 studies, specificity varied widely (15% to 88%), and CIs around these measures were high. Pooling of data was not possible because of study heterogeneity.

CONCLUSIONS: There is inadequate evidence evaluating the use of uMb as a predictor of ARF in patients with suspected rhabdomyolysis.

BACKGROUND: Routine prenatal diagnosis of chromosomal anomalies is based on invasive procedures, which carry a risk of approximately 1%–2% for loss of pregnancy. An alternative to these inherently invasive techniques is to isolate fetal DNA circulating in the pregnant mother's plasma. Free fetal DNA circulates in maternal plasma primarily as fragments of lengths <500 bp, with a majority being <300 bp. Separating these fragments by size facilitates an increase in the ratio of fetal to maternal DNA.

METHODS: We describe our development of a microsystem for the enrichment and isolation of cell-free fetal DNA from maternal plasma. The first step involves a high-volume extraction from large samples of maternal plasma. The resulting 80-µL eluate is introduced into a polymeric microsystem within which DNA is trapped and preconcentrated. This step is followed by a transient isotachophoresis step in which the sample stacks within a neighboring channel for subsequent size separation and is recovered via an outlet at the end of the channel.

RESULTS: Recovered fractions of fetal DNA were concentrated 4–8 times over those in preconcentration samples. With plasma samples from pregnant women, we detected the fetal SRY gene (sex determining region Y) exclusively in the fragment fraction of <500 bp, whereas a LEP gene (leptin) fragment was detected in both the shorter and longer recovery fractions.

CONCLUSIONS: The microdevice we have described has the potential to open new perspectives in noninvasive prenatal diagnosis by facilitating the isolation of fetal DNA from maternal plasma in an integrated, inexpensive, and easy-to-use microsystem.