Genetic Copy Number Variations Research Articles

Challenges in Multi-Task Learning for fMRI-Based Diagnosis: Benefits for Psychiatric Conditions and CNVs Would Likely Require Thousands of Patients

Abstract There is a growing interest in using machine learning (ML) models to perform automatic diagnosis of psychiatric conditions; however, generalising the prediction of ML models to completely independent data can lead to sharp decrease in performance. Patients with different psychiatric diagnoses have traditionally been studied independently, yet there is a growing recognition of neuroimaging signatures shared across them as well as rare genetic copy number variants (CNVs). In this work, we assess the potential of multi-task learning (MTL) to improve accuracy by characterising multiple related conditions with a single model, making use of information shared across diagnostic categories and exposing the model to a larger and more diverse dataset. As a proof of concept, we first established the efficacy of MTL in a context where there is clearly information shared across tasks: the same target (age or sex) is predicted at different sites of data collection in a large fMRI dataset compiled from multiple studies. MTL generally led to substantial gains relative to independent prediction at each site. Performing scaling experiments on the UK Biobank, we observed that performance was highly dependent on sample size: for large sample sizes (N>6000) sex prediction was better using MTL across three sites (N=K per site) than prediction at a single site (N=3K), but for small samples (N<500) MTL was actually detrimental for age prediction. We then used established machine learning methods to benchmark the diagnostic accuracy of each of the 7 CNVs (N=19-103) and 4 psychiatric conditions (N=44-472) independently, replicating the accuracy previously reported in the literature on psychiatric conditions. We observed that MTL hurt performance when applied across the full set of diagnoses, and complementary analyses failed to identify pairs of conditions which would benefit from MTL. Taken together, our results show that if a successful multi-task diagnostic model of psychiatric conditions were to be developed with resting-state fMRI, it would likely require datasets with thousands of patients across different diagnoses.

Discovering the gene-brain-behavior link in autism via generative machine learning.

Autism is traditionally diagnosed behaviorally but has a strong genetic basis. A genetics-first approach could transform understanding and treatment of autism. However, isolating the gene-brain-behavior relationship from confounding sources of variability is a challenge. We demonstrate a novel technique, 3D transport-based morphometry (TBM), to extract the structural brain changes linked to genetic copy number variation (CNV) at the 16p11.2 region. We identified two distinct endophenotypes. In data from the Simons Variation in Individuals Project, detection of these endophenotypes enabled 89 to 95% test accuracy in predicting 16p11.2 CNV from brain images alone. Then, TBM enabled direct visualization of the endophenotypes driving accurate prediction, revealing dose-dependent brain changes among deletion and duplication carriers. These endophenotypes are sensitive to articulation disorders and explain a portion of the intelligence quotient variability. Genetic stratification combined with TBM could reveal new brain endophenotypes in many neurodevelopmental disorders, accelerating precision medicine, and understanding of human neurodiversity.

Microbiota profiling reveals alteration of gut microbial neurotransmitters in a mouse model of autism-associated 16p11.2 microduplication.

The gut-brain axis is evident in modulating neuropsychiatric diseases including autism spectrum disorder (ASD). Chromosomal 16p11.2 microduplication 16p11.2dp/+ is among the most prevalent genetic copy number variations (CNV) linked with ASD. However, the implications of gut microbiota status underlying the development of ASD-like impairments induced by 16p11.2dp/+ remains unclear. To address this, we initially investigated a mouse model of 16p11.2dp/+, which exhibits social novelty deficit and repetitive behavior characteristic of ASD. Subsequently, we conducted a comparative analysis of the gut microbial community and metabolomic profiles between 16p11.2dp/+ and their wild-type counterparts using 16S rRNA sequencing and liquid chromatography-mass spectrometry (LC/MS). Our microbiota analysis revealed structural dysbiosis in 16p11.2dp/+ mice, characterized by reduced biodiversity and alterations in species abundance, as indicated by α/β-diversity analysis. Specifically, we observed reduced relative abundances of Faecalibaculum and Romboutsia, accompanied by an increase in Turicibacter and Prevotellaceae UCG_001 in 16p11.2dp/+ group. Metabolomic analysis identified 19 significantly altered metabolites and unveiled enriched amino acid metabolism pathways. Notably, a disruption in the predominantly histamine-centered neurotransmitter network was observed in 16p11.2dp/+ mice. Collectively, our findings delineate potential alterations and correlations among the gut microbiota and microbial neurotransmitters in 16p11.2dp/+ mice, providing new insights into the pathogenesis of and treatment for 16p11.2 CNV-associated ASD.

