Exploring methods to summarize gut microbiota composition for microbiability estimation and phenotypic prediction in swine

The microbial composition resemblance among individuals in a group can be summarized in a square covariance matrix and fitted in linear models. We investigated eight approaches to create the matrix that quantified the resemblance between animals based on the gut microbiota composition. We aimed to compare the performance of different methods in estimating trait microbiability and predicting growth and body composition traits in three pig breeds. This study included 651 purebred boars from either breed: Duroc (n = 205), Landrace (n = 226), and Large White (n = 220). Growth and body composition traits, including body weight (BW), ultrasound backfat thickness (BF), ultrasound loin depth (LD), and ultrasound intramuscular fat (IMF) content, were measured on live animals at the market weight (156 ± 2.5 days of age). Rectal swabs were taken from each animal at 158 ± 4 days of age and subjected to 16S rRNA gene sequencing. Eight methods were used to create the microbial similarity matrices, including four kernel functions (Linear Kernel, LK; Polynomial Kernel, PK; Gaussian Kernel, GK; Arc-cosine Kernel with one hidden layer, AK1), two dissimilarity methods (Bray-Curtis, BC; Jaccard, JA), and two ordination methods (Metric Multidimensional Scaling, MDS; Detrended Correspondence analysis, DCA). Based on the matrix used, microbiability estimates ranged from 0.07 to 0.21 and 0.12 to 0.53 for Duroc, 0.03 to 0.21 and 0.05 to 0.44 for Landrace, and 0.02 to 0.24 and 0.05 to 0.52 for Large White pigs averaged over traits in the model with sire, pen, and microbiome, and model with the only microbiome, respectively. The GK, JA, BC, and AK1 obtained greater microbiability estimates than the remaining methods across traits and breeds. Predictions were made within each breed group using four-fold cross-validation based on the relatedness of sires in each breed group. The prediction accuracy ranged from 0.03 to 0.18 for BW, 0.08 to 0.31 for BF, 0.21 to 0.48 for LD, and 0.04 to 0.16 for IMF when averaged across breeds. The BC, MDS, LK, and JA achieved better accuracy than other methods in most predictions. Overall, the PK and DCA exhibited the worst performance compared to other microbiability estimation and prediction methods. The current study shows how alternative approaches summarized the resemblance of gut microbiota composition among animals and contributed this information to variance component estimation and phenotypic prediction in swine.

Use of Host Feeding Behavior and Gut Microbiome Data in Estimating Variance Components and Predicting Growth and Body Composition Traits in Swine

The purpose of this study was to investigate the use of feeding behavior in conjunction with gut microbiome sampled at two growth stages in predicting growth and body composition traits of finishing pigs. Six hundred and fifty-one purebred boars of three breeds: Duroc (DR), Landrace (LR), and Large White (LW), were studied. Feeding activities were recorded individually from 99 to 163 days of age. The 16S rRNA gene sequences were obtained from each pig at 123 ± 4 and 158 ± 4 days of age. When pigs reached market weight, body weight (BW), ultrasound backfat thickness (BF), ultrasound loin depth (LD), and ultrasound intramuscular fat (IMF) content were measured on live animals. Three models including feeding behavior (Model_FB), gut microbiota (Model_M), or both (Model_FB_M) as predictors, were investigated. Prediction accuracies were evaluated through cross-validation across genetic backgrounds using the leave-one-breed-out strategy and across rearing environments using the leave-one-room-out approach. The proportions of phenotypic variance of growth and body composition traits explained by feeding behavior ranged from 0.02 to 0.30, and from 0.20 to 0.52 when using gut microbiota composition. Overall prediction accuracy (averaged over traits and time points) of phenotypes was 0.24 and 0.33 for Model_FB, 0.27 and 0.19 for Model_M, and 0.40 and 0.35 for Model_FB_M for the across-breed and across-room scenarios, respectively. This study shows how feeding behavior and gut microbiota composition provide non-redundant information in predicting growth in swine.

Use, and acceptability, of digital health technologies in musculoskeletal physical therapy: A survey of physical therapists and patients

Objectives

Determine (a) frequency of digital health use to obtain/record clinical information (pre‐COVID‐19); (b) willingness to use digital technologies among physical therapists and patients with musculoskeletal conditions.

Methods

102 physical therapists, and 103 patients were recruited in Australia. An electronic survey ascertained (a) demographic/clinical characteristics, (b) frequency of methods to obtain and record clinical information; (c) willingness to use digital technologies to support musculoskeletal care.

Results

Physical therapists mostly used non‐digital methods to obtain subjective (e.g., face‐to‐face questioning, n = 98; 96.1%) and objective information (e.g., visual estimation, n = 95; 93.1%). The top three digital health technologies most frequently used by therapists: photo‐based image capture (n = 19; 18.6%), accessing information logged/tracked by patients into a mobile app (n = 14; 13.7%), and electronic systems to capture subjective information that the patient fills in (n = 13; 12.7%). The top three technologies used by patients: activity trackers (n = 27; 26.2%), logging/tracking health information on mobile apps or websites (n = 12; 11.7%), and entering information on a computer (n = 12; 7.8%). Physical therapists were most willing to use technologies for: receiving diagnostic imaging results (n = 99; 97.1%), scheduling appointments (n = 92; 90.2%) and capturing diagnostic results (n = 92; 90.2%). Patients were most willing to use technologies for receiving notifications about health test results (n = 91; 88.4%), looking up health information (n = 83; 80.6%) and receiving personalised alerts/reminders (n = 80; 77.7%).

Conclusions

Physical therapists and patients infrequently use digital health technologies to support musculoskeletal care, but expressed some willingness to consider using them for select functions.

Honey authenticity: the opacity of analytical reports-part 2, forensic evaluative reporting as a potential solution

The analytical techniques applied to verify honey authenticity are multifaceted and often result in complex data rich certificates of analysis that are open to interpretation and may be opaque to stakeholders without specialist knowledge. In these cases, the drawing of an independent overarching opinion is challenging. Two questions arise: (Q1) Is it acceptable to report interpretation, particularly if it is adverse, without exhibiting the supporting data? (Q2) How may a valid overarching opinion on authenticity be derived from a large, partially conflicting, dataset? To Q1, it is demonstrated that full disclosure of the data used in interpretation is mandatory. To Q2 it is proposed, with worked examples, to adopt ‘evaluative reporting’; a formalised likelihood ratio thought process used in forensic science for evaluation of findings and their strength assessment. In the absence of consensus on techniques for honey authenticity adoption of reporting conventions will allow objective assessments of reports, with equity to all and provide a better basis to identify and address fraud.

Exploring the role of gut microbiota in host feeding behavior among breeds in swine

BACKGROUND

The interplay between the gut microbiota and feeding behavior has consequences for host metabolism and health. The present study aimed to explore gut microbiota overall influence on feeding behavior traits and to identify specific microbes associated with the traits in three commercial swine breeds at three growth stages. Feeding behavior measures were obtained from 651 pigs of three breeds (Duroc, Landrace, and Large White) from an average 73 to 163 days of age. Seven feeding behavior traits covered the information of feed intake, feeder occupation time, feeding rate, and the number of visits to the feeder. Rectal swabs were collected from each pig at 73 ± 3, 123 ± 4, and 158 ± 4 days of age. DNA was extracted and subjected to 16 S rRNA gene sequencing.

RESULTS

Differences in feeding behavior traits among breeds during each period were found. The proportion of phenotypic variances of feeding behavior explained by the gut microbial composition was small to moderate (ranged from 0.09 to 0.31). A total of 21, 10, and 35 amplicon sequence variants were found to be significantly (q-value < 0.05) associated with feeding behavior traits for Duroc, Landrace, and Large White across the three sampling time points. The identified amplicon sequence variants were annotated to five phyla, with Firmicutes being the most abundant. Those amplicon sequence variants were assigned to 28 genera, mainly including Christensenellaceae_R-7_group, Ruminococcaceae_UCG-004, Dorea, Ruminococcaceae_UCG-014, and Marvinbryantia.

