Lynch syndrome associated with two MLH1 promoter variants and allelic imbalance of MLH1 expression.

Lynch syndrome is a hereditary cancer syndrome caused by a constitutional mutation in one of the mismatch repair genes. The implementation of predictive testing and targeted preventative surveillance is hindered by the frequent finding of sequence variants of uncertain significance in these genes. We aimed to determine the pathogenicity of previously reported variants (c.-28A>G and c.-7C>T) within the MLH1 5'untranslated region (UTR) in two individuals from unrelated suspected Lynch syndrome families. We investigated whether these variants were associated with other pathogenic alterations using targeted high-throughput sequencing of the MLH1 locus. We also determined their relationship to gene expression and epigenetic alterations at the promoter. Sequencing revealed that the c.-28A>G and c.-7C>T variants were the only potentially pathogenic alterations within the MLH1 gene. In both individuals, the levels of transcription from the variant allele were reduced to 50% compared with the wild-type allele. Partial loss of expression occurred in the absence of constitutional epigenetic alterations within the MLH1 promoter. We propose that these variants may be pathogenic due to constitutional partial loss of MLH1 expression, and that this may be associated with intermediate penetrance of a Lynch syndrome phenotype. Our findings provide further evidence of the potential importance of noncoding variants in the MLH1 5'UTR in the pathogenesis of Lynch syndrome.

EEG phase patterns reflect the selectivity of neural firing.

Oscillations are pervasive in encephalographic signals and supposedly reflect cognitive processes and sensory representations. While the relation between oscillation amplitude (power) and sensory-cognitive variables has been extensively studied, recent work reveals that the dynamic oscillation signature (phase pattern) can carry information about such processes to a greater degree than amplitude. To elucidate the neural correlates of oscillatory phase patterns, we compared the stimulus selectivity of neural firing rates and auditory-driven electroencephalogram (EEG) oscillations. We employed the same naturalistic sound stimuli in 2 experiments, one recording scalp EEGs in humans and one recording intracortical local field potentials (LFPs) and single neurons in macaque auditory cortex. Using stimulus decoding techniques, we show that stimulus selective firing patterns imprint on the phase rather than the amplitude of slow (theta band) oscillations in LFPs and EEG. In particular, we find that stimuli which can be discriminated by firing rates can also be discriminated by phase patterns but not by oscillation amplitude and that stimulus-specific phase patterns also persist in the absence of increases of oscillation power. These findings support a neural basis for stimulus selective and entrained EEG phase patterns and reveal a level of interrelation between encephalographic signals and neural firing beyond simple amplitude covariations in both signals.

A precluding but not ensuring role of entrained low-frequency oscillations for auditory perception.

Oscillatory activity in sensory cortices reflects changes in local excitation-inhibition balance, and recent work suggests that phase signatures of ongoing oscillations predict the perceptual detection of subsequent stimuli. Low-frequency oscillations are also entrained by dynamic natural scenes, suggesting that the chance of detecting a brief target depends on the relative timing of this to the entrained rhythm. We tested this hypothesis in humans by implementing a cocktail-party-like scenario requiring subjects to detect a target embedded in a cacophony of background sounds. Using EEG to measure auditory cortical oscillations, we find that the chance of target detection systematically depends on both power and phase of theta-band (2-6 Hz) but not alpha-band (8-12 Hz) oscillations before target. Detection rates were higher and responses faster when oscillatory power was low and both detection rate and response speed were modulated by phase. Intriguingly, the phase dependency was stronger for miss than for hit trials, suggesting that phase has a inhibiting but not ensuring role for detection. Entrainment of theta range oscillations prominently occurs during the processing of attended complex stimuli, such as vocalizations and speech. Our results demonstrate that this entrainment to attended sensory environments may have negative effects on the detection of individual tokens within the environment, and they support the notion that specific phase ranges of cortical oscillations act as gatekeepers for perception.

Dominant vertical orientation processing without clustered maps: early visual brain dynamics imaged with voltage-sensitive dye in the pigeon visual Wulst.

