Low-burden TP53 mutations represent frequent genetic events in CLL with an increased risk for treatment initiation.

TP53 aberrations predict chemoresistance and represent a contraindication for the use of standard chemoimmunotherapy in chronic lymphocytic leukaemia (CLL). Recent next-generation sequencing (NGS)-based studies have identified frequent low-burden TP53 mutations with variant allele frequencies below 10%, but the clinical impact of these low-burden TP53 mutations is still a matter of debate. In this study, we aimed to scrutinise the subclonal architecture and clinical impact of TP53 mutations using a sensitive, NGS-based mutation analysis in a 'real-world' cohort of 901 patients with CLL. In total, 225 TP53 mutations were identified in 17.5% (158/901) of the patients; 48% of these alterations represented high-burden mutations, while 52% were low-burden TP53 mutations. Low-burden mutations as sole alterations were identified in 39% (62/158) of all mutated cases with 82% (51/62) of these being represented by a single low-burden TP53 mutation. Patients harbouring low-burden TP53 mutations had significantly lower time to first treatment compared to patients with wild-type TP53. Our study has expanded the knowledge on the frequency, clonal architecture, and clinical impact of low-burden TP53 mutations. By demonstrating that patients with sole low-burden TP53 variants represent more than one-third of patients with TP53 mutations and have an increased risk for treatment initiation, our findings strengthen the need to redefine the threshold of TP53 variant reporting to below 10% in the routine diagnostic setting.

A Novel Measure Inspired by Lyapunov Exponents for the Characterization of Dynamics in State-Transition Networks.

The combination of network sciences, nonlinear dynamics and time series analysis provides novel insights and analogies between the different approaches to complex systems. By combining the considerations behind the Lyapunov exponent of dynamical systems and the average entropy of transition probabilities for Markov chains, we introduce a network measure for characterizing the dynamics on state-transition networks with special focus on differentiating between chaotic and cyclic modes. One important property of this Lyapunov measure consists of its non-monotonous dependence on the cylicity of the dynamics. Motivated by providing proper use cases for studying the new measure, we also lay out a method for mapping time series to state transition networks by phase space coarse graining. Using both discrete time and continuous time dynamical systems the Lyapunov measure extracted from the corresponding state-transition networks exhibits similar behavior to that of the Lyapunov exponent. In addition, it demonstrates a strong sensitivity to boundary crisis suggesting applicability in predicting the collapse of chaos.

Infraslow oscillations in human sleep spindle activity.

BACKGROUND: It has previously been reported that EEG sigma (10-15 Hz) activity during sleep exhibits infraslow oscillations (ISO) with a period of 50 s. However, a detailed analysis of the ISO of individually identified sleep spindles is not available. NEW METHOD: We investigated basic properties of ISO during baseline sleep of 34 healthy young human participants using new and established methods. The analyses focused on fast sleep spindle and sigma activity (13-15 Hz) in NREM stage 2 and slow wave sleep (SWS). To describe ISO in sigma activity we analyzed power of power of the EEG signal. For the study of ISO in sleep spindle activity we applied a new method in which the EEG signal was reduced to a spindle on/off binary square signal. Its spectral properties were contrasted to that of a square signal wherein the same spindles and also the inter spindle intervals were permutated randomly. This approach was validated using surrogate data with imposed ISO modulation. RESULTS: We confirm the existence of ISO in sigma activity albeit with a frequency below the previously reported 0.02 Hz. These ISO are most prominent in the high sigma band and over the centro-parieto-occipital regions. A similar modulation is present in spindle activity. ISO in sleep spindles are most prominent in the centro-parieto-occipital regions, left hemisphere and second half of the night independent of the number of spindles. CONCLUSIONS: The comparison of spectral properties of binary event signals and permutated event signals is effective in detecting slow oscillatory phenomena.

Association of symptoms of insomnia and sleep parameters among kidney transplant recipients.

OBJECTIVE: Insomnia complaints are frequent among kidney transplant (kTx) recipients and are associated with fatigue, depression, lower quality of life and increased morbidity. However, it is not known if subjective insomnia symptoms are associated with objective parameters of sleep architecture. Thus, we analyze the association between sleep macrostructure and EEG activity versus insomnia symptoms among kTx recipients. METHODS: Participants (n1=100) were selected from prevalent adult transplant recipients (n0=1214) followed at a single institution. Insomnia symptoms were assessed by the Athens Insomnia Scale (AIS) and standard overnight polysomnography was performed. In a subgroup of patients (n2=56) sleep microstructure was also analyzed with power spectral analysis. RESULTS: In univariable analysis AIS score was not associated with sleep macrostructure parameters (sleep latency, total sleep time, slow wave sleep, wake after sleep onset), nor with NREM and REM beta or delta activity in sleep microstructure. In multivariable analysis after controlling for covariables AIS score was independently associated with the proportion of slow wave sleep (ß=0.263; CI: 0.026-0.500) and REM beta activity (ß=0.323; CI=0.041-0.606) (p<0.05 for both associations). CONCLUSIONS: Among kTx recipients the severity of insomnia symptoms is independently associated with higher proportion of slow wave sleep and increased beta activity during REM sleep but not with other parameters sleep architecture. The results suggest a potential compensatory sleep protective mechanism and a sign of REM sleep instability associated with insomnia symptoms among this population.