CONCLUSIONS

This study demonstrated the importance of the gut microbial composition in interacting with the host feeding behavior and identified multiple archaea and bacteria associated with feeding behavior measures in pigs from either Duroc, Landrace, or Large White breeds at three growth stages. Our study provides insight into the interaction between gut microbiota and feeding behavior and highlights the genetic background and age effects in swine microbial studies.

The feasibility of an online educational lifestyle program for people with multiple sclerosis: A qualitative analysis of participant semi-structured interviews

Objective

To explore the feasibility of a randomised controlled trial of a multiple sclerosis online course (MSOC) via qualitative analysis of participant semi-structured interviews.

Methods

The MSOC was developed in two arms: intervention arm which contained evidence-based lifestyle modification recommendations, and standard-care arm which delivered information from MS websites reflecting standard advice. Participants were recruited via online advertisements, completed a baseline questionnaire, and randomised. Seven modules were delivered over six weeks. Course completers were invited to participate in semi-structured interviews. Within a qualitative paradigm, interviews were analysed using reflexive thematic analysis.

Results

Fourteen of the 17 course completers were interviewed: 86% (12/14) female; mean age 50 years; residing in Australia, New Zealand, and the USA, predominantly had relapsing-remitting MS, mean time from diagnosis 9.5 years, and patient-determined disease steps disability assessment distributed evenly across all three categories. Four themes were identified: 1) “Hearing our stories” (hope for the future, feeling represented, exploring the journey of others with MS, learning from diversity, and wanting to connect with others); 2) “Taking the plunge” (not wanting to be first, feelings of nervousness or reluctance and feeling confronted); 3) “The accessibility and safety of being online” (ease of access, going at your own pace, making it work and not letting others down); and 4) “unpacking the course” (ease of navigation, visuals, understandability, and length and timing).

Conclusion

Participants felt represented, found the course accessible and content was easy to understand. These experiences provide important insights and considerations for this digital health intervention.

Characteristics of mHealth app use in an international sample of people with multiple sclerosis

The management of multiple sclerosis (MS) has progressed significantly with the emergence of mHealth technologies. Uptake of mHealth apps amongst people with MS, and clinical and demographic characteristics of mHealth adopters is unknown outside North America. Participants of the HOLISM study were queried about their mHealth apps use. We summarize mHealth app usage, and clinical and demographic characteristics of mHealth app adopters using descriptive statistics. Overall, 3.1% of respondents reported using an mHealth app, most of whom were located in Australasia and North America. This study provides insight regarding mHealth app usage within a large international cohort of people with MS.

426 PREVALENCE OF, AND RISK FACTORS FOR, DEMENTIA IN ADULT OUTPATIENT REFERRALS TO A REGIONAL REFERRAL HOSPITAL IN ARUSHA, TANZANIA

Introduction

The global burden of dementia is increasing, with the greatest increase predicted to occur in sub-Saharan Africa (SSA). Despite this there are limited previous data on the prevalence of, and risk factors for, dementia in SSA. This study aimed to estimate the prevalence of dementia, and investigate its associations, in those aged 60 years and older attending the outpatient department of Mount Meru Hospital in northern Tanzania. This is the first hospital-based outpatient dementia prevalence and risk factors study to be conducted in an east African population.

Methods

This was a one-phase cross-sectional study. Adults aged 60 years and over attending medical outpatients were screened for dementia using The Identification and Intervention for Dementia in Elderly Africans cognitive screening tool. Those who scored ≤9 were clinically assessed using the DSM-IV criteria. Demographic, medical comorbidity and lifestyle information were collected during a clinical assessment.

Results

Prevalence of dementia was 5.0% (95% confidence interval: 3.7–6.3). Binary logistic regression found female sex (odds ratio (OR) = 2.778), having no formal education (OR = 6.088), quantity of alcohol consumption (units/week) (OR = 1.080), uncorrected visual impairment (OR = 4.260), body mass index &lt;18.5 kg/m2 (OR = 6.588) and stroke (OR = 15.790 with wide 95% confidence interval (3.48–74.475)) to be significantly, independently associated with dementia.

Conclusions

The prevalence of dementia in this population is lower than previously reported community-based rates in Tanzania, and similar to those in high-income countries. This is the first time the association between uncorrected visual impairment and dementia has been reported in SSA. Other associations identified are in keeping with previous literature. Further research on the management of dementia and its risk factors, and the support and education of carers and patients in east African populations is required.

93 Genomic basis of antibody response to porcine reproductive and respiratory syndrome virus vaccination

Antibody (Ab) response to natural infection with porcine reproductive and respiratory syndrome (PRRS) virus has been shown to be highly heritable (~0.40), to be genetically correlated with farrowing performance in PRRSV-infected sows, be controlled by two major QTL on chromosome 7, among others, and have moderate genomic prediction accuracy. However, waiting for PRRS outbreaks to occur to collect data limits the use of Ab response to select for increased PRRS resilience. Thus, we investigated the genomic basis of Ab response to PRRS vaccination with a modified live PRRSV vaccine as a strategy to generate data for this purpose. Nine hundred and six commercial F1 replacement gilts (189±16 days old) were vaccinated with a commercial PRRS modified live virus vaccine. Blood samples were collected 52 days after vaccination to measure Ab response, as sample-to-positive (S/P) ratio using a commercial ELISA, and for SNP genotyping (~50K). BayesC0 was used to estimate heritability for S/P ratio using in a model with contemporary group (CG) as fixed effect and SNP effects as random. Genome-wide association study and genomic prediction for S/P ratio were performed with BayesB (Pi=0.99). For genomic prediction, a three-fold cross-validation was used, in which each CG (n=3) was used as validation dataset. Accuracy of genomic prediction was defined as the correlation between genomic estimated breeding values and phenotypes adjusted for estimates of fixed effects, weighed by the number of individuals in the validation dataset. Heritability of S/P was moderate (0.35±0.04). A QTL was identified on chromosome 7 (25 Mb) explaining ~28% of the genetic variance. Accuracy of genomic prediction was fairly high (0.60±0.15). This is the first study describing the genomic basis of Ab response to PRRS vaccination with modified-live virus vaccine. Additional work is needed to evaluate the genetic correlation of Ab response to vaccination with resilience traits in pigs.

PSV-11 Accuracies of genomic prediction for reproductive traits in PRRSV-infected sows

Recent studies on host-genetics of response to porcine reproductive and respiratory syndrome virus (PRRSV) infection have shown that genetic markers can be used to predict performance in growing pigs. On the other hand, no work has been done on the genomic prediction of reproductive performance in PRRSV-infected sows. Thus, the objective of this work was to assess the accuracies of genomic prediction for reproductive traits in PRRSV-infected sows. A total of 475 Duroc and 405 Landrace sows with ~30K SNP genotypes had farrowing performance data during the outbreak on: number of piglets born alive (NBA), stillborn piglets (NSB), mummified piglets (NM), piglets born dead (NBD; NSB+NM), total number of piglets born (TNB; NBA+NBD), and piglets weaned (NW). Genomic prediction was performed by Bayes-B with a model fitting parity as fixed-effect and SNP effects as random. Analyses were performed for two scenarios: within-breed and between-breed. For the within-breed prediction, 4-fold cross-validation was used. For the between-breed prediction, all data for each breed were used. Accuracy of genomic prediction (AGP) was calculated as the correlation between genomic estimated breeding values and pre-adjusted phenotype, divided by square-root of heritability. For the within-breed prediction, AGP (± standard deviation) for NBA, NBD, NM, NSB, NW, and TNB were 0.24±0.05, 0.07±0.10, -0.27±0.06, -0.24±0.09, -0.05±0.05, 0.19±0.03, respectively, for Duroc, and 0.37±0.02, 0.38±0.11, 0.30±0.07, 0.60±0.10, 0.09±0.11, 0.15±0.10, respectively, for Landrace. For the between-breed prediction, AGP for NBA, NBD, NM, NSB, NW, and TB were 0.28, -0.17, -0.01, 0.37, 0.27, and 0.29, respectively, when training on Landrace and validating on Duroc, and 0.28, -0.14, 0.01, 0.15, 0.23, and -0.01, respectively, when training on Duroc and validating on Landrace. Results show that the accuracies of genomic prediction for reproductive traits during a PRRSV outbreak are low to moderate.