The pigeon is a widely established behavioral model of visual cognition, but the processes along its most basic visual pathways remain mostly unexplored. Here, we report the neuronal population dynamics of the visual Wulst, an assumed homolog of the mammalian striate cortex, captured for the first time with voltage-sensitive dye imaging. Responses to drifting gratings were characterized by focal emergence of activity that spread extensively across the entire Wulst, followed by rapid adaptation that was most effective in the surround. Using additional electrophysiological recordings, we found cells that prefer a variety of orientations. However, analysis of the imaged spatiotemporal activation patterns revealed no clustered orientation map-like arrangements as typically found in the primary visual cortices of many mammalian species. Instead, the vertical orientation was overrepresented, both in terms of the imaged population signal, as well as the number of neurons preferring the vertical orientation. Such enhanced selectivity for the vertical orientation may result from horizontal motion vectors that trigger adaptation to the extensive flow field input during natural behavior. Our findings suggest that, although the avian visual Wulst is homologous to the primary visual cortex in terms of its gross anatomical connectivity and topology, its detailed operation and internal organization is still shaped according to specific input characteristics.

Association of molecular marker O(6)Methylguanine DNA methyltransferase and concomitant chemoradiotherapy with survival in Southern Chinese glioblastoma patients.

OBJECTIVES: (1) To compare the survival of concomitant chemotherapy and radiotherapy with radiotherapy alone in Chinese patients with primary glioblastoma. (2) To determine the methylation status of O(6)Methylguanine DNA methyltransferase in Chinese primary glioblastoma, and to assess the prognostic value of O(6)Methylguanine DNA methyltransferase methylation status in such patients. DESIGN: Retrospective correlative analysis. SETTING: University teaching hospital, Hong Kong. PATIENTS: Patients diagnosed with histologically proven primary glioblastoma in the period of March 2005 to June 2007 were recruited. Genomic DNA was isolated from formalin-fixed and paraffin-embedded sections of glioblastoma tissues. Methylation-specific polymerase chain reaction for O(6)Methylguanine DNA methyltransferase was performed. Patients' information at presentation was collected (age, performance status, steroid use, extent of resection, complications, radiotherapy data, use of chemotherapy). Primary outcome was measured by overall survival while secondary outcome was measured by progression-free survival. Overall and progression-free survivals were estimated by the Kaplan-Meier technique. Outcomes were assessed for groups with and without concomitant chemoradiotherapy and for groups with and without O(6)Methylguanine DNA methyltransferase methylation. RESULTS: A total of 35 glioblastoma patients were recruited; 27 were male and 8 female. Their mean age was 50 years. In all, 17 received concomitant chemoradiotherapy, and 18 received radiotherapy only. Their median overall survival was 12 (range, 7-17) months and the median progression-free survival was 5 (range, 3-6) months. In the radiotherapy alone group, the median progression-free survival and overall survival was 4 (range, 3-5) months and 6 (range, 2-10) months, respectively. In the concomitant radiochemotherapy group, the median progression-free survival and overall survival was 6 (range, 2-10) months and 13 (range, 8-18) months, respectively. Fifteen (43%) of the tumour samples showed methylation of O(6)Methylguanine DNA methyltransferase. There was a trend towards overall longer survival in the group with methylated tumours compared to those with unmethylated tumours; respective values for median survival (ranges) were 17 (13-21) versus 10 (6-14) months (P=0.105). CONCLUSIONS: Our single-centre results indicated that Chinese glioblastoma patients who had received concomitant chemoradiotherapy showed a trend towards longer overall survival compared to those receiving radiotherapy alone. Approximately 43% of our Chinese glioblastoma samples showed methylation of O(6)Methylguanine DNA methyltransferase. O(6)Methylguanine DNA methyltransferase methylation may be a significant prognostic factor in Chinese glioblastoma patients.

Perspectives of Adult Singaporeans toward Potential Policies to Reduce the Consumption of Sugar Sweetened Beverages-A Cross-Sectional Study.

