Developing Policy Infrastructure to Guide Genomics-Informed Oncology Nursing in Canada: An Interpretive Descriptive Study.

BACKGROUND: Genomic technologies such as genetic testing and precision treatments are rapidly becoming routine in oncology care, and nurses play an increasingly important role in supporting the growing demands for genomics-informed healthcare. Policy infrastructure such as competencies, standards, scope of practice statements, and education and curriculum frameworks are urgently needed to guide these practice and education changes. PURPOSE: This study is part of a larger three-phase project to develop recommendations and catalyze action for genomics-informed oncology nursing education and practice for the Canadian Association of Nurses in Oncology and the Canadian Association of Schools of Nursing. This phase aimed to enhance understanding of policy needs and action drivers for genomics-informed oncology nursing education and practice through the perspectives of Canadian oncology nurses and patient partners. METHODS: Interpretive description methodology guided the study. Twenty semi-structured virtual interviews were conducted; 17 with oncology nurses in various domains of practice, and three with patient partner representatives. Data collection and analysis occurred concurrently. RESULTS: Our analysis identified three themes: 1) nurses and patients recognize that it is time for action, 2) nurses and patients see advantages to executing intentional, strategic, and collaborative policy development, and 3) leadership and advocacy are required to drive action. CONCLUSION: Nursing policy infrastructure is required to increase genomic literacy, support nurses in providing safe patient care, and establish clear roles, responsibilities, and accountabilities within the interdisciplinary team. Strong leadership and advocacy at the practice, organizational, and systems levels are vital to accelerating action.

A cluster-randomized trial of water, sanitation, handwashing and nutritional interventions on stress and epigenetic programming.

A regulated stress response is essential for healthy child growth and development trajectories. We conducted a cluster-randomized trial in rural Bangladesh (funded by the Bill & Melinda Gates Foundation, ClinicalTrials.gov NCT01590095) to assess the effects of an integrated nutritional, water, sanitation, and handwashing intervention on child health. We previously reported on the primary outcomes of the trial, linear growth and caregiver-reported diarrhea. Here, we assessed additional prespecified outcomes: physiological stress response, oxidative stress, and DNA methylation (N = 759, ages 1-2 years). Eight neighboring pregnant women were grouped into a study cluster. Eight geographically adjacent clusters were block-randomized into the control or the combined nutrition, water, sanitation, and handwashing (N + WSH) intervention group (receiving nutritional counseling and lipid-based nutrient supplements, chlorinated drinking water, upgraded sanitation, and handwashing with soap). Participants and data collectors were not masked, but analyses were masked. There were 358 children (68 clusters) in the control group and 401 children (63 clusters) in the intervention group. We measured four F2-isoprostanes isomers (iPF(2α)-III; 2,3-dinor-iPF(2α)-III; iPF(2α)-VI; 8,12-iso-iPF(2α)-VI), salivary alpha-amylase and cortisol, and methylation of the glucocorticoid receptor (NR3C1) exon 1F promoter including the NGFI-A binding site. Compared with control, the N + WSH group had lower concentrations of F2-isoprostanes isomers (differences ranging from -0.16 to -0.19 log ng/mg of creatinine, P < 0.01), elevated post-stressor cortisol (0.24 log µg/dl; P < 0.01), higher cortisol residualized gain scores (0.06 µg/dl; P = 0.023), and decreased methylation of the NGFI-A binding site (-0.04; P = 0.037). The N + WSH intervention enhanced adaptive responses of the physiological stress system in early childhood.

Stress biomarkers and child development in young children in Bangladesh.

