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1.
Cell ; 180(3): 568-584.e23, 2020 02 06.
Article in English | MEDLINE | ID: mdl-31981491

ABSTRACT

We present the largest exome sequencing study of autism spectrum disorder (ASD) to date (n = 35,584 total samples, 11,986 with ASD). Using an enhanced analytical framework to integrate de novo and case-control rare variation, we identify 102 risk genes at a false discovery rate of 0.1 or less. Of these genes, 49 show higher frequencies of disruptive de novo variants in individuals ascertained to have severe neurodevelopmental delay, whereas 53 show higher frequencies in individuals ascertained to have ASD; comparing ASD cases with mutations in these groups reveals phenotypic differences. Expressed early in brain development, most risk genes have roles in regulation of gene expression or neuronal communication (i.e., mutations effect neurodevelopmental and neurophysiological changes), and 13 fall within loci recurrently hit by copy number variants. In cells from the human cortex, expression of risk genes is enriched in excitatory and inhibitory neuronal lineages, consistent with multiple paths to an excitatory-inhibitory imbalance underlying ASD.


Subject(s)
Autistic Disorder/genetics , Cerebral Cortex/growth & development , Exome Sequencing/methods , Gene Expression Regulation, Developmental , Neurobiology/methods , Case-Control Studies , Cell Lineage , Cohort Studies , Exome , Female , Gene Frequency , Genetic Predisposition to Disease , Humans , Male , Mutation, Missense , Neurons/metabolism , Phenotype , Sex Factors , Single-Cell Analysis/methods
2.
Cell ; 170(5): 927-938.e20, 2017 Aug 24.
Article in English | MEDLINE | ID: mdl-28841418

ABSTRACT

We present an exceptional case of a patient with high-grade serous ovarian cancer, treated with multiple chemotherapy regimens, who exhibited regression of some metastatic lesions with concomitant progression of other lesions during a treatment-free period. Using immunogenomic approaches, we found that progressing metastases were characterized by immune cell exclusion, whereas regressing and stable metastases were infiltrated by CD8+ and CD4+ T cells and exhibited oligoclonal expansion of specific T cell subsets. We also detected CD8+ T cell reactivity against predicted neoepitopes after isolation of cells from a blood sample taken almost 3 years after the tumors were resected. These findings suggest that multiple distinct tumor immune microenvironments co-exist within a single individual and may explain in part the heterogeneous fates of metastatic lesions often observed in the clinic post-therapy. VIDEO ABSTRACT.


Subject(s)
Cystadenocarcinoma, Serous/pathology , Neoplasm Metastasis/immunology , Ovarian Neoplasms/pathology , Tumor Microenvironment , Antigens, Neoplasm/immunology , Cystadenocarcinoma, Serous/genetics , Cystadenocarcinoma, Serous/immunology , Cystadenocarcinoma, Serous/therapy , Female , Gene Expression Regulation, Neoplastic , Humans , Mutation , Neoplasm Metastasis/genetics , Neoplasm Metastasis/therapy , Ovarian Neoplasms/genetics , Ovarian Neoplasms/immunology , Ovarian Neoplasms/therapy , T-Lymphocytes/immunology , Transcriptome
3.
Mol Psychiatry ; 27(12): 5020-5027, 2022 12.
Article in English | MEDLINE | ID: mdl-36224258

ABSTRACT

Tourette Syndrome (TS) is a heritable, early-onset neuropsychiatric disorder that typically begins in early childhood. Identifying rare genetic variants that make a significant contribution to risk in affected families may provide important insights into the molecular aetiology of this complex and heterogeneous syndrome. Here we present a whole-genome sequencing (WGS) analysis from the 11-generation pedigree (>500 individuals) of a densely affected Costa Rican family which shares ancestry from six founder pairs. By conducting an identity-by-descent (IBD) analysis using WGS data from 19 individuals from the extended pedigree we have identified putative risk haplotypes that were not seen in controls, and can be linked with four of the six founder pairs. Rare coding and non-coding variants present on the haplotypes and only seen in haplotype carriers show an enrichment in pathways such as regulation of locomotion and signal transduction, suggesting common mechanisms by which the haplotype-specific variants may be contributing to TS-risk in this pedigree. In particular we have identified a rare deleterious missense variation in RAPGEF1 on a chromosome 9 haplotype and two ultra-rare deleterious intronic variants in ERBB4 and IKZF2 on the same chromosome 2 haplotype. All three genes play a role in neurodevelopment. This study, using WGS data in a pedigree-based approach, shows the importance of investigating both coding and non-coding variants to identify genes that may contribute to disease risk. Together, the genes and variants identified on the IBD haplotypes represent biologically relevant targets for investigation in other pedigree and population-based TS data.