Excessive consumption of sugar sweetened beverages (SSB) is of growing concern, and several countries are implementing measures to reduce SSB consumption. Understanding perceptions towards SSB policies is crucial to prioritize policy actions and to effectively frame public communication. We conducted a cross-sectional study in a sample of 754 adult Singaporeans to examine support towards 10 hypothetical policies to reduce SSB consumption. Policy scenarios were presented to participants and support was assessed using a 5-point Likert scale. Opinions about policies were elicited by asking participants "What other thoughts do you have about this policy?". We used logistic regression to examine determinants of policy support, and thematic analyses to understand opinions about policies. We observed good public support for a variety of SSB policies. In general, less restrictive policies such as traffic light labels (85.0% agreed/strongly agreed) and free access to water at eateries (77.1%) were better supported as compared to restrictive policies such as portion-size restrictions (64.5%) and taxation (55.0%). There was limited variation by age, ethnicity, income, physical activity and body mass index. Concerns about policies largely centered on loss of personal autonomy and economic implications for businesses. Nevertheless, participants also recognized that policies could support healthier beverage consumption by increasing awareness and enabling informed decision making. Findings from this study provide insights into consumer's perceptions of SSB policies, and can inform public health advocacy and government action in this area.

Whole genome and biomarker analysis of patients with recurrent glioblastoma on bevacizumab: A subset analysis of the CABARET trial.

The CABARET trial (ACTRN12610000915055) reported no difference in overall survival (OS) between patients with recurrent glioblastoma (GBM) randomized to either bevacizumab monotherapy or bevacizumab plus carboplatin. However, a subset of patients showed durable responses and prolonged survival, with recorded survival times of over 30 months in five of 122 patients (4%). Patient selection for bevacizumab therapy would be enhanced if a predictive biomarker of response or survival could be identified; this biomarker sub-study attempted to identify novel biomarkers. Patients who opted to participate in this sub-study and who had adequate biospecimens for analysis (n = 54) were retrospectively evaluated for the expression of a series of tumor proteins. Immunohistochemistry (IHC) was used to measure the expression of 19 proteins previously implicated in cancer treatment response to bevacizumab. MGMT promoter methylation was also assessed. Tumor DNA from five patients with outlying survival duration ('poor' and 'exceptional' survivors) was subjected to whole genome sequencing (WGS). No single protein expression level, including VEGF-A, predicted OS in the cohort. WGS of poor and exceptional survivors identified a gain in Chromosome 19 that was exclusive to the exceptional survivors. Validation of this finding requires examination of a larger independent cohort.

A case study of a long-term glioblastoma survivor with unmethylated MGMT and hypermutated genotype.

Effective treatments that extend survival of malignant brain tumor glioblastoma (GBM) have not changed in more than a decade; however, there exists a minority patient group (<5%) whose survival is longer than 3 yr. We herein present a case report of a long-term surviving 51-yr-old female diagnosed with a MGMT unmethylated GBM. The patient was progression-free for 23 mo. Fresh primary and recurrent tumor samples were collected and processed for patient-derived model development. Whole-genome sequencing (WGS) was performed concurrently with additional standard of care diagnostics. WGS revealed a hypermutated genotype in the germline tissue and in both the primary and recurrent tumor samples. Specific to the matched tumors, an average of 30 cancer driver genes were mutated. Noteworthy was the identification of a nonsynonymous mutation in the POLE gene. As a possible instigator of the hypermutational genotype observed in the tumors, we identified nonsynonymous germline mutations within the mismatch repair genes, MLH1 and PMS2 Mutations within these genes are often indicative of the pan-cancer phenotype known as Lynch syndrome; however, their pathogenicity remains unreported. We performed a drug screen of 165 compounds, which identified one compound, YM155, an experimental survivin inhibitor, that showed effectivity to the patient-derived cell lines of both tumors. Treatment selection based on a patient's genome to individualize treatment for GBM patients could potentially be useful in the clinic. This is a promising avenue for further translational research, with larger databases and integrated platforms to increase the efficiency of analyzing and interpreting the individual genomic data of GBM.

I-AbACUS: a Reliable Software Tool for the Semi-Automatic Analysis of Invasion and Migration Transwell Assays.

The quantification of invasion and migration is an important aspect of cancer research, used both in the study of the molecular processes involved in this collection of diseases and the evaluation of the efficacy of new potential treatments. The transwell assay, while being one of the most widely used techniques for the evaluation of these characteristics, shows a high dependence on the operator's ability to correctly identify the cells and a low protocol standardization. Here we present I-AbACUS, a software tool specifically designed to aid the analysis of transwell assays that automatically and specifically recognizes cells in images of stained membranes and provides the user with a suggested cell count. A complete description of this instrument, together with its validation against the standard analysis technique for this assay is presented. Furthermore, we show that I-AbACUS is versatile and able to elaborate images containing cells with different morphologies and that the obtained results are less dependent on the operator and their experience. We anticipate that this instrument, freely available (Gnu Public Licence GPL v2) at www.marilisacortesi.com as a standalone application, could significantly improve the quantification of invasion and migration of cancer cells.