PSV-15 Genomic basis of reproductive performance in PRRSV-infected sows

Previous studies have shown that reproductive traits in sows during porcine reproductive and respiratory syndrome (PRRS) outbreaks are lowly heritable. However, little is known about the genomic basis of reproductive performance in PRRS virus (PRRSV)-infected sows. Thus, the objective of this work was to evaluate the genomic basis of reproductive performance in PRRSV-infected sows. Farrowing data from 475 Duroc and 405 Landrace sows that experienced a PRRS outbreak were used. Heritability and genome-wide association studies (GWAS) based on ~30K SNP genotypes were performed for each breed separately, for number of piglets born alive (NBA), stillborn piglets (NSB), mummified piglets (NM), piglets born dead (NBD; NSB+NM), total number of piglets born (TNB; NBA+NBD), and piglets weaned (NW). Heritabilities were estimated with ASReml using a model with the fixed-effect of parity and an animal random-effect, using a genomic-relationship matrix. GWAS was performed using Bayes-B in GenSel with a model fitting parity as fixed-effect and SNP effects as random. Heritability estimates (± standard error) for NBA, NSB, NM, NBD, TNB, and NW were 0.07±0.07, 0.02±0.11, 0.04±0.10, 0.08±0.08, 0.08±0.07, 0.06±0.04, respectively, for Duroc, and 0.09±0.07, 0.10±0.07, 0.10±0.08, 0.11±0.07, 0.07±0.08, 0.07±0.08, respectively, for Landrace. For Duroc, GWAS identified a quantitative trait locus (QTL) on chromosome (chr) 3 [114-120 megabases (Mb)] explaining 3.9% of the genetic variance (GV) for NBA, on chr 13 (189-193 Mb) explaining 2.7% GV for NBD, and on chr 5 (36-41 Mb) explaining 4.3% GV for TNB. For Landrace, GWAS identified a QTL on chr 13 (154-162 Mb) explaining 12.8% GV for NBA, on chr 14 (59-69 Mb) explaining 2.5% GV for NBD, and on chr 10 (7-9 Mb) explaining 4.1% GV for NW. These results indicate that reproductive traits are lowly heritable during a PRRS outbreak with few QTL identified in Duroc and Landrace sows.

Evidence for recombination variability in purebred swine populations

This study aimed to investigate interpopulation variation due to sex, breed and age, and the intrapopulation variation in the form of genetic variance for recombination in swine. Genome-wide recombination rate and recombination occurrences (RO) were traits studied in Landrace (LR) and Large White (LW) male and female populations. Differences were found for sex, breed, sex-breed interaction, and age effects for genome-wide recombination rate and RO at one or more chromosomes. Dams were found to have a higher genome-wide recombination rate and RO at all chromosomes than sires. LW animals had higher genome-wide recombination rate and RO at seven chromosomes but lower at two chromosomes than LR individuals. The sex-breed interaction effect did not show any pattern not already observable by sex. Recombination increased with increasing parity in females, while in males no effect of age was observed. We estimated heritabilities and repeatabilities for both investigated traits and obtained the genetic correlation between male and female genome-wide recombination rate within each of the two breeds studied. Estimates of heritability and repeatability were low (h²  = 0.01-0.26; r = 0.18-0.42) for both traits in all populations. Genetic correlations were high and positive, with estimates of 0.98 and 0.94 for the LR and LW breeds, respectively. We performed a GWAS for genome-wide recombination rate independently in the four sex/breed populations. The results of the GWAS were inconsistent across the four populations with different significant genomic regions identified. The results of this study provide evidence of variability for recombination in purebred swine populations.

Genomics of Heat Tolerance in Reproductive Performance Investigated in Four Independent Maternal Lines of Pigs

Improving swine climatic resilience through genomic selection has the potential to minimize welfare issues and increase the industry profitability. The main objective of this study was to investigate the genetic and genomic determinism of tolerance to heat stress in four independent purebred populations of swine. Three female reproductive traits were investigated: total number of piglets born (TNB), number of piglets born alive (NBA) and average birth weight (ABW). More than 80,000 phenotypic and 12,000 genotyped individuals were included in this study. Genomic random-regression models were fitted regressing the phenotypes of interest on a set of 95 environmental covariates extracted from public weather station records. The models yielded estimates of (genomic) reactions norms for individual pigs, as indicator of heat tolerance. Heat tolerance is a heritable trait, although the heritabilities are larger under comfortable than heat-stress conditions (larger than 0.05 vs. 0.02 for TNB; 0.10 vs. 0.05 for NBA; larger than 0.20 vs. 0.10 for ABW). TNB showed the lowest genetic correlation (-38%) between divergent climatic conditions, being the trait with the strongest impact of genotype by environment interaction, while NBA and ABW showed values slightly negative or equal to zero reporting a milder impact of the genotype by environment interaction. After estimating genetic parameters, a genome-wide association study was performed based on the single-step GBLUP method. Heat tolerance was observed to be a highly polygenic trait. Multiple and non-overlapping genomic regions were identified for each trait based on the genomic breeding values for reproductive performance under comfortable or heat stress conditions. Relevant regions were found on chromosomes (SSC) 1, 3, 5, 6, 9, 11, and 12, although there were important regions across all autosomal chromosomes. The genomic region located on SSC9 appears to be of particular interest since it was identified for two traits (TNB and NBA) and in two independent populations. Heat tolerance based on reproductive performance indicators is a heritable trait and genetic progress for heat tolerance can be achieved through genetic or genomic selection. Various genomic regions and candidate genes with important biological functions were identified, which will be of great value for future functional genomic studies.

Fructans in Foods and Food Products, Ion-Exchange Chromatographic Method: Collaborative Study

Nine collaborating laboratories assayed 6 blind duplicate pairs of food samples containing the fructans inulin or oligofructose. The 6 sample pairs ranged from low (4%) to high levels (40%). Following the proposed method, the samples were treated with amyloglucosidase and inulinase enzymes and the released sugars were determined byion exchange chromatography. Repeatability standard deviation ranged from 2.9 to 5.8%; reproducibility standard deviation ranged from 4.7 to 11.1%. The ion-exchange chromatographic method for determinationof fructans in food and food products has been adopted first action by AOAC INTERNATIONAL (997.08)

211 Changes in genetic parameters of fitness and growth traits under genomic selection in pigs

Genomic selection increases intensity of selection and decreases generation interval. However, intensive selection reduces genetic variation and can strengthen undesirable genetic correlations. The purpose of this study was to investigate changes in genetic parameters of litter size (LS), number born alive (NBA), number born dead (NBD) and average daily gain (ADG) and weight at off-test (WT) in pigs over time. The data set contained 20,086 (LS), 21,230 (NBA), 21,230 (NBD), 144,717 (ADG) and 144,718 (WT) phenotypic records. Pedigree file included 369,776 animals born between 2001 and 2018, of which 39,038 were genotyped. Two trait models were evaluated (LS-ADG, LS-WT, NBA-ADG, NBA-WT, NBD-ADG and NBD-WT) using 3-year sliding subsets starting from 2010. Variance components and genetic parameters were estimated using GIBBS2F90 program. Computations were performed with (BLUP) or without (ssGBLUP) genotypes. For BLUP (ssGBLUP), the changes in heritability from 2010–2012 to 2015–2018 were 0.08 to 0.09 (0.08 to 0.06) for LS, 0.33 to 0.24 (0.37 to 0.16) for ADG, 0.11 to 0.07 (0.10 to 0.07) for NBD, and 0.32 to 0.24 (0.38 to 0.17) for WT. Differences were also observed for genetic correlations as they were -0.23 to -0.73 (-0.31 to -0.58) for LS-ADG, -0.24 to -0.74 (-0.31 to -0.50) for LS-WT, -0.33 to -0.65 (-0.41 to -0.53) for NBA-ADG, -0.35 to -0.66 (-0.42 to -0.45) for NBA-WT, 0.12 to 0.04 (0.12 to 0.16) for NBD-ADG, and 0.11 to 0.05 (0.11 to 0.22) for NBD-WT. Genomic selection in pigs reduced heritabilities and emphasized the antagonistic relationship that are under strong selection. Heritabilities estimated from ssGBLUP declined more than those by BLUP while changes in the genetic correlations were smaller and more gradual by ssGBLUP. Differences between ssGBLUP and BLUP could be caused by genomic pre-selection unaccounted for by BLUP.

