Longitudinal profiling identifies co-occurring BRCA1/2 reversions, TP53BP1, RIF1 and PAXIP1 mutations in PARP inhibitor-resistant advanced breast cancer

BACKGROUND

Resistance to therapies that target homologous recombination deficiency (HRD) in breast cancer limits their overall effectiveness. Multiple, preclinically validated, mechanisms of resistance have been proposed, but their existence and relative frequency in clinical disease are unclear, as is how to target resistance.

PATIENTS AND METHODS

Longitudinal mutation and methylation profiling of circulating tumour (ct)DNA was carried out in 47 patients with metastatic BRCA1-, BRCA2- or PALB2-mutant breast cancer treated with HRD-targeted therapy who developed progressive disease-18 patients had primary resistance and 29 exhibited response followed by resistance. ctDNA isolated at multiple time points in the patient treatment course (before, on-treatment and at progression) was sequenced using a novel >750-gene intron/exon targeted sequencing panel. Where available, matched tumour biopsies were whole exome and RNA sequenced and also used to assess nuclear RAD51.

RESULTS

BRCA1/2 reversion mutations were present in 60% of patients and were the most prevalent form of resistance. In 10 cases, reversions were detected in ctDNA before clinical progression. Two new reversion-based mechanisms were identified: (i) intragenic BRCA1/2 deletions with intronic breakpoints; and (ii) intragenic BRCA1/2 secondary mutations that formed novel splice acceptor sites, the latter being confirmed by in vitro minigene reporter assays. When seen before commencing subsequent treatment, reversions were associated with significantly shorter time to progression. Tumours with reversions retained HRD mutational signatures but had functional homologous recombination based on RAD51 status. Although less frequent than reversions, nonreversion mechanisms [loss-of-function (LoF) mutations in TP53BP1, RIF1 or PAXIP1] were evident in patients with acquired resistance and occasionally coexisted with reversions, challenging the notion that singular resistance mechanisms emerge in each patient.

CONCLUSIONS

These observations map the prevalence of candidate drivers of resistance across time in a clinical setting, information with implications for clinical management and trial design in HRD breast cancers.

IgM marks persistent IgG anti-human leukocyte antigen antibodies in highly sensitized heart transplant patients

BACKGROUND

Sensitization to human leukocyte antigens (HLA) is a persistent problem in heart transplant (HT) candidates. We sought to characterize the anti-HLA antibody and circulating B cell repertoire in a cohort of highly sensitized HT candidates.

METHODS

We assessed immunoglobulin G (IgG) and immunoglobulin M (IgM) anti-HLA antibodies using Luminex single antigen bead assays in a cohort of 11 highly sensitized (HS; calculated panel reactive antibody ≥ 90%) and 3 mildly sensitized (MS) candidates. We also performed B cell receptor repertoire sequencing (BCRseq) in HS candidates and 33 non-candidate controls. HLA antibody strength was measured by mean fluorescence intensity (MFI).

RESULTS

We found that IgM anti-HLA antibodies were present in all HS candidates, but with a lower breadth and strength as compared to IgG. When anti-HLA IgG specificities intersected with IgM, binding strength was higher. In contrast, there were IgM but no intersecting IgG specificities for the MS group. In four candidates in the HS group, IgG anti-HLA antibodies decreased in both breadth and strength after HT, but the decrease in strength was smaller if the IgG possessed a specificity that intersected with pre-transplant IgM. BCRseq revealed larger B cell clonotypes in HS candidates but similar diversity as compared to controls.

CONCLUSIONS

IgM marks IgG anti-HLA antibodies with higher strength before HT and persistence after HT. The presence of IgM intersecting IgG for an anti-HLA specificity may be a useful approach to determine which donor HLA should be avoided for a sensitized candidate.

Developmental changes in obstructive sleep apnea and sleep architecture in Down syndrome

BACKGROUND

Down syndrome (DS, also known as Trisomy 21) is a condition associated with abnormal neurodevelopment and a higher risk for sleep apnea. Our study sought to better understand and characterize the age-related developmental differences in sleep architecture and obstructive sleep apnea (OSA) severity in children with DS compared to euploid individuals.

METHODS

Retrospective review of polysomnograms in over 4151 infants, children, and adolescents in the pediatric sleep center at Children's National Hospital in Washington D.C. (0-18 years) including 218 individuals with DS.

RESULTS

The primary findings of our study are that: (1) severe OSA (obstructive apnea-hypopnea index ≥ 10/h) was more prevalent in the DS group (euploid 18% vs. DS 34%, p < 0.001) with the highest OSA severity being present in young children (<3 years old) and adolescents (>10 years old), (2) abnormalities in sleep architecture in children with DS were characterized by a prolonged rapid-eye movement (REM) sleep onset latency (SOL) (euploid 119 min vs. DS 144 min, p < 0.001) and greater arousal indexes (euploid 10.7/h vs. DS 12.2/h, p < 0.001), (3) developmental changes in the amount of REM sleep or slow wave sleep were not different in DS individuals relative to euploid children, (4) multivariate analyses showed that OSA and REM sleep latency differences between DS and euploid individuals were still present after adjusting by age, biological sex, and body mass index.

CONCLUSION

Severe OSA is highly prevalent in children with DS and follows an age-dependent "U" distribution with peaks in newborns/infants and children >10 years of age. Children with DS also have disturbances in sleep architecture characterized by a longer REM SOL and elevated arousal indexes. As sleep cycle generation and continuity play crucial roles in neuroplasticity and cognitive development, these findings offer clinically relevant insights to guide anticipatory guidance for infants, children, and adolescents with DS.

Real-world data evaluation of PAP responsiveness in pediatric obstructive sleep apnea

STUDY OBJECTIVES

The use of positive airway pressure (PAP) in children is a complex process determined by multiple factors. There are limited data on the response of the pediatric population to PAP therapy at home. The goal of the study was to examine real-world responses using PAP home monitoring in children with obstructive sleep apnea.

