The Modality Specificity of the Slow Negative Wave

Event-related potentials were recorded in a simple reaction time task using a 3-sec interval between S₁ and S₂. The sensory modalities of S₁ and S₂ were varied across 4 conditions to yield all possible combinations of tones and flashes. A negative component which peaked between 600 and 800 msec after S₁ was specific in scalp distribution to the modality of S₁ but not S₂. It was concluded that this negative component is a response to S₁ and not related to processes associated with anticipation of S₂. A slow negative shift which peaked at S₂ was largest at the vertex in all conditions, suggesting its motor origin. A trend for the latter activity to be more negative in posterior recordings when S₂ was visual than auditory leaves open the possibility that the terminal CNV is a combination of motor activities and anticipation of the sensory modality of S₂.     

Mental fatigue and task control: planning and preparation

The effects of mental fatigue on planning and preparation for future actions were examined, using a task switching paradigm. Fatigue was induced by "time on task," with subjects performing a switch task continuously for 2 hr. Subjects had to alternate between tasks on every second trial, so that a new task set was required on every second trial. Manipulations of response-stimulus intervals (RSIs) were used to examine whether subjects prepared themselves for the task change. Behavioral measurements, event-related potentials (ERPs), and mood questionnaires were used to assess the effects of mental fatigue. Reaction times (RTs) were faster on trials in which no change in task set was required in comparison with switch trials, requiring a new task set. Long RSIs were used efficiently to prepare for the processing of subsequent stimuli. With increasing mental fatigue, preparation processes seemed to become less adequate and the number of errors increased. A clear poststimulus parietal negativity was observed on repetition trials, which reduced with time on task. This attention-related component was less pronounced in switch trials; instead, ERPs elicited in switch trials showed a clear frontal negativity. This negativity was also diminished by time on task. ERP differences between repetition and switch trials became smaller with increasing time on task.     

Spatial Distribution of the Contingent Negative Variation (CNV) and the Relationship between CNV and Reaction Time

Multichannel recording of scalp CNV (Contingent Negative Variation) and RT (Reaction Time) was carried out on 12 normal adult Ss in a fixed foreperiod RT experiment. Single trial responses were stored on digital tape and averaged off-line. Strict control over eye movement artifact was exerted through fixation techniques coupled with mechanical and electro-oculographic monitoring of movement. Analysis of single-trial data gave an intra-individual picture of correlation apparently in conflict with the across picture gained from averages. A rationalization is attempted of these results and some evidence is offered that, in the individual S, a negative and probably nonlinear relationship holds between CNV amplitude and RT. Analysis of average data demonstrates the distribution of CNV across the scalp and shows a lack of correlation between CNV and RT in prefrontal areas, in contrast with that found in central-parietal areas. It is suggested that the CNV is an index of functionally different processes in these areas.     

Role of chromosomal imbalances in the pathogenesis of DSD: A retrospective analysis of 115 prenatal samples

Differences of sex development (DSDs) are a group of congenital conditions characterized by a discrepancy between chromosomal, gonadal, and genital sex development of an individual, with significant impact on medical, psychological and reproductive life. The genetic heterogeneity of DSDs complicates the diagnosis and almost half of the patients remains undiagnosed. In this context, chromosomal imbalances in syndromic DSD patients may help to identify new genes implicated in DSDs. In this study, we aimed at describing the burden of chromosomal imbalances including submicroscopic ones (copy number variants or CNVs) in a cohort of prenatal syndromic DSD patients, and review their role in DSDs. Our patients carried at least one pathogenic or likely pathogenic chromosomal imbalance/CNV or low-level mosaicism for aneuploidy. Almost half of the cases resulted from an unbalanced chromosomal rearrangement. Chromosome 9p/q, 4p/q, 3q and 11q anomalies were more frequently observed. Review of the literature confirmed the causative role of CNVs in DSDs, either in disruption of known DSD-causing genes (SOX9, NR0B1, NR5A1, AR, ATRX, …) or as a tool to suspect new genes in DSDs (HOXD cluster, ADCY2, EMX2, CAMK1D, …). Recurrent CNVs of regulatory elements without coding sequence content (i.e. duplications/deletions upstream of SOX3 or SOX9) confirm detection of CNVs as a mean to explore our non-coding genome. Thus, CNV detection remains a powerful tool to explore undiagnosed DSDs, either through routine techniques or through emerging technologies such as long-read whole genome sequencing or optical genome mapping.     