209 Genomic selection for multiple maternal and growth traits in large white pigs using Single-Step GBLUP

The objective of this study was to implement a multi-trait genomic evaluation for maternal and growth traits in a swine population. Phenotypes for preweaning mortality, litter size, weaning weight, and average daily gain were available for 282K Large White pigs. The pedigree included 314k individuals, of which 35,731 were genotyped for 45K SNPs. Variance components were estimated in a multi-trait animal model without genomic information by AIREMLF90. Genomic breeding values were estimated using the genomic information by single-step GBLUP. The algorithm for proven and young (APY) was used to reduce computing time. Genetic correlation between proportion and the total number of preweaning deaths was 0.95. A strong, positive genetic correlation was also observed between weaning weight and average daily gain (r = 0.94). Conversely, the genetic correlations between mortality and growth traits were negative, with an average of -0.7. To avoid computations by expensive threshold models, preweaning mortality was transformed from a binary trait to two linear dam traits: proportion and a total number of piglets dead before weaning. Because of the high genetic correlations within groups of traits, inclusion of only one growth and one mortality trait in the model decreases computing time and allows for the inclusion of other traits. Reduction in computing time for the evaluation using APY was up to 20x, and no differences in EPD ranking were observed. The algorithm for proven and young improves the efficiency of genomic evaluation in swine without harming the quality of predictions. For this population, a binary trait of mortality can be replaced by a linear trait of the dam, resulting in a similar ranking for the selection candidates.

219 Relationship between host-genetics and the vaginal microbiome in commercial gilts

The objective of this study was to investigate host-genetic contributions to the vaginal microbiome of commercial gilts vaccinated for Porcine Reproductive and Respiratory Syndrome (PRRS). Vaginal swab samples (n = 576) from 308 F1 gilts (183±12 days old) were collected on day 4 (D4) and 52 (D52) post-vaccination with a commercial modified live virus PRRS vaccine. Samples were used to profile the vaginal microbiome by 16S rRNA gene sequencing, with sequences clustered into operational taxonomic units (OTUs) and taxonomically classified. All animals were genotyped for 45,536 SNPs. Arcsine of the square root-transformed OTUs abundance data were analyzed using a linear mixed animal model with age at vaccination as a covariate and animal (random) for estimation of genetic parameters. The same model was used for GWAS for the 100 most abundant OTUs but with addition of genotype of SNPs as a covariate, one at a time. For D4, heritability estimates ranged from &lt; 0.001±0.01(13 OTUs) to 0.60±0.13 (Fusobacterium), with OTUs corresponding to the genera Fusobacterium, Pasteurellaceae, Clostridiales, Prevotellaceae, and Lactobacillus having high estimates (0.41±0.13 to 0.60±0.13). For D52, heritability estimates ranged from &lt; 0.001±0.01 (10 OTUs) to 0.63±0.12 (Terrisporobacter), with OTUs corresponding to Clostridium, Terrisporobacter, Romboutsia, Turicibacter, Phascolarctobacterium, Muribaculaceae, and Ruminococcaceae having high estimates (0.42±0.14 to 0.63±0.12). Forty-six QTLs were significantly (P &lt; 0.00001) associated with OTU across days. Among these, one main QTL on chromosome 12 (20–23Mb), a gene-rich region with previously identified QTL for immune-related traits, was identified for 5 and 6 OTUs on D4 and D52, respectively. These OTUs were mainly of the phyla Proteobacteria and Firmicutes on D4 and D52, respectively. In conclusion, there is evidence of substantial host genetic variation for vaginal microbiome in commercial PRRS-vaccinated gilts, including the identification of many QTLs. Additional research is needed to investigate the genetic relationship between vaginal microbiome, health, and production in pigs.

Genetic parameters of meat quality, carcass composition, and growth traits in commercial swine

Swine industry breeding goals are mostly directed towards meat quality and carcass traits due to their high economic value. Yet, studies on meat quality and carcass traits including both phenotypic and genotypic information remain limited, particularly in commercial crossbred swine. The objectives of this study were to estimate the heritabilities for different carcass composition traits and meat quality traits and to estimate the genetic and phenotypic correlations between meat quality, carcass composition, and growth traits in 2 large commercial swine populations: The Maschhoffs LLC (TML) and Smithfield Premium Genetics (SPG), using genotypes and phenotypes data. The TML data set consists of 1,254 crossbred pigs genotyped with 60K SNP chip and phenotyped for meat quality, carcass composition, and growth traits. The SPG population included over 35,000 crossbred pigs phenotyped for meat quality, carcass composition, and growth traits. For TML data sets, the model included fixed effects of dam line, contemporary group (CG), gender, as well as random additive genetic effect and pen nested within CG. For the SPG data set, fixed effects included parity, gender, and CG, as well as random additive genetic effect and harvest group. Analyses were conducted using BLUPF90 suite of programs. Univariate and bivariate analyses were implemented to estimate heritabilities and correlations among traits. Primal yield traits were uniquely created in this study. Heritabilities [high posterior density interval] of meat quality traits ranged from 0.08 [0.03, 0.16] for pH and 0.08 [0.03, 0.1] for Minolta b* to 0.27 [0.22, 0.32] for marbling score, except intramuscular fat with the highest estimate of 0.52 [0.40, 0.62]. Heritabilities of primal yield traits were higher than that of primal weight traits and ranged from 0.17 [0.13, 0.25] for butt yield to 0.45 [0.36, 0.55] for ham yield. The genetic correlations of meat quality and carcass composition traits with growth traits ranged from moderate to high in both directions. High genetic correlations were observed for male and female for all traits except pH. The genetic parameter estimates of this study indicate that a multitrait approach should be considered for selection programs aimed at meat quality and carcass composition in commercial swine populations.

PSIII-9 Heritability estimates for sow prolapse

Vaginal and rectal prolapse incidence has been increasing in the commercial breeding sow population in the U.S. This has resulted in increased sow breeding mortality rates in the U.S. in recent years. The objective of the present study was to estimate the potential role that genetics plays in the prolapse incidence of the U.S. commercial sow population. Data from 22,577 LW x LR crossbred sows from commercial breeding herds were used in this study. Genetic parameters for prolapse incidence were estimated using AIREMLF90 and THRGIBBS1F90 where an animal and threshold models were implemented. The fixed effects in the models included: contemporary group as farm and year-month of removal and removal parity. A random effect for sow and pedigree based relationship matrix was also included in the model. The highest rectal and reproductive tract prolapse incidence were observed in the 1st and 2nd parities. Moreover, sows born in 2013 were investigated greatest incidence of both prolapse incidence. Heritability estimates for prolapse incidence were 0.03 and 0.003 by using the animal and threshold models. The results from this study indicated that there is very little of any genetic impact on the prolapse incidence. Pork producers identify the environmental effects contributing to prolapse incidence.

A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive

Background

In this study we integrated the CNV (copy number variation) and WssGWAS (weighted single-step approach for genome-wide association) analyses to increase the knowledge about number of piglets born alive, an economically important reproductive trait with significant impact on production efficiency of pigs.

Results

A total of 3892 samples were genotyped with the Porcine SNP80 BeadChip. After quality control, a total of 57,962 high-quality SNPs from 3520 Duroc pigs were retained. The PennCNV algorithm identified 46,118 CNVs, which were aggregated by overlapping in 425 CNV regions (CNVRs) ranging from 2.5 Kb to 9718.4 Kb and covering 197 Mb (~ 7.01%) of the pig autosomal genome. The WssGWAS identified 16 genomic regions explaining more than 1% of the additive genetic variance for number of piglets born alive. The overlap between CNVR and WssGWAS analyses identified common regions on SSC2 (4.2–5.2 Mb), SSC3 (3.9–4.9 Mb), SSC12 (56.6–57.6 Mb), and SSC17 (17.3–18.3 Mb). Those regions are known for harboring important causative variants for pig reproductive traits based on their crucial functions in fertilization, development of gametes and embryos. Functional analysis by the Panther software identified 13 gene ontology biological processes significantly represented in this study such as reproduction, developmental process, cellular component organization or biogenesis, and immune system process, which plays relevant roles in swine reproductive traits.