METHODS

The study included PAP therapy data for 195 children aged between 1 month and 18 years with obstructive sleep apnea and polysomnogram baseline study. We collected demographics, clinical variables, and polysomnogram parameters in all study participants. The individual response to PAP therapy was calculated comparing the apnea-hypopnea index (AHI) in the initial polysomnogram with the mean AHI provided by the download of PAP devices. Multivariate models (logistic regression) were used to examine the predictors of positive PAP response defined as a reduction in AHI ≥ 75%.

RESULTS

We found excellent responses to PAP therapy in children (median 85% AHI reduction). However, there was substantial heterogeneity in AHI reductions while on PAP therapy. The best PAP responses were linked to more severe obstructive sleep apnea and higher PAP levels. We also identified that the response to PAP was higher in obese children and lower in males. The best predictive model for individual PAP response was biological sex, obesity, and obstructive AHI ≥ 20 events/h (area under the receiver operating characteristic curve of 0.791).

CONCLUSIONS

Real-world data show that PAP is overall an effective therapy in children but the response is heterogeneous. Obstructive sleep apnea parameters and individual factors can be used to predict individual AHI reductions while on PAP and optimize PAP responses at home.

CITATION

Aguilar H, Kahanowitch R, Weiss M, et al. Real-world data evaluation of PAP responsiveness in pediatric obstructive sleep apnea. J Clin Sleep Med. 2023;19(7):1313-1319.

Safety, Tolerability, and Preliminary Efficacy of TAR-200 in Patients With Muscle-invasive Bladder Cancer Who Refused or Were Unfit for Curative-intent Therapy: A Phase 1 Study

PURPOSE

Half of patients with muscle-invasive bladder cancer worldwide may not receive curative-intent therapy. Elderly or frail patients are most affected by this unmet need. TAR-200 is a novel, intravesical drug delivery system that provides sustained, local release of gemcitabine into the bladder over a 21-day dosing cycle. The phase 1 TAR-200-103 study evaluated the safety, tolerability, and preliminary efficacy of TAR-200 in patients with muscle-invasive bladder cancer who either refused or were unfit for curative-intent therapy.

MATERIALS AND METHODS

Eligible patients had cT2-cT3bN0M0 urothelial carcinoma of the bladder. TAR-200 was inserted for 4 consecutive 21-day cycles over 84 days. The primary end points were safety and tolerability at 84 days. Secondary end points included rates of clinical complete response and partial response as determined by cystoscopy, biopsy, and imaging; duration of response; and overall survival.

RESULTS

Median age of the 35 enrolled patients was 84 years, and most were male (24/35, 68.6%). Treatment-emergent adverse events related to TAR-200 occurred in 15 patients. Two patients experienced treatment-emergent adverse events leading to removal of TAR-200. At 3 months, complete response and partial response rates were 31.4% (11/35) and 8.6% (3/35), respectively, yielding an overall response rate of 40.0% (14/35; 95% CI 23.9-57.9). Median overall survival and duration of response were 27.3 months (95% CI 10.1-not estimable) and 14 months (95% CI 10.6-22.7), respectively. Progression-free rate at 12 months was 70.5%.

CONCLUSIONS

TAR-200 was generally safe, well tolerated, and had beneficial preliminary efficacy in this elderly and frail cohort with limited treatment options.

Reducing the Frequency of Follow-up Cystoscopy in Low-grade pTa Non-muscle-invasive Bladder Cancer Using the ADXBLADDER Biomarker

BACKGROUND

Non-muscle-invasive bladder cancer (NMIBC) is one of the most expensive cancers owing to frequent follow-up cystoscopies for detection of recurrence.

OBJECTIVE

To assess if the noninvasive ADXBLADDER urine test could permit a less intensive surveillance schedule for patients with low-grade (LG) pTa tumor without carcinoma in situ (CIS) at the previous diagnosis.

DESIGN, SETTING, AND PARTICIPANTS

In a prospective, double-blind, multicenter study, 629 patients underwent follow-up cystoscopy, transurethral resection of bladder tumor/biopsy of suspect lesions, and ADXBLADDER testing.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Diagnostic test accuracy and decision curve analysis were used to evaluate the impact of ADXBLADDER on decision-making on whether to perform follow-up cystoscopy. The primary endpoint was the negative predictive value (NPV) of ADXBLADDER for detection of high-grade and/or CIS (HG/CIS) recurrence and its impact on reducing unnecessary cystoscopies.

RESULTS AND LIMITATIONS

ADXBLADDER had sensitivity of 66.7% (95% confidence interval [CI] 34.9-90.1%) and an NPV of 99.15% (95% CI 97.8-99.8%) for detection of HG/CIS recurrence. The probability of HG/CIS recurrence was 5.0% for ADXBLADDER-positive patients and 0.85% for ADXBLADDER-negative patients. For HG/CIS recurrence threshold probabilities between 0.85% and 5.0%, ADXBLADDER yields a net benefit with omission of cystoscopy for ADXBLADDER-negative patients. The corresponding net reduction in unnecessary cystoscopies ranges from 11 to 62 per 100 patients.

CONCLUSIONS

Patients with LG pTa tumor at the previous diagnosis, for which the risk of HG/CIS recurrence is low and the ADXBLADDER NPV for ruling out HG/CIS recurrence is 99.15%, are ideally suited for a less intensive, personalized follow-up surveillance strategy using ADXBLADDER, with omission of cystoscopy for ADXBLADDER-negative patients.

PATIENT SUMMARY

ADXBLADDER is a urine test that can predict the probability of recurrence of bladder cancer. Patients diagnosed with low-grade cancer confined to the bladder mucosa are ideally suited for less intensive follow-up using this test, which could reduce unnecessary cystoscopy procedures for those with a negative result, potentially improve quality of life, and reduce overall health care costs.

