Biology subjects

Scott, R.

Publications and source records attributed to Scott, R..

17 recordsLinked to original sources

bioRxiv2025

Normalization of Prefrontal Network Dynamics Prevents Cognitive Impairments After Developmental Insult

The neurodevelopmental period is highly sensitive; insults during this period impair neural network connectivity, causing lasting cognitive deficits associated with many neuropsychiatric disorders. Medial prefrontal cortex (mPFC) networks subserve flexible behavior, but the mechanisms underlying their disruption after developmental insults remain unclear. We used an early-life seizure (ELS) model to investigate how mPFC networks become impaired and tested whether adrenocorticotropic hormone (ACTH), a clinically relevant neuroprotective peptide, could restore network function. Using in-vivo single-unit recordings during baseline and fear extinction learning, we found ELS-induced dysfunction was characterized by reduced neuronal firing, rigid spike-timing, and weakened functional connectivity, all predicting impaired extinction learning. ACTH treatment prevented these deficits, preserving dynamic spike-timing, flexible connectivity, and network organization. Advanced graph neural network modeling identified neuronal features predictive of cognitive outcomes, revealing potential biomarkers broadly relevant to other developmental disorders. These findings highlight fundamental mechanisms of mPFC network dysfunction and emphasize the translational potential of targeting network dynamics to restore cognition in neurodevelopmental disorders.

neuroscience↗

bioRxiv2025

Characterization Eclosion Hormone Receptor function reveals differential hormonal control of ecdysis during Drosophila development.

Neuromodulators and peptide hormones play important roles in regulating animal behavior. A well-studied example is ecdysis, which is used by insects to shed their exoskeleton at the end of each molt. Ecdysis is initiated by Ecdysis Triggering Hormone (ETH) and Eclosion Hormone (EH), which interact via positive feedback to coordinate the sequence of behavioral and physiological changes that cause exoskeleton shedding. Whereas the cell types targeted by ETH are well characterized, those targeted by EH have remained largely unknown due to limited characterization of the EH receptor (EHR). A gene encoding an EHR has been described in the oriental fruit fly, B. dorsalis, and in the desert locust, Schistocerca gregaria. However, little is known in these species about its expression pattern and its precise role at ecdysis, and no other insect EHRs are known. Here we analyze CG10738, the Drosophila ortholog of the B. dorsalis gene encoding EHR, and show that expressing it in cells confers sensitivity to EH. In addition, mutations of CG10738 specifically disrupt ecdysis, phenocopying the knockout of the EH gene. Together, these results indicate that CG10738 encodes the Drosophila EHR. As in B. dorsalis, EHR is expressed in the ETH-producing Inka cells; in addition, it is expressed in many known targets of ETH, including the neurons responsible for the secretion of other ecdysis-related peptides, such as CCAP and EH itself. Our results from targeted knockdown and rescue experiments reveal that EHR is required for ecdysis in diverse cell types and that the role of EHR in different targets differs with developmental stage. Our findings indicate extensive convergence of EH and ETH signaling and provide an exemplar of the complex mechanisms by which hormones control animal behavior. AUTHOR SUMMARYHormones and neuromodulators are important regulators of animal behavior. In insects, one of the best studied behaviors influenced by hormones is ecdysis, which allows the animal to shed the remains of its exoskeleton at the end of each molt. Ecdysis is controlled by two key hormones: Ecdysis Triggering Hormone (ETH) and Eclosion Hormone (EH). Whereas most targets of ETH have been identified, those of EH have remained largely unknown due to the limited characterization of its receptor, EHR. Previous studies identified a gene encoding EHR in the oriental fruit fly, Bactrocera dorsalis, and in the desert locust, Schistocerca gregaria, but little is known about its expression pattern or its precise role. Here, we show that CG10738 encodes the Drosophila EHR. We found that EHR is expressed in ETH-producing Inka cells, in neurons that secrete other ecdysis-related peptides, in addition to other neuronal classes and non-neuronal cells. Targeted knockdown and rescue experiments revealed that EHR is essential for ecdysis in various cell types, and that its role can vary depending on the developmental stage. Our findings reveal that the role of EH at ecdysis is complex and provides insights into how hormones and neuromodulators regulate animal behavior.