Conclusion

Our research helps to improve the understanding of the genetic architecture of number of piglets born alive, given that the combination of GWAS and CNV analyses allows for a more efficient identification of the genomic regions and biological processes associated with this trait in Duroc pigs. Pig breeding programs could potentially benefit from a more accurate discovery of important genomic regions.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5687-0) contains supplementary material, which is available to authorized users.

Abstract OT2-04-03: Examining personalized radiation therapy (EXPERT): A randomised phase III trial of adjuvant radiotherapy vs observation in patients with molecularly characterized luminal A breast cancer

Background

Radiation therapy (RT) after breast conserving surgery (BCS) is the current standard of care for patients with early stage breast cancer. However, individual absolute recurrence risks and hence benefits of RT vary substantially. A study showed significant association between local recurrence (LR) risk and PAM50-defined intrinsic subtypes and Risk of Recurrence scores (ROR).1

The objective of EXPERT, a co-lead study of Breast Cancer Trials-Australia & New Zealand (BCT-ANZ), and Breast International Group (BIG), is to optimize local therapy for early breast cancer through precise individualized quantification of LR risk to identify patients for whom RT after BCS may be safely omitted.

Trial design

This is a randomized, non-inferiority, phase III study of women who plan to receive adjuvant endocrine therapy for Prosigna (PAM50)-defined luminal A breast cancer with ROR ≤60 resected by BCS.

Women are randomized to receive adjuvant whole breast RT and endocrine therapy or endocrine therapy alone and followed-up for 10 years after randomization.

Major eligibility criteria

Females aged ≥50 years; histologically confirmed invasive breast carcinoma ≤2 cm, grade 1 or 2, ER and PgR ≥10%, HER2-negative and node-negative; treated by BCS with negative margins for invasive carcinoma and associated DCIS; Prosigna (PAM50)-defined Luminal A subtype and ROR ≤60; and plan to receive adjuvant endocrine therapy.

Specific aims

Primary: To determine if omission of RT is not inferior to RT in terms of LR-free interval after BCS.

Secondary: To evaluate the impact of omission of RT on regional, local-regional and distant recurrence-free interval; disease-free survival (DFS); invasive DFS; overall survival; salvage RT or mastectomy rate; toxicity; endocrine therapy adherence; patient reported outcomes; and health economic outcomes.

Statistical methods

An estimated 5-year LR rate in the target population is expected to be 1% with RT. A rate of 4% is considered non-inferior as a worthwhile trade-off against RT toxicity. Using O'Brien-Fleming boundary for rejecting non-inferiority, 29 LR events are required for final analysis expected 8 years after the first patient is randomized. Two interim analyses will be conducted after 10 and 21 events. If the stratified log-rank test statistic exceeds the upper boundary at interim or final analysis, the hypothesis of non-inferiority will be rejected and it will be concluded that no RT is inferior to RT.

Accrual: Target (1170), actual: 82 (June 2018)

The study was activated in Australia in August 2017, with global activation planned for Q4 2018. Recruitment is expected to be completed in 4.5 years.

Contact information

Professor Boon Chua, UNSW Sydney and Prince of Wales Hospital, NSW, Australia; email boon.chua@health.nsw.gov.au; T +61 2 49255239. Registration: NCT02889874

References

Fitzal F, Filipits M, Fesl C, et al. Predicting local recurrence using PAM50 in postmenopausal endocrine responsive breast cancer patients. JCO 2014;32(15 suppl):1008.

Citation Format: Chua BH, Gray K, Krishnasamy M, Regan M, Zdenkowski N, Loi S, Mann B, Forbes JF, Wilcken N, Spillane A, Martin A, Badger H, Jafari S, Fong A, Mavin C, Corachan S, Arahmani A, Martinez J-L, Francis P. Examining personalized radiation therapy (EXPERT): A randomised phase III trial of adjuvant radiotherapy vs observation in patients with molecularly characterized luminal A breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr OT2-04-03.

Abstract P4-14-01: Estrogen levels in premenopausal patients (pts) with hormone-receptor positive (HR+) early breast cancer (BC) receiving adjuvant triptorelin (Trip) plus exemestane (E) or tamoxifen (T) in the SOFT trial: SOFT-EST substudy final analysis

Background: Optimal endocrine therapy for premenopausal pts with early HR+ BC may depend on complete estrogen suppression with GnRH analog, which is crucial when using concurrent aromatase inhibitors (AIs). SOFT-EST is a prospective substudy of the phase 3 SOFT trial aiming to describe estradiol (E2), estrone (E1) and estrone sulphate (E1S) during the first 4 years (y) of monthly Trip+E/T and to assess if there were suboptimally estrogen suppressed (SES) pts in the E+Trip group. Secondary objectives included associations of baseline (BL) factors with SES, early SES with later SES, and SES with disease-free survival (DFS; exploratory objective).

Methods: Patients from select centers who consented and enrolled in SOFT, selected Trip as ovarian function suppression method, and were randomized to E+Trip or T+Trip were eligible for SOFT-EST until the accrual goal (120 pts: 90 E+Trip; 30 T+Trip). Prem status for SOFT eligibility was based on local E2. Blood sampling timepoints were 0, 3, 6, 12, 18, 24, 36 & 48 months (m) until Trip stopped. Serum estrogens were measured centrally by high specificity/sensitivity GC/MSMS and were not available during the study. For 4y analyses, SES was defined as E2 levels &gt;2.72 pg/mL in ≥2 post-BL samples (E2 levels not consistent with postmenopausal (PM) status on AIs [Smith IE, JCO 2006]), or vaginal bleeding &gt;3m after Trip start, or pregnancy. We explored 2 additional cutoffs: &gt;10 pg/mL (clearly inconsistent with PM status on AIs) and &gt;20 pg/mL (inconsistent with GnRH analog-related PM status). The analysis is intention-to-treat based on E/T assignment; as-treated analyses are forthcoming.

Results: From Mar 2009 to Jan 2011,109 pts (E/T=83/26) started Trip and had ≥2 samples drawn. In pts assigned E+Trip, median reductions from BL in E1, E2 and E1S were &gt;95% at all timepoints and significantly lower than in T+Trip. Post-BL E2 geometric mean ranged 0.8-1.3 pg/mL in E+Trip and 16.5-18.3 pg/mL in T+Trip. 21 (25%), 11 (13%) and 6 (7%) pts assigned to E+Trip had E2&gt;2.72, &gt;10, and &gt;20 pg/mL in ≥2 post BL samples or vaginal bleeding (n=3), respectively. Early SES [(≥1 E2 value &gt;2.72 pg/mL or vaginal bleeding in the firsty] predicted later SES [≥1 E2 value &gt;2.72 or vaginal bleeding thereafter (n=1); p&lt;0.001]. BL factors related to SES were higher E2, lower FSH and lower LH values (p=0.02, p&lt;0.01, p&lt;0.01 respectively). 12m FSH levels were not related to SES. In pts assigned E+Trip, after 6y median follow-up, DFS events were seen in 0 of 21 pts with SES vs 5 of 62 pts without SES.

Conclusions: Most pts on E+Trip had a profound E2 drop consistent with postmenopausal status on AI, but &gt;20% assigned to E+Trip had ≥2 E2 values &gt;2.72 pg/mL and 4% had vaginal bleeding, with those having higher E2, lower FSH/LH at BL being at higher risk. SES at 12m predicted subsequent SES. Few DFS events limit the ability to assess clinical relevance of SES with disease outcomes.

