Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes

Background

The extent of intratumoral mutational heterogeneity remains unclear in gliomas, the most common primary brain tumors, especially with respect to point mutation. To address this, we applied single molecule molecular inversion probes targeting 33 cancer genes to assay both point mutations and gene amplifications within spatially distinct regions of 14 glial tumors.

Results

We find evidence of regional mutational heterogeneity in multiple tumors, including mutations in TP53 and RB1 in an anaplastic oligodendroglioma and amplifications in PDGFRA and KIT in two glioblastomas (GBMs). Immunohistochemistry confirms heterogeneity of TP53 mutation and PDGFRA amplification. In all, 3 out of 14 glial tumors surveyed have evidence for heterogeneity for clinically relevant mutations.

Conclusions

Our results underscore the need to sample multiple regions in GBM and other glial tumors when devising personalized treatments based on genomic information, and furthermore demonstrate the importance of measuring both point mutation and copy number alteration while investigating genetic heterogeneity within cancer samples.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0530-z) contains supplementary material, which is available to authorized users.     

The Effects of Physical Exercise with Music on Cognitive Function of Elderly People: Mihama-Kiho Project

Background

Physical exercise has positive effects on cognitive function in elderly people. It is unknown, however, if combinations of non-pharmaceutical interventions can produce more benefits than single ones. This study aimed to identify if physical exercise combined with music improves cognitive function in normal elderly people more than exercise alone.

Methods

We enrolled 119 subjects (age 65–84 years old). Forty subjects performed physical exercise (once a week for an hour with professional trainers) with musical accompaniment (ExM group), developed by YAMAHA Music Foundation; 40 subjects performed the same exercise without music (Ex group); 39 subjects were the control group (Cont group). Before and after the year-long intervention, each patient was assessed by neuropsychological batteries. MRIs were performed before and after intervention; the Voxel-based Specific Regional analysis system for Alzheimer''s Disease (VSRAD) was used to assess medial temporal lobe atrophy.

Results

Analysis of variance (ANOVA) was significant only in visuospatial function. The multiple comparison (ExM vs. Ex, ExM vs. Cont, Ex vs. Cont) was significant between the ExM and Cont group. Intra-group analyses before and after intervention revealed significant improvement in visuospatial function in the ExM group, and significant improvements in other batteries in all three groups. The VSRAD score significantly worsened in the ExM and Ex groups.

Conclusions

Physical exercise combined with music produced more positive effects on cognitive function in elderly people than exercise alone. We attributed this improvement to the multifaceted nature of combining physical exercise with music, which can act simultaneously as both cognitive and physical training.

Trial Registration

UMIN Clinical Trials Registry (UMIN-CTR) UMIN000012148     

Involvement of Interleukin-17A-Induced Hypercontractility of Intestinal Smooth Muscle Cells in Persistent Gut Motor Dysfunction

Background and Aim

The etiology of post-inflammatory gastrointestinal (GI) motility dysfunction, after resolution of acute symptoms of inflammatory bowel diseases (IBD) and intestinal infection, is largely unknown, however, a possible involvement of T cells is suggested.

Methods

Using the mouse model of T cell activation-induced enteritis, we investigated whether enhancement of smooth muscle cell (SMC) contraction by interleukin (IL)-17A is involved in postinflammatory GI hypermotility.

Results

Activation of CD3 induces temporal enteritis with GI hypomotility in the midst of, and hypermotility after resolution of, intestinal inflammation. Prolonged upregulation of IL-17A was prominent and IL-17A injection directly enhanced GI transit and contractility of intestinal strips. Postinflammatory hypermotility was not observed in IL-17A-deficient mice. Incubation of a muscle strip and SMCs with IL-17A in vitro resulted in enhanced contractility with increased phosphorylation of Ser19 in myosin light chain 2 (p-MLC), a surrogate marker as well as a critical mechanistic factor of SMC contractility. Using primary cultured murine and human intestinal SMCs, IκBζ- and p38 mitogen-activated protein kinase (p38MAPK)-mediated downregulation of the regulator of G protein signaling 4 (RGS4), which suppresses muscarinic signaling of contraction by promoting inactivation/desensitization of Gα_q/11 protein, has been suggested to be involved in IL-17A-induced hypercontractility. The opposite effect of L-1β was mediated by IκBζ and c-jun N-terminal kinase (JNK) activation.