Aetiology of severe mental retardation and further genetic analysis by high‐resolution microarray in a population‐based series of 6‐ to 17‐year‐old children

Aim: To investigate the prevalence, co‐morbidities and aetiologies of severe mental retardation (SMR) in a cohort of Swedish children and to further penetrate aetiologies in the group with undetermined causes by application of updated clinical‐genetic methods. Methods: The study was population‐based and included children living in the County of Halland in western Sweden in 2004 (born 1987–1998; 46 000 children). Patients were identified through habilitation centres, paediatric clinics and school health services. Patients with unclear prenatal aetiology were investigated with single nucleotide polymorphism (SNP)‐array. Results: Severe mental retardation was identified in 133 children from 132 families, corresponding to a prevalence of 2.9 per 1000 children. There were more males than females (90:43).The aetiology was prenatal in 82 (62%), perinatal in 14 (10%) and postnatal in 8 (6%). In 29 (22 %) children, mainly males with autism, the cause could not be related to the time of birth. In the prenatal group, genetic causes dominated, but still 23 children remained undiagnosed; in 5/19 of these patients, a diagnosis could be made after SNP‐array analysis. One or more associated neurological handicaps were found in more than half of the children. Conclusion: Prevalence and co‐morbidity were similar to previous Scandinavian studies. High‐resolution chromosomal micro‐array techniques are valuable diagnostic tools, reducing the number of patients with unexplained SMR.     

Contrasting mechanisms of de novo copy number mutagenesis suggest the existence of different classes of environmental copy number mutagens

While gene copy number variations (CNVs) are abundant in the human genome, and often are associated with disease consequences, the mutagenic pathways and environmental exposures that cause these large structural mutations are understudied relative to conventional nucleotide substitutions in DNA. The members of the environmental mutagenesis community are currently seeking to remedy this deficiency, and there is a renewed interest in the development of mutagenicity assays to identify and characterize compounds that may induce de novo CNVs in humans. To achieve this goal, it is critically important to acknowledge that CNVs exist in two very distinct classes: nonrecurrent and recurrent CNVs. The goal of this commentary is to emphasize the deep contrasts that exist between the proposed pathways that lead to these two mutation classes. Nonrecurrent de novo CNVs originate primarily in mitotic cells through replication‐dependent DNA repair pathways that involve microhomologies (<10 bp), and are detected at higher frequency in children of older fathers. In contrast, recurrent de novo CNVs are most often formed in meiotic cells through homologous recombination between nonallelic large low‐copy repeats (>10,000 bp), without an associated paternal age effect. Given the biological differences between the two CNV classes, it is our belief that nonrecurrent and recurrent CN mutagens will probably differ substantially in their modes of action. Therefore, each CNV class may require their own uniquely designed assays, so that we as a field may succeed in uncovering the broadest possible spectrum of environmental CN mutagens. Environ. Mol. Mutagen. 57:3–9, 2016. © 2015 Wiley Periodicals, Inc.     

