Analytical Validation of Esopredict, an Epigenetic Prognostic Assay for Patients with Barrett's Esophagus.

EsopredictTM is a prognostic assay that risk-stratifies Barrett's esophagus patients to predict future progression to high-grade dysplasia (HGD) or esophageal adenocarcinoma (EAC). Established based on foundational studies at Johns Hopkins University, a risk algorithm was developed and clinically validated in two independent studies (n = 320). EsopredictTM is currently offered as a clinical test under the Clinical Laboratory Improvement Amendments (CLIA) guidelines. Here we present the analytical validation by repeated testing of FFPE tissues (n = 26 patients), cell lines, and contrived DNA controls to determine assay performance regarding analytical sensitivity (as defined by the limit of detection (LOD)), analytical specificity (as defined by the limit of blank (LOB)), accuracy as determined from the average positive and negative agreement, repeatability, and reproducibility. The LOD for the assay at 1.5% DNA methylation was significantly higher than the LOB, as determined by an unmethylated DNA control (0% methylated DNA). Inter- and intra-assay average positive agreement (APA) were 88% and 94%, respectively, while average negative agreement (ANA) values were 90% and 94%, respectively. Average inter- and intra-assay precision were <9% and <5% coefficient of variation (CV), respectively. These results confirm that EsopredictTM is a highly reproducible, sensitive, and specific risk categorization assay for the prediction of progression to HGD or EAC within 5 years.

Clinical performance and utility: A microsimulation model to inform the design of screening trials for a multi-cancer early detection test.

OBJECTIVES: Designing cancer screening trials for multi-cancer early detection (MCED) tests presents a significant methodology challenge, as natural histories of cell-free DNA-shedding cancers are not yet known. A microsimulation model was developed to project the performance and utility of an MCED test in cancer screening trials. METHODS: Individual natural history of preclinical progression through cancer stages for 23 cancer classes was simulated by a stage-transition model under a broad range of cancer latency parameters. Cancer incidences and stage distributions at clinical presentation in simulated trials were set to match the data from Surveillance, Epidemiology, and End Results program. One or multiple rounds of annual screening using a targeted methylation-based MCED test (GalleriⓇ) was conducted to detect preclinical cancers. Mortality benefit of early detection was simulated by a stage-shift model. RESULTS: In simulated trials, accounting for healthy volunteer effect and varying test sensitivity, positive predictive value in the prevalence screening round reached 48% to 61% in 6 natural history scenarios. After 3 rounds of annual screening, the cumulative proportions of stage I/II cancers increased by approximately 9% to 14%, the incidence of stage IV cancers was reduced by 37% to 46%, the reduction of stages III and IV cancer incidences was 9% to 24%, and the reduction of mortality reached 13% to 16%. Greater reductions of late-stage cancers and cancer mortality were achieved by five rounds of MCED screening. CONCLUSIONS: Simulation results guide trial design and suggest that adding this MCED test to routine screening in the United States may shift cancer detection to earlier stages, and potentially save lives.

Circulating cell-free messenger RNA secretome characterization of primary sclerosing cholangitis.

BACKGROUND: Primary sclerosing cholangitis (PSC) is a rare chronic cholestatic liver disease characterized by multifocal bile duct strictures. To date, underlying molecular mechanisms of PSC remain unclear, and therapeutic options are limited. METHODS: We performed cell-free messenger RNA (cf-mRNA) sequencing to characterize the circulating transcriptome of PSC and noninvasively investigate potentially bioactive signals that are associated with PSC. Serum cf-mRNA profiles were compared among 50 individuals with PSC, 20 healthy controls, and 235 individuals with NAFLD. Tissue and cell type-of-origin genes that are dysregulated in subjects with PSC were evaluated. Subsequently, diagnostic classifiers were developed using PSC dysregulated cf-mRNA genes. RESULTS: Differential expression analysis of the cf-mRNA transcriptomes of PSC and healthy controls resulted in identification of 1407 dysregulated genes. Furthermore, differentially expressed genes between PSC and healthy controls or NAFLD shared common genes known to be involved in liver pathophysiology. In particular, genes from liver- and specific cell type-origin, including hepatocyte, HSCs, and KCs, were highly abundant in cf-mRNA of subjects with PSC. Gene cluster analysis revealed that liver-specific genes dysregulated in PSC form a distinct cluster, which corresponded to a subset of the PSC subject population. Finally, we developed a cf-mRNA diagnostic classifier using liver-specific genes that discriminated PSC from healthy control subjects using gene transcripts of liver origin. CONCLUSIONS: Blood-based whole-transcriptome cf-mRNA profiling revealed high abundance of liver-specific genes in sera of subjects with PSC, which may be used to diagnose patients with PSC. We identified several unique cf-mRNA profiles of subjects with PSC. These findings may also have utility for noninvasive molecular stratification of subjects with PSC for pharmacotherapy safety and response studies.