Subject(s)
Neurogenesis , Tourette Syndrome , Child, Preschool , Humans , Costa Rica , Haplotypes , Pedigree , Signal Transduction , Tourette Syndrome/genetics , Neurogenesis/genetics , Polymorphism, Genetic , Whole Genome Sequencing , Guanine Nucleotide-Releasing Factor 2/genetics
4.
Conserv Genet ; 24(2): 181-191, 2023.
Article in English | MEDLINE | ID: mdl-36683963

ABSTRACT

Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity's (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.

5.
Toxicol Appl Pharmacol ; 438: 115885, 2022 03 01.
Article in English | MEDLINE | ID: mdl-35090952

ABSTRACT

In a Phase 2 clinical trial, BMS-986020, a lysophosphatidic acid receptor-1 (LPA1) antagonist, produced hepatobiliary toxicity (increased ALT, AST, and ALP; cholecystitis) and increases in plasma bile acids (BA). Nonclinical investigations conducted to identify a potential mechanism(s) for this toxicity examined BMS-986020 and two LPA1 antagonists structurally distinct from BMS-986020 (BMS-986234 and BMS-986278). BMS-986020 inhibited hepatic BA efflux transporters BSEP (IC50 1.8 µM), MRP3 (IC50 22 µM), and MRP4 (IC50 6.2 µM) and inhibited BA canalicular efflux in human hepatocytes (68% at 10 µM). BMS-986020 inhibited mitochondrial function (basal and maximal respiration, ATP production, and spare capacity) in human hepatocytes and cholangiocytes at ≥10 µM and inhibited phospholipid efflux in human hepatocytes (MDR3 IC50 7.5 µM). A quantitative systems toxicology analysis (DILIsym®), considering pharmacokinetics, BA homeostasis, mitochondrial function, oxidative phosphorylation, and reactive intermediates performed for BMS-986020 recapitulated clinical findings ascribing the effects to BA transporter and mitochondrial electron transport chain inhibition. BMS-986234 and BMS-986278 minimally inhibited hepatic BA transporters (IC50 ≥20 µM) and did not inhibit MDR3 activity (IC50 >100 µM), nor did BMS-986234 inhibit BA efflux (≤50 µM) or mitochondrial function (≤30 µM) (BMS-986278 not evaluated). Multiple mechanisms may be involved in the clinical toxicity observed with BMS-986020. The data indicate that this toxicity was unrelated to LPA1 antagonism since the mechanisms that likely influenced the adverse clinical outcome of BMS-986020 were not observed with equipotent LPA1 antagonists BMS-986234 and BMS-986278. This conclusion is consistent with the lack of hepatobiliary toxicity in nonclinical and clinical safety studies with BMS-986278.


Subject(s)
Chemical and Drug Induced Liver Injury/metabolism , Digestive System Diseases/chemically induced , Idiopathic Pulmonary Fibrosis/drug therapy , Liver/drug effects , Receptors, Lysophosphatidic Acid/antagonists & inhibitors , ATP Binding Cassette Transporter, Subfamily B/metabolism , Bile Acids and Salts/metabolism , Biological Transport/physiology , Cell Line , Cell Line, Tumor , Electron Transport/physiology , HEK293 Cells , Hep G2 Cells , Hepatocytes/drug effects , Humans , Mitochondria/drug effects
6.
Bioethics ; 36(9): 964-969, 2022 11.
Article in English | MEDLINE | ID: mdl-36134462

