Evidence that the methylation state of the monoamine oxidase A (MAOA) gene predicts brain activity of MAO A enzyme in healthy men

Human brain function is mediated by biochemical processes, many of which can be visualized and quantified by positron emission tomography (PET). PET brain imaging of monoamine oxidase A (MAO A)—an enzyme metabolizing neurotransmitters—revealed that MAO A levels vary widely between healthy men and this variability was not explained by the common MAOA genotype (VNTR genotype), suggesting that environmental factors, through epigenetic modifications, may mediate it. Here, we analyzed MAOA methylation in white blood cells (by bisulphite conversion of genomic DNA and subsequent sequencing of cloned DNA products) and measured brain MAO A levels (using PET and [¹¹C]clorgyline, a radiotracer with specificity for MAO A) in 34 healthy non-smoking male volunteers. We found significant interindividual differences in methylation status and methylation patterns of the core MAOA promoter. The VNTR genotype did not influence the methylation status of the gene or brain MAO A activity. In contrast, we found a robust association of the regional and CpG site-specific methylation of the core MAOA promoter with brain MAO A levels. These results suggest that the methylation status of the MAOA promoter (detected in white blood cells) can reliably predict the brain endophenotype. Therefore, the status of MAOA methylation observed in healthy males merits consideration as a variable contributing to interindividual differences in behavior.     

The limited spatial scale of dispersal in soil arthropods revealed with whole‐community haplotype‐level metabarcoding

Soil arthropod communities are highly diverse and critical for ecosystem functioning. However, our knowledge of spatial structure and the underlying processes of community assembly are scarce, hampered by limited empirical data on species diversity and turnover. We implement a high‐throughput sequencing approach to generate comparative data for thousands of arthropods at three hierarchical levels: genetic, species and supra‐specific lineages. A joint analysis of the spatial arrangement across these levels can reveal the predominant processes driving the variation in biological assemblages at the local scale. This multihierarchical approach was performed using haplotype‐level COI metabarcoding of entire communities of mites, springtails and beetles from three Iberian mountain regions. Tens of thousands of specimens were extracted from deep and superficial soil layers and produced comparative phylogeographic data for >1,000 codistributed species and nearly 3,000 haplotypes. Local assemblage composition differed greatly between grasslands and forests and, within each habitat, showed strong spatial structure and high endemicity. Distance decay was high at all levels, even at the scale of a few kilometres or less. The local distance decay patterns were self‐similar for the haplotypes and higher hierarchical entities, and this fractal structure was similar in all regions, suggesting that uniform processes of limited dispersal determine local‐scale community assembly. Our results from whole‐community metabarcoding provide insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. If generalized across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod diversity on Earth.     

Single nucleotide polymorphisms in the insulin‐like growth factor 1 (IGF1) gene are associated with growth‐related traits in farmed Atlantic salmon

Understanding the genetic basis of variation in traits related to growth and fillet quality in Atlantic salmon is of importance to the aquaculture industry. Several growth‐related QTL have been identified via the application of genetic markers. The IGF1 gene is considered a highly conserved and crucial growth‐regulating gene in salmonid species. However, the association between polymorphisms in the IGF1 gene and growth‐related traits in Atlantic salmon is unknown. Therefore, in this study, regions of the Atlantic salmon IGF1 gene were sequenced, aligned and compared across individuals. Three SNPs were identified in the putative promoter (SNP1, g.5763G>T; GenBank no. AGKD01012745 ), intron 1 (SNP2, g.7292C>T; GenBank no. AGKD01012745 ) and intron 3 (SNP3, g.4671A>C; GenBank no. AGKD01133398 ) regions respectively. These SNPs were genotyped in a population of 4800 commercial Atlantic salmon with data on several weight and fillet traits measured at harvest (at approximately 3 years of age). In a mixed model, association analysis of individual SNPs, SNP1 and SNP3 were both significantly associated with several weight traits (P < 0.05). The estimated additive effect on overall harvest weight was approximately 35 and 110 g for SNPs 1 and 3 respectively. A haplotype analysis confirmed the association between genetic variation in the IGF1 gene with overall body weight (P < 0.05) and fillet component traits (P < 0.05). Our findings suggest the identified nucleotide polymorphisms of the IGF1 gene may either affect farmed Atlantic salmon growth directly or be in population‐wide linkage disequilibrium with causal variation, highlighting their possible utility as candidates for marker‐assisted selection in the aquaculture industry.     