BL characteristicsN-109Prior chemo60 (55%)Amenorrhea39 (36%)Age &lt;35y8 (7%) Median (range)Age, y44 (25-53)BMI, kg/m224 (22-28)Estrogen (pg/mL) E252 (7-119)E141 (24-70)E1S894 (304-1320)FSH/LH (IU/L) FSH15 (7-47)LH11 (6-26)

Citation Format: Bellet M, Gray K, Francis P, Láng I, Ciruelos E, Lluch A, Ángel Climent M, Catalán G, Avella A, Bohn U, González-Martin A, Zaman K, Ferrer R, Azaro A, Rajasekaran A, De la Peña L, Fleming G, Regan MM. Estrogen levels in premenopausal patients (pts) with hormone-receptor positive (HR+) early breast cancer (BC) receiving adjuvant triptorelin (Trip) plus exemestane (E) or tamoxifen (T) in the SOFT trial: SOFT-EST substudy final analysis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-14-01.

Current, future and potential use of mobile and wearable technologies and social media data in the ABCD study to increase understanding of contributors to child health

Mobile and wearable technologies and novel methods of data collection are innovating health-related research. These technologies and methods allow for multi-system level capture of data across environmental, physiological, behavioral, and psychological domains. In the Adolescent Brain Cognitive Development (ABCD) Study, there is great potential for harnessing the acceptability, accessibility, and functionality of mobile and social technologies for in-vivo data capture to precisely measure factors, and interactions between factors, that contribute to childhood and adolescent neurodevelopment and psychosocial and health outcomes. Here we discuss advances in mobile and wearable technologies and methods of analysis of geospatial, ecologic, social network and behavioral data. Incorporating these technologies into the ABCD study will allow for interdisciplinary research on the effects of place, social interactions, environment, and substance use on health and developmental outcomes in children and adolescents.

Abstract P1-10-06: A randomized phase II trial evaluating the endocrine activity and efficacy of neoadjuvant degarelix versus triptorelin in premenopausal patients receiving letrozole for primary endocrine responsive breast cancer (TREND; IBCSG 41-13)

Background: Neoadjuvant endocrine therapy (NET) with gonadotropin-releasing hormone (GnRH) agonist and aromatase inhibitors is effective in selected premenopausal patients (pts). Degarelix, an antagonist of GnRH, has immediate onset of action through binding to GnRH receptors in the pituitary gland and thereby suppressing the production of LH and FSH. Its suppressing activity in premenopausal women might be faster and free of estrodial breakthrough on continued treatment compared with a GnRH angonist, and thereby provide significant clinical value for pts who are candidates for short-term NET.

Methods: Eligible pts were premenopausal women with cT2-4b, any nodal stage, ER and PgR &gt;50%, HER2-negative (by IHC and/or ISH) breast cancer who were not candidates for breast conserving surgery. Premenopausal status was determined locally with estradiol (E2) levels &gt;54 pg/mL (or &gt;198 pmol/L), measured within 14 days prior to randomization. Pts were randomized 1:1 to Triptorelin (T) 3.75 mg i.m. on day 1 of every cycle or Degarelix (D) 240 mg s.c. given as two injections of 120 mg on day 1 of cycle 1, then 80 mg s.c. on day 1 of cycles 2-6 with letrozole (L) 2.5 mg/day for 6 cycles. Each cycle was 28 days. Definitive surgery was performed within 2-3 weeks after the last administration of T or D. Serum was collected prior to the first injection (baseline), 24 and 72 hours, 7 and 14 days, then prior to injection on day 1 of cycles 2-6. The primary endpoint was time to optimal ovarian function suppression (OFS) calculated as time from the first injection of D or T to the first assessment of centrally assessed 17-β-estradiol (E2) level in the range of optimal OFS (≤2.72 pg/mL or ≤10 pmol/L) during the 6 cycles of NET. The trial had 90% power to detect a difference using a logrank test, 2-sided α=0.05. Secondary endpoints included tolerability, Ki67changes, PEPI score, best overall response. NCT02005887

Results: TREND completed accrual of 51 pts in January 2017. A preliminary analysis based on the first 45 pts is reported here. 89% of patients were ≥40 yrs, 76% had T1-2 and 22% T3 tumors, and 51% were node-positive. Dominant histology type was ductal (93%). The table summarizes centrally-assessed E2 according to treatment at baseline and for the first 5 assessment time points indicating immediate suppression for the D+L arm. E2 levels on day 1 of cycles 2-6 were all below the limit of quantification (0.625 pg/mL) for the D+L arm. For the T+L arm continued OFS was not maintained in 4 pts.

 BaselineCycle 1Cycle 2Day:01371429No. Pts      D+L222221212221T+L232321232222Median (IQR)     D+L96.2 (64.2,206.8)10.1 (4.0,21.8)0.6 (0.6,1.0)0.6 (0.6,0.6)0.6 (0.6,0.6)0.6 (0.6, 0.6)T+L85.1 (49.7,118.0)37.4 (17.9,59.2)12.8 (7.7,23.8)9.0 (1.2,29.7)0.6 (0.6,1.4)0.6 (0.6, 0.6)

Conclusion: Evidence from this first analysis demonstrates rapid and maintained OFS with the combination of D+L as a NET in premenopausal breast cancer patients. The final analysis of the total population, including secondary endpoints, will be presented at the symposium.

Citation Format: Colleoni M, Gray K, Munzone E, Dellapasqua S, Zamagni C, Gianni L, Johansson H, Viale G, Kammler R, Maibach R, Rabaglio-Poretti M, Di Leo A, Coates AS, Gelber RD, Regan MM, Goldhirsch A. A randomized phase II trial evaluating the endocrine activity and efficacy of neoadjuvant degarelix versus triptorelin in premenopausal patients receiving letrozole for primary endocrine responsive breast cancer (TREND; IBCSG 41-13) [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-10-06.

Modeling response to heat stress in pigs from nucleus and commercial farms in different locations in the United States

The purpose of this study was to analyze the impact of seasonal losses due to heat stress in different environments and genetic group combinations. Data were available for 2 different swine populations: purebred Duroc animals raised in nucleus farms in Texas and North Carolina and crosses of Duroc and F females (Landrace × Large White) raised in commercial farms in Missouri and North Carolina; pedigrees provided links between animals from different states. Traits included BW at harvest age for purebred animals and HCW for crossbred animals. Weather data were collected at airports located close to the farms. Heat stress was quantified by a heat load function, defined by the units of temperature-humidity of temperature-humidity index (THI) greater than a certain threshold for 30 to 70 d before phenotype collection. Heat stress responses were quantified by a linear regression of phenotype on heat load. The greatest coefficient of determination occurred with a length of 30 d before phenotype measurements for all states and genetic groups. In the crossbreed data, THI thresholds were 67 in Missouri and 72 in North Carolina. For pure breeds, heat load had the best fit for THI thresholds greater than 70 in North Carolina, although differences in coefficient of determinations were negligible. On the other hand, no optimal THI threshold existed in Texas. In this study, heat stress had a greater impact in commercial farms than in nucleus farms and the effect of heat stress on weight varied by year and state.

Predictive equations of selenium accessibility of dry pet foods

The trace element selenium is essential to both dogs and cats. Dry diets are formulated with a large range of ingredients, which may vary in selenium concentration and accessibility. This paper reports equations to predict the average in vitro selenium accessibility from dry pet foods based on essential dietary nutrient concentrations, including crude protein, amino acids and crude fat. Predictive equations were made using stepwise linear regression for extruded and pelleted diets. The equations can be used to aid diet formulation to optimize selenium accessibility within the diet and to prevent selenium deficiency or toxicity.

The effect of 48-hour fasting on taurine status in healthy adult dogs

Low circulating taurine concentrations may be a risk factor for dilated cardiomyopathy (DCM) in dogs. Circulating taurine is typically measured in the clinic 4-5 h after feeding, largely because the impact of later sampling is not known. The objective of this study was to measure taurine in the blood during a 48-h fast in 12 healthy adult Labrador Retrievers to refine sampling methodology for determination of taurine status. Plasma and whole blood (WB) taurine concentrations did not fall to levels indicative of clinical deficiency throughout fasting; WB was the more reliable indicator of taurine status. This study shows that blood samples can be taken for assessment of taurine status any time up to 48 h after ingestion of a meal in healthy adult dogs.