The interaction of glutathione S-transferase M1-null variants with tobacco smoke exposure and the development of childhood asthma

Background The glutathione S -transferase M1 (GSTM1)-null variant is a common copy number variant associated with adverse pulmonary outcomes, including asthma and airflow obstruction, with evidence of important gene-by-environment interactions with exposures to oxidative stress.
Objective To explore the joint interactive effects of GSTM1 copy number and tobacco smoke exposure on the development of asthma and asthma-related phenotypes in a family-based cohort of childhood asthmatics.
Methods We performed quantitative PCR-based genotyping for GSTM1 copy number in children of self-reported white ancestry with mild to moderate asthma in the Childhood Asthma Management Program. Questionnaire data regarding intrauterine (IUS) and post-natal, longitudinal smoke exposure were available. We performed both family-based and population-based tests of association for the interaction between GSTM1 copy number and tobacco smoke exposure with asthma and asthma-related phenotypes.
Results Associations of GSTM1-null variants with asthma ( P =0.03), younger age of asthma symptom onset ( P =0.03), and greater airflow obstruction (reduced forced expiratory volume in 1 s / forced vital capacity, P =0.01) were observed among the 50 children (10% of the cohort) with exposure to IUS. In contrast, no associations were observed between GSTM1-null variants and asthma-related phenotypes among children without IUS exposure. Presence of at least one copy of GSTM1 conferred protection.
Conclusion These findings support an important gene-by-environment interaction between two common factors: increased risk of asthma and asthma-related phenotypes conferred by GSTM1-null homozygosity in children is restricted to those with a history of IUS exposure.     

Hypoxia drives transient site-specific copy gain and drug-resistant gene expression

Copy number heterogeneity is a prominent feature within tumors. The molecular basis for this heterogeneity remains poorly characterized. Here, we demonstrate that hypoxia induces transient site-specific copy gains (TSSGs) in primary, nontransformed, and transformed human cells. Hypoxia-driven copy gains are not dependent on HIF1α or HIF2α; however, they are dependent on the KDM4A histone demethylase and are blocked by inhibition of KDM4A with a small molecule or the natural metabolite succinate. Furthermore, this response is conserved at a syntenic region in zebrafish cells. Regions with site-specific copy gain are also enriched for amplifications in hypoxic primary tumors. These tumors exhibited amplification and overexpression of the drug resistance gene CKS1B, which we recapitulated in hypoxic breast cancer cells. Our results demonstrate that hypoxia provides a biological stimulus to create transient site-specific copy alterations that could result in heterogeneity within tumors and cell populations. These findings have major implications in our understanding of copy number heterogeneity and the emergence of drug resistance genes in cancer.     

Concurrent DNA Copy‐Number Alterations and Mutations in Genes Related to Maintenance of Genome Stability in Uninvolved Mammary Glandular Tissue from Breast Cancer Patients

Somatic mosaicism for DNA copy‐number alterations (SMC‐CNAs) is defined as gain or loss of chromosomal segments in somatic cells within a single organism. As cells harboring SMC‐CNAs can undergo clonal expansion, it has been proposed that SMC‐CNAs may contribute to the predisposition of these cells to genetic disease including cancer. Herein, the gross genomic alterations (>500 kbp) were characterized in uninvolved mammary glandular tissue from 59 breast cancer patients and matched samples of primary tumors and lymph node metastases. Array‐based comparative genomic hybridization showed 10% (6/59) of patients harbored one to 359 large SMC‐CNAs (mean: 1,328 kbp; median: 961 kbp) in a substantial portion of glandular tissue cells, distal from the primary tumor site. SMC‐CNAs were partially recurrent in tumors, albeit with considerable contribution of stochastic SMC‐CNAs indicating genomic destabilization. Targeted resequencing of 301 known predisposition and somatic driver loci revealed mutations and rare variants in genes related to maintenance of genomic integrity: BRCA1 (p.Gln1756Profs*74, p.Arg504Cys), BRCA2 (p.Asn3124Ile), NCOR1 (p.Pro1570Glnfs*45), PALB2 (p.Ser500Pro), and TP53 (p.Arg306*). Co‐occurrence of gross SMC‐CNAs along with point mutations or rare variants in genes responsible for safeguarding genomic integrity highlights the temporal and spatial neoplastic potential of uninvolved glandular tissue in breast cancer patients.