Identification and Characterization of a Class of MALAT1-like Genomic Loci.

The MALAT1 (Metastasis-Associated Lung Adenocarcinoma Transcript 1) gene encodes a noncoding RNA that is processed into a long nuclear retained transcript (MALAT1) and a small cytoplasmic tRNA-like transcript (mascRNA). Using an RNA sequence- and structure-based covariance model, we identified more than 130 genomic loci in vertebrate genomes containing the MALAT1 3' end triple-helix structure and its immediate downstream tRNA-like structure, including 44 in the green lizard Anolis carolinensis. Structural and computational analyses revealed a co-occurrence of components of the 3' end module. MALAT1-like genes in Anolis carolinensis are highly expressed in adult testis, thus we named them testis-abundant long noncoding RNAs (tancRNAs). MALAT1-like loci also produce multiple small RNA species, including PIWI-interacting RNAs (piRNAs), from the antisense strand. The 3' ends of tancRNAs serve as potential targets for the PIWI-piRNA complex. Thus, we have identified an evolutionarily conserved class of long noncoding RNAs (lncRNAs) with similar structural constraints, post-transcriptional processing, and subcellular localization and a distinct function in spermatocytes.

Stochastic graph Voronoi tessellation reveals community structure.

Given a network, the statistical ensemble of its graph-Voronoi diagrams with randomly chosen cell centers exhibits properties convertible into information on the network's large scale structures. We define a node-pair level measure called Voronoi cohesion which describes the probability for sharing the same Voronoi cell, when randomly choosing g centers in the network. This measure provides information based on the global context (the network in its entirety), a type of information that is not carried by other similarity measures. We explore the mathematical background of this phenomenon and several of its potential applications. A special focus is laid on the possibilities and limitations pertaining to the exploitation of the phenomenon for community detection purposes.

Slow wave sleep and accelerated forgetting.

We investigated whether the benefit of slow wave sleep (SWS) for memory consolidation typically observed in healthy individuals is disrupted in people with accelerated long-term forgetting (ALF) due to epilepsy. SWS is thought to play an active role in declarative memory in healthy individuals and, furthermore, electrographic epileptiform activity is often more prevalent during SWS than during wakefulness or other sleep stages. We studied the relationship between SWS and the benefit of sleep for memory retention using a word-pair associates task. In both the ALF and the healthy control groups, sleep conferred a memory benefit. However, the relationship between the amount of SWS and sleep-related memory benefits differed significantly between the groups. In healthy participants, the amount of SWS correlated positively with sleep-related memory benefits. In stark contrast, the more SWS, the smaller the sleep-related memory benefit in the ALF group. Therefore, contrary to its role in healthy people, SWS-associated brain activity appears to be deleterious for memory in patients with ALF.

Sleep deficits but no metabolic deficits in premanifest Huntington's disease.

OBJECTIVE: Huntington disease (HD) is a fatal autosomal dominant, neurodegenerative condition characterized by progressively worsening motor and nonmotor problems including cognitive and neuropsychiatric disturbances, along with sleep abnormalities and weight loss. However, it is not known whether sleep disturbances and metabolic abnormalities underlying the weight loss are present at a premanifest stage. METHODS: We performed a comprehensive sleep and metabolic study in 38 premanifest gene carrier individuals and 36 age- and sex-matched controls. The study consisted of 2 weeks of actigraphy at home, 2 nights of polysomnography and multiple sleep latency tests in the laboratory, and body composition assessment using dual energy x-ray absorptiometry scanning with energy expenditure measured over 10 days at home by doubly labeled water and for 36 hours in the laboratory by indirect calorimetry along with detailed cognitive and clinical assessments. We performed a principal component analyses across all measures within each studied domain. RESULTS: Compared to controls, premanifest gene carriers had more disrupted sleep, which was best characterized by a fragmented sleep profile. These abnormalities, as well as a theta power (4-7Hz) decrease in rapid eye movement sleep, were associated with disease burden score. Objectively measured sleep problems coincided with the development of cognitive, affective, and subtle motor deficits and were not associated with any metabolic alterations. INTERPRETATION: The results show that among the earliest abnormalities in premanifest HD is sleep disturbances. This raises questions as to where the pathology in HD begins and also whether it could drive some of the early features and even possibly the pathology.

Circadian regulation of slow waves in human sleep: Topographical aspects.

