Gene co-expression networks represent modules of genes with shared biological function, and have been widely used to model biological pathways in gene expression data. Co-expression networks ...associated with a specific trait can be constructed and identified using weighted gene co-expression network analysis (WGCNA), which is especially useful for the study of transcriptional signatures in disease. WGCNA networks are typically constructed using both disease and wildtype samples, so molecular pathways associated with disease are identified. However, it would be advantageous to study such co-expression networks in their disease context across spatiotemporal conditions, but currently there is no comprehensive software implementation for this type of analysis.
Here, we introduce a WGCNA-based procedure, multiWGCNA, that is tailored to datasets with variable spatial or temporal traits. As well as constructing the combined network, multiWGCNA also generates a network for each condition separately, and subsequently maps these modules between and across designs, and performs relevant downstream analyses, including module-trait correlation and module preservation. When applied to astrocyte-specific RNA-sequencing (RNA-seq) data from various brain regions of mice with experimental autoimmune encephalitis, multiWGCNA resolved the de novo formation of the neurotoxic astrocyte transcriptional program exclusively in the disease setting. Using time-course RNA-seq from mice with tau pathology (rTg4510), we demonstrate how multiWGCNA can also be used to study the temporal evolution of pathological modules over the course of disease progression.
The multiWGCNA R package can be applied to expression data with two dimensions, which is especially useful for the study of disease-associated modules across time or space. The source code and functions are freely available at: https://github.com/fogellab/multiWGCNA .
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
IMPORTANCE: Clinical exome sequencing (CES) is rapidly becoming a common molecular diagnostic test for individuals with rare genetic disorders. OBJECTIVE: To report on initial clinical indications ...for CES referrals and molecular diagnostic rates for different indications and for different test types. DESIGN, SETTING, AND PARTICIPANTS: Clinical exome sequencing was performed on 814 consecutive patients with undiagnosed, suspected genetic conditions at the University of California, Los Angeles, Clinical Genomics Center between January 2012 and August 2014. Clinical exome sequencing was conducted as trio-CES (both parents and their affected child sequenced simultaneously) to effectively detect de novo and compound heterozygous variants or as proband-CES (only the affected individual sequenced) when parental samples were not available. MAIN OUTCOMES AND MEASURES: Clinical indications for CES requests, molecular diagnostic rates of CES overall and for phenotypic subgroups, and differences in molecular diagnostic rates between trio-CES and proband-CES. RESULTS: Of the 814 cases, the overall molecular diagnosis rate was 26% (213 of 814; 95% CI, 23%-29%). The molecular diagnosis rate for trio-CES was 31% (127 of 410 cases; 95% CI, 27%-36%) and 22% (74 of 338 cases; 95% CI, 18%-27%) for proband-CES. In cases of developmental delay in children (<5 years, n = 138), the molecular diagnosis rate was 41% (45 of 109; 95% CI, 32%-51%) for trio-CES cases and 9% (2 of 23, 95% CI, 1%-28%) for proband-CES cases. The significantly higher diagnostic yield (P value = .002; odds ratio, 7.4 95% CI, 1.6-33.1) of trio-CES was due to the identification of de novo and compound heterozygous variants. CONCLUSIONS AND RELEVANCE: In this sample of patients with undiagnosed, suspected genetic conditions, trio-CES was associated with higher molecular diagnostic yield than proband-CES or traditional molecular diagnostic methods. Additional studies designed to validate these findings and to explore the effect of this approach on clinical and economic outcomes are warranted.
IMPORTANCE: Cerebellar ataxias are a diverse collection of neurologic disorders with causes ranging from common acquired etiologies to rare genetic conditions. Numerous genetic disorders have been ...associated with chronic progressive ataxia and this consequently presents a diagnostic challenge for the clinician regarding how to approach and prioritize genetic testing in patients with such clinically heterogeneous phenotypes. Additionally, while the value of genetic testing in early-onset and/or familial cases seems clear, many patients with ataxia present sporadically with adult onset of symptoms and the contribution of genetic variation to the phenotype of these patients has not yet been established. OBJECTIVE: To investigate the contribution of genetic disease in a population of patients with predominantly adult- and sporadic-onset cerebellar ataxia. DESIGN, SETTING, AND PARTICIPANTS: We examined a consecutive series of 76 patients presenting to a tertiary referral center for evaluation of chronic progressive cerebellar ataxia. MAIN OUTCOMES AND MEASURES: Next-generation exome sequencing coupled with comprehensive bioinformatic analysis, phenotypic analysis, and clinical correlation. RESULTS: We identified clinically relevant genetic information in more than 60% of patients studied (n = 46), including diagnostic pathogenic gene variants in 21% (n = 16), a notable yield given the diverse genetics and clinical heterogeneity of the cerebellar ataxias. CONCLUSIONS AND RELEVANCE: This study demonstrated that clinical exome sequencing in patients with adult-onset and sporadic presentations of ataxia is a high-yield test, providing a definitive diagnosis in more than one-fifth of patients and suggesting a potential diagnosis in more than one-third to guide additional phenotyping and diagnostic evaluation. Therefore, clinical exome sequencing is an appropriate consideration in the routine genetic evaluation of all patients presenting with chronic progressive cerebellar ataxia.