ABSTRACT

Some argue that it is ethically justifiable to unilaterally withdraw life-sustaining treatment during crisis standards of care without the patient's consent in order to reallocate it to another patient with a better chance of survival. This justification has been supported by two lines of argument: the equivalence thesis and the rule of the double effect. We argue that there are theoretical issues with the first and practical ones with the second, as supported by an experiment aimed at exploring whether the Knobe effect, which affects the folk concept of intention, applies to situations of unilateral withdrawal. Fifty-two critical care physicians from one university were asked to ascribe intention in two hypothetical scenarios A and B in which outcomes differ-the patient from whom life-sustaining treatment is withdrawn dies in scenario A but survives in scenario B-but the intention, to save the other patient regardless of the outcome of the other, is the same. The survey was administered via a web-based survey and all answers were anonymous. A paired proportion test was used to compare responses to both questions. All 52 surveyed individuals responded in scenario A and 30 (57.7%) ascribed intention when outcomes were unfavorable, whereas 50 responded in scenario B and 8 (16%) ascribed intention when outcomes were favorable, a difference that was statistically significant (p < 0.001). There are theoretical and practical issues with the arguments proposed to justify the unilateral withdrawal of life-sustaining treatment based on the equivalence thesis and the rule of double effect.


Subject(s)
Life Support Care , Physicians , Humans , Withholding Treatment , Standard of Care , Dissent and Disputes
7.
Sugar Tech ; 24(3): 882-889, 2022.
Article in English | MEDLINE | ID: mdl-35194347

ABSTRACT

The natural variation of sucrose concentration in maple tree sap is investigated using time-domain magnetic resonance (MR). The current study, which includes a concise introduction to the relevant MR properties, is a demonstration of principle showing how the relaxation time constant T 2 and the self-diffusion coefficient relate to the amount of sucrose and ionic content present in the collected sap samples. T 2 and self-diffusion coefficient for maple saps from six different trees, each sampled weekly in the spring of 2019, were measured using MR. The results were plotted against the sucrose concentration of each sample with the aim of determining if either quantity could serve as the basis for a non-invasive sucrose measurement for maple trees. The T 2 relaxation time constant was found not to be a reliable proxy for sucrose content in maple sap as it showed sensitivity to the slight changes in sap chemistry throughout the season and natural variation from tree to tree. The diffusion coefficient, determined through a standard pulsed-gradient spin-echo experiment, was insensitive to the changes in sap chemistry and showed a strong relationship to sucrose content. A diffusion measurement is thus proposed as the most suitable candidate for a non-invasive sucrose measurement for maple tree sap.

8.
J Clin Psychopharmacol ; 41(1): 53-57, 2021.
Article in English | MEDLINE | ID: mdl-33347024

ABSTRACT

BACKGROUND: Cognitive impairments, negative symptoms, affective symptoms, and low energy are highly prevalent features of schizophrenia. Mitochondrial dysfunction has been hypothesized as one of the numerous factors to underlie the manifestation of these symptoms. The objective of this study was to evaluate whether Coenzyme Q10 (CoQ10) has a role in the treatment of schizophrenia and schizoaffective disorder. METHODS: A double-blind, randomized, placebo-controlled trial was conducted to assess the effects of CoQ10 supplementation (300 mg/day) on the co-primary outcomes of attention and working memory performance after 3 and 6 months. Secondary outcomes included plasma CoQ10 levels, mitochondrial function, energy, depression, anxiety, negative symptoms, and quality oflife. FINDINGS: In total, 72 patients were randomized to intervention groups. Overall, there was no effect of CoQ10 supplementation on the primary outcome measures at 3 or 6 months. Further, with the exception of plasma CoQ10 levels, CoQ10 supplementation also had no effect on the secondary outcomes. At 3 months, CoQ10 concentration was significantly higher in the CoQ10 group (3.85 µg/mL) compared with placebo (1.13 µg/mL); this difference was not present at 6 months. CONCLUSIONS: The results of the study suggest that CoQ10 supplementation at 300 mg/day for 6 months is unlikely to be beneficial for cognitive, psychological and health-related outcomes in schizophrenia and schizoaffective disorder. However, a number of limitations including low adherence, modest sample size, and attrition, likely reduce estimates of effects. As such, results should be considered preliminary.


