TP53 mutation prevalence in normal airway epithelium as a biomarker for lung cancer risk.

BACKGROUND: There is a need for biomarkers that improve accuracy compared with current demographic risk indices to detect individuals at the highest lung cancer risk. Improved risk determination will enable more effective lung cancer screening and better stratification of lung nodules into high or low-risk category. We previously reported discovery of a biomarker for lung cancer risk characterized by increased prevalence of TP53 somatic mutations in airway epithelial cells (AEC). Here we present results from a validation study in an independent retrospective case-control cohort. METHODS: Targeted next generation sequencing was used to identify mutations within three TP53 exons spanning 193 base pairs in AEC genomic DNA. RESULTS: TP53 mutation prevalence was associated with cancer status (P < 0.001). The lung cancer detection receiver operator characteristic (ROC) area under the curve (AUC) for the TP53 biomarker was 0.845 (95% confidence limits 0.749-0.942). In contrast, TP53 mutation prevalence was not significantly associated with age or smoking pack-years. The combination of TP53 mutation prevalence with PLCOM2012 risk score had an ROC AUC of 0.916 (0.846-0.986) and this was significantly higher than that for either factor alone (P < 0.03). CONCLUSIONS: These results support the validity of the TP53 mutation prevalence biomarker and justify taking additional steps to assess this biomarker in AEC specimens from a prospective cohort and in matched nasal brushing specimens as a potential non-invasive surrogate specimen.

Cyclic GMP-AMP synthase contributes to epithelial homeostasis in intestinal inflammation via Beclin-1-mediated autophagy.

Inflammatory bowel disease (IBD) represents a set of idiopathic and chronic inflammatory diseases of the gastrointestinal tract. Central to the pathogenesis of IBD is a dysregulation of normal intestinal epithelial homeostasis. cGAS is a DNA-sensing receptor demonstrated to promote autophagy, a mechanism that removes dysfunctional cellular components. Beclin-1 is a crucial protein involved in the initiation of autophagy. We hypothesized that cGAS plays a key role in intestinal homeostasis by upregulating Beclin-1-mediated autophagy. We evaluated intestinal cGAS levels in humans with IBD and in murine colonic tissue after performing a 2% dextran sulfate sodium (DSS) colitis model. Autophagy and cell death mechanisms were studied in cGAS KO and WT mice via qPCR, WB analysis, H&E, IF, and TUNEL staining. Autophagy was measured in stimulated intestinal epithelial cells (IECs) via WB analysis. Our data demonstrates cGAS to be upregulated during human and murine colitis. Furthermore, cGAS deficiency leads to worsened colitis and decreased levels of autophagy proteins including Beclin-1 and LC3-II. Co-IP demonstrates a direct binding between cGAS and Beclin-1 in IECs. Transfection of cGAS in stimulated HCT-116 cells leads to increased autophagy. IECs isolated from cGAS KO have diminished autophagic flux. cGAS KO mice subjected to DSS have increased cell death and cleaved caspase-3. Lastly, treatment of cGAS KO mice with rapamycin decreased the severity of colitis. Our data suggest that cGAS maintains intestinal epithelial homeostasis during human IBD and murine colitis by upregulating Beclin-1-mediated autophagy and preventing IEC death. Rescue of autophagy can attenuate the severity of colitis associated with cGAS deficiency.

Biosimilars for Pediatric Patients With Inflammatory Bowel Disease: Pediatric Gastroenterology Clinical Practice Survey.

BACKGROUND: Biosimilars are biological agents that have been demonstrated to have similar safety and efficacy profiles as the originator. The objective of this study was to evaluate the perspectives of pediatric gastroenterologists in the United States (U.S.) toward biosimilar use and to explore factors that impact their comfort level with prescribing infliximab biosimilars. METHODS: A cross-sectional survey was developed and distributed to pediatric gastroenterology physicians from the U.S. via a listserv (Pediatric gastroenterology Bulletin Board). Respondent's demographics were recorded. Using a 6-point Likert scale, the survey assessed the respondent's perceptions toward biosimilars and initiating switches from the originator to biosimilar agent along with factors impacting provider's comfort level. Fischer exact tests were used to detect statistically significant differences in responses for hypotheses of interest. RESULTS: One hundred thirty-nine pediatric gastroenterologists completed the online survey (response rate 5.4%). Eighty-seven percent of respondents reported being comfortable prescribing infliximab biosimilars to anti-tumor necrosis factor naive patients, and 69% reported being comfortable doing a one-time switch if the patient was in clinical remission. Factors that negatively impacted a respondent's comfort level included respondents not practicing at an ImproveCareNow (ICN) center and managing less than 50 patients with inflammatory bowel diseases (IBD). CONCLUSIONS: Nearly 90% of pediatric gastroenterologists felt comfortable prescribing an infliximab biosimilar, and 70% felt comfortable with a one-time switch to the biosimilar if the patient was in clinical remission. Involvement in ICN a learning health system and caring for higher numbers of patients with IBD was associated with increased provider comfort with biosimilar use.