ImmunoTyper-SR: A computational approach for genotyping immunoglobulin heavy chain variable genes using short-read data

Human immunoglobulin heavy chain (IGH) locus on chromosome 14 includes more than 40 functional copies of the variable gene (IGHV), which are critical for the structure of antibodies that identify and neutralize pathogenic invaders as a part of the adaptive immune system. Because of its highly repetitive sequence composition, the IGH locus has been particularly difficult to assemble or genotype when using standard short-read sequencing technologies. Here, we introduce ImmunoTyper-SR, an algorithmic tool for the genotyping and CNV analysis of the germline IGHV genes on Illumina whole-genome sequencing (WGS) data using a combinatorial optimization formulation that resolves ambiguous read mappings. We have validated ImmunoTyper-SR on 12 individuals, whose IGHV allele composition had been independently validated, as well as concordance between WGS replicates from nine individuals. We then applied ImmunoTyper-SR on 585 COVID patients to investigate the associations between IGHV alleles and anti-type I IFN autoantibodies, which were previously associated with COVID-19 severity.

Blood pressure reduction in higher cardiovascular risk patients in the Global SYMPLICITY Registry

Background/Introduction

The Global SYMPLICITY Registry (GSR) was designed to evaluate the safety and efficacy of renal denervation (RDN) in real-world patients. Inclusion and exclusion criteria are limited to allow assessment of the effects of RDN on patients with a wide range of comorbidities. The current analysis examines blood pressure (BP) reduction after RDN in higher cardiovascular risk patients.

Purpose

To evaluate blood pressure reduction after RDN in higher cardiovascular risk patients in GSR.

Methods

GSR is a prospective all-comers registry to evaluate the safety and efficacy of RDN. Patients are enrolled in GSR and receive radiofrequency RDN using the Symplicity Flex or Symplicity Spyral catheter. Office and ambulatory BP are measured at each follow-up (3, 6, 12, 24, and 36 months). In this post-hoc analysis, changes from baseline in office and 24-hour ambulatory systolic blood pressure were assessed in patients at higher cardiovascular risk. Higher risk was defined using baseline office systolic or diastolic BP as well as additional risk factors (Figure 1).

Results

As of March 2021, there were 2621 patients characterized as higher cardiovascular risk in GSR. Baseline characteristics included mean age 60.7±12.1 years, 57.6% male, 37.9% type 2 diabetes, 35.8% hypocholesterolemia, 19.7% eGFR &lt;60 mL/min/1.73 m2, 16.2% left ventricular hypertrophy, 10.2% previous stroke and 9.3% previous myocardial infarction. Baseline office systolic BP (OSBP) was 168.8±22.7 mmHg and baseline ambulatory systolic BP (ASBP) 155.3±18.6 mmHg. Mean OSBP reductions after RDN in this higher risk population ranged from −13.1 mmHg at 3 months to −17.5 mmHg at 24 months and −18.9 mmHg at 36 months, and mean ASBP reductions ranged from −7.8 mmHg at 3 months to −9.8 mmHg at 24 months and −9.3 mmHg at 36 months (Figure).

Conclusions

Higher risk patients in GSR had sustained office and ambulatory systolic BP reductions out to 3 years after catheter-based radiofrequency RDN.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): Medtronic

ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data

Human immunoglobulin heavy chain (IGH) locus on chromosome 14 includes more than 40 functional copies of the variable gene (IGHV), which, together with the joining genes (IGHJ), diversity genes (IGHD), constant genes (IGHC) and immunoglobulin light chains, code for antibodies that identify and neutralize pathogenic invaders as a part of the adaptive immune system. Because of its highly repetitive sequence composition, the IGH locus has been particularly difficult to assemble or genotype through the use of standard short read sequencing technologies. Here we introduce ImmunoTyper-SR, an algorithmic method for genotype and CNV analysis of the germline IGHV genes using Illumina whole genome sequencing (WGS) data. ImmunoTyper-SR is based on a novel combinatorial optimization formulation that aims to minimize the total edit distance between reads and their assigned IGHV alleles from a given database, with constraints on the number and distribution of reads across each called allele. We have validated ImmunoTyper-SR on 12 individuals with Illumina WGS data from the 1000 Genomes Project, whose IGHV allele composition have been studied extensively through the use of long read and targeted sequencing platforms, as well as nine individuals from the NIAID COVID Consortium who have been subjected to WGS twice. We have then applied ImmunoTyper-SR on 585 samples from the NIAID COVID Consortium to investigate associations between distinct IGHV alleles and anti-type I IFN autoantibodies which have been linked to COVID-19 severity.

Prognostic Factors in De Novo Metastatic Renal Cell Carcinoma: A Report From the Latin American Renal Cancer Group

PURPOSE

To assess the effect of clinical and pathological variables on cancer-specific and overall survival (OS) in de novo metastatic patients from a collaborative of primarily Latin American countries.

PATIENTS AND METHODS

Of 4,060 patients with renal cell carcinoma diagnosed between 1990 and 2015, a total of 530 (14.5%) had metastasis at clinical presentation. Relationships between clinical and pathological parameters and treatment-related outcomes were analyzed by Cox regression and the log-rank method.

RESULTS

Of 530 patients, 184 (90.6%) had died of renal cell carcinoma. The median OS of the entire cohort was 24 months. American Society of Anesthesiology classification 3-4 (hazard ratio [HR]: 1.64), perirenal fat invasion (HR: 2.02), and ≥ 2 metastatic organ sites (HR: 2.19) were independent prognostic factors for 5-year OS in multivariable analyses. We created a risk group stratification with these variables: no adverse risk factors (favorable group), median OS not reached; one adverse factor (intermediate group), median OS 33 months (HR: 2.04); and two or three adverse factors (poor risk group), median OS 14 months (HR: 3.58).

CONCLUSION

Our study defines novel prognostic factors that are relevant to a Latin American cohort. With external validation, these easily discerned clinical variables can be used to offer prognostic information across low- and middle-income countries.