Subject(s)
Cognition/drug effects , Schizophrenia/drug therapy , Schizophrenic Psychology , Ubiquinone/analogs & derivatives , Adult , Aged , Attention/drug effects , Double-Blind Method , Female , Humans , Male , Memory, Short-Term/drug effects , Middle Aged , Ubiquinone/blood , Ubiquinone/therapeutic use , Young Adult
9.
Geophys Res Lett ; 48(5): e2020GL091987, 2021 Mar 16.
Article in English | MEDLINE | ID: mdl-33785974

ABSTRACT

Throughout spring and summer 2020, ozone stations in the northern extratropics recorded unusually low ozone in the free troposphere. From April to August, and from 1 to 8 kilometers altitude, ozone was on average 7% (≈4 nmol/mol) below the 2000-2020 climatological mean. Such low ozone, over several months, and at so many stations, has not been observed in any previous year since at least 2000. Atmospheric composition analyses from the Copernicus Atmosphere Monitoring Service and simulations from the NASA GMI model indicate that the large 2020 springtime ozone depletion in the Arctic stratosphere contributed less than one-quarter of the observed tropospheric anomaly. The observed anomaly is consistent with recent chemistry-climate model simulations, which assume emissions reductions similar to those caused by the COVID-19 crisis. COVID-19 related emissions reductions appear to be the major cause for the observed reduced free tropospheric ozone in 2020.

10.
J Clin Psychol ; 77(1): 241-253, 2021 01.
Article in English | MEDLINE | ID: mdl-32783219

ABSTRACT

OBJECTIVE: This study investigated associations between childhood trauma, parental bonding, and social cognition (i.e., Theory of Mind and emotion recognition) in patients with schizophrenia and healthy adults. METHODS: Using cross-sectional data, we examined the recollections of childhood trauma experiences and social cognitive abilities in 74 patients with schizophrenia and 116 healthy adults. RESULTS: Patients had significantly higher scores compared with healthy participants on childhood trauma, and lower scores on parental bonding and social cognitive measures. Physical neglect was found to be the strongest predictor of emotion recognition impairments in both groups. Optimal parental bonding attenuated the impact of childhood trauma on emotion recognition. CONCLUSION: The present study provides evidence of an association between physical neglect and emotion recognition in patients with schizophrenia and healthy individuals and shows that both childhood trauma and parental bonding may influence social cognitive development. Psychosocial interventions should be developed to prevent and mitigate the long-term effects of childhood adversities.


Subject(s)
Schizophrenia , Theory of Mind , Adult , Cognition , Cross-Sectional Studies , Emotions , Humans , Parents , Social Cognition , Social Perception
11.
Br J Psychiatry ; 216(5): 275-279, 2020 05.
Article in English | MEDLINE | ID: mdl-31964429

ABSTRACT

BACKGROUND: Copy number variants (CNVs) play a significant role in disease pathogenesis in a small subset of individuals with schizophrenia (~2.5%). Chromosomal microarray testing is a first-tier genetic test for many neurodevelopmental disorders. Similar testing could be useful in schizophrenia. AIMS: To determine whether clinically identifiable phenotypic features could be used to successfully model schizophrenia-associated (SCZ-associated) CNV carrier status in a large schizophrenia cohort. METHOD: Logistic regression and receiver operating characteristic (ROC) curves tested the accuracy of readily identifiable phenotypic features in modelling SCZ-associated CNV status in a discovery data-set of 1215 individuals with psychosis. A replication analysis was undertaken in a second psychosis data-set (n = 479). RESULTS: In the discovery cohort, specific learning disorder (OR = 8.12; 95% CI 1.16-34.88, P = 0.012), developmental delay (OR = 5.19; 95% CI 1.58-14.76, P = 0.003) and comorbid neurodevelopmental disorder (OR = 5.87; 95% CI 1.28-19.69, P = 0.009) were significant independent variables in modelling positive carrier status for a SCZ-associated CNV, with an area under the ROC (AUROC) of 74.2% (95% CI 61.9-86.4%). A model constructed from the discovery cohort including developmental delay and comorbid neurodevelopmental disorder variables resulted in an AUROC of 83% (95% CI 52.0-100.0%) for the replication cohort. CONCLUSIONS: These findings suggest that careful clinical history taking to document specific neurodevelopmental features may be informative in screening for individuals with schizophrenia who are at higher risk of carrying known SCZ-associated CNVs. Identification of genomic disorders in these individuals is likely to have clinical benefits similar to those demonstrated for other neurodevelopmental disorders.