P046 Tofacitinib Induced Resolution of Severe Colitis and Reactive Atypia in an Adolescent Patient With IBD.

CASE: Tofacitinib is an anti-JAK/STAT small molecule approved for treatment of adults (but not children and adolescents) with moderate to severe ulcerative colitis. Data is limited in children and teens although two major centers have shown efficacy as both mono- and dual - combination therapy using tofacitinib in pediatric patients refractory to anti-TNF agents. We present a 16-year-old female diagnosed with inflammatory ileocolonic Crohn's disease without upper gastrointestinal involvement after presenting with several months of abdominal pain, diarrhea, and unintentional weight loss. Laboratory evaluation was notable for normal inflammatory markers, albumin and complete blood count and an elevated stool lactoferrin. Initial endoscopic evaluation revealed moderate to severe pancolitis and patchy ileitis; biopsies noted mild chronic active ileitis and moderate to severe chronic active pancolitis without dysplastic or atypical changes. She was started on infliximab for induction and maintenance therapy and dosage was increased due to suboptimal levels and marginal symptomatic improvement. However, despite increased dosing plus a course of budesonide (Uceris), she had minimal improvement in her symptoms and ongoing elevation of her lactoferrin. Given an equivocal result on a Clostridium difficile testing (GDH antigen positive only), she was started on oral vancomycin which resulted in mild improvement, but not resolution, of diarrhea and abdominal pain. This was continued after completion of a 14-day course (and subsequent negative testing) due to increased stool frequency with discontinuation of the medication and improvement with reinitiating it. She had severe pancolitis (Mayo 2 - 3) but normal TI on repeat colonoscopy 5 months after diagnosis. Biopsies (reviewed by a panel of adult GI pathologists) were notable for reactive atypia with features concerning for early dysplasia in the ascending and descending colon. Due to disease severity and rapid progression plus histologic changes concerning for possible dysplasia despite optimized therapy with infliximab and repeat negative C. difficile testing, she was started on tofacitinib 10 mg twice daily along with oral vancomycin. She had complete resolution of diarrhea, abdominal pain, and early satiety within a week; repeat fecal lactoferrin was negative (<30). She underwent repeat colonoscopy with chromoendoscopy 5 months after initiation of tofacitinib which revealed mild acute ileitis but no active colonic inflammation, atypia or dysplasia. This is the first report to our knowledge that an adolescent patient with colonic predominant Crohn's disease has complete resolution of atypia and possible early dysplasia with tofacitinib therapy.

Technical advance in targeted NGS analysis enables identification of lung cancer risk-associated low frequency TP53, PIK3CA, and BRAF mutations in airway epithelial cells.

BACKGROUND: Standardized Nucleic Acid Quantification for SEQuencing (SNAQ-SEQ) is a novel method that utilizes synthetic DNA internal standards spiked into each sample prior to next generation sequencing (NGS) library preparation. This method was applied to analysis of normal appearing airway epithelial cells (AEC) obtained by bronchoscopy in an effort to define a somatic mutation field effect associated with lung cancer risk. There is a need for biomarkers that reliably detect those at highest lung cancer risk, thereby enabling more effective screening by annual low dose CT. The purpose of this study was to test the hypothesis that lung cancer risk is characterized by increased prevalence of low variant allele frequency (VAF) somatic mutations in lung cancer driver genes in AEC. METHODS: Synthetic DNA internal standards (IS) were prepared for 11 lung cancer driver genes and mixed with each AEC genomic (g) DNA specimen prior to competitive multiplex PCR amplicon NGS library preparation. A custom Perl script was developed to separate IS reads and respective specimen gDNA reads from each target into separate files for parallel variant frequency analysis. This approach identified nucleotide-specific sequencing error and enabled reliable detection of specimen mutations with VAF as low as 5 × 10- 4 (0.05%). This method was applied in a retrospective case-control study of AEC specimens collected by bronchoscopic brush biopsy from the normal airways of 19 subjects, including eleven lung cancer cases and eight non-cancer controls, and the association of lung cancer risk with AEC driver gene mutations was tested. RESULTS: TP53 mutations with 0.05-1.0% VAF were more prevalent (p < 0.05) and also enriched for tobacco smoke and age-associated mutation signatures in normal AEC from lung cancer cases compared to non-cancer controls matched for smoking and age. Further, PIK3CA and BRAF mutations in this VAF range were identified in AEC from cases but not controls. CONCLUSIONS: Application of SNAQ-SEQ to measure mutations in the 0.05-1.0% VAF range enabled identification of an AEC somatic mutation field of injury associated with lung cancer risk. A biomarker comprising TP53, PIK3CA, and BRAF somatic mutations may better stratify individuals for optimal lung cancer screening and prevention outcomes.