Genetic analysis of sow longevity and sow lifetime reproductive traits using censored data

Sow longevity is a key component for efficient and profitable pig farming; however, approximately 50% of sows are removed annually from a breeding herd. There is no consensus in the scientific literature regarding a definition for sow longevity; however, it has been suggested that it can be measured using several methods such as stayability and economic indicators such as lifetime piglets produced. Sow longevity can be improved by genetic selection; however, it is rarely included in genetic evaluations. One reason is elongated time intervals required to collect complete lifetime data. The effect of genetic parameter estimation software in handling incomplete data (censoring) and possible early indicator traits were evaluated analysing a 30% censored data set (12 725 pedigreed Landrace × Large White sows that included approximately 30% censored data) with DMU6, THRGIBBS1F90 and GIBBS2CEN. Heritability estimates were low for all the traits evaluated. The results show that the binary stayability traits benefited from being analysed with a threshold model compared to analysing with a linear model. Sires were ranked very similarly regardless if the program handled censoring when all available data were included. Accumulated born alive and stayability were good indicators for lifetime born alive traits. Number of piglets born alive within each parity could be used as an early indicator trait for sow longevity.

Cognitive training as a resolution for early executive function difficulties in children with intellectual disabilities

Core executive functions (EF) such as attention, and working memory have been strongly associated with academic achievement, language development and behavioral stability. In the case of children who are vulnerable to cognitive and learning problems because of an underlying intellectual disability, EF difficulties will likely exacerbate an already compromised cognitive system. The current review examines cognitive training programs that aim to improve EF, specifically focusing on the potential of this type of intervention for children who have intellectual disabilities. We conclude that despite considerable discrepancies regarding reported intervention effects, these inconsistencies can be attributed to flaws in both program and study design. We discuss the steps needed to address these limitations and to facilitate the advancement of non-pharmaceutical interventions for children with intellectual disabilities.

Potent and specific inhibition of the biological activity of the type-II transmembrane serine protease matriptase by the cyclic microprotein MCoTI-II

Matriptase is a type-II transmembrane serine protease involved in epithelial homeostasis in both health and disease, and is implicated in the development and progression of a variety of cancers. Matriptase mediates its biological effects both via as yet undefined substrates and pathways, and also by proteolytic cleavage of a variety of well-defined protein substrates, several of which it shares with the closely-related protease hepsin. Development of targeted therapeutic strategies will require discrimination between these proteases. Here we have investigated cyclic microproteins of the squash Momordica cochinchinensis trypsin-inhibitor family (generated by total chemical synthesis) and found MCoTI-II to be a high-affinity (Ki 9 nM) and highly selective (> 1,000-fold) inhibitor of matriptase. MCoTI-II efficiently inhibited the proteolytic activation of pro-hepatocyte growth factor (HGF) by matriptase but not by hepsin, in both purified and cell-based systems, and inhibited HGF-dependent cell scattering. MCoTI-II also selectively inhibited the invasion of matriptase-expressing prostate cancer cells. Using a model of epithelial cell tight junction assembly, we also found that MCoTI-II could effectively inhibit the re-establishment of tight junctions and epithelial barrier function in MDCK-I cells after disruption, consistent with the role of matriptase in regulating epithelial integrity. Surprisingly, MCoTI-II was unable to inhibit matriptase-dependent proteolytic activation of prostasin, a GPI-anchored serine protease also implicated in epithelial homeostasis. These observations suggest that the unusually high selectivity afforded by MCoTI-II and its biological effectiveness might represent a useful starting point for the development of therapeutic inhibitors, and further highlight the role of matriptase in epithelial maintenance.

Abstract S6-05: High levels of APOBEC3B, a DNA deaminase and an enzymatic source of C-to-T transitions, are a validated marker of poor outcome in estrogen receptor-positive breast cancer

Two recent observations have connected the innate immune DNA cytosine deaminase APOBEC3B to the genetic evolution of breast cancer. First, APOBEC3B was shown to be up-regulated in the majority of breast cancers, and, in breast cancer cell lines, its activity was causally linked to a doubling of the number of C-to-T transitions over time and to a delay in cell cycle progression (1). Second, sequencing of the complete genome of 21 breast cancers independently suggested that APOBEC deaminase activity could be responsible for 2 of 5 mutational imprints identified, which involved clustered (also called kataegis) and dispersed C-to-T transition mutations in the context of 5’TC dinucleotide motifs (2).

In the current study, we addressed a possible association of APOBEC3B expression with outcome in clinical breast cancer. For this we measured using real-time RT-PCR APOBEC3B mRNA levels in 1,491 primary invasive breast cancers and correlated these levels with disease-free survival (DFS), metastasis-free survival (MFS) and overall survival (OS) using univariate and multivariable Cox regression analysis. In addition, we independently validated our findings in available gene expression datasets with appropriate follow-up.

In univariate analyses including all patients, increasing levels of APOBEC3B mRNA analyzed as a continuous variable were significantly associated with shorter DFS, MFS and OS (Hazard Ratio [HR] = 1.29, 1.31 and 1.36, respectively, all P&lt;0.001). To determine the relation of APOBEC3B mRNA expression with the natural course of the disease without the potential confounding effects of systemic adjuvant therapy, we restricted our next analyses to MFS in 829 patients with lymph node-negative disease who had not received any (neo)adjuvant systemic therapy. This analysis showed that APOBEC3B mRNA expression was, in univariate, and in multivariable analysis, including the traditional prognostic factors (age, menopausal status, tumor size, grade and steroid hormone receptors), a marker of pure prognosis specifically in patients with estrogen receptor-positive (ER+) disease (univariate HR = 1.30; P = 0.003; multivariate HR = 1.22, P = 0.042).

To substantiate and validate our findings, we analysed 4 independent available datasets containing in total 5,760 breast cancer cases in which APOBEC3B mRNA expression was measured by probes on microarrays and found that higher APOBEC3B mRNA expression (dichotomised by mean) was significantly associated with poor outcome in all 4 cohorts ([Metabric, 1,491 ER+ cases, HR = 1.82; P&lt;0.001], [Affymetrix compiled dataset-1, 2,407 cases, HR = 2.22; P = 0.001], and [BIG 1-98; 1,207 cases, HR = 2.13; P&lt;0.001 of late recurrence&gt;5 years], and [Affymetrix dataset-2, 643 ER+ cases, HR = 2.04; P = 0.001]).

Altogether, our analyses show that APOBEC3B mRNA - and as a result likely DNA deamination – is a validated predictor of poor outcome in breast cancer, supporting the notion that APOBEC3B is a potentially interesting clinical target for therapeutic intervention to prevent breast cancer progression and metastasis, particularly in ER+ disease.

1. Burns, M.B. et al. Nature 494, 366-70 (2013); 2. Nik-Zainal, S. et al. Cell 149, 979-93 (2012).

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr S6-05.

Changes in chondrocyte gene expression following in vitro impaction of porcine articular cartilage in an impact injury model

Our objective was to monitor chondrocyte gene expression at 0, 3, 7, and 14 days following in vitro impaction to the articular surface of porcine patellae. Patellar facets were either axially impacted with a cylindrical impactor (25 mm/s loading rate) to a load level of 2,000 N or not impacted to serve as controls. After being placed in organ culture for 0, 3, 7, or 14 days, total RNA was isolated from full thickness cartilage slices and gene expression measured for 17 genes by quantitative real-time RT-PCR. Targeted genes included those encoding proteins involved with biological stress, inflammation, or anabolism and catabolism of cartilage extracellular matrix. Some gene expression changes were detected on the day of impaction, but most significant changes occurred at 14 days in culture. At 14 days in culture, 10 of the 17 genes were differentially expressed with col1a1 most significantly up-regulated in the impacted samples, suggesting impacted chondrocytes may have reverted to a fibroblast-like phenotype.

Abstract PD10-03: Predictive value of a proliferation score (MS) in postmenopausal women with endocrine-responsive breast cancer: results from International Breast Cancer Study Group (IBCSG) Trial IX

Background: While representing the largest fraction of women diagnosed with primary breast cancer, older postmenopausal women with ER+, HER2− tumors are less responsive to chemoendocrine therapy than younger women and have been underrepresented in molecular profiling of randomized trials. IBCSG Trial IX, a randomized controlled trial in postmenopausal women, median age 61y, with node negative disease, failed to demonstrate the benefit of preceding tamoxifen (T) by 3 cycles of CMF for ER+ tumors. We sought to determine if MS, a proliferation score, could identify a subset of women who differentially benefit from addition of chemotherapy to T in this trial.