Subject(s)
DNA Copy Number Variations/genetics , Medical History Taking , Schizophrenia/diagnosis , Schizophrenia/genetics , Female , Humans , Logistic Models , Male , Neurodevelopmental Disorders/diagnosis , Neurodevelopmental Disorders/genetics , ROC Curve , Retrospective Studies , Young Adult
12.
Psychol Med ; 50(11): 1852-1861, 2020 08.
Article in English | MEDLINE | ID: mdl-31391132

ABSTRACT

BACKGROUND: Previous studies using resting-state functional neuroimaging have revealed alterations in whole-brain images, connectome-wide functional connectivity and graph-based metrics in groups of patients with schizophrenia relative to groups of healthy controls. However, it is unclear which of these measures best captures the neural correlates of this disorder at the level of the individual patient. METHODS: Here we investigated the relative diagnostic value of these measures. A total of 295 patients with schizophrenia and 452 healthy controls were investigated using resting-state functional Magnetic Resonance Imaging at five research centres. Connectome-wide functional networks were constructed by thresholding correlation matrices of 90 brain regions, and their topological properties were analyzed using graph theory-based methods. Single-subject classification was performed using three machine learning (ML) approaches associated with varying degrees of complexity and abstraction, namely logistic regression, support vector machine and deep learning technology. RESULTS: Connectome-wide functional connectivity allowed single-subject classification of patients and controls with higher accuracy (average: 81%) than both whole-brain images (average: 53%) and graph-based metrics (average: 69%). Classification based on connectome-wide functional connectivity was driven by a distributed bilateral network including the thalamus and temporal regions. CONCLUSION: These results were replicated across the three employed ML approaches. Connectome-wide functional connectivity permits differentiation of patients with schizophrenia from healthy controls at single-subject level with greater accuracy; this pattern of results is consistent with the 'dysconnectivity hypothesis' of schizophrenia, which states that the neural basis of the disorder is best understood in terms of system-level functional connectivity alterations.


Subject(s)
Brain/physiopathology , Connectome , Schizophrenia/diagnostic imaging , Adult , Case-Control Studies , Female , Humans , Magnetic Resonance Imaging , Male , Middle Aged , Schizophrenia/physiopathology , Severity of Illness Index , Support Vector Machine , Young Adult
13.
Nutr Neurosci ; 23(10): 756-769, 2020 Oct.
Article in English | MEDLINE | ID: mdl-30537908

ABSTRACT

Objective: Mitochondrial dysfunction has been implicated in the pathophysiology of schizophrenia and other neuropsychiatric disorders. Though the exact mechanisms and clinical implications for this dysfunction are not fully determined, there is a hypothesis that deficiency in coenzyme Q10 (CoQ10) may contribute to mitochondrial impairments and be reflected in cognitive, affective, and energy disturbances in the disorders. CoQ10 is a critical component of the mitochondrial respiratory chain and an essential free radical scavenger, necessary for mitochondrial function. Here, we review the results of CoQ10 supplementation interventions for adults with various neurological and neuropsychiatric disorders and consider the therapeutic potential of CoQ10 supplementation for schizophrenia in light of these studies. Methods: A literature review of randomised controlled trials and open-label studies investigating the effect of CoQ10 as a single intervention in adults with neurological and neuropsychiatric disorders was conducted. Results: CoQ10 supplementation has some positive effects on fatigue, cognitive impairment and affective difficulties in several neurological and neuropsychiatric conditions with associated mitochondrial dysfunction. Discussion: CoQ10 may be of therapeutic value to schizophrenia given evidence of mitochondrial dysfunction in the disorder.