BACKGROUND: Hundreds of millions of children in low- and middle-income countries are exposed to chronic stressors, such as poverty, poor sanitation and hygiene, and sub-optimal nutrition. These stressors can have physiological consequences for children and may ultimately have detrimental effects on child development. This study explores associations between biological measures of chronic stress in early life and developmental outcomes in a large cohort of young children living in rural Bangladesh. METHODS: We assessed physiologic measures of stress in the first two years of life using measures of the hypothalamic-pituitary-adrenal (HPA) axis (salivary cortisol and glucocorticoid receptor gene methylation), the sympathetic-adrenal-medullary (SAM) system (salivary alpha-amylase, heart rate, and blood pressure), and oxidative status (F2-isoprostanes). We assessed child development in the first two years of life with the MacArthur-Bates Communicative Development Inventories (CDI), the WHO gross motor milestones, and the Extended Ages and Stages Questionnaire (EASQ). We compared development outcomes of children at the 75th and 25th percentiles of stress biomarker distributions while adjusting for potential confounders using generalized additive models, which are statistical models where the outcome is predicted by a potentially non-linear function of predictor variables. RESULTS: We analyzed data from 684 children (49% female) at both 14 and 28 months of age; we included an additional 765 children at 28 months of age. We detected a significant relationship between HPA axis activity and child development, where increased HPA axis activity was associated with poor development outcomes. Specifically, we found that cortisol reactivity (coefficient -0.15, 95% CI (-0.29, -0.01)) and post-stressor levels (coefficient -0.12, 95% CI (-0.24, -0.01)) were associated with CDI comprehension score, post-stressor cortisol was associated with combined EASQ score (coefficient -0.22, 95% CI (-0.41, -0.04), and overall glucocorticoid receptor methylation was associated with CDI expression score (coefficient -0.09, 95% CI (-0.17, -0.01)). We did not detect a significant relationship between SAM activity or oxidative status and child development. CONCLUSIONS: Our observations reveal associations between the physiological evidence of stress in the HPA axis with developmental status in early childhood. These findings add to the existing evidence exploring the developmental consequences of early life stress.

The impact of farming on prehistoric culinary practices throughout Northern Europe.

To investigate changes in culinary practices associated with the arrival of farming, we analysed the organic residues of over 1,000 pottery vessels from hunter-gatherer-fisher and early agricultural sites across Northern Europe from the Lower Rhine Basin to the Northeastern Baltic. Here, pottery was widely used by hunter-gatherer-fishers prior to the introduction of domesticated animals and plants. Overall, there was surprising continuity in the way that hunter-gatherer-fishers and farmers used pottery. Both aquatic products and wild plants remained prevalent, a pattern repeated consistently across the study area. We argue that the rapid adaptation of farming communities to exploit coastal and lagoonal resources facilitated their northerly expansion, and in some cases, hunting, gathering, and fishing became the most dominant subsistence strategy. Nevertheless, dairy products frequently appear in pottery associated with the earliest farming groups often mixed with wild plants and fish. Interestingly, we also find compelling evidence of dairy products in hunter-gatherer-fisher Ertebølle pottery, which predates the arrival of domesticated animals. We propose that Ertebølle hunter-gatherer-fishers frequently acquired dairy products through exchange with adjacent farming communities prior to the transition. The continuity observed in pottery use across the transition to farming contrasts with the analysis of human remains which shows substantial demographic change through ancient DNA and, in some cases, a reduction in marine consumption through stable isotope analysis. We postulate that farmers acquired the knowledge and skills they needed to succeed from local hunter-gatherer-fishers but without substantial admixture.

Stress Biomarkers and Child Development in Young Children in Bangladesh.

Background: Hundreds of millions of children in low- and middle-income countries are exposed to chronic stressors, such as poverty, poor sanitation and hygiene, and sub-optimal nutrition. These stressors can have physiological consequences for children and may ultimately have detrimental effects on child development. This study explores associations between biological measures of chronic stress in early life and developmental outcomes in a large cohort of young children living in rural Bangladesh. Methods: We assessed physiologic measures of stress in the first two years of life using measures of the hypothalamic-pituitary-adrenal (HPA) axis (salivary cortisol and glucocorticoid receptor gene methylation), the sympathetic-adrenal-medullary (SAM) system (salivary alpha-amylase, heart rate, and blood pressure), and oxidative status (F2-isoprostanes). We assessed child development in the first two years of life with the MacArthur-Bates Communicative Development Inventories (CDI), the WHO gross motor milestones, and the Extended Ages and Stages Questionnaire (EASQ). We compared development outcomes of children at the 75th and 25th percentiles of stress biomarker distributions while adjusting for potential confounders (hereafter referred to as contrasts) using generalized additive models, which are statistical models where the outcome is predicted by a potentially non-linear function of predictor variables. Results: We analyzed data from 684 children (49% female) at both 14 and 28 months of age; we included an additional 765 children at 28 months of age. We observed 135 primary contrasts of the differences in child development outcomes at the 75th and 25th percentiles of stress biomarkers, where we detected significant relationships in 5 out of 30 contrasts (17%) of HPA axis activity, 1 out of 30 contrasts (3%) of SAM activity, and 3 out of 75 contrasts (4%) of oxidative status. These findings revealed that measures of HPA axis activity were associated with poor development outcomes. We did not find consistent evidence that markers of SAM system activity or oxidative status were associated with developmental status. Conclusions: Our observations reveal associations between the physiological evidence of stress in the HPA axis with developmental status in early childhood. These findings add to the existing evidence exploring the developmental consequences of early life stress.