Redefining breast cancer subtypes to guide treatment prioritization and maximize response: Predictive biomarkers across 10 cancer therapies.

Using pre-treatment gene expression, protein/phosphoprotein, and clinical data from the I-SPY2 neoadjuvant platform trial (NCT01042379), we create alternative breast cancer subtypes incorporating tumor biology beyond clinical hormone receptor (HR) and human epidermal growth factor receptor-2 (HER2) status to better predict drug responses. We assess the predictive performance of mechanism-of-action biomarkers from ∼990 patients treated with 10 regimens targeting diverse biology. We explore >11 subtyping schemas and identify treatment-subtype pairs maximizing the pathologic complete response (pCR) rate over the population. The best performing schemas incorporate Immune, DNA repair, and HER2/Luminal phenotypes. Subsequent treatment allocation increases the overall pCR rate to 63% from 51% using HR/HER2-based treatment selection. pCR gains from reclassification and improved patient selection are highest in HR+ subsets (>15%). As new treatments are introduced, the subtyping schema determines the minimum response needed to show efficacy. This data platform provides an unprecedented resource and supports the usage of response-based subtypes to guide future treatment prioritization.

Noninvasive stratification of nonalcoholic fatty liver disease by whole transcriptome cell-free mRNA characterization.

Hepatic fibrosis stage is the most important determinant of outcomes in patients with nonalcoholic fatty liver disease (NAFLD). There is an urgent need for noninvasive tests that can accurately stage fibrosis and determine efficacy of interventions. Here, we describe a novel cell-free (cf)-mRNA sequencing approach that can accurately and reproducibly profile low levels of circulating mRNAs and evaluate the feasibility of developing a cf-mRNA-based NAFLD fibrosis classifier. Using separate discovery and validation cohorts with biopsy-confirmed NAFLD (n = 176 and 59, respectively) and healthy subjects (n = 23), we performed serum cf-mRNA RNA-Seq profiling. Differential expression analysis identified 2,498 dysregulated genes between patients with NAFLD and healthy subjects and 134 fibrosis-associated genes in patients with NAFLD. Comparison between cf-mRNA and liver tissue transcripts revealed significant overlap of fibrosis-associated genes and pathways indicating that the circulating cf-mRNA transcriptome reflects molecular changes in the livers of patients with NAFLD. In particular, metabolic and immune pathways reflective of known underlying steatosis and inflammation were highly dysregulated in the cf-mRNA profile of patients with advanced fibrosis. Finally, we used an elastic net ordinal logistic model to develop a classifier that predicts clinically significant fibrosis (F2-F4). In an independent cohort, the cf-mRNA classifier was able to identify 50% of patients with at least 90% probability of clinically significant fibrosis. We demonstrate a novel and robust cf-mRNA-based RNA-Seq platform for noninvasive identification of diverse hepatic molecular disruptions and for fibrosis staging with promising potential for clinical trials and clinical practice.NEW & NOTEWORTHY This work is the first study, to our knowledge, to utilize circulating cell-free mRNA sequencing to develop an NAFLD diagnostic classifier.

Fungal endophytes in germinated seeds of the common bean, Phaseolus vulgaris.

We conducted a survey of fungal endophytes in 582 germinated seeds belonging to 11 Colombian cultivars of the common bean (Phaseolus vulgaris). The survey yielded 394 endophytic isolates belonging to 42 taxa, as identified by sequence analysis of the ribosomal DNA internal transcribed spacer (ITS) region. Aureobasidium pullulans was the dominant endophyte, isolated from 46.7 % of the samples. Also common were Fusarium oxysporum, Xylaria sp., and Cladosporium cladosporioides, but found in only 13.4 %, 11.7 %, and 7.6 % of seedlings, respectively. Endophytic colonization differed significantly among common bean cultivars and seedling parts, with the highest colonization occurring in the first true leaves of the seedlings.

A quantitative analysis of torn and cut duct tape physical end matching.

Forensic scientists are often asked to physically compare duct tape samples found in association with criminal activity. This study was designed to statistically evaluate the error and accuracy rates associated with duct tape physical end matching. The experimental design consisted of a blind study in which three researchers independently analyzed eight types of tape subjected to four methods of separation. The lowest mean accuracy observed was 98.15%, the highest mean false-positive rate observed was 3.33%, and the highest mean false-negative rate was 2.67%. Overall, high accuracy with low false-positive and false-negative error rates were observed. This study confirms the use of physical end matching in identifying duct tape samples as matching or nonmatching and that the differences between analysts, brands, tape grades, tape color, and methods of separation have varying contributions to misidentifications and inconclusive results. This study also demonstrates the importance of peer review in duct tape analysis.