Subject(s)
Mental Disorders/drug therapy , Nervous System Diseases/drug therapy , Schizophrenia/drug therapy , Ubiquinone/analogs & derivatives , Vitamins/administration & dosage , Humans , Mental Disorders/metabolism , Mitochondria/drug effects , Mitochondria/metabolism , Nervous System Diseases/metabolism , Oxidative Stress/drug effects , Randomized Controlled Trials as Topic , Schizophrenia/metabolism , Treatment Outcome , Ubiquinone/administration & dosage , Ubiquinone/deficiency
14.
Am J Med Genet B Neuropsychiatr Genet ; 183(8): 445-453, 2020 12.
Article in English | MEDLINE | ID: mdl-32918526

ABSTRACT

Multiple genome-wide association studies of schizophrenia have reported associations between genetic variants within the MHC region and disease risk, an association that has been partially accounted for by alleles of the complement component 4 (C4) gene. Following on previous findings of association between both C4 and other complement-related variants and memory function, we tested the hypothesis that polygenic scores calculated based on identified schizophrenia risk alleles within the "complement" system would be broadly associated with memory function and associated brain structure. We tested this using a polygenic risk score (PRS) calculated for complement genes, but excluding C4 variants. Higher complement-based PRS scores were observed to be associated with lower memory scores for the sample as a whole (N = 620, F change = 8.25; p = .004). A significant association between higher PRS and lower hippocampal volume was also observed (N = 216, R2 change = 0.016, p = .015). However, after correcting for further testing of association with the more general indices of cortical thickness, surface area or total brain volume, none of which were associated with complement, the association with hippocampal volume became non-significant. A post-hoc analysis of hippocampal subfields suggested an association between complement PRS and several hippocampal subfields, findings that appeared to be particularly driven by the patient sample. In conclusion, our study yielded suggestive evidence of association between complement-based schizophrenia PRS and variation in memory function and hippocampal volume.


Subject(s)
Brain/pathology , Cerebral Cortex/pathology , Genetic Markers , Immunologic Factors/genetics , Multifactorial Inheritance , Polymorphism, Single Nucleotide , Psychotic Disorders/pathology , Adult , Brain/metabolism , Case-Control Studies , Cerebral Cortex/metabolism , Complement C4/genetics , Female , Follow-Up Studies , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Ireland/epidemiology , Male , Prognosis , Psychotic Disorders/epidemiology , Psychotic Disorders/genetics , Risk Factors
15.
EMBO J ; 34(4): 448-65, 2015 Feb 12.
Article in English | MEDLINE | ID: mdl-25471072

ABSTRACT

Paradoxically, the thymidine kinase (TK) encoded by Kaposi sarcoma-associated herpesvirus (KSHV) is an extremely inefficient nucleoside kinase, when compared to TKs from related herpesviruses. We now show that KSHV-TK, in contrast to HSV1-TK, associates with the actin cytoskeleton and induces extensive cell contraction followed by membrane blebbing. These dramatic changes in cell morphology depend on the auto-phosphorylation of tyrosines 65, 85 and 120 in the N-terminus of KSHV-TK. Phosphorylation of tyrosines 65/85 and 120 results in an interaction with Crk family proteins and the p85 regulatory subunit of PI3-Kinase, respectively. The interaction of Crk with KSHV-TK leads to tyrosine phoshorylation of this cellular adaptor. Auto-phosphorylation of KSHV-TK also induces a loss of FAK and paxillin from focal adhesions, resulting in activation of RhoA-ROCK signalling to myosin II and cell contraction. In the absence of FAK or paxillin, KSHV-TK has no effect on focal adhesion integrity or cell morphology. Our observations demonstrate that by acting as a tyrosine kinase, KSHV-TK modulates signalling and cell morphology.


Subject(s)
Focal Adhesions/enzymology , Focal Adhesions/metabolism , Herpesvirus 8, Human/enzymology , Protein-Tyrosine Kinases/metabolism , rho GTP-Binding Proteins/metabolism , Animals , COS Cells , Chlorocebus aethiops , HeLa Cells , Humans , Immunoblotting , Immunoprecipitation , Paxillin/metabolism , Phosphatidylinositol 3-Kinases/metabolism , Phosphorylation , Proto-Oncogene Proteins c-crk/metabolism
16.
Am J Med Genet B Neuropsychiatr Genet ; 180(3): 223-231, 2019 04.
Article in English | MEDLINE | ID: mdl-30801977