Leading Canadian Nurses into the Genomic Era of Healthcare.

Genomics is having a profound impact on every aspect of healthcare. To support nurses to develop genomic literacy and integrate genomics into care, an engagement framework was created. The framework uses principles of nursing intraprofessional collaboration, the knowledge-to-action cycle and the diffusion of innovations theory. This framework was used to identify six key priorities for action and leadership strategies to accelerate and sustain the nurses' engagement with genomics. With leadership and genomic literacy, nurses can fully participate in the creation and implementation of new care pathways, deliver education, advance research linked to genomics and improve patient experience and health outcomes.

Suppression weakens unwanted memories via a sustained reduction of neural reactivation.

Aversive events sometimes turn into intrusive memories. However, prior evidence indicates that such memories can be controlled via a mechanism of retrieval suppression. Here, we test the hypothesis that suppression exerts a sustained influence on memories by deteriorating their neural representations. This deterioration, in turn, would hinder their subsequent reactivation and thus impoverish the vividness with which they can be recalled. In an fMRI study, participants repeatedly suppressed memories of aversive scenes. As predicted, this process rendered the memories less vivid. Using a pattern classifier, we observed that suppression diminished the neural reactivation of scene information both globally across the brain and locally in the parahippocampal cortices. Moreover, the decline in vividness was associated with reduced reinstatement of unique memory representations in right parahippocampal cortex. These results support the hypothesis that suppression weakens memories by causing a sustained reduction in the potential to reactivate their neural representations.

Neural Correlates of Successful Memory Encoding in Kindergarten and Early Elementary School Children: Longitudinal Trends and Effects of Schooling.

From age 5 to 7, there are remarkable improvements in children's cognitive abilities ("5-7 shift"). In many countries, including Germany, formal schooling begins in this age range. It is, thus, unclear to what extent exposure to formal schooling contributes to the "5-7 shift." In this longitudinal study, we investigated if schooling acts as a catalyst of maturation. We tested 5-year-old children who were born close to the official cutoff date for school entry and who were still attending a play-oriented kindergarten. One year later, the children were tested again. Some of the children had experienced their first year of schooling whereas the others had remained in kindergarten. Using 2 functional magnetic resonance imaging tasks that assessed episodic memory formation (i.e., subsequent memory effect), we found that children relied strongly on the medial temporal lobe (MTL) at both time points but not on the prefrontal cortex (PFC). In contrast, older children and adults typically show subsequent memory effects in both MTL and PFC. Both children groups improved in their memory performance, but there were no longitudinal changes nor group differences in neural activation. We conclude that successful memory formation in this age group relies more heavily on the MTL than in older age groups.

The oral 13C-bicarbonate technique for determination of energy expenditure in dogs: dietary and environmental factors affecting the respiratory quotient and 13C recovery factor.

