CNV-ClinViewer: Enhancing the clinical interpretation of large copy-number variants online

Purpose Large copy number variants (CNVs) can cause a heterogeneous spectrum of rare and severe disorders. However, most CNVs are benign and are part of natural variation in human genomes. CNV pathogenicity classification, genotype-phenotype analyses, and therapeutic target identification are challenging and time-consuming tasks that require the integration and analysis of information from multiple scattered sources by experts. Methods We developed a web-application combining >250,000 patient and population CNVs together with a large set of biomedical annotations and provide tools for CNV classification based on ACMG/ClinGen guidelines and gene-set enrichment analyses. Results Here, we introduce the CNV-ClinViewer (https://cnv-ClinViewer.broadinstitute.org), an open-source web-application for clinical evaluation and visual exploration of CNVs. The application enables real-time interactive exploration of large CNV datasets in a user-friendly designed interface. Conclusion Overall, this resource facilitates semi-automated clinical CNV interpretation and genomic loci exploration and, in combination with clinical judgment, enables clinicians and researchers to formulate novel hypotheses and guide their decision-making process. Subsequently, the CNV-ClinViewer enhances for clinical investigators patient care and for basic scientists translational genomic research

The psychological science accelerator’s COVID-19 rapid-response dataset

In response to the COVID-19 pandemic, the Psychological Science Accelerator coordinated three large-scale psychological studies to examine the effects of loss-gain framing, cognitive reappraisals, and autonomy framing manipulations on behavioral intentions and affective measures. The data collected (April to October 2020) included specific measures for each experimental study, a general questionnaire examining health prevention behaviors and COVID-19 experience, geographical and cultural context characterization, and demographic information for each participant. Each participant started the study with the same general questions and then was randomized to complete either one longer experiment or two shorter experiments. Data were provided by 73,223 participants with varying completion rates. Participants completed the survey from 111 geopolitical regions in 44 unique languages/dialects. The anonymized dataset described here is provided in both raw and processed formats to facilitate re-use and further analyses. The dataset offers secondary analytic opportunities to explore coping, framing, and self-determination across a diverse, global sample obtained at the onset of the COVID-19 pandemic, which can be merged with other time-sampled or geographic data

A global experiment on motivating social distancing during the COVID-19 pandemic

Finding communication strategies that effectively motivate social distancing continues to be a global public health priority during the COVID-19 pandemic. This cross-country, preregistered experiment (n = 25,718 from 89 countries) tested hypotheses concerning generalizable positive and negative outcomes of social distancing messages that promoted personal agency and reflective choices (i.e., an autonomy-supportive message) or were restrictive and shaming (i.e., a controlling message) compared with no message at all. Results partially supported experimental hypotheses in that the controlling message increased controlled motivation (a poorly internalized form of motivation relying on shame, guilt, and fear of social consequences) relative to no message. On the other hand, the autonomy-supportive message lowered feelings of defiance compared with the controlling message, but the controlling message did not differ from receiving no message at all. Unexpectedly, messages did not influence autonomous motivation (a highly internalized form of motivation relying on one’s core values) or behavioral intentions. Results supported hypothesized associations between people’s existing autonomous and controlled motivations and self-reported behavioral intentions to engage in social distancing. Controlled motivation was associated with more defiance and less long-term behavioral intention to engage in social distancing, whereas autonomous motivation was associated with less defiance and more short- and long-term intentions to social distance. Overall, this work highlights the potential harm of using shaming and pressuring language in public health communication, with implications for the current and future global health challenges

Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome

Background: Genomics enables individualized diagnosis and treatment, but large challenges remain to functionally interpret rare variants. To date, only one causative variant has been described for KCNK9 imprinting syndrome (KIS). The genotypic and phenotypic spectrum of KIS has yet to be described and the precise mechanism of disease fully understood. Methods: This study discovers mechanisms underlying KCNK9 imprinting syndrome (KIS) by describing 15 novel KCNK9 alterations from 47 KIS-affected individuals. We use clinical genetics and computer-assisted facial phenotyping to describe the phenotypic spectrum of KIS. We then interrogate the functional effects of the variants in the encoded TASK3 channel using sequence-based analysis, 3D molecular mechanic and dynamic protein modeling, and in vitro electrophysiological and functional methodologies. Results: We describe the broader genetic and phenotypic variability for KIS in a cohort of individuals identifying an additional mutational hotspot at p.Arg131 and demonstrating the common features of this neurodevelopmental disorder to include motor and speech delay, intellectual disability, early feeding difficulties, muscular hypotonia, behavioral abnormalities, and dysmorphic features. The computational protein modeling and in vitro electrophysiological studies discover variability of the impact of KCNK9 variants on TASK3 channel function identifying variants causing gain and others causing loss of conductance. The most consistent functional impact of KCNK9 genetic variants, however, was altered channel regulation. Conclusions: This study extends our understanding of KIS mechanisms demonstrating its complex etiology including gain and loss of channel function and consistent loss of channel regulation. These data are rapidly applicable to diagnostic strategies, as KIS is not identifiable from clinical features alone and thus should be molecularly diagnosed. Furthermore, our data suggests unique therapeutic strategies may be needed to address the specific functional consequences of KCNK9 variation on channel function and regulation

The Psychological Science Accelerator’s COVID-19 rapid-response dataset

In response to the COVID-19 pandemic, the Psychological Science Accelerator coordinated three large-scale psychological studies to examine the effects of loss-gain framing, cognitive reappraisals, and autonomy framing manipulations on behavioral intentions and affective measures. The data collected (April to October 2020) included specific measures for each experimental study, a general questionnaire examining health prevention behaviors and COVID-19 experience, geographical and cultural context characterization, and demographic information for each participant. Each participant started the study with the same general questions and then was randomized to complete either one longer experiment or two shorter experiments. Data were provided by 73,223 participants with varying completion rates. Participants completed the survey from 111 geopolitical regions in 44 unique languages/dialects. The anonymized dataset described here is provided in both raw and processed formats to facilitate re-use and further analyses. The dataset offers secondary analytic opportunities to explore coping, framing, and self-determination across a diverse, global sample obtained at the onset of the COVID-19 pandemic, which can be merged with other time-sampled or geographic data

A multi-country test of brief reappraisal interventions on emotions during the COVID-19 pandemic.

The COVID-19 pandemic has increased negative emotions and decreased positive emotions globally. Left unchecked, these emotional changes might have a wide array of adverse impacts. To reduce negative emotions and increase positive emotions, we tested the effectiveness of reappraisal, an emotion-regulation strategy that modifies how one thinks about a situation. Participants from 87 countries and regions (n = 21,644) were randomly assigned to one of two brief reappraisal interventions (reconstrual or repurposing) or one of two control conditions (active or passive). Results revealed that both reappraisal interventions (vesus both control conditions) consistently reduced negative emotions and increased positive emotions across different measures. Reconstrual and repurposing interventions had similar effects. Importantly, planned exploratory analyses indicated that reappraisal interventions did not reduce intentions to practice preventive health behaviours. The findings demonstrate the viability of creating scalable, low-cost interventions for use around the world