Estimate of genetic variants using CNV-Seq for fetuses with oligohydramnios or polyhydramnios.

Oligohydramnios or polyhydramnios, is associated with chromosomal aberrations, particularly aneuploidy. However, its correlation with copy number variation (CNV) remains unclear. We retrospectively analyzed 428 cases with an abnormal level of amniotic fluid, comprising of 139 cases of single ultrasound findings (SU group) and 289 cases of multiple ultrasound findings (MU group), by CNV sequencing (CNV-Seq) and followed their pregnancy outcomes. The overall detection rate of clinically significant findings was 8%, with 5% in the SU group and 11% in MU group. Besides, 18 microdeletion/microduplication syndromes were detected, with the highest rate of renal cysts and diabetes syndrome (22%, 4/18). Also, the rate of termination of pregnancy in MU group was much higher than that in the SU group (29% vs. 10%, ***p < 0.001), and in the MU-oligohydramnios subgroup, it was the highest (34%), regardless of cases with chromosomal anomaly and lost to follow-up. Our results showed that the abnormal level of amniotic fluid, especially combined with other ultrasound abnormalities, is closely related to chromosomal abnormalities and genetic CNVs. CNV-Seq may be useful in investigating pregnancies with an abnormal amniotic fluid level.

PRECISION MEDICINE AND GENOMICALLY GUIDED TREATMENT IN AUTISM SPECTRUM DISORDER: ARE WE THERE YET?

Genetic factors make up a large proportion of autism spectrum disorder (ASD) liability, and guidelines recommend genetic testing for all youth with ASD. However, the practicalities of how to implement and interpret this testing are not always clear. This series of talks will be able to answer some of these questions. In highlighting recent work they and others have conducted, the speakers will provide some context and guidance regarding 5 relevant aspects of genetic testing for ASD: 1) how to implement it in an inpatient setting; 2) how to implement it in an outpatient setting; 3) how and when to order pharmacogenomic testing; 4) what to do when a patient’s genetic test comes back positive for a single-gene change; and 5) the role that genetic copy number variation may play in defining and understanding ASD subtypes. In a series of brief talks, 5 speakers will describe different aspects of the state of knowledge regarding genetic testing in ASD. Afterwards, an independent discussant will reflect on the material presented, relating it to his own expertise and experience. In an inpatient setting, medical genetics education for child and adolescent psychiatry fellows may improve genetic testing rates. In the outpatient clinic, numerous parallel strategies, including administrative support, agreements with genetic testing providers, and a dedicated genomic psychiatry consult service, all may increase the rate at which genetic tests are ordered. Pharmacogenomic testing in ASD is supported by limited evidence, and broad genetic screening is not warranted currently, although current commercial testing may yield clinically actionable information. Several single-gene changes associated with ASD may have implications for clinical treatment. Copy number variants with distinct presentations may serve as models for meaningful ASD subtypes. The presentations and subsequent discussion will provide attendees with up-to-date knowledge regarding genetic testing in ASD, much of which will be directly applicable to their clinical practice.

Genetic alternations and immune characteristics in patients with small cell lung cancer

Genetic alternations and immune characteristics in patients with small cell lung cancer

Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells.