RNAseq analysis of bronchial epithelial cells to identify COPD-associated genes and SNPs.

BACKGROUND: There is a need for more powerful methods to identify low-effect SNPs that contribute to hereditary COPD pathogenesis. We hypothesized that SNPs contributing to COPD risk through cis-regulatory effects are enriched in genes comprised by bronchial epithelial cell (BEC) expression patterns associated with COPD. METHODS: To test this hypothesis, normal BEC specimens were obtained by bronchoscopy from 60 subjects: 30 subjects with COPD defined by spirometry (FEV1/FVC < 0.7, FEV1% < 80%), and 30 non-COPD controls. Targeted next generation sequencing was used to measure total and allele-specific expression of 35 genes in genome maintenance (GM) genes pathways linked to COPD pathogenesis, including seven TP53 and CEBP transcription factor family members. Shrinkage linear discriminant analysis (SLDA) was used to identify COPD-classification models. COPD GWAS were queried for putative cis-regulatory SNPs in the targeted genes. RESULTS: On a network basis, TP53 and CEBP transcription factor pathway gene pair network connections, including key DNA repair gene ERCC5, were significantly different in COPD subjects (e.g., Wilcoxon rank sum test for closeness, p-value = 5.0E-11). ERCC5 SNP rs4150275 association with chronic bronchitis was identified in a set of Lung Health Study (LHS) COPD GWAS SNPs restricted to those in putative regulatory regions within the targeted genes, and this association was validated in the COPDgene non-hispanic white (NHW) GWAS. ERCC5 SNP rs4150275 is linked (D' = 1) to ERCC5 SNP rs17655 which displayed differential allelic expression (DAE) in BEC and is an expression quantitative trait locus (eQTL) in lung tissue (p = 3.2E-7). SNPs in linkage (D' = 1) with rs17655 were predicted to alter miRNA binding (rs873601). A classifier model that comprised gene features CAT, CEBPG, GPX1, KEAP1, TP73, and XPA had pooled 10-fold cross-validation receiver operator characteristic area under the curve of 75.4% (95% CI: 66.3%-89.3%). The prevalence of DAE was higher than expected (p = 0.0023) in the classifier genes. CONCLUSIONS: GM genes comprised by COPD-associated BEC expression patterns were enriched for SNPs with cis-regulatory function, including a putative cis-rSNP in ERCC5 that was associated with COPD risk. These findings support additional total and allele-specific expression analysis of gene pathways with high prior likelihood for involvement in COPD pathogenesis.

A lung cancer risk classifier comprising genome maintenance genes measured in normal bronchial epithelial cells.