The oral 13C-bicarbonate technique (o13CBT) can be used for short-term measurements of CO2 production (RCO2) and energy expenditure (EEx). The method relies on appropriate estimates for the respiratory quotient (RQ) and recovery factor (RF) of 13C. Four Retriever dogs were included in four experiments to validate the o13CBT against indirect calorimetry (IC), and determine RQ and RF; Expt. 1: feeding different protein:fat:carbohydrate ratios [in % of metabolisable energy]: 25:33:42 in a maintenance (Mnt.) diet; 38:26:36 in a high-protein high-fibre (HFibre) diet and 27:56:17 in a high-fat (HFat) diet, simultaneously with start of measurements (T0); Expt. 2: the Mnt. diet at T0 or 4 h postprandial (T4); Expt. 3: T4 at different ambient temperatures, 22°C and 15°C; Expt. 4: T4 after 1 h physical activity. The RCO2 and EEx were determined from the respiration chamber measurements made simultaneously with IC and the o13CBT (o13CBTonline), and in Expts. 1 and 2, also on two consecutive days using o13CBT with collection of breath into breath bags (o13CBTbreathbags). The RQ values obtained at T0 reflected dietary compositions, with the highest least square mean (LSM) of 0.954  for the Mnt. diet, 0.905 for the HFibre and 0.877 for the HFat diet (p < 0.05). An increased interval between meal and measurement period decreased RQ significantly (p < 0.05) in Expt. 2, LSM being 0.954 at T0 and 0.909 at T4. Ambient temperature (Expt. 3) and physical activity (Expt. 4) did not influence postprandial RQ. The RF values were not significantly affected by diet (Expt. 1). Measurements starting at T0 (Expt. 2) resulted in higher (p < 0.05) RF values than at T4 (LSM = 0.971 and 0.836, respectively). The ambient temperatures (Expt. 3) did not influence postprandial RF. However, when dogs were physically active prior to measurements (Expt. 4), RF values (LSM = 1.019) were higher (p < 0.05) than when resting only (LSM = 0.836). Calculations based on RQ and RF determined in each experiment resulted in RCO2 and EEx values which were not different regardless of method used, except for Expt. 1 where EEx-values [kJ · kg BW-0.75 · d-1] were higher (p < 0.05) when measured with o13CBTbreathbags (460) than by IC (421) and o13CBTonline (420). Provided accurate RQ and RF values, the o13CBTbreathbags can be used as an independent and minimally invasive research tool to determine EEx in dogs under carefully standardised conditions.

The influence of obesity on folate status, DNA methylation and cancer-related gene expression in normal breast tissues from premenopausal women.

Epidemiological studies have established obesity as a critical risk factor for postmenopausal breast cancer (post-BC), whereas a reverse association holds prior to menopause. A significant scientific gap exists in understanding the mechanism(s) underpinning this epidemiological phenomenon, particularly the reverse association between obesity and premenopausal breast cancer (pre-BC). This study aimed to understand how folate metabolism and DNA methylation inform the association between obesity and pre-BC. Fifty normal breast tissue samples were collected from premenopausal women who underwent reduction mammoplasty. We modified the Lactobacillus Casei microbiological folate assay and measured folate levels in our breast tissue samples. The DNA methylation of LINE-1, a biomarker of genome-wide methylation, and the expression of a panel of breast cancer-related genes was measured by pyrosequencing and real-time PCR. We found that a high BMI is associated with an increase of folate levels in mammary tissue, with an increase of 2.65 ng/g of folate per every 5-unit increase of BMI (p < 0.05). LINE-1 DNA methylation was significantly associated with BMI (p < 0.05), and marginally associated with folate concentration (p = 0.087). A high expression of SFRP1 was observed in subjects with high BMI or high folate status (p < 0.05). This study demonstrated that, in premenopausal women, obesity is associated with increased mammary folate status, genome-wide DNA methylation and SFRP1 gene expression. Our findings indicated that the improved folate and epigenetic status represents a novel mechanism responsible for the reverse association between obesity and pre-BC.

Memory suppression and its deficiency in psychological disorders: A focused meta-analysis.

It is still debated whether suppressing the retrieval of unwanted memories causes forgetting and whether this constitutes a beneficial mechanism. To shed light on these 2 questions, we scrutinize the evidence for such suppression-induced forgetting (SIF) and examine whether it is deficient in psychological disorders characterized by intrusive thoughts. Specifically, we performed a focused meta-analysis of studies that have used the think/no-think procedure to test SIF in individuals either affected by psychological disorders or exhibiting high scores on related traits. Overall, across 96 effects from 25 studies, we found that avoiding retrieval leads to significant forgetting in healthy individuals, with a small to moderate effect size (0.28, 95% CI [0.14, 0.43]). Importantly, this effect was indeed larger than for more anxious (-0.21, 95% CI [-0.41, -0.02]) or depressed individuals (0.05, 95% CI [-0.19, 0.29])-though estimates for the healthy may be inflated by publication bias. In contrast, individuals with a stronger repressive coping style showed greater SIF (0.42, 95% CI [0.32, 0.52]). Furthermore, moderator analyses revealed that SIF varied with the exact suppression mechanism that participants were instructed to engage. For healthy individuals, the effect sizes were considerably larger when instructions induced specific mechanisms of direct retrieval suppression or thought substitution than when they were unspecific. These results suggest that intact suppression-induced forgetting is a hallmark of psychological well-being, and that inducing more specific suppression mechanisms fosters voluntary forgetting. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

MYC DNA Methylation in Prostate Tumor Tissue Is Associated with Gleason Score.