Final Selection of Quality Protein Popcorn Hybrids

Quality Protein Popcorn (QPP) BC2F5 inbred lines were produced through an interpopulation breeding system between Quality Protein Maize dent (QPM) and elite popcorn germplasm. In 2019, five QPP F1 hybrids were selected for further evaluation due to superior agronomics, endosperm protein quality, and popping quality traits. Though these BC2F5 QPP hybrids were phenotypically similar to their popcorn parents, the QPP cultivars conveyed slightly inferior popping characteristics when compared to the original popcorn germplasm. The objective of this study was twofold. First, BC2F5 inbred lines were crossed to their popcorn parents and BC3F4 inbred lines were produced for hybridization to test the agronomic, protein, and popping trait effects from an additional QPP by popcorn backcross. Second, BC2- and BC3-hybrids were simultaneously evaluated alongside ConAgra Brands® elite cultivars and ranked for potential commercialization in the spring of 2020. These 10 QPP hybrids were grown alongside five ConAgra Brands® elite popcorn cultivars in three locations and agronomic, protein quality, and popping quality traits were evaluated. Significant improvements in popcorn quality traits were observed in the QPP BC3 cultivars compared to their BC2 counterparts, and yield averages were significantly lower in BC3-derived QPP hybrids compared to the BC2 population. Protein quality traits were not significantly different between QPP backcrossing populations and significantly superior to ConAgra elite popcorn varieties. Utilizing a previously published ranking system, six QPP hybrids, three from the BC2F5 population and three from the BC3F4 population, were evaluated as candidates for final selection. The successful evaluation and ranking system methodology employed is transferable to other hybrid production and testing programs. Incorporating this analysis with concurrent sensory studies, two QPP hybrids were chosen as premier cultivars for potential commercialization.

Impact of coronary atherosclerotic plaque metrics and CT reader skills on inter-observer variation of repeated on-site CT-FFR

Funding Acknowledgements

Type of funding sources: None.

Background and Purpose

 

Little is known about the on-site CT-FFR inter-reader reproducibility and its variability in different atherosclerotic plaque scenarios. The aim of this study was to determine the variation of repeated CT-FFR analyses between two CCTA readers with different training skills across different atherosclerotic features. 

Methods

 

Patients referred for invasive coronary angiography who accepted to undergo a CCTA/CT-FFR study were prospectively included. Patients with contraindications for CCTA, atrial fibrillation, chronic total occlusions or previous coronary revascularization were excluded. Quantification of atherosclerotic plaque metrics and CT-FFR was performed for each coronary vessel by two different CT readers, one Level I and one Level III. Inter-reader agreement for CT-FFR was assessed using kappa index, Bland-Altman and Lin’s concordance correlation agreement (LCCA). The impact of each atherosclerotic feature was assessed by dividing the dataset based on the corresponding median and assessing inter-reader variability for both the lower and upper half.

Results

47 patients (137 vessels) were included. Mean age was 66 ± 10 years, 89% were males, 63% had hypertension, 76% dyslipidemia and 38% diabetes. Degree of stenosis was moderate (50-69%) in 29% and severe (≥70%) in 28% of vessels with a positive CT-FFR (≤0.80) in 39%. CT-FFR showed good correlation between the two readers based on a kappa index of 0.77 with a mean CT-FFR difference of -0.017 ± 0.12. The inter-reader agreement was good in the main epicardial vessels (LCCA of 0.70 for LAD, 0.74 for LCX and 0.76 for RCA, p &lt; 0.001 for all) and better in proximal than in distal segments (LCCA of 0.83 vs 0.63, p &lt; 0.001). Likewise, in different atherosclerotic plaque scenarios, the agreement was better in those vessels with lower plaque volume, less calcified and longer lesions (see table 1). 

Conclusions

 

In our cohort, on-site CT-FFR showed good inter-reader agreement without relevant impact by reader experience level and atherosclerotic plaque features.

Table 1 Mean difference Bland-Altman Lin’s concordance correlation coefficient p value Plaque volume &lt; median (556 mm3) -0.01 ± 0.12 0.85 &lt;0.001 Plaque volume &gt; median (556 mm3) -0.035 ± 0.13 0.64 &lt;0.001 Calcified plaque burden &lt; median (34%) -0.03 ± 0.11 0.82 &lt;0.001 Calcified plaque burden &gt; median (34%) -0.02 ± 0.14 0.75 &lt;0.001 Lesion length &lt; median (55 mm) -0.005 ± 0.12 0.68 &lt;0.001 Lesion length &gt; median (55 mm) -0.031 ± 0.12 0.83 &lt;0.001 *p values indicate inter-reader agreement by two independent observers for each category

Comparison of the performances of the ADXBLADDER test and urinary cytology in the follow-up of non-muscle-invasive bladder cancer: a blinded prospective multicentric study

Objective

To compare directly the performance of the ADXBLADDER test with that of cytology in the detection of non‐muscle‐invasive bladder cancer (NMIBC) recurrences.

Background

ADXBLADDER is a urine test based on the detection of MCM5, a DNA licensing factor expressed in all cells capable of dividing. Expression is usually restricted to the basal stem cell compartment; however, in malignancy, MCM5‐expressing cells can be found throughout the epithelium. Detection of MCM5 in urine sediment can be indicative of the presence of a bladder tumour.

Patients and Methods

A multicentre prospective, blinded study was carried out from August 2017 and July 2019 at 21 European Union centres, 14 of which collected matching cytology data. Urine was collected from patients prior to cystoscopy. Urine cytology and ADXBLADDER were performed and compared to the diagnosis obtained by cystoscopy. The performance of cytology and ADXBLADDER were then compared.

Results

The overall performance of ADXBLADDER demonstrated a sensitivity of 51.9%, a specificity of 66.4%, and a negative predictive value (NPV) of 92%. The sensitivity of ADXBLADDER for low‐ and high‐grade recurrences was 44.1% and 58.8%, respectively. By contrast, cytology sensitivity was 16.7%, specificity was 98% and NPV was 90.7%. Cytology sensitivity for both low‐ and high‐grade disease was 17.6%.

Conclusions

ADXBLADDER detection of both low‐ and high‐grade NMIBC recurrence is superior to that of cytology, with ADXBLADDER able to exclude the presence of high‐grade recurrence in 97.8% of cases compared to 97.1% with cytology. These results show that ADXBLADDER has promise as a more reliable alternative to urine cytology in the follow‐up of NMIBC.