Inducible knockdown of pregnancy‐associated plasma protein‐A gene expression in adult female mice extends life span

Pregnancy‐associated plasma protein‐A (PAPP‐A) knockout (KO) mice, generated through homologous recombination in embryonic stem cells, have a significantly increased lifespan compared to wild‐type littermates. However, it is unknown whether this longevity advantage would pertain to PAPP‐A gene deletion in adult animals. In the present study, we used tamoxifen (Tam)‐inducible Cre recombinase‐mediated excision of the floxed PAPP‐A (fPAPP‐A) gene in mice at 5 months of age. fPAPP‐A mice, which were either positive (pos) or negative (neg) for Tam‐Cre, received Tam treatment with quarterly boosters. Only female mice could be used with this experimental design. fPAPP‐A/neg and fPAPP‐A/pos mice had similar weights at the start of the experiment and showed equivalent weight gain. We found that fPAPP‐A/pos mice had a significant extension of life span (P = 0.005). The median life span was increased by 21% for fPAPP‐A/pos compared to fPAPP‐A/neg mice. Analysis of mortality in life span quartiles indicated that the proportion of deaths of fPAPP‐A/pos mice were lower than fPAPP‐A/neg mice at young adult ages (P = 0.002 for 601–800 days) and higher than fPAPP‐A/neg mice at older ages (P = 0.004 for >1000 days). Thus, survival curves and age‐specific mortality indicate that female mice with knockdown of PAPP‐A gene expression as adults have an extended healthy life span.     

Replicated association of the NR4A3 gene with smoking behaviour in schizophrenia and in bipolar disorder

Schizophrenia and bipolar disorder are associated with dopamine neurotransmission and show high comorbidity with tobacco dependence. Recent evidence indicates that the family of the NR4A orphan nuclear receptors, which are expressed in dopamine neurons and in dopaminoceptive brain areas, may play a role in dopamine‐mediated effects. We have, therefore, analysed the association of six single nucleotide polymorphisms (SNPs) within the three genes belonging to the NR4A orphan nuclear receptor family, NR4A1 (rs2603751, rs2701124), NR4A2 (rs12803, rs834835) and NR4A3 (rs1131339, rs1405209), with the degree of smoking in a sample of 204 unrelated schizophrenia patients, which included 126 smokers and 78 non‐smokers. SNPs within the NR4A3 gene (rs1131339 and rs1405209) were significantly associated with heavy smoking in this cohort, using a stepwise analysis of the escalated number of cigarettes smoked per day (P = 0.008 and 0.006, respectively; satisfying the Nyholt significance threshold of 0.009, an adjustment for multiple testing). We then repeated the association analysis of the NR4A3 markers (rs1131339 and rs1405209) in a larger cohort of 319 patients with bipolar disorder, which included 167 smokers and 152 non‐smokers. We have replicated the positive association with smoking of the NR4A3 SNP rs1131339 in this group (P = 0.04), providing an important confirmation of the involvement of the NR4A3 gene in nicotine addiction in patients with mental health disease, a population significantly at risk for nicotine addiction.     

Conformational changes within the HLA‐A1:MAGE‐A1 complex induced by binding of a recombinant antibody fragment with TCR‐like specificity

Although there is X‐ray crystallographic evidence that the interaction between major histocompatibility complex (MHC, in humans HLA) class I molecules and T cell receptors (TCR) or killer cell Ig‐like receptors (KIR) may be accompanied by considerable changes in the conformation of selected residues or even entire loops within TCR or KIR, conformational changes between receptor‐bound and ‐unbound MHC class I molecules of comparable magnitude have not been observed so far. We have previously determined the structure of the MHC class I molecule HLA‐A1 bound to a melanoma antigen‐encoding gene (MAGE)‐A1‐derived peptide in complex with a recombinant antibody fragment with TCR‐like specificity, Fab‐Hyb3. Here, we compare the X‐ray structure of HLA‐A1:MAGE‐A1 with that complexed with Fab‐Hyb3 to gain insight into structural changes of the MHC molecule that might be induced by the interaction with the antibody fragment. Apart from the expulsion of several water molecules from the interface, Fab‐Hyb3 binding results in major rearrangements (up to 5.5 Å) of heavy chain residues Arg65, Gln72, Arg145, and Lys146. Residue 65 is frequently and residues 72 and 146 are occasionally involved in TCR binding‐induced conformational changes, as revealed by a comparison with MHC class I structures in TCR‐liganded and ‐unliganded forms. On the other hand, residue 145 is subject to a reorientation following engagement of HLA‐Cw4 and KIR2DL1. Therefore, conformational changes within the HLA‐A1:MAGE‐A1:Fab‐Hyb3 complex include MHC residues that are also involved in reorientations in complexes with natural ligands, pointing to their central importance for the peptide‐dependent recognition of MHC molecules.     