The biological roles of DNA methylation have been elucidated by profiling methods based on whole-genome or reduced-representation bisulfite sequencing, but these approaches do not efficiently survey the vast numbers of non-coding regulatory elements in mammalian genomes. Here we present an extended-representation bisulfite sequencing (XRBS) method for targeted profiling of DNA methylation. Our design strikes a balance between expanding coverage of regulatory elements and reproducibly enriching informative CpG dinucleotides in promoters, enhancers and CTCF binding sites. Barcoded DNA fragments are pooled before bisulfite conversion, allowing multiplex processing and technical consistency in low-input samples. Application of XRBS to single leukemia cells enabled us to evaluate genetic copy number variations and methylation variability across individual cells. Our analysis highlights heterochromatic H3K9me3 regions as having the highest cell-to-cell variability in their methylation, likely reflecting inherent epigenetic instability of these late-replicating regions, compounded by differences in cell cycle stages among sampled cells.

An ALYREF-MYCN coactivator complex drives neuroblastoma tumorigenesis through effects on USP3 and MYCN stability

To achieve the very high oncoprotein levels required to drive the malignant state cancer cells utilise the ubiquitin proteasome system to upregulate transcription factor levels. Here our analyses identify ALYREF, expressed from the most common genetic copy number variation in neuroblastoma, chromosome 17q21-ter gain as a key regulator of MYCN protein turnover. We show strong co-operativity between ALYREF and MYCN from transgenic models of neuroblastoma in vitro and in vivo. The two proteins form a nuclear coactivator complex which stimulates transcription of the ubiquitin specific peptidase 3, USP3. We show that increased USP3 levels reduce K-48- and K-63-linked ubiquitination of MYCN, thus driving up MYCN protein stability. In the MYCN-ALYREF-USP3 signal, ALYREF is required for MYCN effects on the malignant phenotype and that of USP3 on MYCN stability. This data defines a MYCN oncoprotein dependency state which provides a rationale for future pharmacological studies.

Actionable and incidental neuroradiological findings in twins with neurodevelopmental disorders

While previous research has investigated neuroradiological findings in autism spectrum disorder (ASD) and attention-deficit hyperactivity disorder (ADHD), the entire range of neurodevelopmental disorders (NDDs) has not yet been well-studied using magnetic resonance imaging (MRI). Considering the overlap among NDDs and simultaneous development of the brain and face, guided by molecular signaling, we examined the relationship of actionable and incidental (non-actionable) MRI findings and NDD diagnoses together with facial morphological variants and genetic copy number variants (CNVs). A cross-sectional study was conducted with a twin cohort 8–36 years of age (57% monozygotic, 40% dizygotic), including 372 subjects (46% with NDDs; 47% female) imaged by MRI, 280 with data for facial morphological variants, and 183 for CNVs. Fifty-one percent of participants had MRI findings. Males had a statistically significantly higher percentage of MRI findings (57.7%) compared with females (43.8%, p = 0.03). Twin zygosity was not statistically significantly correlated with incidence or severity of specific MRI findings. No statistically significant association was found between MRI findings and any NDD diagnosis or facial morphological variants; however, MRI findings were statistically significantly associated with the number of CNVs (OR 1.20, 95% CI 1.00–1.44, p = 0.05, adjusted OR for sex 1.24, 95% CI 1.03–1.50, p = 0.02). When combining the presence of MRI findings, facial morphological variants, and CNVs, statistically significant relationships were found with ASD and ADHD diagnoses (p = 0.0006 and p = 0.002, respectively). The results of this study demonstrate that the ability to identify NDDs from combined radiology, morphology, and CNV assessments may be possible. Additionally, twins do not appear to be at increased risk for neuroradiological variants.

