Complementation testing identifies genes mediating effects at quantitative trait loci underlying fear-related behavior

Knowing the genes involved in quantitative traits provides an entry point to understanding the biological bases of behavior, but there are very few examples where the pathway from genetic locus to behavioral change is known. To explore the role of specific genes in fear behavior, we mapped three fear-related traits, tested fourteen genes at six quantitative trait loci (QTLs) by quantitative complementation, and identified six genes. Four genes, Lamp, Ptprd, Nptx2, and Sh3gl, have known roles in synapse function; the fifth, Psip1, was not previously implicated in behavior; and the sixth is a long non-coding RNA, 4933413L06Rik, of unknown function. Variation in transcriptome and epigenetic modalities occurred preferentially in excitatory neurons, suggesting that genetic variation is more permissible in excitatory than inhibitory neuronal circuits. Our results relieve a bottleneck in using genetic mapping of QTLs to uncover biology underlying behavior and prompt a reconsideration of expected relationships between genetic and functional variation.

Complementation testing identifies causal genes at quantitative trait loci underlying fear related behavior

Knowing the genes involved in quantitative traits provides a critical entry point to understanding the biological bases of behavior, but there are very few examples where the pathway from genetic locus to behavioral change is known. Here we address a key step towards that goal by deploying a test that directly queries whether a gene mediates the effect of a quantitative trait locus (QTL). To explore the role of specific genes in fear behavior, we mapped three fear-related traits, tested fourteen genes at six QTLs, and identified six genes. Four genes, Lsamp, Ptprd, Nptx2 and Sh3gl, have known roles in synapse function; the fifth gene, Psip1, is a transcriptional co-activator not previously implicated in behavior; the sixth is a long non-coding RNA 4933413L06Rik with no known function. Single nucleus transcriptomic and epigenetic analyses implicated excitatory neurons as likely mediating the genetic effects. Surprisingly, variation in transcriptome and epigenetic modalities between inbred strains occurred preferentially in excitatory neurons, suggesting that genetic variation is more permissible in excitatory than inhibitory neuronal circuits. Our results open a bottleneck in using genetic mapping of QTLs to find novel biology underlying behavior and prompt a reconsideration of expected relationships between genetic and functional variation.

Single-cell methylation analysis of brain tissue prioritizes mutations that alter transcription

Relating genetic variants to behavior remains a fundamental challenge. To assess the utility of DNA methylation marks in discovering causative variants, we examined their relationship to genetic variation by generating single-nucleus methylomes from the hippocampus of eight inbred mouse strains. At CpG sequence densities under 40 CpG/Kb, cells compensate for loss of methylated sites by methylating additional sites to maintain methylation levels. At higher CpG sequence densities, the exact location of a methylated site becomes more important, suggesting that variants affecting methylation will have a greater effect when occurring in higher CpG densities than in lower. We found this to be true for a variant's effect on transcript abundance, indicating that candidate variants can be prioritized based on CpG sequence density. Our findings imply that DNA methylation influences the likelihood that mutations occur at specific sites in the genome, supporting the view that the distribution of mutations is not random.

Improving Activity Estimation in Passive Gamma Scanning for Radioactive Waste Drums

A method to improve radioactive waste drum activity estimation in Segmented Gamma Scanning (SGS) systems was developed for homogenous content. We describe a method to quantify the activity of spatially distributed gamma-emitting isotopes (‘hot spots’) in homogenous content waste drums without the use of a collimator. Instead of averaging all the detector's readings we treat it as many different spatial samples as if we have multiple detectors surrounding the waste drum ("virtual detectors"). From these readings, we form a general linear model. Next, we derive the Maximum Likelihood Estimator (MLE) for the multiple sources position and activity. We solve this hyper-dimensional search problem using an Alternating Projections (AP) technique which transforms the problem into a simpler one-dimensional maximization problem. We tested this method using a mathematical simulation with a various number of sources, at random activities and positions for several energy bands. The preliminary results are consistent and show large improvement of the accuracy with comparison to industrial SGS systems and the same accuracy as new methods which exploits the spatial samples. Furthermore, since this method eliminates the need for heavy led collimator, none of the sources is blocked for the whole measurement period, which provides increased count rates and decreases the total measurement time.