Increasing evidence suggests a role of epigenetic mechanisms at chromosome 8q24, an important cancer genetic susceptibility region, in prostate cancer. We investigated whether MYC DNA methylation at 8q24 (six CpG sites from exon 3 to the 3' UTR) in prostate tumor was associated with tumor aggressiveness (based on Gleason score, GS), and we incorporated RNA expression data to investigate the function. We accessed radical prostatectomy tissue for 50 Caucasian and 50 African American prostate cancer patients at the University of Maryland Medical Center, selecting an equal number of GS 6 and GS 7 cases per group. MYC DNA methylation was lower in tumor than paired normal prostate tissue for all six CpG sites (median difference: -14.74 to -0.20 percentage points), and we observed similar results for two nearby sites in The Cancer Genome Atlas (p < 0.0001). We observed significantly lower methylation for more aggressive (GS 7) than less aggressive (GS 6) tumors for three exon 3 sites (for CpG 212 (chr8:128753145), GS 6 median = 89.7%; GS 7 median = 85.8%; p-value = 9.4 × 10-4). MYC DNA methylation was not associated with MYC expression, but was inversely associated with PRNCR1 expression after multiple comparison adjustment (q-value = 0.04). Findings suggest that prostate tumor MYC exon 3 hypomethylation is associated with increased aggressiveness.

Early life stress and voluntary alcohol consumption in relation to Maoa methylation in male rats.

Early life stress (ELS) or alcohol consumption can influence DNA methylation and affect gene expression. Monoamine oxidase A (Maoa) encodes the enzyme that metabolizes monoaminergic neurotransmitters crucial for the stress response, alcohol reward, and reinforcement. Previously, we reported lower Maoa expression in the nucleus accumbens and dorsal striatum of male rats exposed to ELS during the first three postnatal weeks, and to voluntary alcohol consumption in adulthood, compared with controls. The present study continued to investigate the effect of ELS and alcohol consumption on Maoa methylation, and its relation to Maoa expression in these animals. We selected candidate CpGs after performing next-generation bisulfite sequencing of the Maoa promoter, intron 1-5, and exons 5 and 6, together composed of 107 CpGs (5'-cytosine-phosphate-guanosine-3'), in a subgroup of rats. Pyrosequencing was used to analyze the methylation of 10 candidate CpGs in the promoter and intron 1 in the entire sample. ELS and alcohol displayed an interactive effect on CpG-specific methylation in the dorsal striatum. CpG-specific methylation correlated with Maoa expression, corticosterone levels, and alcohol consumption in a brain region-specific manner. CpG-specific methylation in the Maoa promoter was a potential moderator of the interaction of ELS with alcohol consumption on Maoa expression in the NAc. However, the findings were sparse, did not survive correction for multiple testing, and the magnitude of differences in methylation levels was small. In conclusion, CpG-specific Maoa methylation in the promoter and intron 1 may associate with ELS, alcohol consumption, and Maoa expression in reward-related brain regions.

Identification of genetic variation in equine collagenous lectins using targeted resequencing.

Collagenous lectins are a family of soluble pattern recognition receptors that play an important role in innate immune resistance to infectious disease. Through recognition of carbohydrate motifs on the surface of pathogens, some collagenous lectins can activate the lectin pathway of complement, providing an effective means of host defense. Genetic polymorphisms in collagenous lectins have been shown in several species to predispose animals to a variety of infectious diseases. Infectious diseases are an important cause of morbidity in horses, however little is known regarding the role of equine collagenous lectins. Using a high-throughput, targeted re-sequencing approach, the relationship between genetic variation in equine collagenous lectin genes and susceptibility to disease was investigated. DNA was isolated from tissues obtained from horses submitted for post-mortem examination. Animals were divided into two populations, those with infectious or autoinflammatory diseases (n = 37) and those without (n = 52), and then subdivided by dominant pathological process for a total of 21 pools, each containing 4-5 horses. DNA was extracted from each horse and pooled in equimolar amounts, and the exons, introns, upstream (approximately 50 kb) and downstream (approximately 3 kb) regulatory regions for the 11 equine collagenous lectin genes and related MASP genes were targeted for re-sequencing. A custom target capture kit was used to prepare a sequencing library, which was sequenced on an Illumina MiSeq. After implementing quality control filters, 4559 variants were identified. Of these, 92 were present in the coding regions (43 missense, 1 nonsense, and 48 synonymous), 1414 in introns, 3029 in the upstream region, and 240 in the downstream region. In silico analysis of the missense short nucleotide variants identified 12 mutations with potential to disrupt collagenous lectin protein structure or function, 280 mutations located within predicted transcription factor binding sites, and 95 mutations located within predicted microRNA binding elements. Analysis of allelic association identified 113 mutations that segregated between the infectious/autoinflammatory and non-infectious populations. The variants discovered in this experiment represent potential genetic contributors to disease susceptibility of horses, and will serve as candidates for further population-level genotyping. This study contributes to the growing body of evidence that pooled, high-throughput sequencing is a viable strategy for cost-effective variant discovery.