Conclusions

We propose and discuss the possible involvement of IL-17A and its downstream signaling cascade in SMCs in diarrheal hypermotility in various GI disorders.     

Evolution of craniofacial novelty in parrots through developmental modularity and heterochrony

Parrots (order Psittaciformes) have developed novel cranial morphology. At the same time, they show considerable morphological diversity in the cranial musculoskeletal system, which includes two novel structures: the suborbital arch and the musculus (M.) pseudomasseter. To understand comprehensively the evolutionary pattern and process of novel cranial morphology in parrots, phylogenetic and developmental studies were conducted. Firstly, we undertook phylogenetic analyses based on mitochondrial ribosomal RNA gene sequences to obtain a robust phylogeny among parrots, and secondly we surveyed the cranial morphology of parrots extensively to add new information on the character states. Character mapping onto molecular phylogenies indicated strongly the repeated evolution of both the suborbital arch and the well-developed M. pseudomasseter within parrots. These results also suggested that the direction of evolutionary change is not always identical in the two characters, implying that these characters are relatively independent or decoupled structures behaving as separate modules. Finally, we compared the developmental pattern of jaw muscles among bird species and found a difference in the timing of M. pseudomasseter differentiation between the cockatiel Nymphicus hollandicus (representative of a well-developed condition) and the peach-faced lovebird Agapornis roseicollis (representative of an underdeveloped condition). On the basis of this study, we suggest that in the development of novel traits, modularity and heterochrony facilitate the diversification of parrot cranial morphology.     

Developmental origins of species-specific muscle pattern

Vertebrate jaw muscle anatomy is conspicuously diverse but developmental processes that generate such variation remain relatively obscure. To identify mechanisms that produce species-specific jaw muscle pattern we conducted transplant experiments using Japanese quail and White Pekin duck, which exhibit considerably different jaw morphologies in association with their particular modes of feeding. Previous work indicates that cranial muscle formation requires interactions with adjacent skeletal and muscular connective tissues, which arise from neural crest mesenchyme. We transplanted neural crest mesenchyme from quail to duck embryos, to test if quail donor-derived skeletal and muscular connective tissues could confer species-specific identity to duck host jaw muscles. Our results show that duck host jaw muscles acquire quail-like shape and attachment sites due to the presence of quail donor neural crest-derived skeletal and muscular connective tissues. Further, we find that these species-specific transformations are preceded by spatiotemporal changes in expression of genes within skeletal and muscular connective tissues including Sox9, Runx2, Scx, and Tcf4, but not by alterations to histogenic or molecular programs underlying muscle differentiation or specification. Thus, neural crest mesenchyme plays an essential role in generating species-specific jaw muscle pattern and in promoting structural and functional integration of the musculoskeletal system during evolution.     

Activation of Leukemia-associated RhoGEF by G��13 with Significant Conformational Rearrangements in the Interface