Methods: From 1988–1999, 1669 eligible patients (1040 with ER+, HER2− tumors) were randomized to CMF→T vs T. Disease-free survival (DFS) was the primary trial endpoint; breast cancer-free interval (BCFI) which excludes second (non-breast) malignancies and censors deaths without prior cancer event was also evaluated. Analysis was limited to the first 7 years of follow-up. From 671 (ER+, HER2−) available subjects, 568 were successfully profiled by RT-PCR. The mRNA expression levels of 14 equally-weighted proliferation genes and 3 normalization genes were used to generate MS; predetermined binary categorization of MS was used. Analysis of this post hoc, pre-specified study used results from centralized laboratory IHC and Cox models to assess the predictive value of MS on DFS and BCFI, adjusting for traditional risk factors of local treatment, age, ER, PR, Ki67, tumor size and grade.

Results: Subgroups of MS (low, 169 samples (30%) and high, 399 samples (70%)) were identified. MS by treatment interaction was significant for DFS and BCFI (each p ≤ 0.004). Among patients with low MS, CMF→T improved DFS (HR 0.19, 95% CI 0.06–0.59) and BCFI (HR 0.19, 95% CI 0.05–0.72) vs T; 7y DFS was 95% vs 83% with CMF→T vs T. Among patients with high MS, CMF→T did not improve DFS (HR 1.27, 95% CI 0.79–2.05) or BCFI (HR 1.37, 95% CI 0.80–2.33) and 7y DFS of 81% for CMF→T and T. Continuous MS was moderately correlated with log Ki67 (r = 0.47) but not correlated with ER or PR. The MS by treatment interaction remained significant with Ki67 in the model.

Conclusions: Low MS was associated with differential benefit favoring those women receiving CMF→T vs T alone for both DFS and BCFI in the first 7 years. The effect was independent of traditional risk factors including Ki67. Hence this study, which is unconfounded by chemotherapy-induced ovarian ablation in younger women, identifies a subset of postmenopausal women with ER+, HER2− tumors that benefit from CMF chemotherapy. This seemingly incongruous observation is consistent with a) the prior observation that only the low-proliferation subgroup by PAM50 11-gene signature benefits from the addition of weekly paclitaxel to adjuvant FEC (GEICAM/9906), b) the ability of MS to identify a subset of women with tumors with disseminated luminal progenitor cells activated through the agonistic activity of tamoxifen, and c) the repetitive dosing of cyclophosphamide and taxol being hypothesized to act via tumor stroma/anti-angiogenesis. The relative contribution of these factors is under investigation.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD10-03.

Haemophilus influenzae serotype B (Hib) seroprevalence in England and Wales in 2009

A national seroprevalence study was performed to determine the prevalence of Haemophilus influenzae type b (Hib) antibodies in England and Wales in 2009, when Hib disease incidence was the lowest ever recorded. A total of 2,693 anonymised residual sera from routine diagnostic testing submitted by participating National Health Service hospital laboratories were tested for Hib anti-polyribosyl-ribitol phosphate (PRP) IgG antibodies using a fluorescent bead assay. Median anti-PRP IgG concentrations were highest in toddlers aged 1–4 years (2.65 μg/ml), followed by children aged 5–9 years (1.95 μg/ml). Antibody concentrations were significantly lower after this age, but were still significantly higher among 10–19 year-olds (0.54 μg/ml) compared with adults aged >20 years (0.16 μg/ ml; p<0.0001). Half of the adults (51%) did not have Hib antibody concentrations ≥0.15 μg/ml, the level considered to confer short-term protection. Thus, the current excellent Hib control appears to be the result of high anti-PRP antibody concentrations in children aged up to 10 years, achieved through the various childhood vaccination campaigns offering booster immunisation. The lack of seroprotection in adults emphasises the importance of maintaining control of the disease and, most probably carriage, in children, therefore raising the question as to whether long-term routine boosting of either pre-school children or adolescents may be required.

mRNA profiling of the cancer degradome in oesophago-gastric adenocarcinoma

Background:

Degradation of the extracellular matrix is fundamental to tumour development, invasion and metastasis. Several protease families have been implicated in the development of a broad range of tumour types, including oesophago–gastric (OG) adenocarcinoma. The aim of this study was to analyse the expression levels of all core members of the cancer degradome in OG adenocarcinoma and to investigate the relationship between expression levels and tumour/patient variables associated with poor prognosis.

Methods:

Comprehensive expression profiling of the protease families (matrix metalloproteinases (MMPs), members of the ADAM metalloproteinase-disintegrin family (ADAMs)), their inhibitors (tissue inhibitors of metalloproteinase), and molecules involved in the c-Met signalling pathway, was performed using quantitative real-time reverse transcription polymerase chain reaction in a cohort of matched malignant and benign peri-tumoural OG tissue (n=25 patients). Data were analysed with respect to clinico-pathological variables (tumour stage and grade, age, sex and pre-operative plasma C-reactive protein level).

Results:

Gene expression of MMP1, 3, 7, 9, 10, 11, 12, 16 and 24 was upregulated by factors >4-fold in OG adenocarcinoma samples compared with matched benign tissue (P<0.01). Expression of ADAM8 and ADAM15 correlated significantly with tumour stage (P=0.048 and P=0.044), and ADAM12 expression correlated with tumour grade (P=0.011).

Conclusion:

This study represents the first comprehensive quantitative analysis of the expression of proteases and their inhibitors in human OG adenocarcinoma. These findings implicate elevated ADAM8, 12 and 15 mRNA expression as potential prognostic molecular markers.

A structured course teaching junior doctors invasive medical procedures results in sustained improvements in self-reported confidence

Pressure on working hours has led to a decrease in opportunities for training in invasive medical procedures for junior doctors. The effect of a structured course on immediate and medium-term changes in self-reported confidence was investigated. A one-day model-based practical course was run on two separate occasions teaching central venous line placement, lumbar puncture, Seldinger-technique chest drain insertion and knee joint aspiration. Attendees were asked to indicate their confidence in each procedure on a 10-point Likert scale before, immediately after and three months after the course. Significant improvements in self-reported confidence were seen for all procedures which were sustained at three months. Feedback was universally positive. Practical preclinical training may be a useful adjunct to patient-based training in invasive procedures. The course was particularly popular with foundation year trainees: ideally this training should be available before trainees' first exposure in the clinical setting.

Roles and regulation of membrane-associated serine proteases

Pericellular proteolytic activity affects many aspects of cellular behaviour, via mechanisms involving processing of the extracellular matrix, growth factors and receptors. The serine proteases have exquisitely sensitive regulatory mechanisms in this setting, involving both receptor-bound and transmembrane proteases. Receptor-bound proteases are exemplified by the uPA (urokinase plasminogen activator)/uPAR (uPAR receptor) plasminogen activation system. The mechanisms initiating the activity of this proteolytic system on the cell surface, a critical regulatory point, are poorly understood. We have found that the expression of the TTSP (type II transmembrane serine protease) matriptase is highly regulated in leucocytes, and correlates with the presence of active uPA on their surface. Using siRNA (small interfering RNA), we have demonstrated that matriptase specifically activates uPAR-associated pro-uPA. The uPA/uPAR system has been implicated in the activation of the plasminogen-related growth factor HGF (hepatocyte growth factor). However, we find no evidence for this, but instead that HGF can be activated by both matriptase and the related TTSP hepsin in purified systems. Hepsin is of particular interest, as the proteolytic cleavage sequence of HGF is an 'ideal substrate' for hepsin and membrane-associated hepsin activates HGF with high efficiency. Both of these TTSPs can be activated autocatalytically at the cell surface, an unusual mechanism among the serine proteases. Therefore these TTSPs have the capacity to be true upstream initiators of proteolytic activity with subsequent downstream effects on cell behaviour.