Prospective study of DNA methylation at chromosome 8q24 in peripheral blood and prostate cancer risk.

BACKGROUND: Chromosome 8q24 has emerged as an important genetic susceptibility region for several cancers, including prostate cancer; however, little is known about the contribution of DNA methylation in this region to risk. METHODS: We prospectively evaluated DNA methylation at 8q24 in relation to prostate cancer using pre-diagnostic blood samples from 694 prostate cancer cases (including 172 aggressive cases) and 703 controls in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. We used logistic regression to estimate odds ratios and 95% confidence intervals. RESULTS: Although none remained significant after adjustment for multiple testing (q>0.05), of the 50 CpG sites meeting quality control, we identified 8 sites that were nominally associated with prostate cancer (Ptrend<0.05), including 6 correlated (Spearman ρ: 0.20-0.52) sites in POU5F1B and 2 intergenic sites (most significant site: Chr8:128428897 in POU5F1B, Ptrend=0.01). We also identified two correlated (ρ=0.39) sites in MYC (Chr8:128753187 and Chr8:128753154) that were associated with aggressive (Ptrend=0.02 and 0.03), but not non-aggressive disease (Ptrend=0.70 and 0.20; Pheterogeneity=0.01 and 4.6 × 10-3). These findings persisted after adjustment for the top 8q24 prostate cancer variants in our study. CONCLUSIONS: Although requiring replication, our findings provide some evidence that 8q24 DNA methylation levels may be associated with prostate cancer risk.

Surface Roughness of Initial Enamel Caries Lesions in Human Teeth After Resin Infiltration.

BACKGROUND: Low viscosity resin infiltration of initial caries lesions is a modern microinvasive method to treat initial cries lesions. However, only scarce information is available about the long-term surface alterations of infiltrated lesions. METHODS: Twenty-eight premolar teeth exhibiting non-cavitated initial caries lesions (International Caries Detection and Assessment System (ICDAS code 1&2)) were divided into two groups, one of which was infiltrated with resin, and the other remained untreated. The teeth underwent two thermocycling procedures. The surface roughness was determined quantitatively, and the results were evaluated statistically. In addition, the surfaces of the lesions were investigated by scanning electron microscopy (SEM), and the surface was analyzed visually with respect to surface irregularities. RESULTS: The results showed a reduction in the surface roughness that was significant after 2500 thermocycles compared to the untreated surface. In the control specimens, no change in the surface roughness was found. The qualitative SEM data also showed a smooth surface after thermocycling, which supported the statistical findings. CONCLUSION: After thermocycling, resin-infiltrated enamel surfaces become smoother and had no additional risk for plaque accumulation.

Genome Sequence of the Urethral Isolate Pseudomonas aeruginosa RN21.

Pseudomonas aeruginosa is known to cause complicated urinary tract infections (UTI). The improved 7.0-Mb draft genome sequence of P. aeruginosa RN21, isolated from a patient with an acute UTI, was determined. It carries three (pro)phage genomes, genes for two restriction/modification systems, and a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system.

Outcome of patients with classical infantile pompe disease receiving enzyme replacement therapy in Germany.