Exploring intra-splicing and its regulatory potential

Die Diversität des menschlichen Proteoms ist das Ergebnis einer Kaskade regulativer Interaktionen, die genetisch kodierte Informationen nutzen und diesen durch einen transformativen Prozess führen. Dies erlaubt eine Maximierung der Diversität. Einer dieser Prozesse, und möglicherweise der mit dem größten Diversifikationspotential ist Transkription und die daran gekoppelten RNA Prozessierung. Viele regulative Ebenen dieser Prozesse, von Transkription bis Prozessierung, wurden bereits entdeckt und untersucht. Die führt zu einem bereits heute komplexen Gesamtbild, dieser zellulären Vorgänge. Diese Entdeckungen beinhalten molekulare Interaktionen und Interaktoren, kombinatorische Events, die das Transkriptom effektiv, als Antwort auf externe Stimuli, interne Anforderungen oder zelluläre Diversifikation formen. In der vorliegenden Arbeit präsentiere ich eine weitere regulative Ebene, welche durch den bereits intensiv erforschten Splicingmechanismus agiert. Intra-splicing, ursprünglich ein hypothetischer Mechanismus des langen-Intron-splicings wurde inzwischen experimentell verifiziert. Diesem wurde in jüngeren Studien eine weitere regulative Funktion zugeschrieben: recursive Exons. Diese erlauben eine flexible Einbindung zusätzlicher genetischer Information in langen Introns und ermöglichen außerdem, höchstwahrscheinlich, das Spleißen dieser langen Introns. Aufbauend auf diesem Ansatz habe ich weitere Intra-splicing Events genomweit identifiziert. Dies führte einerseits zu einer neuen Perspektive der RNA-Prozessierung und andererseits zu der Identifikation einiger Intra-splicing spezifischer regulativer Mechanismen. Die im Detail studierten Fälle beeinflussten Genexpression quantitativ und qualitativ. Teilweise Intronretention, beziehungsweise erhöhte RNA-Prozessierungseffizienz regulierten die Abundanz spezifischer Transkripte, während potentielle rekursive splicing Events in einer Art positioniert sind, die alternatives Splicing ermöglichen und, möglicherweise, forcieren. Die vorliegende Arbeit bildet das theoretische Grundgerüst der während des Doktorats durchgeführten praktischen Arbeiten und den daraus resultierten Publikationen.The diversity of the human proteome is the consequence of a cascade of regulatory network interactions that use the rather limited pool of direct genetically encoded information and push it through extensive transformative processes, allowing for maximum, or rather required, diversity. One of these processes, and arguably the one with the biggest diversification potential is transcription and its coupled RNA processing steps. Many regulatory layers in these processes, touching all aspects of transcription and RNA processing, have already been uncovered, drawing a complex interactive network. This includes the continuous discovery of molecular interactions and interactors and combinatorial events that allow for efficient shaping of the transcriptome in response to external stimuli, internal requirements or cellular diversification attempts. In this thesis, I want to present yet another layer of regulation via the extensively studied splicing process. Intra-splicing, previously hypothesized and later experimentally validated as a mechanism of long intron splicing, recently was accredited with a novel impact on gene expression: recursive exons. These allow for a flexible inclusion of additional genetic information in long introns and presumably facilitate long intron removal. Extending on this approach, I identified intrasplicing events on a genome-wide scale which allows for a more processing-focused approach to gene expression and additionally lead to the discovery of a number of regulatory splicing events that, in the cases studied in detail, lead to gene expression and isoform regulation. Down-regulation is achieved via partial intron retention, and increased gene expression via more efficient intron removal. The impact on isoform selection is hypothesized based on a novel intersection between recursive splicing and exon selection. This thesis provides the theoretical basis for the work performed in this doctorate and the resulting manuscripts attached

Automated image analysis of stained cytospins to quantify Schwann cell purity and proliferation.

In response to injury, adult Schwann cells (SCs) re-enter the cell cycle, change their expression profile, and exert repair functions important for wound healing and the re-growth of axons. While this phenotypical instability of SCs is essential for nerve regeneration, it has also been implicated in cancer progression and de-myelinating neuropathies. Thus, SCs became an important research tool to study the molecular mechanisms involved in repair and disease and to identify targets for therapeutic intervention. A high purity of isolated SC cultures used for experimentation must be demonstrated to exclude that novel findings are derived from a contaminating fibroblasts population. In addition, information about the SC proliferation status is an important parameter to be determined in response to different treatments. The evaluation of SC purity and proliferation, however, usually depends on the time consuming, manual assessment of immunofluorescence stainings or comes with the sacrifice of a large amount of SCs for flow cytometry analysis. We here show that rat SC culture derived cytospins stained for SC marker SOX10, proliferation marker EdU, intermediate filament vimentin and DAPI allowed the determination of SC identity and proliferation by requiring only a small number of cells. Furthermore, the CellProfiler software was used to develop an automated image analysis pipeline that quantified SCs and proliferating SCs from the obtained immunofluorescence images. By comparing the results of total cell count, SC purity and SC proliferation rate between manual counting and the CellProfiler output, we demonstrated applicability and reliability of the established pipeline. In conclusion, we here combined the cytospin technique, a multi-colour immunofluorescence staining panel, and an automated image analysis pipeline to enable the quantification of SC purity and SC proliferation from small cell aliquots. This procedure represents a solid read-out to simplify and standardize the quantification of primary SC culture purity and proliferation