Children's tonsillectomy experiences: influencing factors.

The aim of this study was to explore factors influencing children's (7-13 years) tonsillectomy experiences and outcomes. A prospective, repeated measures, design was used to investigate the effect of age, gender, ethnicity, time, and previous pain, hospitalization and surgery on children's (N = 60) perceptions of anxiety, pain intensity, quality of pain and sleep, and oral intake. The relationship between postoperative pain and anxiety was also examined. Using a diary, three days of data were collected. Descriptive statistics, Pearson correlation coefficient, and a mixed linear regression model were used for analysis. Children's tonsillectomy experiences and outcomes were affected by time, previous experience, age, and anxiety. Moderate correlations were found between level of anxiety and pain intensity. These findings provide clinicians with additional knowledge to guide their perioperative practice and care of children.

Magnitude and complexity of rectal mucosa HIV-1-specific CD8+ T-cell responses during chronic infection reflect clinical status.

BACKGROUND: The intestinal mucosa displays robust virus replication and pronounced CD4+ T-cell loss during acute human immunodeficiency virus type 1 (HIV-1) infection. The ability of HIV-specific CD8+ T-cells to modulate disease course has prompted intensive study, yet the significance of virus-specific CD8+ T-cells in mucosal sites remains unclear. METHODS AND FINDINGS: We evaluated five distinct effector functions of HIVgag-specific CD8+ T-cells in rectal mucosa and blood, individually and in combination, in relationship to clinical status and antiretroviral therapy (ART). In subjects not on ART, the percentage of rectal Gag-specific CD8+ T-cells capable of 3, 4 or 5 simultaneous effector functions was significantly related to blood CD4 count and inversely related to plasma viral load (PVL) (p<0.05). Polyfunctional rectal CD8+ T-cells expressed higher levels of MIP-1beta and CD107a on a per cell basis than mono- or bifunctional cells. The production of TNFalpha, IFN-gamma, and CD107a by Gag-specific rectal CD8+ T-cells each correlated inversely (p<0.05) with PVL, and MIP-1beta expression revealed a similar trend. CD107a and IFN-gamma production were positively related to blood CD4 count (p<0.05), with MIP-1beta showing a similar trend. IL-2 production by rectal CD8+ T-cells was highly variable and generally low, and showed no relationship to viral load or blood CD4 count. CONCLUSIONS: The polyfunctionality of rectal Gag-specific CD8+ T-cells appears to be related to blood CD4 count and inversely related to PVL. The extent to which these associations reflect causality remains to be determined; nevertheless, our data suggest a potentially important role for mucosal T-cells in limiting virus replication during chronic infection.

Children's pre-operative tonsillectomy pain education: clinical outcomes.

OBJECTIVE: To examine the effects of pre-operative tonsillectomy pain education on children's (7-13 years) self-reported pre-operative anxiety and post-operative clinical outcomes (i.e., anxiety, pain intensity, quality of pain and sleep, oral intake, perceptions of pre-operative education, and pain expectation). METHOD: A prospective, repeated measures, quasi-experimental design using an age appropriate pain education booklet (n = 30) and a standard care comparison group (n = 30) was employed to investigate children's pre- and post-education anxiety and post-operative tonsillectomy with or without adenoidectomy subjective experiences in the hospital and home settings. Group comparisons were performed using the Wilcoxon test, Fisher's exact test, repeated measures analysis of variance, and mixed model regression. RESULTS: There were no significant differences between groups for measures of anxiety, pain intensity, quality of pain and sleep, oral intake, or expected pain. There was no change in anxiety before or after pre-operative education (P = 0.85). Ninety-six percent (n = 25) of the children in the intervention group reported that pre-operative pain education helped with their post-operative pain and 72% (n = 16) in the control group stated that it would be helpful to learn about pain before surgery. The majority of children in both the intervention and control groups (96%, 91%, respectively) stated learning about the 0-10 numeric pain intensity scale helped or would be helpful to learn pre-operatively. CONCLUSION: Pre-operative pain education did not affect anxiety. Children valued pre-operative pain education. Pre-operative pain education may influence children's perceptions of medical care.

Initial validation of a numeric zero to ten scale to measure children's state anxiety.