Evidence for interplay between genes and maternal stress in utero: monoamine oxidase A polymorphism moderates effects of life events during pregnancy on infant negative emotionality at 5 weeks

The low activity variant of the monoamine oxidase A (MAOA) functional promoter polymorphism, MAOA‐LPR, in interaction with adverse environments (G × E) is associated with child and adult antisocial behaviour disorders. MAOA is expressed during foetal development so in utero G × E may influence early neurodevelopment. We tested the hypothesis that MAOA G × E during pregnancy predicts infant negative emotionality soon after birth. In an epidemiological longitudinal study starting in pregnancy, using a two stage stratified design, we ascertained MAOA‐LPR status (low vs. high activity variants) from the saliva of 209 infants (104 boys and 105 girls), and examined predictions to observed infant negative emotionality at 5 weeks post‐partum from life events during pregnancy. In analyses weighted to provide estimates for the general population, and including possible confounders for life events, there was an MAOA status by life events interaction (P = 0.017). There was also an interaction between MAOA status and neighbourhood deprivation (P = 0.028). Both interactions arose from a greater effect of increasing life events on negative emotionality in the MAOA‐LPR low activity, compared with MAOA‐LPR high activity infants. The study provides the first evidence of moderation by MAOA‐LPR of the effect of the social environment in pregnancy on negative emotionality in infancy, an early risk for the development of child and adult antisocial behaviour disorders .     

Inference of patient‐specific subpathway activities reveals a functional signature associated with the prognosis of patients with breast cancer

Breast cancer is one of the most deadly forms of cancer in women worldwide. Better prediction of breast cancer prognosis is essential for more personalized treatment. In this study, we aimed to infer patient‐specific subpathway activities to reveal a functional signature associated with the prognosis of patients with breast cancer. We integrated pathway structure with gene expression data to construct patient‐specific subpathway activity profiles using a greedy search algorithm. A four‐subpathway prognostic signature was developed in the training set using a random forest supervised classification algorithm and a prognostic score model with the activity profiles. According to the signature, patients were classified into high‐risk and low‐risk groups with significantly different overall survival in the training set (median survival of 65 vs 106 months, P = 1.82e‐13) and test set (median survival of 75 vs 101 months, P = 4.17e‐5). Our signature was then applied to five independent breast cancer data sets and showed similar prognostic values, confirming the accuracy and robustness of the subpathway signature. Stratified analysis suggested that the four‐subpathway signature had prognostic value within subtypes of breast cancer. Our results suggest that the four‐subpathway signature may be a useful biomarker for breast cancer prognosis.     

Neuron‐specific non‐classical release of prothymosin alpha: a novel neuroprotective damage‐associated molecular patterns

Prothymosin alpha (ProTα), a nuclear protein devoid of signal sequence, has been shown to possess a number of cellular functions including cell survival. Most recently, we demonstrated that ProTα is localized in the nuclei of neurons, while it is found in both nuclei and cytoplasm in the astrocytes and microglia of adult brain. However, the cell type‐specific non‐classical release of ProTα under cerebral ischemia is yet unknown. In this study, we report that ProTα is non‐classically released along with S100A13 from neurons in the hippocampus, striatum and somatosensory cortex at 3 h after cerebral ischemia, but amlexanox (an anti‐allergic compound) reversibly blocks this neuronal ProTα release. We found that none of ProTα is released from astrocytes and microglia under ischemic stress. Indeed, ProTα intensity is increased gradually in astrocytes and microglia through 24 h after the cerebral ischemia. Interestingly, Z‐Val‐Ala‐Asp fluoromethyl ketone, a caspase 3 inhibitor, pre‐treatment induces ProTα release from astrocytes in the ischemic brain, but this release is reversibly blocked by amlexanox. However, Z‐Val‐Ala‐Asp fluoromethyl ketone as well as amlexanox has no effect on ProTα distribution in microglia upon cerebral ischemia. Taken together, these results suggest that only neurons have machineries to release ProTα upon cerebral ischemic stress in vivo.     

Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single‐nucleotide polymorphism array

With the access to draft genome sequence assemblies and whole‐genome resequencing data from population samples, molecular ecology studies will be able to take truly genome‐wide approaches. This now applies to an avian model system in ecological and evolutionary research: Old World flycatchers of the genus Ficedula, for which we recently obtained a 1.1 Gb collared flycatcher genome assembly and identified 13 million single‐nucleotide polymorphism (SNP)s in population resequencing of this species and its sister species, pied flycatcher. Here, we developed a custom 50K Illumina iSelect flycatcher SNP array with markers covering 30 autosomes and the Z chromosome. Using a number of selection criteria for inclusion in the array, both genotyping success rate and polymorphism information content (mean marker heterozygosity = 0.41) were high. We used the array to assess linkage disequilibrium (LD) and hybridization in flycatchers. Linkage disequilibrium declined quickly to the background level at an average distance of 17 kb, but the extent of LD varied markedly within the genome and was more than 10‐fold higher in ‘genomic islands’ of differentiation than in the rest of the genome. Genetic ancestry analysis identified 33 F₁ hybrids but no later‐generation hybrids from sympatric populations of collared flycatchers and pied flycatchers, contradicting earlier reports of backcrosses identified from much fewer number of markers. With an estimated divergence time as recently as <1 Ma, this suggests strong selection against F₁ hybrids and unusually rapid evolution of reproductive incompatibility in an avian system.