neuroscience↗

bioRxiv2025

Structural, biophysical and biological analysis and characterisation of IRF4 DNA-binding domain mutations associated with multiple myeloma

IRF4, a transcription factor in the interferon regulatory factor family, is a key regulator in immune cell differentiation indicated to have an essential role in the development of lymphoid malignancies. Genome-wide association studies previously identified a set of overlapping mutations within the IRF4 DNA-binding domain in T-cell lymphoma and multiple myeloma, several of which appeared to be associated with better prognosis. Mapping these mutations to the known crystal structure of the IRF4:PU.1:DNA ternary complex and a new structure of the IRF4 DNA-binding domain in the apo state suggested they might interfere with DNA-binding, directly or via destabilisation of domain structure. We characterised these cancer-associated IRF4 mutants experimentally using the recombinant IRF4 DNA-binding domain (DBD) in vitro and examined the clinically relevant mutant K123R in cellulo. Using fluorescence polarisation, surface plasmon resonance, differential scanning fluorimetry and molecular dynamics, we find that mutation may give rise to significant differences in DNA-binding kinetics and thermal stability without compromising the affinity of IRF4 DNA-binding. The K123R IRF4 mutant showed increased transcriptional activity via a luciferase reporter assay and increased nuclear partitioning, which may be preferentially selected for in multiple myeloma. We discuss our observations in relation to the improved prognosis conferred by this mutation.

biophysics↗

bioRxiv2024

Na+/Ca2+ exchanger triggers transient disruption of axon initial segments in hippocampal granule cells after brief ischemia.

The axon initial segment (AIS) is the site of action potential initiation in many cell types. The large density of Na+ channels and the small intraluminal volume of the AIS underlie the largest spike-dependent Na+ raise along the neuron. Our Na+ and Ca2+ imaging experiments in dentate granule cells reveal that the Na+/Ca2+ exchanger contributes to fast Na+ clearance at the expense of Ca2+ entry specifically at the AIS during short bursts of action potentials. The AIS is thought to be irreversibly disrupted during brain ischemia by the Ca2+-dependent protease calpain, as an early step leading to neuronal death. We find here that brief transitory ischemia produces a similar calpain-dependent disruption of the AIS in the dentate gyrus. However, this is not an irreversible process: a few days following the brief ischemic stress, intact initial segments re-appear, and calpain activity in the dentate gyrus returns to normal. Moreover, pharmacological blockade of Ca2+ entry through the Na+/Ca2+ exchanger prevents AIS disruption in vivo and in slice preparations. Our results unveil a highly dynamic anoxia driven disruption-reconstruction of AIS, which is mediated by a previously unnoticed Ca2+ entry through the Na+/Ca2+ exchanger in the axon initial segment of hippocampal granule cells.

neuroscience↗

bioRxiv2024

An Exploratory EEG Comparison of Good and Bad Readers

Reading is a crucial skill for critical thinking and cognitive development, yet many individuals experience difficulties that impact their daily lives. This study examines the neurophysiological differences between proficient and struggling readers using electroencephalography (EEG). The analysis focuses on the alpha (8-12 Hz) and beta (13-30 Hz) frequency bands, which are prominently involved in cognitive and language-related processes, although other frequency bands also contribute significantly to language comprehension and cognitive control. Eighteen participants (9 good readers and 9 poor readers) were selected based on standardized reading assessments. Resting-state EEG recordings were collected with a 64-channel system while participants were at rest with their eyes closed. After preprocessing to remove artifacts, the power spectra were analyzed, emphasizing relative power and alpha peak activity. Functional connectivity was measured using the corrected imaginary part of the phase-locking value (ciPLV), ensuring accuracy by minimizing volume conduction effects. Results revealed that good readers displayed increased beta power in frontal regions and enhanced synchronization within fronto-central-parietal networks compared to poor readers. Alpha band activity showed complex associations with factors such as age, reading skills, and verbal fluency, indicating nuanced relationships between neural development and literacy. The heightened beta activity in good readers is consistent with its role in cognitive control and language processing, while their stronger network connectivity suggests more efficient neural communication. These findings provide valuable insights into the neural basis of reading proficiency and emphasize the importance of distributed brain networks in skilled reading. Future research should replicate these results with larger samples and longitudinal designs to better understand the neural mechanisms underlying literacy development.