Genetic copy number variants, cognition and psychosis: a meta-analysis and a family study

The burden of large and rare copy number genetic variants (CNVs) as well as certain specific CNVs increase the risk of developing schizophrenia. Several cognitive measures are purported schizophrenia endophenotypes and may represent an intermediate point between genetics and the illness. This paper investigates the influence of CNVs on cognition. We conducted a systematic review and meta-analysis of the literature exploring the effect of CNV burden on general intelligence. We included ten primary studies with a total of 18,847 participants and found no evidence of association. In a new psychosis family study, we investigated the effects of CNVs on specific cognitive abilities. We examined the burden of large and rare CNVs (>200 kb, <1% MAF) as well as known schizophrenia-associated CNVs in patients with psychotic disorders, their unaffected relatives and controls (N = 3428) from the Psychosis Endophenotypes International Consortium (PEIC). The carriers of specific schizophrenia-associated CNVs showed poorer performance than non-carriers in immediate (P = 0.0036) and delayed (P = 0.0115) verbal recall. We found suggestive evidence that carriers of schizophrenia-associated CNVs had poorer block design performance (P = 0.0307). We do not find any association between CNV burden and cognition. Our findings show that the known high-risk CNVs are not only associated with schizophrenia and other neurodevelopmental disorders, but are also a contributing factor to impairment in cognitive domains such as memory and perceptual reasoning, and act as intermediate biomarkers of disease risk.

Copy Number Variation in MUC5AC and Susceptibility to Allergic Rhinitis: A Low-Coverage Whole-Genome Sequencing and Validation Cohort Study

Background: The contribution of genetic copy number variations (CNVs) to allergic rhinitis (AR) remains unknown. The aim of this study was to identify genetic CNVs related to AR in the Han Chinese population. Methods: A case/parent trio of patients of Han Chinese descent affected with AR was examined using low-coverage whole-genome sequencing. Select CNVs were also explored for AR association in a validation cohort of 696 diagnosed AR patients and 528 matched controls. AccuCopy™, a multiplex fluorescence competitive polymerase chain reaction (PCR) assay, was used for genotyping of the CNV and was further validated with real-time PCR. Results: In the case/parent trio study, 67 CNVs were found in the Database of Genomic Variants and shared by patients within the family; 7 of these CNVs had a frequency higher than 0.05. A duplication at 11P15.5 was found involving three mucin-encoding genes (MUC2, MUC5AC, and MUC5B) previously identified as candidate genes for asthma and other chronic inflammatory upper airway diseases. In the validation cohort, no CNVs for MUC2 or MUC5B were identified. However, in the case group, 36.21% of individuals had a duplication of MUC5AC, and 28.03% of controls had MUC5AC duplication (χ2 = 9.123; p = 0.0025). The association of MUC5AC copy number with AR was significant in a multivariable logistic regression analysis after adjusting for age and sex (Padj = 0.0010; OR = 2.073; 95% CI, 1.625-2.805). Real-time PCR validation confirmed duplication of MUC5AC, and the CNV genotype detected with the AccuCopy assay was validated for 58 (96.67%) individuals. Furthermore, individuals with a high MUC5AC copy number showed enhanced total blood eosinophil counts in both the total sample group and the case group (Spearman's ρ: 0.162, p < 0.001; Spearman's ρ: 0.240, p < 0.001). Conclusions: MUC5AC copy number is associated with AR susceptibility. Additional validation and functional studies are warranted to elucidate the effect of MUC5AC CNV on gene expression and AR risk.

Identifying schizophrenia patients who carry pathogenic genetic copy number variants using standard clinical assessment: retrospective cohort study

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. 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. 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). 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. 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.

Genetic Copy Number Variants, Cognition and Psychosis: A Meta-analysis and a Family Study

Genetic Copy Number Variants, Cognition and Psychosis: A Meta-analysis and a Family Study

Cell-free fetal DNA screening for detection of microdeletion syndromes: a cost-effectiveness analysis