Abstract P6-03-03: The Q-CROC-3 project reveals novel genomic alterations in triple negative breast cancers in residual tumors after neoadjuvant chemotherapy

The prognosis of triple negative breast cancer that shows resistance and/or incomplete response to cytotoxic chemotherapy is poor. In order to understand the mechanisms of resistance to chemotherapy and the genomic evolution of TNBCs treated with chemotherapy, an international multi-center biopsy-driven clinical trial was created for the collection and study of drug-resistant primary and metastatic freshly frozen tumors (Q-CROC-03: NCT01276899). We consented 60 patients with operable TNBC undergoing neoadjuvant Anthracycline/Taxane-based chemotherapy for pre and post-treatment biopsies as well as collection of residual tumor at the time of surgery and serial blood sampling. In 12-15 patients, adequate residual tumor material was available for genomic studies, which included whole exome sequencing, array CGH, gene expression microarray profiling and RNAseq of paired tumors. Whole exome sequencing revealed clonal shifts as well as the relatively infrequent appearance of novel mutations in individual tumors, without any recurrently detected variants. Array CGH revealed a remarkable stability in the number of DNA copy number alterations with a few functional alterations enriched for in the residual tumor, including an amplicon involving the NFIB gene. Finally, gene expression profiling showed shifts towards the immune-modulatory and basal TNBC subtypes after chemotherapy as well as an increase in the expression of several targetable genes, including DUSP1, a dual specificity phosphatase. In the 4 cases of primary and matching metastatic tumors, the post-NAC residual tumor had acquired changes many of which persisted in the metastatic sites, indicating that the analysis of the residual tumors can provide a partial picture of genomic changes present in metastases but not in the primary tumor. In summary, the genomic characterization of residual post-NAC tumor tissue provides important information for the development of novel therapeutic strategies for drug-resistant TNBCs as well as a portrait of genomic evolution of TNBCs subjected to chemotherapy.

Citation Format: Basik M, Aguilar-Mahecha A, Lafleur J, Bareke E, Przybytkowski E, Alirezaie N, Discepola F, Légaré S, Kovacina B, Lan C, Mihalcioiu CL, Robidoux A, Marcus E, Roy J-A, Pelmus M, Aleynikova O, Nabavi S, Tonellato P, Majewski J. The Q-CROC-3 project reveals novel genomic alterations in triple negative breast cancers in residual tumors after neoadjuvant chemotherapy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-03.

Evidence for effective interventions to reduce mental health-related stigma and discrimination in the medium and long term: systematic review

BACKGROUND

Most research on interventions to counter stigma and discrimination has focused on short-term outcomes and has been conducted in high-income settings.

AIMS

To synthesise what is known globally about effective interventions to reduce mental illness-based stigma and discrimination, in relation first to effectiveness in the medium and long term (minimum 4 weeks), and second to interventions in low- and middle-income countries (LMICs).

METHOD

We searched six databases from 1980 to 2013 and conducted a multi-language Google search for quantitative studies addressing the research questions. Effect sizes were calculated from eligible studies where possible, and narrative syntheses conducted. Subgroup analysis compared interventions with and without social contact.

RESULTS

Eighty studies (n = 422 653) were included in the review. For studies with medium or long-term follow-up (72, of which 21 had calculable effect sizes) median standardised mean differences were 0.54 for knowledge and -0.26 for stigmatising attitudes. Those containing social contact (direct or indirect) were not more effective than those without. The 11 LMIC studies were all from middle-income countries. Effect sizes were rarely calculable for behavioural outcomes or in LMIC studies.

CONCLUSIONS

There is modest evidence for the effectiveness of anti-stigma interventions beyond 4 weeks follow-up in terms of increasing knowledge and reducing stigmatising attitudes. Evidence does not support the view that social contact is the more effective type of intervention for improving attitudes in the medium to long term. Methodologically strong research is needed on which to base decisions on investment in stigma-reducing interventions.

Significance and outcome of left heart hypoplasia in fetal congenital diaphragmatic hernia

OBJECTIVE

In patients with a left-sided congenital diaphragmatic hernia (CDH), the left ventricle (LV) is often compressed and smaller than normal. The objective of this study was to investigate whether small left heart dimensions prenatally normalize after birth in patients with CDH, or whether prenatal indices of left heart size and flow predict postnatal outcome.

METHODS

Clinical and echocardiographic data were reviewed for patients diagnosed with left-sided CDH prenatally. Cardiac dimensions and flows were compared with normative data. Among liveborn patients, pre- and postnatal Z-scores of left heart structures were compared, and associations between prenatal indices and outcome were assessed.

RESULTS

Of 125 patients diagnosed prenatally with CDH, 111 had a left-sided defect. Of these, 85 were liveborn, including 20 with congenital heart disease. Gestational age-adjusted dimensions of fetal left heart structures, including aortic valve diameter, mitral valve (MV) diameter, LV long-axis, LV short-axis and LV volume, were all smaller than normal (P < 0.001). On average, the LV contributed 33 +/- 8% of combined ventricular output, lower than the normal 40-50%. Z-scores of left heart structures increased from the prenatal echocardiogram to the postnatal study, with average changes ranging from 0.56 +/- 1.68 (aortic valve) to 1.39 +/- 1.85 (LV volume). Among liveborn patients, there was no association between prenatal left heart Z-scores and postnatal survival.

CONCLUSIONS

Hypoplasia of and reduced flow through the left heart are common among fetuses with CDH. After birth and CDH repair, left heart dimensions generally normalize, with adequate size to support a biventricular circulation, even when there is very low flow through the left heart in mid- and late-gestation.