The GENDULF algorithm: mining transcriptomics to uncover modifier genes for monogenic diseases.

Modifier genes are believed to account for the clinical variability observed in many Mendelian disorders, but their identification remains challenging due to the limited availability of genomics data from large patient cohorts. Here, we present GENDULF (GENetic moDULators identiFication), one of the first methods to facilitate prediction of disease modifiers using healthy and diseased tissue gene expression data. GENDULF is designed for monogenic diseases in which the mechanism is loss of function leading to reduced expression of the mutated gene. When applied to cystic fibrosis, GENDULF successfully identifies multiple, previously established disease modifiers, including EHF, SLC6A14, and CLCA1. It is then utilized in spinal muscular atrophy (SMA) and predicts U2AF1 as a modifier whose low expression correlates with higher SMN2 pre-mRNA exon 7 retention. Indeed, knockdown of U2AF1 in SMA patient-derived cells leads to increased full-length SMN2 transcript and SMN protein expression. Taking advantage of the increasing availability of transcriptomic data, GENDULF is a novel addition to existing strategies for prediction of genetic disease modifiers, providing insights into disease pathogenesis and uncovering novel therapeutic targets.

Characterization of Expression Quantitative Trait Loci in Pedigrees from Colombia and Costa Rica Ascertained for Bipolar Disorder.

The observation that variants regulating gene expression (expression quantitative trait loci, eQTL) are at a high frequency among SNPs associated with complex traits has made the genome-wide characterization of gene expression an important tool in genetic mapping studies of such traits. As part of a study to identify genetic loci contributing to bipolar disorder and other quantitative traits in members of 26 pedigrees from Costa Rica and Colombia, we measured gene expression in lymphoblastoid cell lines derived from 786 pedigree members. The study design enabled us to comprehensively reconstruct the genetic regulatory network in these families, provide estimates of heritability, identify eQTL, evaluate missing heritability for the eQTL, and quantify the number of different alleles contributing to any given locus. In the eQTL analysis, we utilize a recently proposed hierarchical multiple testing strategy which controls error rates regarding the discovery of functional variants. Our results elucidate the heritability and regulation of gene expression in this unique Latin American study population and identify a set of regulatory SNPs which may be relevant in future investigations of complex disease in this population. Since our subjects belong to extended families, we are able to compare traditional kinship-based estimates with those from more recent methods that depend only on genotype information.

Integration of cardiac proteome biology and medicine by a specialized knowledgebase.

RATIONALE: Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts. OBJECTIVE: The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine. METHODS AND RESULTS: We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10,924 proteins in human myocardium. In addition, the Java-coded bioinformatics tools provided by COPaKB enable cardiovascular investigators in all disciplines to retrieve and analyze pertinent organellar protein properties of interest. CONCLUSIONS: COPaKB provides an innovative and interactive resource that connects research interests with the new biological discoveries in protein sciences. With an array of intuitive tools in this unified Web server, nonproteomics investigators can conveniently collaborate with proteomics specialists to dissect the molecular signatures of cardiovascular phenotypes.

Interrogating the Genetic Determinants of Tourette's Syndrome and Other Tic Disorders Through Genome-Wide Association Studies.

OBJECTIVE: Tourette's syndrome is polygenic and highly heritable. Genome-wide association study (GWAS) approaches are useful for interrogating the genetic architecture and determinants of Tourette's syndrome and other tic disorders. The authors conducted a GWAS meta-analysis and probed aggregated Tourette's syndrome polygenic risk to test whether Tourette's and related tic disorders have an underlying shared genetic etiology and whether Tourette's polygenic risk scores correlate with worst-ever tic severity and may represent a potential predictor of disease severity. METHODS: GWAS meta-analysis, gene-based association, and genetic enrichment analyses were conducted in 4,819 Tourette's syndrome case subjects and 9,488 control subjects. Replication of top loci was conducted in an independent population-based sample (706 case subjects, 6,068 control subjects). Relationships between Tourette's polygenic risk scores (PRSs), other tic disorders, ascertainment, and tic severity were examined. RESULTS: GWAS and gene-based analyses identified one genome-wide significant locus within FLT3 on chromosome 13, rs2504235, although this association was not replicated in the population-based sample. Genetic variants spanning evolutionarily conserved regions significantly explained 92.4% of Tourette's syndrome heritability. Tourette's-associated genes were significantly preferentially expressed in dorsolateral prefrontal cortex. Tourette's PRS significantly predicted both Tourette's syndrome and tic spectrum disorders status in the population-based sample. Tourette's PRS also significantly correlated with worst-ever tic severity and was higher in case subjects with a family history of tics than in simplex case subjects. CONCLUSIONS: Modulation of gene expression through noncoding variants, particularly within cortico-striatal circuits, is implicated as a fundamental mechanism in Tourette's syndrome pathogenesis. At a genetic level, tic disorders represent a continuous spectrum of disease, supporting the unification of Tourette's syndrome and other tic disorders in future diagnostic schemata. Tourette's PRSs derived from sufficiently large samples may be useful in the future for predicting conversion of transient tics to chronic tic disorders, as well as tic persistence and lifetime tic severity.

Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.

By analyzing multitissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalog of expression quantitative trait loci (eQTLs) in a nonhuman primate model. This catalog contains more genome-wide significant eQTLs per sample than comparable human resources and identifies sex- and age-related expression patterns. Findings include a master regulatory locus that likely has a role in immune function and a locus regulating hippocampal long noncoding RNAs (lncRNAs), whose expression correlates with hippocampal volume. This resource will facilitate genetic investigation of quantitative traits, including brain and behavioral phenotypes relevant to neuropsychiatric disorders.

Rare Copy Number Variants in NRXN1 and CNTN6 Increase Risk for Tourette Syndrome.

Tourette syndrome (TS) is a model neuropsychiatric disorder thought to arise from abnormal development and/or maintenance of cortico-striato-thalamo-cortical circuits. TS is highly heritable, but its underlying genetic causes are still elusive, and no genome-wide significant loci have been discovered to date. We analyzed a European ancestry sample of 2,434 TS cases and 4,093 ancestry-matched controls for rare (< 1% frequency) copy-number variants (CNVs) using SNP microarray data. We observed an enrichment of global CNV burden that was prominent for large (> 1 Mb), singleton events (OR = 2.28, 95% CI [1.39-3.79], p = 1.2 × 10-3) and known, pathogenic CNVs (OR = 3.03 [1.85-5.07], p = 1.5 × 10-5). We also identified two individual, genome-wide significant loci, each conferring a substantial increase in TS risk (NRXN1 deletions, OR = 20.3, 95% CI [2.6-156.2]; CNTN6 duplications, OR = 10.1, 95% CI [2.3-45.4]). Approximately 1% of TS cases carry one of these CNVs, indicating that rare structural variation contributes significantly to the genetic architecture of TS.

Identification of an Efficient Gene Expression Panel for Glioblastoma Classification.

We present here a novel genetic algorithm-based random forest (GARF) modeling technique that enables a reduction in the complexity of large gene disease signatures to highly accurate, greatly simplified gene panels. When applied to 803 glioblastoma multiforme samples, this method allowed the 840-gene Verhaak et al. gene panel (the standard in the field) to be reduced to a 48-gene classifier, while retaining 90.91% classification accuracy, and outperforming the best available alternative methods. Additionally, using this approach we produced a 32-gene panel which allows for better consistency between RNA-seq and microarray-based classifications, improving cross-platform classification retention from 69.67% to 86.07%. A webpage producing these classifications is available at http://simplegbm.semel.ucla.edu.

Lysine ubiquitination and acetylation of human cardiac 20S proteasomes.

PURPOSE: Altered proteasome functions are associated with multiple cardiomyopathies. While the proteasome targets polyubiquitinated proteins for destruction, it itself is modifiable by ubiquitination. We aim to identify the exact ubiquitination sites on cardiac proteasomes and examine whether they are also subject to acetylations. EXPERIMENTAL DESIGN: Assembled cardiac 20S proteasome complexes were purified from five human hearts with ischemic cardiomyopathy, then analyzed by high-resolution MS to identify ubiquitination and acetylation sites. We developed a library search strategy that may be used to complement database search in identifying PTM in different samples. RESULTS: We identified 63 ubiquitinated lysines from intact human cardiac 20S proteasomes. In parallel, 65 acetylated residues were also discovered, 39 of which shared with ubiquitination sites. CONCLUSION AND CLINICAL RELEVANCE: This is the most comprehensive characterization of cardiac proteasome ubiquitination to date. There are significant overlaps between the discovered ubiquitination and acetylation sites, permitting potential crosstalk in regulating proteasome functions. The information presented here will aid future therapeutic strategies aimed at regulating the functions of cardiac proteasomes.

A novel spectral library workflow to enhance protein identifications.