The transient protein-protein interactions induced by guanine nucleotide-dependent conformational changes of G proteins play central roles in G protein-coupled receptor-mediated signaling systems. Leukemia-associated RhoGEF (LARG), a guanine nucleotide exchange factor for Rho, contains an RGS homology (RH) domain and Dbl homology/pleckstrin homology (DH/PH) domains and acts both as a GTPase-activating protein (GAP) and an effector for Gα₁₃. However, the molecular mechanism of LARG activation upon Gα₁₃ binding is not yet well understood. In this study, we analyzed the Gα₁₃-LARG interaction using cellular and biochemical methods, including a surface plasmon resonance (SPR) analysis. The results obtained using various LARG fragments demonstrated that active Gα₁₃ interacts with LARG through the RH domain, DH/PH domains, and C-terminal region. However, an alanine substitution at the RH domain contact position in Gα₁₃ resulted in a large decrease in affinity. Thermodynamic analysis revealed that binding of Gα₁₃ proceeds with a large negative heat capacity change (ΔCp°), accompanied by a positive entropy change (ΔS°). These results likely indicate that the binding of Gα₁₃ with the RH domain triggers conformational rearrangements between Gα₁₃ and LARG burying an exposed hydrophobic surface to create a large complementary interface, which facilitates complex formation through both GAP and effector interfaces, and activates the RhoGEF. We propose that LARG activation is regulated by an induced-fit mechanism through the GAP interface of Gα₁₃.Heterotrimeric G proteins³ serve as key molecular switches to transduce a large array of extracellular signals into cells by actively alternating their conformations between GDP-bound inactive and GTP-bound active forms. In the current model, the ligand-activated G protein-coupled receptors (GPCRs) catalyze the exchange of GDP for GTP on Gα subunits (1). Upon activation, three switch regions in the Gα subunit undergo significant conformational changes, followed by dissociation of the GTP-bound Gα subunit from the Gβγ subunits. Both Gα-GTP and free Gβγ interact with diverse downstream effectors to transmit intracellular signals. The Gα subunit hydrolyzes bound GTP to GDP by its intrinsic GTPase activity. This deactivation process is further accelerated by GTPase-activating proteins (GAPs) such as regulator of G protein signaling (RGS) proteins (2, 3). Gα-GDP dissociates from effectors and re-associates with Gβγ to terminate the signal.Although this model explains the basic concept of G protein signaling, the molecular dynamics of interactions among GPCR, G protein, RGS protein, and effector during the signaling process is not well understood. It has been suggested that the GPCR signals are integrated into the intracellular signaling network at the level of G proteins (4). Accumulating evidence suggests that the Gα subunit acts as the core of the signaling complex at the membrane, which is formed through the transient protein-protein interactions of multiple signaling components (5, 6). Thus, the quantitative analysis of the dynamic molecular interactions in the GPCR signaling complex will be crucial to understanding various cellular processes.Gα₁₂ and Gα₁₃ subunits have been demonstrated to regulate the activity of Rho GTPase through RhoGEFs, which contain an N-terminal RGS homology domain (RH-RhoGEFs) (7–10). RH-RhoGEFs, which consist of p115RhoGEF/Lsc, PDZ-Rho-GEF/GTRAP48, and LARG in mammalian species, directly link the activation of GPCRs by extracellular ligands to the regulation of Rho activity in cells (10–14). All three RH-RhoGEFs contain an N-terminal RH domain, which specifically recognizes the active form of Gα₁₂ or Gα₁₃ and central DH/PH domains characteristic of GEFs for Rho GTPases. It has been demonstrated in vitro that LARG and p115RhoGEF serve as specific GAPs for Gα_12/13 through their RH domains and also as their effectors to regulate Rho GTPase activation (11–13). A structural study has demonstrated that the interface of the RH domain of p115RhoGEFs and a Gα_13/i1 chimera is different from that of the RGS domain of RGS4 and Gα_i1 (7). The N-terminal small element in the RH domain, which is required for GAP activity toward Gα₁₃, contacts the switch regions and the helical domain of the Gα_13/i1 chimera. The core module of the p115RhoGEF RH domain binds to the region of Gα_13/i1, which is conventionally used for effector binding. These results suggest roles for the RH domain in the stimulation of GEF activity by Gα₁₃ in addition to GAP activity. On the other hand, several studies have also indicated that regions outside of RH domain of RH-RhoGEFs, particularly the DH/PH domains, interact directly with activated Gα₁₃ (11, 14, 15). In addition, we have demonstrated recently that p115RhoGEF interacts with distinct surfaces of Gα₁₃ for the GAP reaction or GEF activity regulation (16). However, the molecular mechanism of LARG activation upon Gα₁₃ binding is not clearly understood.In this study, we have developed a quantitative method for the kinetic and thermodynamic analysis of Gα₁₃-effector interaction using surface plasmon resonance (SPR) with sensor chips on which Gα₁₃ was immobilized. We examined the kinetics and thermodynamics of the Gα₁₃-LARG interaction and assessed LARG activation using both in vitro and cell-based approaches. We present evidence that, in addition to the interaction with the RH domain, the DH/PH domains and C-terminal region of LARG also interact with Gα₁₃ to form the high affinity Gα₁₃-LARG complex and activate RhoGEF activity. We further propose that LARG adopts the active conformation using an induced-fit mechanism through association with the GAP interface of Gα₁₃. A similar mechanism may also be used with other Gα-effector interactions.     