Objective Fetuses with genetic copy number variants are poorly detected through traditional prenatal screening. Microdeletions and duplications are clearly identified with diagnostic testing through chromosomal microarray, and screening of a select number of microdeletions has become available with cell-free DNA (cfDNA). Our study compares the costs and outcomes of cfDNA for five pathogenic microdeletions and aneuploidy to cfDNA for aneuploidy alone in conjunction with ultrasound. Methods A decision-analytic model was constructed using TreeAge software to compare cfDNA with microdeletions versus traditional cfDNA in a theoretical cohort of 4,000,000 pregnancies that would also be screened with ultrasound. Probabilities, costs, and utilities were derived from literature. The primary outcomes were the incremental cost per quality-adjusted life-year (QALY), terminations, and procedure-related losses. Because the microdeletion results are available, but not reported, on all cfDNA testing we set the incremental cost of the cfDNA microdeletion screening test to zero at baseline and varied the cost in sensitivity analysis. Results Screening with cfDNA for microdeletions among all pregnant women would result in 83 fewer anomalous neonates compared to traditional cfDNA with ultrasound. This reduction is due to increased diagnosis and termination of fetuses with microdeletions in this group. Routine use of cfDNA with microdeletions resulted in more procedure-related losses. cfDNA with microdeletions would improve effectiveness by 977 QALYs and decrease costs by $90,991,784. When we varied the specificity of the screening test, we found that it remained cost-effective down to a specificity of 91%. With a threshold of $100,000/QALY, microdeletion screening is cost-effective to an incremental increase in cost over cfDNA for aneuploidy alone of $47.10. Conclusion For detection of fetal subchromosomal abnormalities, use of cfDNA with microdeletions is a cost-effective strategy compared to cfDNA for aneuploidy alone in conjunction with ultrasound. Cell-free DNA for microdeletions is not currently recommended as routine screening for low-risk obstetric populations by the American College of Obstetrics and Gynecologists or the Society for Maternal–Fetal Medicine. The test characteristics of cfDNA with microdeletions require greater examination before being routinely recommended.

Influence of genetic copy number variants of the human GLUT3 glucose transporter gene SLC2A3 on protein expression, glycolysis and rheumatoid arthritis risk: A genetic replication study

ObjectivesThe gene encoding glucose transporter 3 (GLUT3, SLC2A3) is present in the human population at variable copy number. An overt disease phenotype of SLC2A3 copy number variants has not been reported; however, deletion of SLC2A3 has been previously reported to protect carriers from rheumatoid arthritis, implicating GLUT3 as a therapeutic target in rheumatoid arthritis. Here we aim to perform functional analysis of GLUT3 copy number variants in immune cells, and test the reported protective association of the GLUT3 copy number variants for rheumatoid arthritis in a genetic replication study. MethodsCells from genotyped healthy controls were analyzed for SLC2A3/GLUT3 expression and glycolysis capacity. We genotyped the SLC2A3 copy number variant in four independent cohorts of rheumatoid arthritis and controls and one cohort of multiple sclerosis and controls. ResultsHeterozygous deletion of SLC2A3 correlates directly with expression levels of GLUT3 and influences glycolysis rates in the human immune system. The frequency of the SLC2A3 copy number variant is not different between rheumatoid arthritis, multiple sclerosis and control groups. ConclusionsDespite a robust SLC2A3 gene copy number dependent phenotype, our study of large groups of rheumatoid arthritis cases and controls provides no evidence for rheumatoid arthritis disease protection in deletion carriers. These data emphasize the importance of well powered replication studies to confirm or refute genetic associations, particularly for relatively rare variants.

Diagnostic implications of genetic copy number variation in epilepsy plus.