BACKGROUND: Annual low dose CT (LDCT) screening of individuals at high demographic risk reduces lung cancer mortality by more than 20%. However, subjects selected for screening based on demographic criteria typically have less than a 10% lifetime risk for lung cancer. Thus, there is need for a biomarker that better stratifies subjects for LDCT screening. Toward this goal, we previously reported a lung cancer risk test (LCRT) biomarker comprising 14 genome-maintenance (GM) pathway genes measured in normal bronchial epithelial cells (NBEC) that accurately classified cancer (CA) from non-cancer (NC) subjects. The primary goal of the studies reported here was to optimize the LCRT biomarker for high specificity and ease of clinical implementation. METHODS: Targeted competitive multiplex PCR amplicon libraries were prepared for next generation sequencing (NGS) analysis of transcript abundance at 68 sites among 33 GM target genes in NBEC specimens collected from a retrospective cohort of 120 subjects, including 61 CA cases and 59 NC controls. Genes were selected for analysis based on contribution to the previously reported LCRT biomarker and/or prior evidence for association with lung cancer risk. Linear discriminant analysis was used to identify the most accurate classifier suitable to stratify subjects for screening. RESULTS: After cross-validation, a model comprising expression values from 12 genes (CDKN1A, E2F1, ERCC1, ERCC4, ERCC5, GPX1, GSTP1, KEAP1, RB1, TP53, TP63, and XRCC1) and demographic factors age, gender, and pack-years smoking, had Receiver Operator Characteristic area under the curve (ROC AUC) of 0.975 (95% CI: 0.96-0.99). The overall classification accuracy was 93% (95% CI 88%-98%) with sensitivity 93.1%, specificity 92.9%, positive predictive value 93.1% and negative predictive value 93%. The ROC AUC for this classifier was significantly better (p < 0.0001) than the best model comprising demographic features alone. CONCLUSIONS: The LCRT biomarker reported here displayed high accuracy and ease of implementation on a high throughput, quality-controlled targeted NGS platform. As such, it is optimized for clinical validation in specimens from the ongoing LCRT blinded prospective cohort study. Following validation, the biomarker is expected to have clinical utility by better stratifying subjects for annual lung cancer screening compared to current demographic criteria alone.

Haplotype and diplotype analyses of variation in ERCC5 transcription cis-regulation in normal bronchial epithelial cells.

Excision repair cross-complementation group 5 (ERCC5) gene plays an important role in nucleotide excision repair, and dysregulation of ERCC5 is associated with increased lung cancer risk. Haplotype and diplotype analyses were conducted in normal bronchial epithelial cells (NBEC) to better understand mechanisms responsible for interindividual variation in transcript abundance regulation of ERCC5 We determined genotypes at putative ERCC5 cis-regulatory SNPs (cis-rSNP) rs751402 and rs2296147, and marker SNPs rs1047768 and rs17655. ERCC5 allele-specific transcript abundance was assessed by a recently developed targeted sequencing method. Syntenic relationships among alleles at rs751402, rs2296147, and rs1047768 were assessed by allele-specific PCR followed by Sanger sequencing. We then assessed association of ERCC5 allele-specific expression at rs1047768 with haplotype and diplotype structure at cis-rSNPs rs751402 and rs2296147. Genotype analysis revealed significantly (P < 0.005) higher interindividual variation in allelic ratios in cDNA samples relative to matched gDNA samples at both rs1047768 and rs17655. By diplotype analysis, mean expression was higher at the rs1047768 alleles syntenic with rs2296147 T allele compared with rs2296147 C allele. Furthermore, mean expression was lower at rs17655 C allele, which is syntenic with G allele at a linked SNP rs873601 (D' = 0.95). These data support the conclusions that in NBEC, T allele at SNP rs2296147 upregulates ERCC5, variation at rs751402 does not alter ERCC5 regulation, and that C allele at SNP rs17655 downregulates ERCC5 Variation in ERCC5 transcript abundance associated with allelic variation at these SNPs could result in variation in NER function in NBEC and lung cancer risk.

Studying the Epithelial Effects of Intestinal Inflammation In Vitro on Established Murine Colonoids.

The intestinal epithelium plays an essential role in human health, providing a barrier between the host and the external environment. This highly dynamic cell layer provides the first line of defense between microbial and immune populations and helps to modulate the intestinal immune response. Disruption of the epithelial barrier is a hallmark of inflammatory bowel disease (IBD) and is of interest for therapeutic targeting. The 3-dimensional colonoid culture system is an extremely useful in vitro model for studying intestinal stem cell dynamics and epithelial cell physiology in IBD pathogenesis. Ideally, establishing colonoids from the inflamed epithelial tissue of animals would be most beneficial in assessing the genetic and molecular influences on disease. However, we have shown that in vivo epithelial changes are not necessarily retained in colonoids established from mice with acute inflammation. To address this limitation, we have developed a protocol to treat colonoids with a cocktail of inflammatory mediators that are typically elevated during IBD. While this system can be applied ubiquitously to various culture conditions, this protocol emphasizes treatment on both differentiated colonoids and 2-dimensional monolayers derived from established colonoids. In a traditional culture setting, colonoids are enriched with intestinal stem cells, providing an ideal environment to study the stem cell niche. However, this system does not allow for an analysis of the features of intestinal physiology, such as barrier function. Further, traditional colonoids do not offer the opportunity to study the cellular response of terminally differentiated epithelial cells to proinflammatory stimuli. The methods presented here provide an alternative experimental framework to address these limitations. The 2-dimensional monolayer culture system also offers an opportunity for therapeutic drug screening ex vivo. This polarized layer of cells can be treated with inflammatory mediators on the basal side of the cell and concomitantly with putative therapeutics apically to determine their utility in IBD treatment.