neuroscience↗

bioRxiv2024

Disrupted Hippocampal-Prefrontal Networks In A Rat Model Of Fragile X Syndrome: A Study Linking Neural Dynamics To Autism-Like Behavioral Impairments

Fragile X Syndrome (FXS) is associated with autism spectrum disorder (ASD) symptoms that are associated with cognitive, learning, and behavioral challenges. We investigated how known molecular disruptions in the Fmr1 knockout (FMR-KO) rat model of FXS negatively impact hippocampal-prefrontal cortex (H-PFC) neural network activity and consequent behavior. MethodsFMR-KO and control rats underwent a battery of behavioral tests assessing sociability, memory, and anxiety. Single-unit electrophysiology recordings were then conducted to measure patterns of neural activity in H-PFC circuit. Advanced mathematical models were used to characterize the patterns that were then compared between groups using generalized linear mixed models. ResultsFMR-KO rats demonstrated significant behavioral deficits in sociability, spatial learning, and anxiety, aligning with symptoms of ASD. At the neural level, these rats exhibited abnormal firing patterns in the H-PFC circuit that is critical for learning, memory, and social behavior. The neural networks in FMR-KO rats were also less densely connected and more fragmented, particularly in hippocampal-PFC correlated firing. These findings suggest that disruptions in neural network dynamics underlie the observed behavioral impairments in FMR-KO rats. ConclusionFMR-KO significantly disrupts several characteristics of action potential firing in the H-PFC network, leading to deficits in social behavior, memory, and anxiety, as seen in FXS. This disruption is characterized by less organized and less resilient hippocampal-PFC networks. These findings suggest that therapeutic strategies aimed at normalizing neural dynamics, such as with brain stimulation, could potentially improve behavior and cognitive functions in autistic individuals. HIGHLIGHTSO_LIFragile X Syndrome is associated with autism, cognitive challenges and anxiety C_LIO_LIThe loss of Fmr1 protein disrupts processes involved in building neural networks C_LIO_LIThe consequence is abnormal neural dynamics in hippocampal-prefrontal cortex networks C_LIO_LINormalization of dynamics could improve outcomes in FXS and ASD C_LI

neuroscience↗

bioRxiv2024

Effects of Bacillus thuringiensis subsp. kurstaki application on non-target nocturnal macromoth biodiversity in the eastern boreal forest, Canada.

Insect biodiversity is crucial for resilient ecosystems, supporting essential services. Moths play significant roles as herbivores, pollinators, decomposers, and as prey for birds, bats, and predatory invertebrates, emphasizing their conservation importance. However, large-scale studies on the non-target effects of Bacillus thuringiensis subs. kurstaki (Btk) on moth communities are limited, particularly in northern forests where diversity is lower. Btk is commonly used to control pest insect populations, with forest managers in eastern Canada applying it to manage eastern spruce budworm. We established a replicated two-year study in the North American Boreal Forest of western Newfoundland, Canada, using paired Btk-treated and control (untreated) sites. No significant differences in total abundance or richness were found between treated and control sites. In 2021, Hill numbers only differed between our northern treatment and control sites, which may reflect those stands having already received multiple years of treatment compared to just one year in the southern sites. In 2022, control sites showed higher diversity (Shannon and Simpson diversity metrics) compared to treated sites, extending to all locations. Multiple years of Btk treatment led to shifts in community composition and the relative abundance of some common species, without affecting total richness or abundance. Species responses varied, likely due to Btk sensitivity, application timing, and differences in phenology and voltinism, making it difficult to generalize the effects of Btk on moth communities.

ecology↗

bioRxiv2024

Busted: maternal modifiers of the triploid block involved in seed size control.