ABSTRACT

Genome-wide association studies (GWASs) are highly effective at identifying common risk variants for schizophrenia. Rare risk variants are also important contributors to schizophrenia etiology but, with the exception of large copy number variants, are difficult to detect with GWAS. Exome and genome sequencing, which have accelerated the study of rare variants, are expensive so alternative methods are needed to aid detection of rare variants. Here we re-analyze an Irish schizophrenia GWAS dataset (n = 3,473) by performing identity-by-descent (IBD) mapping followed by exome sequencing of individuals identified as sharing risk haplotypes to search for rare risk variants in coding regions. We identified 45 rare haplotypes (>1 cM) that were significantly more common in cases than controls. By exome sequencing 105 haplotype carriers, we investigated these haplotypes for functional coding variants that could be tested for association in independent GWAS samples. We identified one rare missense variant in PCNT but did not find statistical support for an association with schizophrenia in a replication analysis. However, IBD mapping can prioritize both individual samples and genomic regions for follow-up analysis but genome rather than exome sequencing may be more effective at detecting risk variants on rare haplotypes.


Subject(s)
Exome Sequencing/methods , Schizophrenia/genetics , Sequence Analysis, DNA/methods , Adult , Case-Control Studies , Chromosome Mapping , DNA Copy Number Variations , Databases, Genetic , Exome/genetics , Female , Genetic Predisposition to Disease/genetics , Genome-Wide Association Study/methods , Genotype , Haplotypes , Humans , Male , Middle Aged , Risk Factors , Schizophrenia/metabolism
17.
Neurobiol Dis ; 110: 29-36, 2018 02.
Article in English | MEDLINE | ID: mdl-29100987

ABSTRACT

Adenosine A2A receptors are putative therapeutic targets for neurological disorders. The adenosine A2A receptor antagonist istradefylline is approved in Japan for Parkinson's disease and is being tested in clinical trials for this condition elsewhere. A2A receptors on neurons and astrocytes may contribute to Alzheimer's disease (AD) by impairing memory. However, it is not known whether istradefylline enhances cognitive function in aging animals with AD-like amyloid plaque pathology. Here, we show that elevated levels of Aß, C-terminal fragments of the amyloid precursor protein (APP), or amyloid plaques, but not overexpression of APP per se, increase astrocytic A2A receptor levels in the hippocampus and neocortex of aging mice. Moreover, in amyloid plaque-bearing mice, low-dose istradefylline treatment enhanced spatial memory and habituation, supporting the conclusion that, within a well-defined dose range, A2A receptor blockers might help counteract memory problems in patients with Alzheimer's disease.


Subject(s)
Adenosine A2 Receptor Antagonists/pharmacology , Astrocytes/metabolism , Brain/drug effects , Memory Disorders , Purines/pharmacology , Aging , Alzheimer Disease/metabolism , Alzheimer Disease/pathology , Amyloid beta-Peptides , Animals , Brain/pathology , Female , Humans , Male , Mice , Mice, Inbred C57BL , Mice, Transgenic , Plaque, Amyloid/pathology , Receptor, Adenosine A2A
18.
Br J Cancer ; 118(8): 1098-1106, 2018 04.
Article in English | MEDLINE | ID: mdl-29576623

ABSTRACT

BACKGROUND: Optoacoustic tomography (OT) of breast tumour oxygenation is a promising new technique, currently in clinical trials, which may help to determine disease stage and therapeutic response. However, the ability of OT to distinguish breast tumours displaying different vascular characteristics has yet to be established. The aim of the study is to prove OT as a sensitive technique for differentiating breast tumour models with manifestly different vasculatures. METHODS: Multispectral OT (MSOT) was performed in oestrogen-dependent (MCF-7) and oestrogen-independent (MDA-MB-231) orthotopic breast cancer xenografts. Total haemoglobin (THb) and oxygen saturation (SO2MSOT) were calculated. Pathological and biochemical evaluation of the tumour vascular phenotype was performed for validation. RESULTS: MCF-7 tumours show SO2MSOT similar to healthy tissue in both rim and core, despite significantly lower THb in the core. MDA-MB-231 tumours show markedly lower SO2MSOT with a significant rim-core disparity. Ex vivo analysis revealed that MCF-7 tumours contain fewer blood vessels (CD31+) that are more mature (CD31+/aSMA+) than MDA-MB-231. MCF-7 presented higher levels of stromal VEGF and iNOS, with increased NO serum levels. The vasculogenic process observed in MCF-7 was consistent with angiogenesis, while MDA-MB-231 appeared to rely more on vascular mimicry. CONCLUSIONS: OT is sensitive to differences in the vascular phenotypes of our breast cancer models.