Epithelial NAD+ depletion drives mitochondrial dysfunction and contributes to intestinal inflammation.

Introduction: We have previously demonstrated that a pathologic downregulation of peroxisome proliferator-activated receptor-gamma coactivator 1-alpha (PGC1α) within the intestinal epithelium contributes to the pathogenesis of inflammatory bowel disease (IBD). However, the mechanism underlying downregulation of PGC1α expression and activity during IBD is not yet clear. Methods: Mice (male; C57Bl/6, Villincre/+;Pgc1afl/fl mice, and Pgc1afl/fl) were subjected to experimental colitis and treated with nicotinamide riboside. Western blot, high-resolution respirometry, nicotinamide adenine dinucleotide (NAD+) quantification, and immunoprecipitation were used to in this study. Results: We demonstrate a significant depletion in the NAD+ levels within the intestinal epithelium of mice undergoing experimental colitis, as well as humans with ulcerative colitis. While we found no decrease in the levels of NAD+-synthesizing enzymes within the intestinal epithelium of mice undergoing experimental colitis, we did find an increase in the mRNA level, as well as the enzymatic activity, of the NAD+-consuming enzyme poly(ADP-ribose) polymerase-1 (PARP1). Treatment of mice undergoing experimental colitis with an NAD+ precursor reduced the severity of colitis, restored mitochondrial function, and increased active PGC1α levels; however, NAD+ repletion did not benefit transgenic mice that lack PGC1α within the intestinal epithelium, suggesting that the therapeutic effects require an intact PGC1α axis. Discussion: Our results emphasize the importance of PGC1α expression to both mitochondrial health and homeostasis within the intestinal epithelium and suggest a novel therapeutic approach for disease management. These findings also provide a mechanistic basis for clinical trials of nicotinamide riboside in IBD patients.

Evaluating tuberculosis case detection via real-time monitoring of tuberculosis diagnostic services.

RATIONALE: Tuberculosis case-detection rates are below internationally established targets in high-burden countries. Real-time monitoring and evaluation of adherence to widely endorsed standards of tuberculosis care might facilitate improved case finding. OBJECTIVES: To monitor and evaluate the quality of tuberculosis case-detection and management services in a low-income country with a high incidence of tuberculosis. METHODS: We prospectively evaluated tuberculosis diagnostic services at five primary health-care facilities in Uganda for 1 year, after introducing a real-time, electronic performance-monitoring system. We collected data on every clinical encounter, and measured quality using indicators derived from the International Standards of Tuberculosis Care. MEASUREMENTS AND MAIN RESULTS: In 2009, there were 62,909 adult primary-care visits. During the first quarter of 2009, clinicians referred only 21% of patients with cough greater than or equal to 2 weeks for sputum smear microscopy and only 71% of patients with a positive sputum examination for tuberculosis treatment. These proportions increased to 53% and 84%, respectively, in the fourth quarter of 2009. The cumulative probability that a smear-positive patient with cough greater than or equal to 2 weeks would be appropriately evaluated and referred for treatment rose from 11% to 34% (P = 0.005). The quarterly number of tuberculosis cases identified and prescribed treatment also increased four-fold, from 5 to 21. CONCLUSIONS: Poor adherence to internationally accepted standards of tuberculosis care improved after introduction of real-time performance monitoring and was associated with increased tuberculosis case detection. Real-time monitoring and evaluation can strengthen health systems in low-income countries and facilitate operational research on the effectiveness and sustainability of interventions to improve tuberculosis case detection.

Pediatric endoscopy across multiple clinical settings: Efficiency and adverse events.