The triploid block leads to seed abortion in crosses involving tetraploid Col-0 pollen. The genetic basis underlying this phenomenon is established in the endosperm and attributed to parental genomic imprinting. This research utilised the genetic variation in Arabidopsis to identify the genomic regions harbouring the maternal modifiers of the triploid block to produce viable large seeds. Distinct chromosomal regions were identified in Bla-1 and Tsu-0 accessions. The Bla-1 maternal modifier maps to the TTG2 locus at the lower end of chromosome 2 to produce large viable seeds in response to a triploid block. Tsu-0 accession, on the other hand, recruits the TTG1 locus on the upper arm of chromosome 5 as a maternal modifier of the triploid block. TTG1 and TTG2 mutations significantly increased the proportion of large viable seeds in interploidy crosses. Both genes are involved in transcriptional regulation in the flavonoid biosynthesis pathway. However, to regulate seed size in diploids, TTG1 functions synergistically with auxin but does so independently of TTG2. This work contributed to the genetic framework for the TTG1 and TTG2 seed size roles. HIGHLIGHTSO_LIDifferent Arabidopsis accessions recruit maternal modifiers to repress Col-killing in F1 triploids. C_LIO_LIThese maternal modifiers may operate in the same pathway, such as the flavonoid biosynthesis pathway or other interconnected pathways such as auxin. C_LIO_LITTG1 and TTG2 generally increase F1 triploid survival but in an accession-dependent manner. C_LIO_LITTG1 differentially exhibits a strong positive additive interaction with auxin to increase diploid seed size. C_LIO_LIThe TTG1/TTG2 roles in diploid seed size control appear to have diverged somewhere in the auxin branch of the flavonoid biosynthesis pathway. C_LI

plant biology↗

bioRxiv2023

snPATHO-seq: unlocking the pathology archives

Formalin-fixed paraffin-embedded (FFPE) samples are valuable but underutilized in single-cell omics research due to their low DNA and RNA quality. In this study, leveraging recent single-cell genomic technology advances, we introduce a versatile method to derive high-quality single-nucleus transcriptomic data from FFPE samples.

molecular biology↗

bioRxiv2023

U6 snRNA m6A modification is required for accurate and efficient cis- and trans-splicing of C. elegans mRNAs

pre-mRNA splicing is a critical feature of eukaryotic gene expression. Many eukaryotes use cis-splicing to remove intronic sequences from pre-mRNAs. In addition to cis-splicing, many organisms use trans-splicing to replace the 5' ends of mRNAs with a non-coding spliced-leader RNA. Both cis- and trans-splicing rely on accurately recognising splice site sequences by spliceosomal U snRNAs and associated proteins. Spliceosomal snRNAs carry multiple RNA modifications with the potential to affect different stages of pre-mRNA splicing. Here, we show that m6A modification of U6 snRNA A43 by the RNA methyltransferase METT-10 is required for accurate and efficient cis- and trans-splicing of C. elegans pre-mRNAs. The absence of U6 snRNA m6A modification primarily leads to alternative splicing at 5' splice sites. Furthermore, weaker 5' splice site recognition by the unmodified U6 snRNA A43 affects splicing at 3' splice sites. U6 snRNA m6A43 and the splicing factor SNRNP27K function to recognise an overlapping set of 5' splice sites with an adenosine at +4 position. Finally, we show that U6 snRNA m6A43 is required for efficient SL trans-splicing at weak 3' trans-splice sites. We conclude that the U6 snRNA m6A modification is important for accurate and efficient cis- and trans-splicing in C. elegans.

molecular biology↗

bioRxiv2023

Connectome architecture shapes large-scale cortical reorganization in schizophrenia: a worldwide ENIGMA study