Integrated Genetic, Epigenetic, and Transcriptional Profiling Identifies Molecular Pathways in the Development of Laterally Spreading Tumors.

Laterally spreading tumors (LST) are colorectal adenomas that develop into extremely large lesions with predominantly slow progression to cancer, depending on lesion subtype. Comparing and contrasting the molecular profiles of LSTs and colorectal cancers offers an opportunity to delineate key molecular alterations that drive malignant transformation in the colorectum. In a discovery cohort of 11 LSTs and paired normal mucosa, we performed a comprehensive and unbiased screen of the genome, epigenome, and transcriptome followed by bioinformatics integration of these data and validation in an additional 84 large, benign colorectal lesions. Mutation rates in LSTs were comparable with microsatellite-stable colorectal cancers (2.4 vs. 2.6 mutations per megabase); however, copy number alterations were infrequent (averaging only 1.5 per LST). Frequent genetic, epigenetic, and transcriptional alterations were identified in genes not previously implicated in colorectal neoplasia (ANO5, MED12L, EPB41L4A, RGMB, SLITRK1, SLITRK5, NRXN1, ANK2). Alterations to pathways commonly mutated in colorectal cancers, namely, the p53, PI3K, and TGFß pathways, were rare. Instead, LST-altered genes converged on axonal guidance, Wnt, and actin cytoskeleton signaling. These integrated omics data identify molecular features associated with noncancerous LSTs and highlight that mutation load, which is relatively high in LSTs, is a poor predictor of invasive potential. IMPLICATIONS: The novel genetic, epigenetic, and transcriptional changes associated with LST development reveal important insights into why some adenomas do not progress to cancer. The finding that LSTs exhibit a mutational load similar to colorectal carcinomas has implications for the validity of molecular biomarkers for assessing cancer risk. Mol Cancer Res; 14(12); 1217-28. ©2016 AACR.

Development and evaluation of plunger-in-needle liquid-phase microextraction.

In this work, a novel, simple and fast one-step liquid-phase microextraction (LPME) approach, termed plunger-in-needle LPME was developed. In this method, the stainless steel plunger wire of a commercially available plunger-in-needle microsyringe was simply etched by immersion in hydrofluoric acid to form a microporous structure, and was used as the extractant solvent holder. The extractant solvent could be easily held within the pores created by the etching. When the plunger wire with the extractant solvent was exposed to the sample solution, analytes directly diffused from the sample solution to the solvent. After extraction, the plunger wire was directly introduced into the injection port of a gas chromatography-mass spectrometry (GC-MS) system for analysis of the analytes after thermal desorption. Polycyclic aromatic hydrocarbons (PAHs) were used as model analytes to evaluate the extraction performance of this new approach to LPME. Parameters affecting the extraction efficiency were investigated in detail. Under the optimized conditions, the method detection limits for 10PAHs were in the range of 0.003 and 0.136µg/L (at a signal/noise ratio of 3), with relative standard deviations of between 2.9% and 9.6% on the same etched plunger wire. The linearities of the calibration plots were from 0.05 to 50 or from 1 to 50µg/L, depending on the PAHs. When this method was applied for the spiked river water sample, the relative recoveries ranged from 70.1% to 106.4%. The proposed method integrates the extraction and extract introduction into one device, without extraneous sorbent needed, which makes the procedure fast and simple. It is also an environmentally friendly approach as the organic solvent consumed is almost negligible.

Altered promoter nucleosome positioning is an early event in gene silencing.