BACKGROUND: Endoscopic procedures are becoming increasingly important for the diagnosis and treatment of gastrointestinal disorders during childhood, and have evolved from a more infrequent inpatient procedure in the operating room to a routine outpatient procedure conducted in multiple care settings. Demand for these procedures is rapidly increasing and thus there is a need to perform them in an efficient manner. However, there are little data comparing the efficiency of pediatric endoscopic procedures in diverse clinical environments. We hypothesized that there are significant differences in efficiency between settings. AIM: To compare the efficiency and examine adverse effects of pediatric endoscopic procedures across three clinical settings. METHODS: A retrospective chart review was conducted on 1623 cases of esophagogastroduodenoscopy (EGD) or combined EGD and colonoscopy performed between January 1, 2014 and May 31, 2018 by 6 experienced pediatric gastroenterologists in three different clinical settings, including a tertiary care hospital operating room, community hospital operating room, and free-standing pediatric ambulatory endoscopy center at a community hospital. The following strict guidelines were used to schedule patients at all three locations: age greater than 6 mo; American Society of Anesthesiologists class 1 or 2; normal craniofacial anatomy; no anticipated therapeutic intervention (e.g., foreign body retrieval, stricture dilation); and, no planned or anticipated hospitalization post-procedure. Data on demographics, times, admission rates, and adverse events were collected. Endoscopist time (elapsed time from the endoscopist entering the operating room or endoscopy suite to the next patient entering) and patient time (elapsed time from patient registration to that patient exiting the operating room or endoscopy suite) were calculated to assess efficiency. RESULTS: In total, 58% of the cases were performed in the tertiary care operating room. The median age of patients was 12 years and the male-to-female ratio was nearly equal across all locations. Endoscopist time at the tertiary care operating room was 12 min longer compared to the community operating room (63.3 ± 21.5 min vs 51.4 ± 18.9 min, P < 0.001) and 7 min longer compared to the endoscopy center (vs 56.6 ± 19.3 min, P < 0.001). Patient time at the tertiary care operating room was 11 min longer compared to the community operating room (133.2 ± 39.9 min vs 122.3 ± 39.5 min, P < 0.001) and 9 min longer compared to the endoscopy center (vs 124.9 ± 37.9 min; P < 0.001). When comparing endoscopist and patient times for EGD and EGD/colonoscopies among the three locations, endoscopist, and patient times were again shorter in the community hospital and endoscopy center compared to the tertiary care operating room. Adverse events from procedures occurred in 0.1% (n = 2) of cases performed in the tertiary care operating room, with 2.2% (n = 35) of cases from all locations having required an unplanned admission after the endoscopy for management of a primary GI disorder. CONCLUSION: Pediatric endoscopic procedures can be conducted more efficiently in select patients in a community operating room and endoscopy center compared to a tertiary care operating room.

The need for comprehensive multidisciplinary programs, complex interventions, and precision medicine for bicuspid aortic valve disease.

Patients with bicuspid aortic valves commonly require an intervention on their valve and/or aorta. Because of their heterogeneous presentations, recommendations for imaging surveillance and surgery timing are highly individualized. Critical points in care include time of diagnosis, transition from adolescent to adult medicine, and surgery referral. To better support patients with bicuspid aortic valves, we developed a comprehensive program that utilizes the multidisciplinary care team, complex interventions, and translational research protocols. We describe our program structure and experience with this common and sometimes challenging diagnosis.

Microcystin-LR aerosol induces inflammatory responses in healthy human primary airway epithelium.

Harmful algal blooms plague bodies of freshwater globally. These blooms are often composed of outgrowths of cyanobacteria capable of producing the heptapeptide Microcystin-LR (MC-LR) which is a well-known hepatotoxin. Recently, MC-LR has been detected in aerosols generated from lake water. However, the risk for human health effects due to MC-LR inhalation exposure have not been extensively investigated. In this study, we exposed a fully differentiated 3D human airway epithelium derived from 14 healthy donors to MC-LR-containing aerosol once a day for 3 days. Concentrations of MC-LR ranged from 100 pM to 1 µM. Although there were little to no detrimental alterations in measures of the airway epithelial function (i.e. cell survival, tissue integrity, mucociliary clearance, or cilia beating frequency), a distinct shift in the transcriptional activity was found. Genes related to inflammation were found to be upregulated such as C-C motif chemokine 5 (CCL5; log2FC = 0.57, p = 0.03) and C-C chemokine receptor type 7 (CCR7; log2FC = 0.84, p = 0.03). Functionally, conditioned media from MC-LR exposed airway epithelium was also found to have significant chemo-attractive properties for primary human neutrophils. Additionally, increases were found in the concentration of secreted chemokine proteins in the conditioned media such as CCL1 (log2FC = 5.07, p = 0.0001) and CCL5 (log2FC = 1.02, p = 0.046). These results suggest that MC-LR exposure to the human airway epithelium is capable of inducing an inflammatory response that may potentiate acute or chronic disease.

Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples.

BACKGROUND: Clinical laboratories routinely use formalin-fixed paraffin-embedded (FFPE) tissue or cell block cytology samples in oncology panel sequencing to identify mutations that can predict patient response to targeted therapy. To understand the technical error due to FFPE processing, a robustly characterized diploid cell line was used to create FFPE samples with four different pre-tissue processing formalin fixation times. A total of 96 FFPE sections were then distributed to different laboratories for targeted sequencing analysis by four oncopanels, and variants resulting from technical error were identified. RESULTS: Tissue sections that fail more frequently show low cellularity, lower than recommended library preparation DNA input, or target sequencing depth. Importantly, sections from block surfaces are more likely to show FFPE-specific errors, akin to "edge effects" seen in histology, while the inner samples display no quality degradation related to fixation time. CONCLUSIONS: To assure reliable results, we recommend avoiding the block surface portion and restricting mutation detection to genomic regions of high confidence.

Association of Fecal Calprotectin With Endoscopic and Histologic Activity in Pediatric Inflammatory Bowel Disease.

Fecal calprotectin (FC) is a noninvasive marker of intestinal inflammation used for screening and ongoing monitoring of inflammatory bowel disease (IBD); it is unclear the association of specific FC values with disease activity. The aim of our study was to examine the association of FC values with endoscopic and histologic severity. Methods: We performed a retrospective chart review of patients who had FC done between 30 days and 1 day before colonoscopy at our institution. IBD patients were graded using the simple endoscopic score for Crohn's disease or Mayo endoscopic score for ulcerative colitis. Histologic slides were graded using the Geboes method. Results: Three-hundred thirty-one patients were included in the study and 107 had IBD. For endoscopy, median FC was lowest for all IBD patients with no disease (181 µg/g) and highest in severe disease (921 µg/g), with significant difference between no disease and moderate and severe disease (P = 0.019, 0.003), and between mild and severe disease (P = 0.012). For histology, median FC was lowest with no disease (328 µg/g) and highest in severe disease (895 µg/g), with significant difference between no disease and moderate and severe disease (P = 0.021, 0.018). The control population had a significantly lower median FC than the IBD population in endoscopic remission (35.5 versus 181 µg/g; P = 0.018). Conclusions: There was a linear increase in FC values associated with increasing disease severity in the undifferentiated IBD cohort. Values for IBD patients in endoscopic remission were significantly different from our control population. FC may be a useful noninvasive marker to assess disease severity.

Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA.

The primary objective of the FDA-led Sequencing and Quality Control Phase 2 (SEQC2) project is to develop standard analysis protocols and quality control metrics for use in DNA testing to enhance scientific research and precision medicine. This study reports a targeted next-generation sequencing (NGS) method that will enable more accurate detection of actionable mutations in circulating tumor DNA (ctDNA) clinical specimens. To accomplish this, a synthetic internal standard spike-in was designed for each actionable mutation target, suitable for use in NGS following hybrid capture enrichment and unique molecular index (UMI) or non-UMI library preparation. When mixed with contrived ctDNA reference samples, internal standards enabled calculation of technical error rate, limit of blank, and limit of detection for each variant at each nucleotide position in each sample. True-positive mutations with variant allele fraction too low for detection by current practice were detected with this method, thereby increasing sensitivity.

Cis-acting genetic variation at an E2F1/YY1 response site and putative p53 site is associated with altered allele-specific expression of ERCC5 (XPG) transcript in normal human bronchial epithelium.