PURPOSE: Enzyme replacement therapy (ERT) has been shown to improve outcome in classical infantile Pompe disease. The purpose of this study was to assess mortality, morbidity, and shortcomings of ERT in a larger cohort of patients treated outside clinical trials. To accomplish this, we retrospectively analyzed the data of all 23 subjects with classical infantile Pompe disease having started ERT in Germany between January 2003 and December 2010. RESULTS: Ten patients (43%) deceased and four others (17%) became ventilator dependent. Seven infants (30.5%) made no motor progress at all, while seven (30.5%) achieved free sitting, and nine (39%) gained free walking. Besides all the seven patients (100%) attaining no improvement of motor functions, four out of the seven (57%) achieving to sit without support, and three out of the nine (33%) being able to walk independently, secondarily deteriorated, and died or became ventilator dependent. Sustained reduction of systolic function despite reversal of cardiac hypertrophy (n = 3), gastroesophageal reflux (n = 5), swallowing difficulties or failure to thrive (n = 11), recurrent pneumonias (n = 14), port system complications (n = 4), anesthesia-related incidents (n = 2), severe allergic reactions (n = 6), hearing loss (n = 3), and orthopedic deformities (n = 4) were problems frequently encountered. CONCLUSION: Although this study has important shortcomings due to its retrospective nature and because important variables potentially influencing outcome were not available for a substantial amount of patients, these data suggest that classical infantile Pompe disease still remains a life-threatening condition associated with high morbidity and often dismal prognosis. Currently, a relevant number of patients do not benefit definitely from ERT.

DNA methylation levels at chromosome 8q24 in peripheral blood are associated with 8q24 cancer susceptibility loci.

Chromosome 8q24 has emerged as an important region for genetic susceptibility to various cancers, but little is known about the contribution of DNA methylation at 8q24. To evaluate variability in DNA methylation levels at 8q24 and the relationship with cancer susceptibility single nucleotide polymorphisms (SNPs) in this region, we quantified DNA methylation levels in peripheral blood at 145 CpG sites nearby 8q24 cancer susceptibility SNPs or MYC using pyrosequencing among 80 Caucasian men in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. For the 60 CpG sites meeting quality control, which also demonstrated temporal stability over a 5-year period, we calculated pairwise Spearman correlations for DNA methylation levels at each CpG site with 42 8q24 cancer susceptibility SNPs. To account for multiple testing, we adjusted P values into q values reflecting the false discovery rate (FDR). In contrast to the MYC CpG sites, most sites nearby the SNPs demonstrated good reproducibility, high methylation levels, and moderate-high between-individual variation. We observed 10 statistically significant (FDR < 0.05) CpG site-SNP correlations. These included correlations between an intergenic CpG site at Chr8:128393157 and the prostate cancer SNP rs16902094 (ρ = -0.54; P = 9.7 × 10(-7); q = 0.002), a PRNCR1 CpG site at Chr8:128167809 and the prostate cancer SNP rs1456315 (ρ = 0.52; P = 1.4 × 10(-6); q = 0.002), and two POU5F1B CpG sites and several prostate/colorectal cancer SNPs (for Chr8:128498051 and rs6983267, ρ = 0.46; P = 2.0 × 10(-5); q = 0.01). This is the first report of correlations between blood DNA methylation levels and cancer susceptibility SNPs at 8q24, suggesting that DNA methylation at this important susceptibility locus may contribute to cancer risk.

Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication.

Domestication is a multifaceted evolutionary process, involving changes in individual genes, genetic interactions, and emergent phenotypes. There has been extensive discussion of the phenotypic characteristics of plant domestication, and recent research has started to identify the specific genes and mutational mechanisms that control domestication traits. However, there is an apparent disconnect between the simple genetic architecture described for many crop domestication traits, which should facilitate rapid phenotypic change under selection, and the slow rate of change reported from the archeobotanical record. A possible explanation involves the middle ground between individual genetic changes and their expression during development, where gene-by-gene (epistatic) and gene-by-environment interactions can modify the expression of phenotypes and opportunities for selection. These aspects of genetic architecture have the potential to significantly slow the speed of phenotypic evolution during crop domestication and improvement. Here we examine whether epistatic and gene-by-environment interactions have shaped how domestication traits have evolved. We review available evidence from the literature, and we analyze two domestication-related traits, shattering and flowering time, in a mapping population derived from a cross between domesticated foxtail millet and its wild progenitor. We find that compared with wild progenitor alleles, those favored during domestication often have large phenotypic effects and are relatively insensitive to genetic background and environmental effects. Consistent selection should thus be able to rapidly change traits during domestication. We conclude that if phenotypic evolution was slow during crop domestication, this is more likely due to cultural or historical factors than epistatic or environmental constraints.