The role of post-transcriptional gene regulation in human brain development and neurodevelopmental disorders remains mostly uncharacterized. ELAV-like RNA-binding proteins (RNAbps) are a family of ...proteins that regulate several aspects of neuronal function including neuronal excitability and synaptic transmission, both critical to the normal function of the brain in cognition and behavior. Here, we identify the downstream neuronal transcriptional and splicing networks of ELAVL2, an RNAbp with previously unknown function in the brain. Expression of ELAVL2 was reduced in human neurons and RNA-sequencing was utilized to identify networks of differentially expressed and alternatively spliced genes resulting from haploinsufficient levels of ELAVL2. These networks contain a number of autism-relevant genes as well as previously identified targets of other important RNAbps implicated in autism spectrum disorder (ASD) including RBFOX1 and FMRP. ELAVL2-regulated co-expression networks are also enriched for neurodevelopmental and synaptic genes, and include genes with human-specific patterns of expression in the frontal pole. Together, these data suggest that ELAVL2 regulation of transcript expression is critical for neuronal function and clinically relevant to ASD.
Summary Among the hereditary ataxias, autosomal recessive spinocerebellar ataxias comprise a diverse group of neurodegenerative disorders. Clinical phenotypes vary from predominantly cerebellar ...syndromes to sensorimotor neuropathy, ophthalmological disturbances, involuntary movements, seizures, cognitive dysfunction, skeletal anomalies, and cutaneous disorders, among others. Molecular pathogenesis also ranges from disorders of mitochondrial or cellular metabolism to impairments of DNA repair or RNA processing functions. Diagnosis can be improved by a systematic approach to the categorisation of these disorders, which is used to direct further, more specific, biochemical and genetic investigations. In this Review, we discuss the clinical characteristics and molecular genetics of the more common autosomal recessive ataxias and provide a framework for assessment and differential diagnosis of patients with these disorders.
Childhood Cerebellar Ataxia Fogel, Brent L.
Journal of child neurology,
09/2012, Letnik:
27, Številka:
9
Journal Article
Recenzirano
Odprti dostop
Childhood presentations of ataxia, an impairment of balance and coordination caused by damage to or dysfunction of the cerebellum, can often be challenging to diagnose. Presentations tend to be ...clinically heterogeneous, but key considerations may vary based on the child’s age at onset, the course of illness, and subtle differences in phenotype. Systematic investigation is recommended for efficient diagnosis. In this review, we outline common etiologies and describe a comprehensive approach to the evaluation of both acquired and genetic cerebellar ataxia in children.
RNA splicing plays a critical role in the programming of neuronal differentiation and, consequently, normal human neurodevelopment, and its disruption may underlie neurodevelopmental and ...neuropsychiatric disorders. The RNA-binding protein, fox-1 homolog (RBFOX1; also termed A2BP1 or FOX1), is a neuron-specific splicing factor predicted to regulate neuronal splicing networks clinically implicated in neurodevelopmental disease, including autism spectrum disorder (ASD), but only a few targets have been experimentally identified. We used RNA sequencing to identify the RBFOX1 splicing network at a genome-wide level in primary human neural stem cells during differentiation. We observe that RBFOX1 regulates a wide range of alternative splicing events implicated in neuronal development and maturation, including transcription factors, other splicing factors and synaptic proteins. Downstream alterations in gene expression define an additional transcriptional network regulated by RBFOX1 involved in neurodevelopmental pathways remarkably parallel to those affected by splicing. Several of these differentially expressed genes are further implicated in ASD and related neurodevelopmental diseases. Weighted gene co-expression network analysis demonstrates a high degree of connectivity among these disease-related genes, highlighting RBFOX1 as a key factor coordinating the regulation of both neurodevelopmentally important alternative splicing events and clinically relevant neuronal transcriptional programs in the development of human neurons.
Late-onset genetic cerebellar ataxias are clinically heterogenous with variable phenotypes. Several of these conditions are commonly associated with dementia. Recognition of the relationship between ...ataxia and dementia can guide clinical genetic evaluation.
Spinocerebellar ataxias often present with variable phenotypes that may include dementia. Genomic studies have begun to identify links between incomplete penetrance and such variable phenotypes in certain hereditary ataxias. Recent studies evaluating the interaction of TBP repeat expansions and STUB1 sequence variants provide a framework to understand how genetic interactions influence disease penetrance and dementia risk in spinocerebellar ataxia types 17 and 48. Further advances in next generation sequencing methods will continue to improve diagnosis and create new insights into the expressivity of existing disorders.
The late-onset hereditary ataxias are a clinically heterogenous group of disorders with complex presentations that can include cognitive impairment and/or dementia. Genetic evaluation of late-onset ataxia patients with dementia follows a systemic testing approach that often utilizes repeat expansion testing followed by next-generation sequencing. Advances in bioinformatics and genomics is improving both diagnostic evaluation and establishing a basis for phenotypic variability. Whole genome sequencing will likely replace exome sequencing as a more comprehensive means of routine testing.
Next-generation sequencing technologies allow for rapid and inexpensive large-scale genomic analysis, creating unprecedented opportunities to integrate genomic data into the clinical diagnosis and ...management of neurological disorders. However, the scale and complexity of these data make them difficult to interpret and require the use of sophisticated bioinformatics applied to extensive datasets, including whole exome and genome sequences. Detailed analysis of genetic data has shown that accurate phenotype information is essential for correct interpretation of genetic variants and might necessitate re-evaluation of the patient in some cases. A multidisciplinary approach that incorporates bioinformatics, clinical evaluation, and human genetics can help to address these challenges. However, despite numerous studies that show the efficacy of next-generation sequencing in establishing molecular diagnoses, pathogenic mutations are generally identified in fewer than half of all patients with genetic neurological disorders, exposing considerable gaps in the understanding of the human genome and providing opportunities to focus research on improving the usefulness of genomics in clinical practice. Looking forward, the emergence of precision health in neurological care will increasingly apply genomic data analysis to pharmacogenetics, preventive medicine, and patient-targeted therapies.
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