While schizophrenia is considered a prototypical network disorder characterized by widespread brain-morphological alterations, it still remains unclear whether distributed structural alterations robustly reflect underlying network layout. Here, we tested whether large-scale structural alterations in schizophrenia relate to normative structural and functional connectome architecture, and systematically evaluated robustness and generalizability of these network-level alterations. Leveraging anatomical MRI scans from 2,439 adults with schizophrenia and 2,867 healthy controls from 26 ENIGMA sites and normative data from the Human Connectome Project (n=207), we evaluated structural alterations of schizophrenia against two network susceptibility models: i) hub vulnerability, which examines associations between regional network centrality and magnitude of disease-related alterations; ii) epicenter mapping, which identify regions whose typical connectivity profile most closely resembles the disease-related morphological alterations. To assess generalizability and specificity, we contextualized the influence of site, disease stages, and individual clinical factors and compared network associations of schizophrenia with that found in affective disorders. Schizophrenia-related structural alterations co-localized with interconnected functional and structural hubs and harbored temporo-paralimbic and frontal epicenters. Findings were robust across sites and related to individual symptom profiles. We observed localized unique epicenters for first-episode psychosis and early stages, and transmodal epicenters that were shared across first-episode to chronic stages. Moreover, transdiagnostic comparisons revealed overlapping epicenters in schizophrenia and bipolar, but not major depressive disorder, yielding insights in pathophysiological continuity within the schizophrenia-bipolar-spectrum. In sum, cortical alterations over the course of schizophrenia robustly follow brain network architecture, emphasizing marked hub susceptibility and temporo-frontal epicenters at both the level of the group and the individual. Subtle variations of epicenters across disease stages suggest interacting pathological processes, while associations with patient-specific symptoms support additional inter-individual variability of hub vulnerability and epicenters in schizophrenia. Our work contributes to recognizing potentially common pathways to better understand macroscale structural alterations, and inter-individual variability in schizophrenia.

neuroscience↗

bioRxiv2023

Cytokine-Mediated Degradation of the Transcription Factor ERG Impacts the Pulmonary Vascular Response to Systemic Inflammatory Challenge

BackgroundDuring infectious diseases, pro-inflammatory cytokines transiently destabilize interactions between adjacent vascular endothelial cells (ECs) to facilitate the passage of immune molecules and cells into tissues. However, in the lung the resulting vascular hyperpermeability can lead to organ dysfunction. Previous work identified the transcription factor ERG as a master regulator of endothelial homeostasis. Here we investigate whether the sensitivity of pulmonary blood vessels to cytokine-induced destabilization is due to organotypic mechanisms affecting the ability of endothelial ERG to protect lung ECs from inflammatory injury. MethodsCytokine-dependent ubiquitination and proteasomal degradation of ERG was analyzed in cultured Human Umbilical Vein ECs (HUVECs). Systemic administration of TNF or the bacterial cell wall component lipopolysaccharide (LPS) was used to cause a widespread inflammatory challenge in mice; ERG protein levels were assessed by immunoprecipitation, immunoblot, and immunofluorescence. Murine Erg deletion was genetically induced in ECs (Ergfl/fl;Cdh5(PAC)CreERT2), and multiple organs were analyzed by histology, immunostaining, and electron microscopy. ResultsIn vitro, TNF promoted the ubiquitination and degradation of ERG in HUVECs, which was blocked by the proteasomal inhibitor MG132. In vivo, systemic administration of TNF or LPS resulted in a rapid and substantial degradation of ERG within lung ECs, but not ECs of the retina, heart, liver, or kidney. Pulmonary ERG was also downregulated in a murine model of influenza infection. Ergfl/fl;Cdh5(PAC)-CreERT2 mice spontaneously recapitulated aspects of inflammatory challenges, including lung-predominant vascular hyperpermeability, immune cell recruitment, and fibrosis. These phenotypes were associated with a lung-specific decrease in the expression of Tek, a gene target of ERG previously implicated in maintaining pulmonary vascular stability during inflammation. ConclusionsCollectively, our data highlight a unique role for ERG in pulmonary vascular function. We propose that cytokine-induced ERG degradation and subsequent transcriptional changes in lung ECs play critical roles in the destabilization of pulmonary blood vessels during infectious diseases.

cell biology↗

bioRxiv2023

UCHL1-dependent control of Hypoxia-Inducible Factor Transcriptional Activity in Liver Disease.