SummaryObjectiveCopy number variations (CNVs) represent a significant genetic risk for several neurodevelopmental disorders including epilepsy. As knowledge increases, reanalysis of existing data is essential. Reliable estimates of the contribution of CNVs to epilepsies from sizeable populations are not available.MethodsWe assembled a cohort of 1255 patients with preexisting array comparative genomic hybridization or single nucleotide polymorphism array based CNV data. All patients had “epilepsy plus,” defined as epilepsy with comorbid features, including intellectual disability, psychiatric symptoms, and other neurological and nonneurological features. CNV classification was conducted using a systematic filtering workflow adapted to epilepsy.ResultsOf 1097 patients remaining after genetic data quality control, 120 individuals (10.9%) carried at least one autosomal CNV classified as pathogenic; 19 individuals (1.7%) carried at least one autosomal CNV classified as possibly pathogenic. Eleven patients (1%) carried more than one (possibly) pathogenic CNV. We identified CNVs covering recently reported (HNRNPU) or emerging (RORB) epilepsy genes, and further delineated the phenotype associated with mutations of these genes. Additional novel epilepsy candidate genes emerge from our study. Comparing phenotypic features of pathogenic CNV carriers to those of noncarriers of pathogenic CNVs, we show that patients with nonneurological comorbidities, especially dysmorphism, were more likely to carry pathogenic CNVs (odds ratio = 4.09, confidence interval = 2.51‐6.68; P = 2.34 × 10−9). Meta‐analysis including data from published control groups showed that the presence or absence of epilepsy did not affect the detected frequency of CNVs.SignificanceThe use of a specifically adapted workflow enabled identification of pathogenic autosomal CNVs in 10.9% of patients with epilepsy plus, which rose to 12.7% when we also considered possibly pathogenic CNVs. Our data indicate that epilepsy with comorbid features should be considered an indication for patients to be selected for a diagnostic algorithm including CNV detection. Collaborative large‐scale CNV reanalysis leads to novel declaration of pathogenicity in unexplained cases and can promote discovery of promising candidate epilepsy genes.

Precise quantitation and sensitive detection of copy number within genetic variations using ligation-mediated droplet digital PCR in plasma

The analysis of cancer-associated genetic copy number variations (CNVs) has been employed for cancer diagnostics, treatment, and prognostic assessments.

MP64-02 THERAPEUTIC TARGETING OF TRANSCRIPTIONAL REPRESSOR BCL-6 FOR CASTRATION-RESISTANT PROSTATE CANCER THROUGH REPRESSING ANDROGEN RECEPTOR VARIANTS.

You have accessJournal of UrologyProstate Cancer: Basic Research & Pathophysiology II1 Apr 2018MP64-02 THERAPEUTIC TARGETING OF TRANSCRIPTIONAL REPRESSOR BCL-6 FOR CASTRATION-RESISTANT PROSTATE CANCER THROUGH REPRESSING ANDROGEN RECEPTOR VARIANTS. Hiroshi Hongo, Takeo Kosaka, Yota Yasumizu, Yasumasa Miyazaki, Eiji Kikuchi, and Mototsugu Oya Hiroshi HongoHiroshi Hongo More articles by this author , Takeo KosakaTakeo Kosaka More articles by this author , Yota YasumizuYota Yasumizu More articles by this author , Yasumasa MiyazakiYasumasa Miyazaki More articles by this author , Eiji KikuchiEiji Kikuchi More articles by this author , and Mototsugu OyaMototsugu Oya More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2018.02.2047AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Enzalutamide (ENZ) is a next-generation antiandrogen approved for castration-resistant prostate cancer (CRPC). However, about 30% of CRPC patients have primary resistance to ENZ and acquired resistance to ENZ is inevitable. In order to analyze the mechanisms of ENZ resistance, we analyzed the gene expression profiles of ENZ-resistant CRPC cell lines and identified a therapeutic target for reprogramming ENZ resistance. METHODS Four cell lines were used: LNCaP, a human prostate cancer cell line that exhibits androgen-dependent proliferation; C4-2, an ENZ-sensitive CRPC cell line; C4-2AT6, an ENZ-resistant CRPC cell line which had been established by incubating C4-2 in androgen ablation conditions; and 22Rv1, a AR-V7 positive CRPC cell line. We analyzed genetic copy number variants in LNCaP, C4-2 and C4-2AT6 cells by array-CGH, and found BCL-6 as a potential therapeutic target gene. RESULTS At first, we examined the efficacy of ENZ for LNCaP and C4-2AT6 cells. In cell viability assay, C4-2AT6 had significant ENZ resistance. To investigate ENZ resistance mechanism, we analyzed genetic copy number variants in LNCaP, C4-2 and C4-2AT6 cells. Array-CGH array demonstrated that BCL-6 expression was higher in the order C4-2AT6 > C4-2 > LNCaP. We validated these results using quantitative PCR and western blotting. The mRNA and protein expression level of BCL-6 was also higher in C4-2AT6 cells.We evaluated the cytotoxic effect of a BCL-6 inhibitor, 79-6, on C4-2AT6 cells. Relative cell viability when treated with 10 μM 79-6 was 65.7 ± 0.8%. Western blotting revealed that 79-6 promoted p53 expression and PARP cleavage in C4-2AT6 cells. We also examined the effect of BCL-6 inhibition by gene knockdown with siRNA. Knockdown of BCL-6 significantly reduces the cell viability of C4-2AT6 cells (78.4 ± 1.4%).We examined the synergistic effect of ENZ and 79-6 on C4-2AT6 cells. The relative cell viability when treated with 1 μM ENZ and 10 μM 79-6 was 43.5 ± 2.1%. Because AR-V7 was focused as mechanism of ENZ resistance, we tested anti-tumor effect of 79-6 for AR-V7 positive CRPC cells. 22Rv1 had AR-V7 expression while LNCaP and C4-2AT6 did not (Fig. a). WST assay demonstrated 79-6 inhibited 22Rv1 proliferation (78.3 ± 1.9%). Western blotting demonstrated AR-V expression was down-regulated after 79-6 administration. 79-6 also sensitized 22Rv1 for ENZ in WST assay like C4-2AT6 (Fig. b). CONCLUSIONS BCL-6 inhibition was able to overcome AR variants positive CRPC. © 2018FiguresReferencesRelatedDetails Volume 199Issue 4SApril 2018Page: e850 Advertisement Copyright & Permissions© 2018MetricsAuthor Information Hiroshi Hongo More articles by this author Takeo Kosaka More articles by this author Yota Yasumizu More articles by this author Yasumasa Miyazaki More articles by this author Eiji Kikuchi More articles by this author Mototsugu Oya More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