Slow waves (SWs, 0.5-4Hz) in field potentials during sleep reflect synchronized alternations between bursts of action potentials and periods of membrane hyperpolarization of cortical neurons. SWs decline during sleep and this is thought to be related to a reduction of synaptic strength in cortical networks and to be central to sleep's role in maintaining brain function. A central assumption in current concepts of sleep function is that SWs during sleep, and associated recovery processes, are independent of circadian rhythmicity. We tested this hypothesis by quantifying all SWs from 12 EEG derivations in 34 participants in whom 231 sleep periods were scheduled across the circadian cycle in a 10-day forced-desynchrony protocol which allowed estimation of the separate circadian and sleep-dependent modulation of SWs. Circadian rhythmicity significantly modulated the incidence, amplitude, frequency and the slope of the SWs such that the peaks of the circadian rhythms in these slow-wave parameters were located during the biological day. Topographical analyses demonstrated that the sleep-dependent modulation of SW characteristics was most prominent in frontal brain areas whereas the circadian effect was similar to or greater than the sleep-dependent modulation over the central and posterior brain regions. The data demonstrate that circadian rhythmicity directly modulates characteristics of SWs thought to be related to synaptic plasticity and that this modulation depends on topography. These findings have implications for the understanding of local sleep regulation and conditions such as ageing, depression, and neurodegeneration which are associated with changes in SWs, neural plasticity and circadian rhythmicity.

Lamin A/C is expressed in pluripotent mouse embryonic stem cells.

The pluripotent nature of embryonic stem cells (ESC) is associated with a dynamic open chromatin state and an irregular nuclear shape. It has been postulated that the absence of Lamin A/C contributes to these features. However, we show that mouse ESCs express low, yet readily detectable, amounts of Lamin A/C at both the RNA and protein levels. Full-length transcripts of both isoforms were readily detected by q-PCR and deep RNA sequencing. Additionally, protein expression was validated in multiple primary and established ESC lines by immunoblotting using several independent antibodies. Immunofluorescence labeling showed localization of Lamin A/C at the nuclear periphery of all Oct4/Nanog double-positive ESC lines examined, as well as in the inner cell mass of blastocysts. Our results demonstrate ESCs do express low levels of Lamin A/C, thus models linking pluripotency and nuclear dynamics with the absence of Lamin A/C need to be revisited.

The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult.

Genome-wide studies have identified thousands of long noncoding RNAs (lncRNAs) lacking protein-coding capacity. However, most lncRNAs are expressed at a very low level, and in most cases there is no genetic evidence to support their in vivo function. Malat1 (metastasis associated lung adenocarcinoma transcript 1) is among the most abundant and highly conserved lncRNAs, and it exhibits an uncommon 3'-end processing mechanism. In addition, its specific nuclear localization, developmental regulation, and dysregulation in cancer are suggestive of it having a critical biological function. We have characterized a Malat1 loss-of-function genetic model that indicates that Malat1 is not essential for mouse pre- and postnatal development. Furthermore, depletion of Malat1 does not affect global gene expression, splicing factor level and phosphorylation status, or alternative pre-mRNA splicing. However, among a small number of genes that were dysregulated in adult Malat1 knockout mice, many were Malat1 neighboring genes, thus indicating a potential cis-regulatory role of Malat1 gene transcription.

Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation.

Although transmission of the gene expression program from mother to daughter cells has been suggested to be mediated by gene bookmarking, the precise mechanism by which bookmarking mediates post-mitotic transcriptional re-activation has been unclear. Here, we used a real-time gene expression system to quantitatively demonstrate that transcriptional activation of the same genetic locus occurs with a significantly more rapid kinetics in post-mitotic cells versus interphase cells. RNA polymerase II large subunit (Pol II) and bromodomain protein 4 (BRD4) were recruited to the locus in a different sequential order on interphase initiation versus post-mitotic re-activation resulting from the recognition by BRD4 of increased levels of histone H4 Lys 5 acetylation (H4K5ac) on the previously activated locus. BRD4 accelerated the dynamics of messenger RNA synthesis by de-compacting chromatin and hence facilitating transcriptional re-activation. Using a real-time quantitative approach, we identified differences in the kinetics of transcriptional activation between interphase and post-mitotic cells that are mediated by a chromatin-based epigenetic mechanism.

Reduced fronto-cortical brain connectivity during NREM sleep in Asperger syndrome: an EEG spectral and phase coherence study.

OBJECTIVE: To investigate whether sleep macrostructure and EEG power spectral density and coherence during NREM sleep are different in Asperger syndrome (AS) compared to typically developing children and adolescents. METHODS: Standard all night EEG sleep parameters were obtained from 18 un-medicated subjects with AS and 14 controls (age range: 7.5-21.5years) after one adaptation night. Spectral, and phase coherence measures were computed for multiple frequency bands during NREM sleep. RESULTS: Sleep latency and wake after sleep onset were increased in AS. Absolute power spectrum density (PSD) was significantly reduced in AS in the alpha, sigma, beta and gamma bands and in all 10 EEG derivations. Relative PSD showed a significant increase in delta and a decrease in the sigma band for frontal, and in beta for centro-temporal derivations. Intrahemispheric coherence measures were markedly lower in AS in the frontal areas, and the right hemisphere over all EEG channels. The most prominent reduction in intrahemispheric coherence was observed over the fronto-central areas in delta, theta, alpha and sigma EEG frequency bands. CONCLUSION: EEG power spectra and coherence during NREM sleep, in particular in fronto-cortical derivations are different in AS compared to typically developing children and adolescents. SIGNIFICANCE: Quantitative analysis of the EEG during NREM sleep supports the hypothesis of frontal dysfunction in AS.