Liver fibrosis is the excessive accumulation of extracellular matrix proteins that occurs in most types of chronic liver diseases. Fibrosis is associated with the activation of hepatic stellate cells (HSCs) which transdifferentiate into a myofibroblast like phenotype that is contractile, proliferative and profibrogenic. Hypoxia-inducible factor 1 (HIF1), an oxygen-sensitive transcription factor, is elevated during HSC activation and promotes the expression of profibrotic mediator HIF target genes. HIF activation during HSC activation can by either due to localised decreases in oxygen levels, or through oxygen-independent mechanisms that are not completely understood. Here we describe a role for the deubiquitinase UCHL1 in regulating HIF levels and activity during HSC activation and liver fibrosis. Increased HIF1 expression correlated with induction of UCHL1 mRNA and protein with HSC activation. Genetic deletion or chemical inhibition of UCHL1 impaired HIF activity through reduction of HIF1 levels. UCHL1 specifically cleaves the degradative ubiquitin chains from HIF1 leading to increased HIF1 levels, even in sufficiently oxygenated cells. Furthermore, our mechanistic studies have shown that UCHL1 elevates HIF activity through specific cleavage of degradative ubiquitin chains, elevates levels of pro-fibrotic gene expression and increases proliferation rates. These results demonstrate how small molecule inhibitors of DUBs can modulate the activity of HIF transcription factors in liver disease. Furthermore, inhibition of HIF activity via modulation of the ubiquitin-proteasomal degradation pathway may represent a therapeutic opportunity with other HIF-related pathologies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/523142v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1d82ee9org.highwire.dtl.DTLVardef@1eff21aorg.highwire.dtl.DTLVardef@1ffb0eforg.highwire.dtl.DTLVardef@1b93dc9_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2022

Bordetella spp. block eosinophil recruitment to suppress lung iBALT formation

A characteristic that differentiates pathogenic and opportunistic bacteria is that pathogens have been selected by their ability to suppress host inflammatory responses allowing colonization and persistence. Bordetella spp. are respiratory pathogens characterized for the arsenal of mechanisms they use to manipulate host immune responses. We have previously characterized a B. bronchiseptica mutant, RB50{Delta}btrS, that is not able to suppress host immune responses, resulting not only in rapid clearance of the infection but also long-term lung sterilizing immunity against reinfection with the three classical Bordetella spp. Interestingly, this strong immune response requires eosinophils. In this work our results indicate that wildtype B. bronchiseptica, RB50, blocks eosinophil pro-inflammatory functions to prevent the rapid recruitment of B and T cells to the lung that results in iBALT formation. Moreover, eosinophils promote a TH17 microenvironment within the iBALT that might be responsible for the long-term robust protective immunity generated by infection with this mutant. Overall, this work provides a novel role for eosinophils as promoters of adaptive immune responses and protective immunity, while also indicating that bacteria actively manipulate those cells to promote long-term persistence and reinfection.

microbiology↗

bioRxiv2019

Novel truncating mutations in CTNND1 cause a dominant craniofacial and cardiac syndrome

AbstractCTNND1 encodes the p120-catenin (p120) protein, which has a wide range of functions, including the maintenance of cell-cell junctions, regulation of the epithelial-mesenchymal transition and transcriptional signaling. Due to advances in next generation sequencing, CTNND1 has been implicated in human diseases including cleft palate and blepharocheilodontic syndrome (BCD) albeit only recently. In this study, we identify eight novel protein-truncating variants, six de novo, in thirteen participants presenting with craniofacial dysmorphisms including cleft palate and hypodontia, as well as congenital cardiac anomalies, limb dysmorphologies and neurodevelopmental disorders. Using conditional deletions in mice as well as CRISPR/Cas9 approaches to target CTNND1 in Xenopus, we identified a subset of phenotypes that can be linked to p120-catenin in epithelial integrity and turnover, and additional phenotypes that suggest mesenchymal roles of CTNND1. We propose that CTNND1 variants have a wider developmental role than previously described, and that variations in this gene underlie not only cleft palate and BCD but may be expanded to a broader velocardiofacial-like syndrome.

genetics↗

bioRxiv2019

tappAS: A comprehensive computational framework for the analysis of the functional impact of differential splicing