Modulating Neuroinflammation to Treat Neuropsychiatric Disorders.

Neuroinflammation is recognised as one of the potential mechanisms mediating the onset of a broad range of psychiatric disorders and may contribute to nonresponsiveness to current therapies. Both preclinical and clinical studies have indicated that aberrant inflammatory responses can result in altered behavioral responses and cognitive deficits. In this review, we discuss the role of inflammation in the pathogenesis of neuropsychiatric disorders and ask the question if certain genetic copy-number variants (CNVs) associated with psychiatric disorders might play a role in modulating inflammation. Furthermore, we detail some of the potential treatment strategies for psychiatric disorders that may operate by altering inflammatory responses.

Integrating Microarrays into Routine Prenatal Diagnosis: Determinants of Decision Making

Objectives: The explosion in genetic technologies, including array comparative genomic hybridization (aCGH), has increased the complexity of genetic counseling. We now offer chorionic villus sampling (CVS) and aCGH to all first-trimester patients, as this allows the prenatal diagnosis of an additional 1% of anomalies not otherwise detectable and can detect genetic copy number variants at a much higher resolution than conventional cytogenetics. Here, we explored some of the determinants of how patients are deciding to use or not use this new technology and evaluate risk-benefit analyses for that decision. Methods: This is a retrospective case-control study of singleton and multiples pregnancies at our center. Those having aCGH testing along with CVS were defined as ‘testers' and those who declined aCGH but had the CVS were ‘nontesters'. Results: Demographic data of 181 educated women who chose CVS were compared. Among those carrying singletons (n = 144), older women, defined as over 35 years of age (or ‘advanced maternal age'; AMA), were more likely to choose the aCGH than younger women. Further, women who had a prior history of genetic testing and who wanted to know the gender of the fetus were more likely to choose the aCGH test. In women carrying multiples (n = 37), AMA ceases to be a predictor of choice. Having had prior genetic counseling remains a strong predictor for choosing aCGH, as does wanting to know the gender of the fetus. Neither prior abortions nor having prior children were significant for women carrying singletons or multiples. Conclusion: Offering pregnant couples an individualized choice regarding aCGH seems an appropriate approach. There are discrete patterns associated with the choice of taking the aCGH that varied depending on whether the patient was carrying a singleton or multiples.