Production and Selection of Quality Protein Popcorn Hybrids Using a Novel Ranking System and Combining Ability Estimates

Popcorn varieties are agronomically sub-optimal and genetically limited compared to other maize subspecies. To increase genetic diversity and improve popcorn agronomics, dent germplasm has been introduced to popcorn with limited success and generally, major loss of popping. Between 2013 and 2018, 12 Quality Protein Popcorn (QPP) inbreds containing Quality Protein Maize (QPM) and popcorn germplasm were produced that maintained popping while carrying the opaque-2 allele conferring elevated kernel lysine. This is an opportune trait in the growing market for healthier snacks and a model for mining QPM traits into popcorn. We crossed QPP inbreds to explore the effects of heterosis on popcorn protein, popping quality, and plant agronomics and selected hybrids for further production. To rank and intermediately prescreen hybrids, we utilized a novel hybrid-ranking model adapted from a rank summation index while examining the inbred general combining ability and hybrid specific combining ability estimates for all traits. We observed a biological manifestation of heterosis by categorizing hybrids by pedigree that resulted in a stepwise progression of trait improvement. These results corroborated our hybrid selection and offered insight in basic heterosis research. Estimates for popcorn quality and agronomic trait covariances also suggest the synergistic introgression of highly vitreous dent maize (QPM) into popcorn, providing a likely explanation for the successfully maintained vitreous endosperm, protein quality and popping traits in line with a remodeled proteome. QPP hybrids maintained improved amino acid profiles although different popping methods variably affected popcorn's protein bound and free amino acid levels. This preliminary screening of QPP hybrids is enabling further quantitative selection for large-scale, complex trait comparison to currently marketed elite popcorn varieties.

Maize genomes to fields (G2F): 2014-2017 field seasons: genotype, phenotype, climatic, soil, and inbred ear image datasets

OBJECTIVES

Advanced tools and resources are needed to efficiently and sustainably produce food for an increasing world population in the context of variable environmental conditions. The maize genomes to fields (G2F) initiative is a multi-institutional initiative effort that seeks to approach this challenge by developing a flexible and distributed infrastructure addressing emerging problems. G2F has generated large-scale phenotypic, genotypic, and environmental datasets using publicly available inbred lines and hybrids evaluated through a network of collaborators that are part of the G2F's genotype-by-environment (G × E) project. This report covers the public release of datasets for 2014-2017.

DATA DESCRIPTION

Datasets include inbred genotypic information; phenotypic, climatic, and soil measurements and metadata information for each testing location across years. For a subset of inbreds in 2014 and 2015, yield component phenotypes were quantified by image analysis. Data released are accompanied by README descriptions. For genotypic and phenotypic data, both raw data and a version without outliers are reported. For climatic data, a version calibrated to the nearest airport weather station and a version without outliers are reported. The 2014 and 2015 datasets are updated versions from the previously released files [1] while 2016 and 2017 datasets are newly available to the public.

P6174On-site CT-derived FFR predicts the need for revascularization

Background and purpose

Coronary computed tomography angiography (CTA) in combination with CT-derived fractional flow reserve (CT-FFR) is a solid tool for assessing both the anatomical and functional impact of coronary atherosclerotic disease (CAD) in a single study. The development of new software for on-site CT-FFR quantification may reduce costs and increase availability. The aim of this study was to analyze the incremental value of CT-FFR over CTA alone and its ability to predict the need for revascularization.

Methods

Patients referred for invasive coronary angiography (ICA) who accepted to undergo a CTA/CT-FFR study were prospectively included. Patients with any contraindication for CT, atrial fibrillation, chronic total occlusions, severe ventricular hypertrophy or previous coronary revascularization were excluded. On-site CT-FFR was calculated for each coronary vessel. Invasive FFR was quantified during ICA, considering ≤0.8 as a surrogate for the need for revascularization.

Results

33 patients (90 vessels) were included. Mean age was 65±10 years, 88% were males, 60% had hypertension, 77% dyslipidaemia and 40% diabetes. The average analysis time of CT-FFR was 16±4 minutes. There was a good correlation between CT-FFR and FFR in all three main epicardial vessels as well as in proximal segments or in moderate to severe stenosis (see Table). 83% of vessels with FFR≤0.8 were predicted by CT-FFR study (89% of LAD lesions, 86% of LCX and 66% of RCA). CT-FFR added incremental diagnostic value over CTA alone to predict FFR≤0.8 (ΔAUC 0.0336 with a net reclassification index 1.4±0.23; p<0.001) (see Image).

n Mean difference from Bland-Altman Pearson's r coefficient p value All-vessels 90 0.037±0.1 0.8 <0.001 Lesions in LAD 40 0.005±0.11 0.81 <0.001 Lesions in LCX 32 0.061±0.094 0.85 <0.001 Lesions in RCA 18 0.06±0.11 0.83 <0.001 Moderate lesions (50–69% QCA stenosis) 24 0.02±0.06 0.88 <0.001 Severe lesions (70–99% QCA stenosis) 25 0.034±0.18 0.4 <0.001 Proximal lesions 42 0.012±0.11 0.84 <0.001 Non-proximal lesions 48 0.061±0.1 0.78 <0.001

Conclusions

On-site CT-FFR is a good predictor of the need for revascularization in all three main coronary vessels and adds incremental diagnostic value over CTA alone. There is higher dispersion of the values in severe stenosis, lesions in LCX or RCA although this do not result in misclassification.

P6185Impact of coronary atherosclerotic plaque metrics on the correlation between on-site CT-FFR and invasive FFR

Background

Developed in the last years, coronary computed tomography-derived fractional flow reserve (CT-FFR) has shown good correlation with invasive fractional flow reserve (FFR). However, little is known about the interaction of coronary atherosclerotic plaque characteristics in the correlation between CT-FFR and FFR.

Purpose

This study sought to determine the effect of main coronary atherosclerotic plaque metrics (APM) on the correlation between on-site CT-FFR and invasive FFR.

Methods

Patients referred for invasive coronary angiography (ICA) who accepted to undergo a CT-FFR study were prospectively included. We excluded patients with atrial fibrillation, chronic total occlusions, severe ventricular hypertrophy or previous coronary revascularization, and those with any contraindication for CT. On-site CT-FFR and APM were calculated for each coronary vessel. Continuous variables of APM were dichotomized as above and below the median and their interaction on the correlation between on-site CT-FFR and invasive FFR was assessed by multiple linear regression model.