Gene silencing in cancer frequently involves hypermethylation and dense nucleosome occupancy across promoter regions. How a promoter transitions to this silent state is unclear. Using colorectal adenomas, we investigated nucleosome positioning, DNA methylation, and gene expression in the early stages of gene silencing. Genome-wide gene expression correlated with highly positioned nucleosomes upstream and downstream of a nucleosome-depleted transcription start site (TSS). Hypermethylated promoters displayed increased nucleosome occupancy, specifically at the TSS. We investigated 2 genes, CDH1 and CDKN2B, which were silenced in adenomas but lacked promoter hypermethylation. Instead, silencing correlated with loss of nucleosomes from the -2 position upstream of the TSS relative to normal mucosa. In contrast, permanent CDH1 silencing in carcinoma cells was characterized by promoter hypermethylation and dense nucleosome occupancy. Our findings suggest that silenced genes transition through an intermediary stage involving altered promoter nucleosome positioning, before permanent silencing by hypermethylation and dense nucleosome occupancy.

NKT and MAIT invariant TCRα sequences can be produced efficiently by VJ gene recombination.

Semi-invariant T cell receptors (TCRs) found on natural killer T (NKT) and mucosal-associated invariant T (MAIT) cells are characterized by the use of invariant variable (V) and joining (J) gene combinations in the TCR α-chain, as well as ubiquitous canonical TCRα amino acid sequences that are dominant in many individuals and similar across species. That they are so prevalent indicates that they occupy an important niche within the immune system. However, these TCRs are produced by a largely random gene recombination process, which seems a risky approach for the immune system to acquire these innate-like cells. We surveyed studies reporting NKT and MAIT TCRα sequences for six and four different species, respectively. Although the germline nature of the canonical human and mouse NKT and mouse MAIT TCRα sequences and an overlap of nucleotides between the mouse MAIT-related Vα and Jα genes have been noted in previous studies, in this study we demonstrate that, for all reported species, the canonical TCRα amino acid sequences can be encoded by at least one germline-derived nucleotide sequence. Moreover, these nucleotide sequences can utilize an overlap between the Vα and Jα genes in their production, which enables them to be produced by a large variety of recombination mechanisms. We investigated the role of these TCRα features in the production of the canonical NKT and MAIT TCRα sequences. In computer simulations of a random recombination process involving the invariant NKT and MAIT TCRα gene combinations for each species, the canonical NKT and MAIT TCRα sequences were the first or second most generated of all sequences with the CDR3α length restrictions associated with NKT and MAIT cells. These results suggest that the immune machinery enables the canonical NKT and MAIT TCRα sequences to be produced with great efficiency through the process of convergent recombination, ensuring their prevalence across individuals and species.

Orientation selective or not? - Measuring significance of tuning to a circular parameter.

Orientation and direction tuning are among the most studied features of the visual system and are routinely measured during experiments to estimate the quality of neuronal responses. However, standard approaches to report orientation selectivity are only narrowly quantitative and strongly depend on the signal quality, while the more sophisticated ones are computationally exhaustive, making them difficult to use during ongoing experiments. We propose a fast and efficient method for reporting the reliability of coding applicable to any circular parameter. Similar to standard deviation in the linear statistics, reproducibility measures trial-to-trial variability of a circular response parameter. Reproducibility is a normalized measure easily transformed to p-values, which provide explicit information about significance of the estimated orientation preference. The proposed approach is applicable to a wide range of signal types. Here, we discuss examples from optical imaging and electrophysiological recordings, and provide a more thorough examination based on tuning curves modeled in silico.

Nasal chemosensory-stimulation evoked activity patterns in the rat trigeminal ganglion visualized by in vivo voltage-sensitive dye imaging.

Mammalian nasal chemosensation is predominantly mediated by two independent neuronal pathways, the olfactory and the trigeminal system. Within the early olfactory system, spatiotemporal responses of the olfactory bulb to various odorants have been mapped in great detail. In contrast, far less is known about the representation of volatile chemical stimuli at an early stage in the trigeminal system, the trigeminal ganglion (TG), which contains neurons directly projecting to the nasal cavity. We have established an in vivo preparation that allows high-resolution imaging of neuronal population activity from a large region of the rat TG using voltage-sensitive dyes (VSDs). Application of different chemical stimuli to the nasal cavity elicited distinct, stimulus-category specific, spatiotemporal activation patterns that comprised activated as well as suppressed areas. Thus, our results provide the first direct insights into the spatial representation of nasal chemosensory information within the trigeminal ganglion imaged at high temporal resolution.