BACKGROUND: Although children experience physical and behavioral consequences from anxiety in many health care settings, anxiety assessment and subsequent management is not often performed because of the lack of clinically useful subjective scales. Current state anxiety scales are either observational or multidimensional self-report measures requiring significant clinician and patient time. Because anxiety is subjective, in this pilot study, we evaluated the validity of a self-report numeric 0-10 anxiety scale that is easy to administer to children in the clinical setting. METHODS: A descriptive correlation research design was used to determine the concurrent validity for a numeric 0-10 anxiety scale with the state portion of the State-Trait Anxiety Inventory for Children (STAIC). During clinic preoperative visits, 60 children, 7-13 yr, provided anxiety scores for the 0-10 scale and the STAIC pre- and posteducation. Simple linear regression and Pearson correlation were performed to determine the strength of the relationship. RESULTS: STAIC was associated with the anxiety scale both preeducation (beta = 1.20, SE[beta] = 0.34, F[1,58] = 12.74, P = 0.0007) and posteducation (beta = 1.97, SE[beta]) = 0.31, F[1,58] = 40.11, P < 0.0001). Correlations were moderate for pre-education (r = 0.424) and posteducation (r = 0.639). CONCLUSIONS: This initial study supports the validity of the numeric 0-10 anxiety self-report scale to assess state anxiety in children as young as 7 yr.

Influence of Verapamil and Cyclosporin A on bile acid metabolism and transport in rat liver slices.

Verapamil (V) is a specific inhibitor of the P-glycoprotein (mdr1) in the hepatocyte canalicular membrane. Cyclosporin A (CsA) as an essential immunosuppressive drug has potentially cholestatic adverse effects on the liver, but increases the expression of mdr1. In precision-cut liver slices from 34- to 40-day-old male Wistar rats 26 individual free and conjugated bile acids (BAs) as markers of hepatic transport and synthesis function were analysed after 4 h incubation with V (100 microM) or CsA (5 microM) in Krebs-Henseleit buffer. Some slices were loaded with cholic acid (CA 5 microM) or tauro-ursodeoxycholic acid (T-UDCA 5 microM) to investigate the V and CsA effects under conditions of BA supplementation. BAs were determined in tissue and medium by HPLC with postcolumn derivatisation and fluorescence detection. V and CsA, influencing different targets in BA transport, enhanced slice concentrations of T- and glyco- (G-) conjugated CA only when exogenous CA was given additionally. This BA accumulation in tissue is more reflected at decreased medium concentrations of these BAs after V and CsA incubations. Both V and CsA also inhibited CA uptake into the slices. The acidic chenodeoxycholic acid (CDCA) synthesis pathway is disturbed: T- and G-CDCA concentrations are diminished in slices and medium after V and CsA incubations. T-UDCA plus V or CsA enhanced not only its own slice concentration but also the concentration of the trihydroxylated tauro-muricholic acid (T-beta-MCA), reflecting the conversion of the accumulated dihydroxylated T-UDCA into the T-beta-MCA. The similar effects of V and CsA on BA transport and metabolism can be explained by mdr1 mediated disturbances of cellular ATP transport rather than by inhibition of individual BA transporters.

Bile acid transport and metabolism in rat liver slices.

To further characterise precision-cut liver slices from 34- to 40-day-old male rats as an in vitro model for bile acid (BA) metabolism and transport, the effect of the primary BAs cholic (CA, 5 microM) and chenodeoxycholic acid (CDCA, 0.15 and 0.75 microM) as well as of the therapeutically used tauroursodeoxycholic acid (T-UDCA, 5 microM) on BA profiles was investigated. After 4 h incubation in 5 ml Krebs-Henseleit buffer (KHB) 26 individual BAs were determined in slices (50 mg liver/5 ml KHB) and medium by HPLC with postcolumn derivatisation and fluorescence detection. In control incubations, mean total BA concentrations were 5.09 nmol/50 mg liver (101.80 nmol/g liver) in slices and 25.71 nmol/5 ml KHB, among them 72% taurine-(T-), 22% glycine-(G-) conjugated and 6% free BAs in tissue and medium. The main BAs were beta-muricholic (beta-MCA and conjugates) and cholic acids (CA and conjugates) in tissue and medium. The following results were obtained after addition of CDCA, CA, and T-UDCA, respectively, to the KHB. The toxic CDCA was quantitatively converted mainly to T-UDCA and taurohyodeoxycholic (T-HDCA) acid. CA was conjugated in equal shares to T- and G-CA, whereas T-UDCA was enriched in slices and hydroxylated half to T-beta-MCA, which is the main BA in rats. In conclusion, rat liver slices are highly effective not only in uptake, conjugation and excretion of BAs but also in conversion of strong detergent into less toxic BAs.