Results

33 patients (90 vessels) were included. Mean age was 65±10 years, 88% were males, 60% had hypertension, 77% dyslipidaemia and 40% diabetes. The mean delay time between CTA and ICA of 21 days. The average analysis time of CT-FFR was 16±4 minutes. Overall, correlation between FFR and CT-FFR showed a Pearson's r coefficient of 0.77±0.06 and a standardized beta coefficient of 0.8 (p<0.001). The beta coefficients between CT-FFR and FFR did not change significantly after the interaction with different APM (p>0.05 for all) (see Table).

Standardized Beta coefficients for on-site CT-FFR with invasive FFR as a gold standard Below the median Above the median p value for interaction Total atheroma volume (TAV) (mm3) 0.66 0.93 0.071 Percent atheroma volume (PAV) (%) 1.00 0.69 0.063 Calcified atheroma plaque volume (%) 0.89 0.68 0.175 Remodeling index 0.94 0.71 0.129 Lesion length (LL) (mm) 0.67 0.89 0.158 Minimal lumen area (mm2) 0.73 0.71 0.955

Conclusions

There is a good correlation between on-site CT-FFR and invasive FFR, which is not affected by main atherosclerotic plaque characteristics.

Relative importance of gene effects for nitrogen-use efficiency in popcorn

The objective of this study was to evaluate the effects of additive and non-additive genes on the efficiency of nitrogen (N) use and N responsiveness in inbred popcorn lines. The parents, hybrids and reciprocal crosses were evaluated in a 10x10 triple lattice design at two sites and two levels of N availability. To establish different N levels in the two experiments, fertilization was carried out at sowing, according to soil analysis reports. However, for the experiments with ideal nitrogen availability, N was sidedressed according to the crop requirement, whereas for the N-poor experiments sidedressing consisted of 30% of that applied in the N-rich environment. Two indices were evaluated, the Harmonic Mean of the Relative Performance (HMRP) and Agronomic Efficiency under Low Nitrogen Availability (AELN), both based on grain yield at both N levels. Both additive and non-additive gene effects were important for selection for N-use efficiency. Moreover, there was allelic complementarity between the lines and a reciprocal effect for N-use efficiency, indicating the importance of the choice of the parents used as male or female. The best hybrids were obtained from inbred popcorn lines with contrasting N-use efficiency and N responsiveness.

Parallels between natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize

Artificial selection has produced varieties of domesticated maize that thrive in temperate climates around the world. However, the direct progenitor of maize, teosinte, is indigenous only to a relatively small range of tropical and subtropical latitudes and grows poorly or not at all outside of this region. Tripsacum, a sister genus to maize and teosinte, is naturally endemic to the majority of areas in the western hemisphere where maize is cultivated. A full-length reference transcriptome for Tripsacum dactyloides generated using long-read Iso-Seq data was used to characterize independent adaptation to temperate climates in this clade. Genes related to phospholipid biosynthesis, a critical component of cold acclimation in other cold-adapted plant lineages, were enriched among those genes experiencing more rapid rates of protein sequence evolution in T. dactyloides. In contrast with previous studies of parallel selection, we find that there is a significant overlap between the genes that were targets of artificial selection during the adaptation of maize to temperate climates and those that were targets of natural selection in temperate-adapted T. dactyloides. Genes related to growth, development, response to stimulus, signaling, and organelles were enriched in the set of genes identified as both targets of natural and artificial selection.

Palladium-Catalyzed Direct α-C(sp3) Heteroarylation of Ketones under Microwave Irradiation

Heteroaryl compounds are valuable building blocks in medicinal chemistry and chemical industry. A palladium-catalyzed direct α-C(sp3) heteroarylation of ketones under microwave irradiation is developed and reported in this study. Under optimized conditions, twenty-eight (28) heteroarylated ketones were prepared in this study to demonstrate the substrate scope of this reaction. The ground-state optimized structure of Pd(0) active catalyst with 2-dicyclohexylphosphino-2',4',6'-triisopropylbiphenyl (XPhos) in toluene, and the products of its reaction with 3-bromopyridine and acetophenone were studied using all-atom density functional theory. This study provided insightful information for palladium catalytic system design to generate heteroaryl compounds.

Generation and Evaluation of Modified Opaque-2 Popcorn Suggests a Route to Quality Protein Popcorn

Introducing traits from dent corn to popcorn is challenging because it is difficult to recover adequate popping characteristics. QPM (Quality Protein Maize) is a dent corn variety carrying the opaque-2 (o2) mutation, specifying increased amounts of normally limiting essential amino acids, and modifier genes which restore the wild type vitreous kernel phenotype. In this study, we introgressed o2 and selected for endosperm modification using vitreousness and high 27-kD gamma zein content. In this way, we recovered high-lysine, fully poppable Quality Protein Popcorn (QPP). BC2F4 individuals with vitreous kernels were confirmed to be o2 mutants by both genotyping and SDS-PAGE. Amino acid profiling of BC2F4 individuals showed that they all have significantly increased lysine compared with popcorn parental lines. Principal Component Analysis of the amino acid profiles showed that all introgressions were grouped with corresponding QPM parental lines. Popping analysis of the BC2F5 individuals showed that while there is variability in popping volume between lines, some lines show equivalent popping to the popcorn parent. In this proof-of-concept study for QPP, we have shown that it is possible to rapidly recover sufficient popcorn characteristics in a modified o2 background using simple phenotypic, biochemical and genetic selection. Furthermore, this shows increased γ-zein is an acceptable substitute for α-zein for full poppability. Since we have developed multiple QPP introgressions, this gives good scope for ongoing hybrid production and future evaluation of agronomic performance and selection of elite hybrids. In a wider context, this study shows the potential for breeding beneficial traits into popcorn for agronomic improvement.

Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets

OBJECTIVES

Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large, well-integrated, multi-year datasets, diverse queries can be made: Which lines perform best in hot, dry environments? Which alleles of specific genes are required for optimal performance in each environment? Such datasets also can be leveraged to predict cultivar performance, even in uncharacterized environments. The maize Genomes to Fields (G2F) Initiative is a multi-institutional organization of scientists working to generate and analyze such datasets from existing, publicly available inbred lines and hybrids. G2F's genotype by environment project has released 2014 and 2015 datasets to the public, with 2016 and 2017 collected and soon to be made available.

DATA DESCRIPTION

Datasets include DNA sequences; traditional phenotype descriptions, as well as detailed ear, cob, and kernel phenotypes quantified by image analysis; weather station measurements; and soil characterizations by site. Data are released as comma separated value spreadsheets accompanied by extensive README text descriptions. For genotypic and phenotypic data, both raw data and a version with outliers removed are reported. For weather data, two versions are reported: a full dataset calibrated against nearby National Weather Service sites and a second calibrated set with outliers and apparent artifacts removed.

Autologous dental pulp mesenchymal stem cells for inferior third molar post-extraction socket healing: A split-mouth randomised clinical trial

Background

Since the discovery of adult mesenchymal stem cells extensive research has been conducted to determine their mechanisms of differentiation and effectiveness in cell therapy and regenerative medicine.

Material and Methods

To assess the efficacy of autologous dental pulp mesenchymal stem cells delivered in a collagen matrix for post-extraction socket healing, a single-centre, double-blind, randomised, split-mouth, controlled clinical trial was performed. Both impacted mandibular third molars were extracted from 32 patients. Dental pulp was collected and dissociated; the resulting cell suspension, obtained by centrifugation, was incorporated into a resorbable collagen matrix and implanted in 32 experimental post-extraction sockets. Collagen matrices alone were implanted in 32 contralateral, control post-extraction sockets. Two neuroradiologists independently assessed the extent of bone repair at 6 months after the extractions. Computed tomography (CT, Philips Brilliance) and an advanced display platform (IntelliSpace Portal) was used to record extraction socket density, expressed as Hounsfield units (HU) and height (mm) of the distal interdental bone septum of the second molar. Measurements at 6 months post-extraction were compared with measurements obtained immediately after extraction. Data were analysed with the statistical program STATA 14.

Results

Two patients dropped out of the study. The final sample consisted of 22 women and 8 men (mean age, 23 years; range: 18–30 years). Clinical, radiological, and surgical characteristics of impacted third molars of the control and experimental groups were homogeneous. Measurements obtained by the two neuroradiologists showed agreement. No significant differences were found in the extent of bone repair during analyses of density (p=0.4203 neuroradiologist 1; p=0.2525 neuroradiologist 2) or interdental septum height (p=0.2280 neuroradiologist 1; p=0.4784 neuroradiologist 2).

Conclusions

In our clinical trial, we were unable to demonstrate that autologous dental pulp mesenchymal stem cells reduce socket bone resorption after inferior third molar extraction.

Key words:Clinical trial, autologous, pulpal stem cells, extraction socket healing.

Long-term Bladder and Upper Urinary Tract Follow-up Recurrence and Progression Rates of G1-2 Non-muscle-invasive Urothelial Carcinoma of the Bladder

OBJECTIVE

To evaluate the risk of long-term tumor recurrence and progression in patients with low- and intermediate-risk non-muscle-invasive bladder cancers, which could facilitate optimization in the follow-up schedules.

MATERIALS AND METHODS

A single-institution, retrospective analysis of 704 patients with primary TaG1, TaG2, T1G1, and T1G2 urothelial carcinomas of the bladder without concomitant carcinoma in situ, treated with transurethral resection, was performed. Response was determined and monitored by routine periodic urine cytology, cystoscopy, and upper tract imaging.

RESULTS

The median follow-up was 64.9 months (maximum, 120 months). Among all of the tumors, 59.3% did not relapse, 36.6% recurred in the bladder during the first 5 years of surveillance, and only 3.6% recurred after 5 years of follow-up. Eight urothelial bladder cancers (1.1%) progressed in stage, and 87.5% of the progressions occurred during the first 5 years of surveillance. An upper urinary tract recurrence was detected in 2.4% of the patients; 94.1% were diagnosed within the upper urinary tract during the first 5 years of follow-up and 5.9% occurred after 5 years of surveillance.

CONCLUSION

G1-2 urothelial bladder cancers recur and progress uncommonly in the long-term period. Although limited by its retrospective nature, the present study provides potential grounds for re-examination of the follow-up schedule for patients with primary non-muscle-invasive bladder cancer G1-2 tumors who remain asymptomatic and disease-free for at least 5 years.

Electron Beam Irradiation Treatment of Cantaloupes: Effect on Product Quality

Despite the impressive advances in electron beam irradiation, the technology is not ready for application to all types of fresh and/or minimally processed fruits and vegetables. The relationships between food product quality (nutrients, colour and texture) and irradiation dose are still needed. Cantaloupes ( Cucumis melo, L.) have become a product of interest due to the recent food-borne illness outbreaks related to their consumption in the United States and other countries. The main goal of this study was to verify whether treatment of cantaloupes using electron beam technology has any detrimental effects on the product quality. Whole and fresh-cut packaged cantaloupes were irradiated using a linear electron beam accelerator with the single beam (10MeV) fixture. Samples were stored at 10°C for zero, 4, 8 and 12 days along with control (non-irradiated) samples and tested for colour, texture (firmness), size (density), sugars and carotene content to determine the effect of irradiation dose level (1.0, 1.5 and 3.1kGy). Results indicated that irradiation of cantaloupes, as whole fruits with dose up to 1.0kGy, caused no significant changes on the fruit’s physical and nutritional quality attributes. Irradiating at higher doses had an undesirable effect on product quality. The fresh-cut packaged cantaloupe may be irradiated up to 1.5kGy without worsening the product quality attributes. In both cases, carotene content slightly increased as irradiation dose increased. In general, samples irradiated with dose levels between 1.0-1.5kGy had better quality attributes than the non-irradiated samples.

