SUMMARY The genetics of complex disease produce alterations in the molecular interactions of cellular pathways whose collective effect may become clear through the organized structure of molecular networks. To characterize molecular systems associated with late-onset Alzheimer’s disease (LOAD), we constructed gene regulatory networks in 1647 post-mortem brain tissues from LOAD patients and non-demented subjects, and demonstrate that LOAD reconfigures specific portions of the molecular interaction structure. Through an integrative network-based approach, we rank-ordered these network structures for relevance to LOAD pathology, highlighting an immune and microglia-specific module dominated by genes involved in pathogen phagocytosis, containing TYROBP as a key regulator and up-regulated in LOAD. Mouse microglia cells over-expressing intact or truncated TYROBP revealed expression changes that significantly overlapped the human brain TYROBP network. Thus the causal network structure is a useful predictor of response to gene perturbations and presents a novel framework to test models of disease mechanisms underlying LOAD.

Type II DNA topoisomerases actively reduce the fractions of knotted and catenated circular DNA below thermodynamic equilibrium values. To explain this surprising finding, we designed a model in which topoisomerases introduce a sharp bend in DNA. Because the enzymes have a specific orientation relative to the bend, they act like Maxwell's demon, providing unidirectional strand passage. Quantitative analysis of the model by computer simulations proved that it can explain much of the experimental data. The required sharp DNA bend was demonstrated by a greatly increased cyclization of short DNA fragments from topoisomerase binding and by direct visualization with electron microscopy.T ype II topoisomerases are essential enzymes that pass one DNA through another and thereby remove DNA entanglements. They make a transient double-stranded break in a gate segment (G segment) that allows passage by another segment (T segment) of the same or another DNA molecule (reviewed in refs. 1 and 2). Thus, these enzymes have the potential to convert real DNA molecules into phantom chains that freely pass through themselves to generate an equilibrium distribution of knots, catenanes, and supercoils.The actual picture is more complex and more interesting. The observed steady-state fractions of knotted, catenated, and supercoiled DNAs produced by type II topoisomerases are up to two orders of magnitude lower than at equilibrium (3). Thermodynamically, there is no contradiction in this finding because the enzymes use the energy of ATP hydrolysis. Active topology simplification by topoisomerases has an important biological consequence. It helps explain how topoisomerases can remove all DNA entanglements under the crowded cellular conditions which favor the opposite outcome. The challenge, though, is to understand how type II topoisomerases actively simplify DNA topology. Topology is a global property of circular DNA molecules, and yet it is determined by the much smaller topoisomerases, which can act only locally.Two models have been suggested to explain active simplification of DNA topology. First, if type II topoisomerases corral the T segment within a small loop of DNA containing the G segment, active disentanglement would result (3). However, it was pointed out when this model was suggested (3) that to account for the large effects observed, the loop trapping would need substantial energy input from ATP hydrolysis for the transport of the DNA along the enzymes, and these enzymes are energetically efficient (4). Moreover, no direct experimental data supporting the model have been presented.Second, a kinetic proofreading model proposed that two successive bindings of T segments are required for strand passage (5). The first binding event converts the enzyme bound with a G segment to an activated state. An assumption of the model is that segment collision in the knotted state occurs about 1͞P k times more often than in the unknotted state, where P k is the equilibrium probability of knotting. Our computer simulations below show that th...

SUMMARY Genome-wide transcriptional profiling was used to characterize the molecular underpinnings of neocortical organization in rhesus macaque, including cortical areal specialization and laminar cell type diversity. Microarray analysis of individual cortical layers across sensorimotor and association cortices identified robust and specific molecular signatures for individual cortical layers and areas, prominently involving genes associated with specialized neuronal function. Overall, transcriptome-based relationships were related to spatial proximity, being strongest between neighboring cortical areas and between proximal layers. Primary visual cortex (V1) displayed the most distinctive gene expression compared to other cortical regions in rhesus and human, both in the specialized layer 4 as well as other layers. Laminar patterns were more similar between macaque and human compared to mouse, as was the unique V1 profile that was not observed in mouse. These data provide a unique resource detailing neocortical transcription patterns in a non-human primate with great similarity in gene expression to human.

PurposeAberrant Notch signaling has been implicated in the pathogenesis of many human cancers. MK-0752 is a potent, oral inhibitor of γ-secretase, an enzyme required for Notch pathway activation. Safety, maximum-tolerated dose, pharmacokinetics (PKs), pharmacodynamics, and preliminary antitumor efficacy were assessed in a phase I study of MK-0752.Patients and MethodsMK-0752 was administered in three different schedules to patients with advanced solid tumors. Hair follicles were collected at higher dose levels to assess a gene signature of Notch inhibition.ResultsOf 103 patients who received MK-0752, 21 patients received a continuous once-daily dosing at 450 and 600 mg; 17 were dosed on an intermittent schedule of 3 of 7 days at 450 and 600 mg; and 65 were dosed once per week at 600, 900, 1,200, 1,500, 1,800, 2,400, 3,200, and 4,200 mg. The most common drug-related toxicities were diarrhea, nausea, vomiting, and fatigue. PKs (area under the concentration-time curve and maximum measured plasma concentration) increased in a less than dose proportional manner, with a half-life of approximately 15 hours. Significant inhibition of Notch signaling was observed with the 1,800- to 4,200-mg weekly dose levels, confirming target engagement at those doses. One objective complete response and an additional 10 patients with stable disease longer than 4 months were observed among patients with high-grade gliomas.ConclusionMK-0752 toxicity was schedule dependent. Weekly dosing was generally well tolerated and resulted in strong modulation of a Notch gene signature. Clinical benefit was observed, and rational combination trials are currently ongoing to maximize clinical benefit with this novel agent.