Traditionally, the functional analysis of gene expression data has used pathway and network enrichment algorithms. These methods are usually gene rather than transcript centric and hence fall short to unravel functional roles associated to posttranscriptional regulatory mechanisms such as Alternative Splicing (AS) and Alternative PolyAdenylation (APA), jointly referred here as Alternative Transcript Processing (AltTP). Moreover, short-read RNA-seq has serious limitations to resolve full-length transcripts, further complicating the study of isoform expression. Recent advances in long-read sequencing open exciting opportunities for studying isoform biology and function. However, there are no established bioinformatics methods for the functional analysis of isoform-resolved transcriptomics data to fully leverage these technological advances. Here we present a novel framework for Functional Iso-Transcriptomics analysis (FIT). This framework uses a rich isoform-level annotation database of functional domains, motifs and sites -both coding and non-coding- and introduces novel analysis methods to interrogate different aspects of the functional relevance of isoform complexity. The Functional Diversity Analysis (FDA) evaluates the variability at the inclusion/exclusion of functional domains across annotated transcripts of the same gene. Parameters can be set to evaluate if AltTP partially or fully disrupts functional elements. FDA is a measure of the potential of a multiple isoform transcriptome to have a functional impact. By combining these functional labels with expression data, the Differential Analysis Module evaluates the relative contribution of transcriptional (i.e. gene level) and post-transcriptional (i.e. transcript/protein levels) regulation on the biology of the system. Measures of isoform relevance such as Minor Isoform Filtering, Isoform Switching Events and Total Isoform Usage Change contribute to restricting analysis to biologically meaningful changes. Finally, novel methods for Differential Feature Inclusion, Co-Feature Inclusion, and the combination of UTR-lengthening with Alternative Polyadenylation analyses carefully dissects the contextual regulation of functional elements resulting from differential isoforms usage. These methods are implemented in the software tappAS, a user-friendly Java application that brings FIT to the hands of non-expert bioinformaticians supporting several model and non-model species. tappAS complements statistical analyses with powerful browsing tools and highly informative gene/transcript/CDS graphs.\n\nWe applied tappAS to the analysis of two mouse Neural Precursor Cells (NPCs) and Oligodendrocyte Precursor Cells (OPCs) whose transcriptome was defined by PacBio and quantified by Illumina. Using FDA we confirmed the high potential of AltTP regulation in our system, in which 90% of multi-isoform genes presented variation in functional features at the transcript or protein level. The Differential Analysis module revealed a high interplay between transcriptional and AltTP regulation in neural development, mainly controlled by differential expression, but where AltTP acts the main driver of important neural development biological mechanisms such as vesicle trafficking, signal transduction and RNA processing. The DFI analysis revealed that, globally, AltTP increased the availability of functional features in differentiated neural cells. DFI also showed that AltTP is a mechanism for altering gene function by changing cellular localization and binding properties of proteins, via the differential inclusion of NLS, transmembrane domains or DNA binding motifs, for example. Some of these findings were experimentally validated by others and us.\n\nIn summary, we propose a novel framework for the functional analysis of transcriptomes at isoform resolution. We anticipate the tappAS tool will be an important resource for the adoption of the Functional Iso-Transcriptomics analysis by functional genomics community.

bioinformatics↗

bioRxiv2019

Genetic predisposition to mosaic Y chromosome loss in blood is associated with genomic instability in other tissues and susceptibility to non-haematological cancers

Mosaic loss of chromosome Y (LOY) in circulating white blood cells is the most common form of clonal mosaicism, yet our knowledge of the causes and consequences of this is limited. Using a newly developed approach, we estimate that 20% of the UK Biobank male population (N=205,011) has detectable LOY. We identify 156 autosomal genetic determinants of LOY, which we replicate in 757,114 men of European and Japanese ancestry. These loci highlight genes involved in cell-cycle regulation, cancer susceptibility, somatic drivers of tumour growth and cancer therapy targets. Genetic susceptibility to LOY is associated with non-haematological health outcomes in both men and women, supporting the hypothesis that clonal haematopoiesis is a biomarker of genome instability in other tissues. Single-cell RNA sequencing identifies dysregulated autosomal gene expression in leukocytes with LOY, providing insights into how LOY may confer cellular growth advantage. Collectively, these data highlight the utility of studying clonal mosaicism to uncover fundamental mechanisms underlying cancer and other ageing-related diseases.

genetics↗