Sorption of indium (III) onto carbon nanotubes

Indium has numerous applications in different industrial sectors and is not an abundant element. Therefore appropriate technology to recover this element from various process wastes is needed. This research reports high adsorption capacity of multiwalled carbon nanotubes (MWCNT) for In(III). The effects of pH, kinetics, isotherms and adsorption mechanism of MWCNT on In(III) adsorption were investigated and discussed in detail. The pH increases improves the adsorption capacity for In(III). The Langmuir adsorption model is the best fit with the experimental data. For the kinetic study, the adsorption onto MWCNT could be fitted to pseudo second-order. The adsorption of indium(III) can be described to a mechanism which consists of a film diffusion controlled process. Metal desorption can be achieved with acidic solutions.

MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis

Network analysis can make variant analysis better. There are existing tools like HotNet2 and dmGWAS that can provide various analytical methods. We developed a prototype of a pipeline called MetaNetVar that allows execution of multiple tools. The code is published at https://github.com/NCBI-Hackathons/Network_SNPs. A working prototype is published as an Amazon Machine Image - ami-4510312f .

[Computerized ranking test in three French universities: Staff experience and students' feedback]

BACKGROUND

The year 2016 will be pivotal for the evaluation of French medical students with the introduction of the first computerized National Ranking Test (ECNi). The SIDES, online electronic system for medical student evaluation, was created for this purpose. All the universities have already organized faculty exams but few a joint computerized ranking test at several universities simultaneously. We report our experience on the organization of a mock ECNi by universities Paris Descartes, Paris Diderot and Paris 13.

METHODS

Docimological, administrative and technical working groups were created to organize this ECNi. Students in their fifth year of medical studies, who will be the first students to sit for the official ECNi in 2016, were invited to attend this mock exam that represented more than 50% of what will be proposed in 2016. A final electronic questionnaire allowed a docimological and organizational evaluation by students. An analysis of ratings and rankings and their distribution on a 1000-point scale were performed.

RESULTS

Sixty-four percent of enrolled students (i.e., 654) attended the three half-day exams. No difference in total score and ranking between the three universities was observed. Students' feedback was extremely positive. Normalized over 1000 points, 99% of students were scored on 300 points only. Progressive clinical cases were the most discriminating test.

CONCLUSION

The organization of a mock ECNi involving multiple universities was a docimological and technical success but required an important administrative, technical and teaching investment.

Phase III, randomized trial (CheckMate 057) of nivolumab (NIVO) versus docetaxel (DOC) in advanced non-squamous cell (non-SQ) non-small cell lung cancer (NSCLC)

LBA109

Background: Options for advanced non-SQ NSCLC patients (pts) who progress after platinum-based doublet chemotherapy (PT-DC) are limited, with minimal improvement in overall survival (OS). We report results from a randomized, global phase III study of NIVO, a fully human IgG4 programmed death-1 (PD-1) immune checkpoint inhibitor antibody, vs DOC in pts with advanced non-SQ NSCLC after failure of PT-DC and tyrosine kinase inhibitor, if eligible. Methods: Pts were randomized to NIVO 3 mg/kg Q2W (n=292) or DOC 75 mg/m2 Q3W (n=290) until progression or discontinuation due to toxicity/other reasons. Primary objective was OS; Secondary objectives were investigator-assessed objective response rate (ORR; per RECIST v1.1), progression-free survival (PFS), efficacy by PD-L1 expression, quality of life, and safety. Results: NIVO demonstrated superior OS (HR=0.73; 96% CI: 0.59, 0.89; P=0.00155) and improved ORR (19.2% vs 12.4%; P=0.0235). HR for PFS was 0.92 (95% CI: 0.77, 1.11; P=0.393). PD-L1 expression was associated with benefit from NIVO (Table). In PD-L1+ pts, NIVO showed improved efficacy across all endpoints at predefined 1%, 5%, and 10% cut- points. Grade 3–5 drug-related AEs occurred in 10.5% (30/287) of NIVO and 53.7% (144/268) of DOC pts. No deaths were related to NIVO vs 1 DOC-related death. After discontinuation, 42.1% of NIVO and 49.7% of DOC pts received subsequent systemic therapy. Conclusions: NIVO demonstrated superior OS vs DOC in pts with advanced non-SQ NSCLC after failure of PT-DC. The safety profile of NIVO 3 mg/kg Q2W was favorable vs DOC. NIVO demonstrated survival benefit across histologies in two randomized phase III trials. Clinical trial information: NCT01673867. [Table: see text]

Association of genetic variants of membrane receptors related to recognition and induction of immune response with Helicobacter pylori infection in Ecuadorian individuals

Helicobacter pylori (Hp) has a worldwide distribution showing its higher prevalence of infection in developing countries. Toll-like receptors (TLRs) and C-type lectin receptors (CLRs) are proteins that recognize pathogen-associated molecular patterns (PAMPs) and initiate an innate immune response by promoting growth and differentiation of specialized hematopoietic cells for host defense. Gastric infections led by Hp induce a Th-1 cellular immune response, regulated mainly by the expression of IFN-γ. In this retrospective case-control study, we evaluated the TLR1 1805T/G, TLR2 2029C/T, TLR4 896A/G, CD209 -336A/G and IFNGR1 -56C/T polymorphisms and their relationship with susceptibility to Hp infection. TLR1 1805T/G showed statistical differences when the control (Hp-) and infected (Hp+) groups (P = 0.041*) were compared; the TLR1 1805G allele had a protective effect towards infection (OR = 0.1; 95% CI = 0.01-0.88, P = 0.033*). Similarly, the IFNGR1 -56C/T polymorphism showed statistical differences between Hp+ and Hp- (P = 0.018*), and the IFNGR1 -56TT genotype exhibited significant risk to Hp infection (OR = 2.9, 95% CI = 1.27-6.54, P = 0.018*). In conclusion, the pro-inflammatory TLR1 1805T and IFNGR1 -56T alleles are related with susceptibility to Hp infection in Ecuadorian individuals. The presence of these polymorphisms in individuals with chronic infection increases the risk of cellular damage and diminishes the cellular immune response efficiency towards colonizing agents.