ERCC5 (XPG) is a key component of the nucleotide excision DNA repair pathway. In two recent case-control studies, we determined that ERCC5 transcript expression pattern in grossly normal human bronchial epithelial cells (NBEC) was different in individuals diagnosed with lung cancer compared with non-lung cancer controls. In this study, we tested the hypothesis that variation at cis-acting sites contributed to observed variation in ERCC5 transcript expression in NBEC. Allele-specific expression (ASE) was measured at transcribed polymorphic site rs1047768 in exon 2 of ERCC5 in NBEC complementary DNA (cDNA) of 22 individuals using allele-specific competitive polymerase chain reaction. ASE at rs1047768 was then assessed for association with allelotype at polymorphic sites rs751402 (E2F1 and YY1 recognition and response site) and rs2296147 (putative P53 recognition site) in the proximal promoter and 5' untranslated region, respectively, of ERCC5. Interindividual variation in recombination between rs751402, rs2296147 and rs1047768 in poly-heterozygotes was controlled for by allele-specific sequencing. Measured rs1047768 T:C allelic ratio was (i) significantly higher in NBEC cDNA compared with genomic DNA controls (P < 0.001) among samples heterozygous at both rs751402 and rs2296147; (ii) less high (P = 0.02) for samples homozygous at rs751402 but heterozygous at rs2296147 and (iii) not significantly different (P = 0.18) for doubly homozygous individuals. Here, we demonstrate that rs751402 A allele and rs2296147 T allele are associated with higher ASE of ERCC5 T allele transcript at rs1047768 in NBEC.

Applications of a Specialty Bicuspid Aortic Valve Program: Clinical Continuity and Translational Collaboration.

Bicuspid aortic valve (BAV) is a common congenital heart diagnosis and is associated with aortopathy. Current guidelines for aortic resection have been validated but are based on aortic diameter, which is insufficient to predict acute aortic events. Clinical and translational collaboration is necessary to identify biomarkers that can individualize the timing of prophylactic surgery for BAV aortopathy. We describe our multidisciplinary BAV program, including research protocols aimed at biomarker discovery and results from our longitudinal clinical registry. From 2012-2018, 887 patients enrolled in our clinical BAV registry with the option to undergo four dimensional flow cardiovascular magnetic resonance imaging (4D flow CMR) and donate serum plasma or tissue samples. Of 887 patients, 388 (44%) had an elective BAV-related procedure after initial presentation, while 499 (56%) continued with medical management. Of medical patients, 44 (9%) had elective surgery after 2.3 ± 1.4 years. Surgery patients' biobank donations include 198 (46%) aorta, 374 (86%) aortic valve, and 314 (73%) plasma samples. The 4D flow CMR was completed for 215 (50%) surgery patients and 243 (49%) medical patients. Patients with BAV aortopathy can be safely followed by a multidisciplinary team to detect indications for surgery. Paired tissue and hemodynamic analysis holds opportunity for biomarker development in BAV aortopathy.

Predictors of Left Ventricular Dysfunction After Surgery for Degenerative Mitral Regurgitation.

BACKGROUND: This study was performed to determine whether strain can supplement the ability of left ventricular (LV) ejection fraction (LVEF) to predict postoperative ventricular dysfunction in patients undergoing mitral valve surgery for degenerative mitral regurgitation (DMR). METHODS: From 2004 to 2017, 520 patients with an LVEF of 60% or more underwent mitral valve surgery (98% repair) for DMR. All patients had preoperative, predischarge, and follow-up (mean, 5.0 ± 3.6 years) echocardiograms. Speckle tracking was performed in 119 of 520 patients (22.9%) to determine LV strain, right ventricular free-wall strain, and left atrial longitudinal strain. Multivariate logistic and Cox regression models were used in this subgroup to evaluate associations with early postoperative LV dysfunction and medium-term overall survival, respectively. RESULTS: Median preoperative LVEF of the entire cohort was 65%. Based on predischarge echocardiogram, 449 patients (86.3%) maintained postoperative LVEF of 50% or greater. Seventy-one patients (13.7%) had a predischarge LVEF of less than 50%, 49 (9.4%) had a predischarge LVEF of 40% to 49%, and 22 (4.2% overall) had a predischarge LVEF of less than 40%. Abnormal preoperative LV, right ventricular, and left atrial strain measurements were significantly associated with the development of postoperative LV dysfunction, but preoperative hemodynamic and non-strain echo parameters did not vary enough in absolute values to be clinically useful as predictors of postoperative LV dysfunction. CONCLUSIONS: Preoperative strain measurements in DMR patients were significantly associated with superior capabilities of detecting underlying LV dysfunction despite preserved preoperative LVEF. Strain analysis may serve as another marker for optimal timing of surgical intervention in DMR patients.