The innovations in mass spectrometry-based investigations in proteome biology enable systematic characterization of molecular details in pathophysiological phenotypes. However, the process of delineating large-scale raw proteomic datasets into a biological context requires high-throughput data acquisition and processing. A spectral library search engine makes use of previously annotated experimental spectra as references for subsequent spectral analyses. This workflow delivers many advantages, including elevated analytical efficiency and specificity as well as reduced demands in computational capacity. In this study, we created a spectral matching engine to address challenges commonly associated with a library search workflow. Particularly, an improved sliding dot product algorithm, that is robust to systematic drifts of mass measurement in spectra, is introduced. Furthermore, a noise management protocol distinguishes spectra correlation attributed from noise and peptide fragments. It enables elevated separation between target spectral matches and false matches, thereby suppressing the possibility of propagating inaccurate peptide annotations from library spectra to query spectra. Moreover, preservation of original spectra also accommodates user contributions to further enhance the quality of the library. Collectively, this search engine supports reproducible data analyses using curated references, thereby broadening the accessibility of proteomics resources to biomedical investigators. This article is part of a Special Issue entitled: From protein structures to clinical applications.

Ansiedad y miedos dentales en escolares hondureños / Anxiety and dental fears among Honduran school children

Anxiety towards dental attention and treatment can affect significantly children’s oral health as well as the quality of dental treatment received. Despite its importance scarce research about childhood dental anxiety has been done in Latin America, specifically in Honduras. In this study dental anxiety was assed in a random sample of 170 school children (6-11 years) from Tegucigalpa’s metropolitan region. Corah Dental Anxiety Scale, Venham Picture Test and Children Fear Survey were used for the assessment. School children showed moderate dental anxiety levels, and only between 14 -15 percent showed significant clinical anxiety levels. No significant differences were found related to dental anxiety between girls and boys. Highly invasive dental procedures account for higher anxiety levels as well as the expectation of visiting the dentist the next day. Children with previous dental experience showed higher anxiety levels as well as children of parents that report fear towards dental treatment. Results demonstrate the relevance of children’s dental anxiety and its relationship with certain previous experience.

La ansiedad a la atención y tratamiento dental puede afectar de forma significativa a la salud oral de los niños así como a la calidad del tratamiento dental recibido. A pesar de su importancia se han realizado muy pocos estudios sobre la ansiedad y miedo dental infantil en Latinoamérica, concretamente en Honduras. En este estudio se evaluó la ansiedad dental de una muestra aleatoria de 170 escolares (6-11 años) de la región metropolitana de Tegucigalpa. La evaluación se realizó mediante la Escala de Ansiedad de Corah, el Test de Dibujos de Venham, y el Escala de Evaluación de los Miedos. Los escolares mostraban niveles moderados de ansiedad dental, y sólo entre el 14-15 % de ellos presentaban niveles de ansiedad clínicamente significativos. No se encontraron diferencias respecto a la ansiedad dental entre niños y niñas. Los procedimientos del tratamiento dental más invasivos provocaron mayores niveles de ansiedad dental, así como la expectativa de ir al dentista al día siguiente. Los niños que tenían experiencia dental previa mostraban niveles más elevados de ansiedad, así como los niños de padres con miedo al tratamiento dental. Los resultados demuestran la relevancia de la ansiedad dental infantil y su relación con ciertas experiencias previas.

Caracterización de pacientes con lesión medular atendidos en un Centro de Rehabilitación (Teletón) en Honduras / Characterization of patients with spinal cord injury at the Rehabilitation Centre Teleton in Honduras

OBJETIVO. Determinar las características clínico-epidemiológicas y la funcionalidad de los pacientes con lesión medular atendidos en el Centro de Rehabilitación Integral Teletón en Tegucigalpa, Honduras. MATERIALES Y MÉTODOS. Estudio prospectivo y descriptivo. Se incluyó a todos los pacientes con lesión medular, referidos por primera vez al centroTeletón de Tegucigalpa, del 1 Octubre del 2005 al 31 de Diciembre del 2006. Para la evaluación neurológica y determinación del grado de dependencia funcional se usó la escala de la Asociación Americana de Lesión Medular y el Clasificador Internacional de Funcionamiento, Discapacidad y Salud de Rehabilitación. RESULTADOS. Se captó 46 pacientes con edad promedio de 35 años, el 80.4 del sexo masculino. En 67.4 la etiología fue traumática, 58 por herida por arma de fuego. El 34.8 se valoró como clase A (lesión completa) y paraplejía en 89, con afección del segmento torácico en 73.7. Las úlceras por presión y las infecciones del tracto urinario fueron las complicaciones agudas y causas de rehospitalización más frecuentes. De los 33 pacientes que completaron 6 meses de tratamiento de rehabilitación, el 48.4 tuvo mejoría en I o II grado de dependencia funcional. En 97 hubo mejoría significativa en porcentaje de dependencia funcional inicial y final.CONCLUSIONES: La mayoría de los pacientes fueron varones en edad productiva. La principal causa de lesión medular fue traumática,principalmente por herida por arma de fuego. El tipo de lesión más frecuente fue la paraplejía completa y la mayoría de los pacientes mejoró con rehabilitación...