Discovery of novel diarylketoxime derivatives as selective and orally active melanin-concentrating hormone 1 receptor antagonists

Optimization of the lead 2a led to the identification of a novel diarylketoxime class of melanin-concentrating hormone 1 receptor (MCH-1R) antagonists. Our focus was directed toward improvement of hERG activity and metabolic stability. The representative derivative 4b showed potent and dose-dependent body weight reduction in diet-induced obese (DIO) C57BL/6J mice after oral administration. The synthesis and structure–activity relationships of the novel diarylketoxime MCH-1R antagonists are described.     

Design,synthesis and evaluation of a novel cyclohexanamine class of neuropeptide Y Y1 receptor antagonists

A novel series of cyclohexanamine derivatives was designed and synthesized as potent and selective human neuropeptide Y Y1 receptor antagonists. Modification of high-throughput screening hit compound 1 resulted in the identification of compound 3i, which displays potent Y1 activity and good selectivity towards hERG K⁺ channel and serotonin transporter.     

Distinct narcolepsy syndromes in Orexin receptor-2 and Orexin null mice: molecular genetic dissection of Non-REM and REM sleep regulatory processes

Narcolepsy-cataplexy, a neurological disorder associated with the absence of hypothalamic orexin (hypocretin) neuropeptides, consists of two underlying problems: inability to maintain wakefulness and intrusion of rapid eye movement (REM) sleep into wakefulness. Here we document, using behavioral, electrophysiological, and pharmacological criteria, two distinct classes of behavioral arrests exhibited by mice deficient in orexin-mediated signaling. Both OX2R(-/-) and orexin(-/-) mice are similarly affected with behaviorally abnormal attacks of non-REM sleep ("sleep attacks") and show similar degrees of disrupted wakefulness. In contrast, OX2R(-/-) mice are only mildly affected with cataplexy-like attacks of REM sleep, whereas orexin(-/-) mice are severely affected. Absence of OX2Rs eliminates orexin-evoked excitation of histaminergic neurons in the hypothalamus, which gate non-REM sleep onset. While normal regulation of wake/non-REM sleep transitions depends critically upon OX2R activation, the profound dysregulation of REM sleep control unique to the narcolepsy-cataplexy syndrome emerges from loss of signaling through both OX2R-dependent and OX2R-independent pathways.     

Tyrosine 220 in the 5th transmembrane domain of the neuromedin B receptor is critical for the high selectivity of the peptoid antagonist PD168368

Peptoid antagonists are increasingly being described for G protein-coupled receptors; however, little is known about the molecular basis of their binding. Recently, the peptoid PD168368 was found to be a potent selective neuromedin B receptor (NMBR) antagonist. To investigate the molecular basis for its selectivity for the NMBR over the closely related receptor for gastrin-releasing peptide (GRPR), we used a chimeric receptor approach and a site-directed mutagenesis approach. Mutated receptors were transiently expressed in Balb 3T3. The extracellular domains of the NMBR were not important for the selectivity of PD168368. However, substitution of the 5th upper transmembrane domain (uTM5) of the NMBR by the comparable GRPR domains decreased the affinity 16-fold. When the reverse study was performed by substituting the uTM5 of NMBR into the GRPR, a 9-fold increase in affinity occurred. Each of the 4 amino acids that differed between NMBR and GRPR in the uTM5 region were exchanged, but only the substitution of Phe(220) for Tyr in the NMBR caused a decrease in affinity. When the reverse study was performed to attempt to demonstrate a gain of affinity in the GRPR, the substitution of Tyr(219) for Phe caused an increase in affinity. These results suggest that the hydroxyl group of Tyr(220) in uTM5 of NMBR plays a critical role for high selectivity of PD168368 for NMBR over GRPR. Receptor and ligand modeling suggests that the hydroxyl of the Tyr(220) interacts with nitrophenyl group of PD168368 likely primarily by hydrogen bonding. This result shows the selectivity of the peptoid PD168368, similar to that reported for numerous non-peptide analogues with other G protein-coupled receptors, is primarily dependent on interaction with transmembrane amino acids.