Subject(s)
Biological Mimicry/physiology , Mammary Neoplasms, Experimental/blood supply , Mammary Neoplasms, Experimental/diagnosis , Mammary Neoplasms, Experimental/pathology , Neovascularization, Pathologic/diagnosis , Photoacoustic Techniques/methods , Tomography/methods , Animals , Breast Neoplasms/blood supply , Breast Neoplasms/diagnosis , Breast Neoplasms/pathology , Cell Line, Tumor , Drug Monitoring/methods , Female , Humans , MCF-7 Cells , Mammary Neoplasms, Experimental/metabolism , Mice , Mice, Inbred BALB C , Mice, Nude , Neoplasm Staging , Neovascularization, Pathologic/pathology , Oxygen Consumption/physiology , Sensitivity and Specificity , Tumor Hypoxia/physiology , Xenograft Model Antitumor Assays
19.
PLoS Biol ; 13(2): e1002083, 2015 Feb.
Article in English | MEDLINE | ID: mdl-25710520

ABSTRACT

In eukaryotes, the highly conserved U3 small nucleolar RNA (snoRNA) base-pairs to multiple sites in the pre-ribosomal RNA (pre-rRNA) to promote early cleavage and folding events. Binding of the U3 box A region to the pre-rRNA is mutually exclusive with folding of the central pseudoknot (CPK), a universally conserved rRNA structure of the small ribosomal subunit essential for protein synthesis. Here, we report that the DEAH-box helicase Dhr1 (Ecm16) is responsible for displacing U3. An active site mutant of Dhr1 blocked release of U3 from the pre-ribosome, thereby trapping a pre-40S particle. This particle had not yet achieved its mature structure because it contained U3, pre-rRNA, and a number of early-acting ribosome synthesis factors but noticeably lacked ribosomal proteins (r-proteins) that surround the CPK. Dhr1 was cross-linked in vivo to the pre-rRNA and to U3 sequences flanking regions that base-pair to the pre-rRNA including those that form the CPK. Point mutations in the box A region of U3 suppressed a cold-sensitive mutation of Dhr1, strongly indicating that U3 is an in vivo substrate of Dhr1. To support the conclusions derived from in vivo analysis we showed that Dhr1 unwinds U3-18S duplexes in vitro by using a mechanism reminiscent of DEAD box proteins.


Subject(s)
DEAD-box RNA Helicases/metabolism , Gene Expression Regulation, Fungal , RNA Precursors/metabolism , RNA, Small Nucleolar/metabolism , Ribosome Subunits, Small, Eukaryotic/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/genetics , Base Pairing , Base Sequence , Cold Temperature , DEAD-box RNA Helicases/genetics , Molecular Sequence Data , Nucleic Acid Conformation , Point Mutation , Protein Biosynthesis , RNA Precursors/chemistry , RNA Precursors/genetics , RNA, Ribosomal, 18S/genetics , RNA, Ribosomal, 18S/metabolism , RNA, Small Nucleolar/chemistry , RNA, Small Nucleolar/genetics , Ribosome Subunits, Small, Eukaryotic/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics
20.
Twin Res Hum Genet ; 21(5): 394-397, 2018 10.
Article in English | MEDLINE | ID: mdl-30001766

ABSTRACT

Hill (Twin Research and Human Genetics, Vol. 21, 2018, 84-88) presented a critique of our recently published paper in Cell Reports entitled 'Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets' (Lam et al., Cell Reports, Vol. 21, 2017, 2597-2613). Specifically, Hill offered several interrelated comments suggesting potential problems with our use of a new analytic method called Multi-Trait Analysis of GWAS (MTAG) (Turley et al., Nature Genetics, Vol. 50, 2018, 229-237). In this brief article, we respond to each of these concerns. Using empirical data, we conclude that our MTAG results do not suffer from 'inflation in the FDR [false discovery rate]', as suggested by Hill (Twin Research and Human Genetics, Vol. 21, 2018, 84-88), and are not 'more relevant to the genetic contributions to education than they are to the genetic contributions to intelligence'.


Subject(s)
Genome-Wide Association Study , Nootropic Agents , Cognition , Genetic Predisposition to Disease , Humans , Polymorphism, Single Nucleotide
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