Integrative analysis identifies key molecular signatures underlying neurodevelopmental deficits in fragile X syndrome

BACKGROUND: Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by epigenetic silencing of FMR1 and loss of FMRP expression. Efforts to understand the molecular underpinnings of the disease have been largely performed in rodent or nonisogenic settings. A detailed examination of the impact of FMRP loss on cellular processes and neuronal properties in the context of isogenic human neurons remains lacking. METHODS: Using CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 to introduce indels in exon 3 of FMR1, we generated an isogenic human pluripotent stem cell model of FXS that shows complete loss of FMRP expression. We generated neuronal cultures and performed genome-wide transcriptome and proteome profiling followed by functional validation of key dysregulated processes. We further analyzed neurodevelopmental and neuronal properties, including neurite length and neuronal activity, using multielectrode arrays and patch clamp electrophysiology. RESULTS: We showed that the transcriptome and proteome profiles of isogenic FMRP-deficient neurons demonstrate perturbations in synaptic transmission, neuron differentiation, cell proliferation and ion transmembrane transporter activity pathways, and autism spectrum disorder-associated gene sets. We uncovered key deficits in FMRP-deficient cells demonstrating abnormal neural rosette formation and neural progenitor cell proliferation. We further showed that FMRP-deficient neurons exhibit a number of additional phenotypic abnormalities, including neurite outgrowth and branching deficits and impaired electrophysiological network activity. These FMRP-deficient related impairments have also been validated in additional FXS patient-derived human-induced pluripotent stem cell neural cells. CONCLUSIONS: Using isogenic human pluripotent stem cells as a model to investigate the pathophysiology of FXS in human neurons, we reveal key neural abnormalities arising from the loss of FMRP.Peer reviewe

Exome Sequencing and Rare Variant Analysis Reveals Multiple Filaggrin Mutations in Bangladeshi Families with Atopic Eczema and Additional Risk Genes

M.P was supported by a Fellowship from the German Research Foundation (DFG). This work received infrastructure support through the DFG Cluster of Excellence “Inflammation at Interfaces” (grants EXC306 and EXC306/2), and was supported by grants (WE2678/6-1, WE2678/6-2, WE2678/9) from the DFG and the e:Med sysINFLAME grant no. 01ZX1306A from the German Federal Ministry of Education and Research (BMBF). J.E.A.C. and X.F.C.C.W. are funded by A*STAR SPF funding for translational skin research and genetic orphan disease

IDENTIFYING AND EXPLOITING SYNTHETIC LETHALITY FOR CANCER THERAPEUTICS

Ph.DDOCTOR OF PHILOSOPHY (SOC

MultiDCoX: Multi-factor analysis of differential co-expression

Abstract Background Differential co-expression (DCX) signifies change in degree of co-expression of a set of genes among different biological conditions. It has been used to identify differential co-expression networks or interactomes. Many algorithms have been developed for single-factor differential co-expression analysis and applied in a variety of studies. However, in many studies, the samples are characterized by multiple factors such as genetic markers, clinical variables and treatments. No algorithm or methodology is available for multi-factor analysis of differential co-expression. Results We developed a novel formulation and a computationally efficient greedy search algorithm called MultiDCoX to perform multi-factor differential co-expression analysis. Simulated data analysis demonstrates that the algorithm can effectively elicit differentially co-expressed (DCX) gene sets and quantify the influence of each factor on co-expression. MultiDCoX analysis of a breast cancer dataset identified interesting biologically meaningful differentially co-expressed (DCX) gene sets along with genetic and clinical factors that influenced the respective differential co-expression. Conclusions MultiDCoX is a space and time efficient procedure to identify differentially co-expressed gene sets and successfully identify influence of individual factors on differential co-expression

Additional file 2: of MultiDCoX: Multi-factor analysis of differential co-expression

Functional analysis of joint and individual influence of co-factors on co-expression of genesets. Summary of GO terms and pathways enriched for joint and individual influence of different cofactors on co-expression of genests. Joint influence of co-factors is evident from the number of pathways and GO terms enriched for genesets whose co-expression is affected by more than one co-factor. (DOC 66 kb

Additional file 1: of MultiDCoX: Multi-factor analysis of differential co-expression

Results of Analysis of Breast Cancer Data. Contains all differentially co-expressed genesets with respective differential co-expression model fit (F-test p-value, coefficient value), gene counts, and permutation results over three factors (ER, p53 and Grade) in breast cancer data. Remarks: Grade + indicates higher grade tumor i.e. 2 and 3, while Grade– indicates lower grade tumour i.e. 1. (XLS 804 kb

Evaluation of novel Parkinson's disease candidate genes in the Chinese population

Recent whole-exome sequencing studies in European patients with Parkinson's disease (PD) have identified potential risk variants across 33 novel PD candidate genes. We aim to determine if these reported candidate genes are similarly implicated in Asians by assessing common, rare, and novel nonsynonymous coding variants by sequencing all 33 genes in 198 Chinese samples and genotyping coding variants in an independent set of 9756 Chinese samples. We carried out further targeted sequencing of CD36 in an additional 576 Chinese and Korean samples. We found that only 8 of 43 reported risk variants were polymorphic in our Chinese samples. We identified several heterozygotes for rare loss-of-function mutations, including the reported CD36 p.Gln74Ter variant, in both cases and controls. We also observed 2 potential compound heterozygotes among PD cases for rare loss-of-function mutations in CD36 and SSPO. The other reported variants were common in East Asians and not associated with PD, completely absent, or only found in controls. Therefore, the 33 reported candidate genes and associated variants are unlikely to confer significant PD risk in the East Asian population.NRF (Natl Research Foundation, S’pore)ASTAR (Agency for Sci., Tech. and Research, S’pore)NMRC (Natl Medical Research Council, S’pore)Accepted versio

Analysis of <i>POFUT1</i> Gene Mutation in a Chinese Family with Dowling-Degos Disease

<div><p>Dowling-Degos disease (DDD) is an autosomal dominant genodermatosis characterized by reticular pigmented anomaly mainly affecting flexures. Though <i>KRT5</i> has been identified to be the causal gene of DDD, the heterogeneity of this disease was displayed: for example, <i>POFUT1</i> and <i>POGLUT1</i> were recently identified and confirmed to be additional pathogenic genes of DDD. To identify other DDD causative genes, we performed genome-wide linkage and exome sequencing analyses in a multiplex Chinese DDD family, in which the <i>KRT5</i> mutation was absent. Only a novel 1-bp deletion (c.246+5delG) in <i>POFUT1</i> was found. No other novel mutation or this deletion was detected in <i>POFUT1</i> in a second DDD family and a sporadic DDD case by Sanger Sequencing. The result shows the genetic-heterogeneity and complexity of DDD and will contribute to the further understanding of DDD genotype/phenotype correlations and to the pathogenesis of this disease.</p></div

Family trees of Family I and Family II.

<p>Shown are the pedigree of family I and family II with DDD. The arrow denotes the proband; “Δ” denotes the individuals used in the linkage analysis; “★” denotes the individuals used in exome sequencing analysis, “⧫” denotes the individuals that were Sanger sequenced for <i>POFUT1</i>.</p