Two variables define the topological state of closed doublestranded DNA: the knot type, K, and ⌬Lk, the linking number difference from relaxed DNA. The equilibrium distribution of probabilities of these states, P(⌬Lk, K), is related to two conditional distributions: P(⌬LkͦK), the distribution of ⌬Lk for a particular K, and P(Kͦ⌬Lk) and also to two simple distributions: P(⌬Lk), the distribution of ⌬Lk irrespective of K, and P(K). We explored the relationships between these distributions. P(⌬Lk, K), P(⌬Lk), and P(Kͦ⌬Lk) were calculated from the simulated distributions of P(⌬LkͦK) and of P(K). The calculated distributions agreed with previous experimental and theoretical results and greatly advanced on them. Our major focus was on P(Kͦ⌬Lk), the distribution of knot types for a particular value of ⌬Lk, which had not been evaluated previously. We found that unknotted circular DNA is not the most probable state beyond small values of ⌬Lk. Highly chiral knotted DNA has a lower free energy because it has less torsional deformation. Surprisingly, even at ͦ⌬Lkͦ > 12, only one or two knot types dominate the P(Kͦ⌬Lk) distribution despite the huge number of knots of comparable complexity. A large fraction of the knots found belong to the small family of torus knots. The relationship between supercoiling and knotting in vivo is discussed. T opological properties of DNA are essential for life. It is simplest to consider the topological properties of circular DNA in which both strands are intact, called closed circular DNA, but linear DNA in vivo is also topologically constrained (1, 2). The topological state of closed circular DNA can be described by two variables. One is the knot type, K, formed by the double helix axis. In particular, a molecule may be unknotted (unknot, trivial knot) or form a non-trivial knot. The second variable, the linking number of the complementary strands, Lk, describes the winding of the strands of the double helix about each other. It is more convenient to use the difference between Lk and that of relaxed DNA (Lk o ), ⌬Lk ϭ Lk Ϫ Lk o , than Lk itself. Circular DNA extracted from cells has negative ⌬Lk (3).Random cyclization of linear DNA molecules results in an equilibrium distribution of topological states, P(⌬Lk, K). Studies of the components of this distribution have greatly advanced our understanding of DNA conformational properties. The measurement in 1975 of the equilibrium distribution of ⌬Lk for unknotted circular DNAs, the conditional distribution P(⌬Lk͉Unknot), led to elegant determinations of the free energy of supercoiling (4, 5). These textbook experiments were elaborated later to include the effect of DNA length, solvent, temperature, and ionic conditions (6-10). A theoretical analysis of P(⌬Lk͉Unknot) allowed the determination of the torsional rigidity of DNA (11-15). The conditional distribution for the simplest knot, P(⌬Lk͉Trefoil), has also been studied theoretically (16) and experimentally (17).The value of Lk is not defined in nicked circular DNA, whose topological state is spec...

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Individual differences in behavioral effects of sleep deprivation are associated with differences in diurnal amplitude of gene expression for genes that show circadian rhythmicity.

BackgroundIn Alzheimer’s disease, there are striking changes in CSF composition that relate to altered choroid plexus (CP) function. Studying CP tissue gene expression at the blood–cerebrospinal fluid barrier could provide further insight into the epithelial and stromal responses to neurodegenerative disease states.MethodsTranscriptome-wide Affymetrix microarrays were used to determine disease-related changes in gene expression in human CP. RNA from post-mortem samples of the entire lateral ventricular choroid plexus was extracted from 6 healthy controls (Ctrl), 7 patients with advanced (Braak and Braak stage III–VI) Alzheimer’s disease (AD), 4 with frontotemporal dementia (FTD) and 3 with Huntington’s disease (HuD). Statistics and agglomerative clustering were accomplished with MathWorks, MatLab; and gene set annotations by comparing input sets to GeneGo (http://www.genego.com) and Ingenuity (http://www.ingenuity.com) pathway sets. Bonferroni-corrected hypergeometric p-values of < 0.1 were considered a significant overlap between sets.ResultsPronounced differences in gene expression occurred in CP of advanced AD patients vs. Ctrls. Metabolic and immune-related pathways including acute phase response, cytokine, cell adhesion, interferons, and JAK-STAT as well as mTOR were significantly enriched among the genes upregulated. Methionine degradation, claudin-5 and protein translation genes were downregulated. Many gene expression changes in AD patients were observed in FTD and HuD (e.g., claudin-5, tight junction downregulation), but there were significant differences between the disease groups. In AD and HuD (but not FTD), several neuroimmune-modulating interferons were significantly enriched (e.g., in AD: IFI-TM1, IFN-AR1, IFN-AR2, and IFN-GR2). AD-associated expression changes, but not those in HuD and FTD, were enriched for upregulation of VEGF signaling and immune response proteins, e.g., interleukins. HuD and FTD patients distinctively displayed upregulated cadherin-mediated adhesion.ConclusionsOur transcript data for human CP tissue provides genomic and mechanistic insight for differential expression in AD vs. FTD vs. HuD for stromal as well as epithelial components. These choroidal transcriptome characterizations elucidate immune activation, tissue functional resiliency, and CSF metabolic homeostasis. The BCSFB undergoes harmful, but also important functional and adaptive changes in neurodegenerative diseases; accordingly, the enriched JAK-STAT and mTOR pathways, respectively, likely help the CP in adaptive transcription and epithelial repair and/or replacement when harmed by neurodegeneration pathophysiology. We anticipate that these precise CP translational data will facilitate pharmacologic/transgenic therapies to alleviate dementia.Electronic supplementary materialThe online version of this article (10.1186/s12987-018-0102-9) contains supplementary material, which is available to authorized users.