Biology subjects

Young, E.

Publications and source records attributed to Young, E..

23 records · Page 2Linked to original sources

bioRxiv2019

Comprehensive Analysis of Human Subtelomeres by Whole Genome Mapping

Detailed comprehensive knowledge of the structures of individual long-range telomere-terminal haplotypes are needed to understand their impact on telomere function, and to delineate the population structure and evolution of subtelomere regions. However, the abundance of large evolutionarily recent segmental duplications and high levels of large structural variations have complicated both the mapping and sequence characterization of human subtelomere regions. Here, we use high throughput optical mapping of large single DNA molecules in nanochannel arrays for 154 human genomes from 26 populations to present a comprehensive look at human subtelomere structure and variation. The results catalog many novel long-range subtelomere haplotypes and determine the frequencies and contexts of specific subtelomeric duplicons on each chromosome arm, helping to clarify the currently ambiguous nature of many specific subtelomere structures as represented in the current reference sequence (HG38). The organization and content of some duplicons in subtelomeres appear to show both chromosome arm and population-specific trends. Based upon these trends we estimate a timeline for the spread of these duplication blocks.\n\nAuthor SummaryThe ends of human chromosomes have caps called telomeres that are essential. These telomeres are influenced by the portions of DNA next to them, a region known as the subtelomere. We need to better understand the subtelomeric region to understand how it impacts the telomeres. This subtelomeric region is not well described in the current references. This is due to large variations in this region and portions that are repeated many times, making current sequencing technologies struggle to capture these regions. Many of these variations are evolutionary recent. Here we use 154 different samples from the 26 geographic regions of the world to gain a better understanding of the variation in these regions. We found many new haplotypes and clarified the haplotypes existing in the current reference. We then examined population and chromosome specific trends.

genomics↗

bioRxiv2019

STAT5: A Target of Antagonism by Neurotropic Flaviviruses

Flaviviruses are a diverse group of arthropod-borne viruses responsible for numerous significant public health threats; therefore, understanding the interactions between these viruses and the human immune response remains vital. Earlier work has found that WNV and ZIKV infect human DCs and can block antiviral immune responses in DCs. Previously, we used mRNA sequencing and weighted gene co-expression network analysis (WGCNA) to define molecular signatures of antiviral DC responses following activation of innate immune signaling (RIG-I, MDA5, or type I IFN signaling) or infection with WNV. Using this approach, we found that several genes involved in T cell co-signaling and antigen processing were not enriched in DCs during WNV infection. Using cis-regulatory sequence analysis, STAT5 was identified as a regulator of DC activation and immune responses downstream of innate immune signaling that was not activated during either WNV or ZIKV infection. Mechanistically, WNV and ZIKV actively blocked STAT5 phosphorylation downstream of RIG-I, IFN{beta}, and IL-4, but not GM-CSF signaling. Unexpectedly, dengue virus serotypes 1-4 (DENV1-4) and the yellow fever 17D vaccine strain (YFV-17D) did not antagonize STAT5 phosphorylation. In contrast to WNV, ZIKV inhibited JAK1 and TYK2 phosphorylation following type I IFN treatment, suggesting divergent mechanisms used by these viruses to inhibit STAT5 activation. Combined, these findings identify STAT5 as a target of antagonism by specific pathogenic flaviviruses to subvert the immune response in infected DCs.\n\nImportanceFlaviviruses are a diverse group of insect-borne viruses responsible for numerous significant public health threats. Previously, we used a computational biology approach to define molecular signatures of antiviral DC responses following activation of innate immune signaling or infection with WNV. In this work, we identify STAT5 as a regulator of DC activation and antiviral immune responses downstream of innate immune signaling that was not activated during either WNV or ZIKV infection. WNV and ZIKV actively blocked STAT5 phosphorylation downstream of RIG-I, IFN{beta}, and IL-4, but not GM-CSF signaling. However, other related flaviviruses, dengue virus serotypes 1-4 and yellow fever 17D vaccine strain, did not antagonize STAT5 phosphorylation. Mechanistically, WNV and ZIKV showed differential inhibition of Jak kinases upstream of STAT5, suggesting divergent countermeasures to inhibit STAT5 activation. Combined, these findings identify STAT5 as a target of antagonism by specific pathogenic flaviviruses to subvert antiviral immune responses in human DCs.

microbiology↗

bioRxiv2019

Single cell q-PCR derived expression profiles of identified sensory neurons

Sensory neurons are chemically and functionally heterogeneous and this heterogeneity has been examined extensively over the last several decades. These studies have employed a variety of different methodologies, including anatomical, electrophysiological and molecular approaches. Recent studies using next generation sequencing techniques have examined the transcriptome of single sensory neurons. Although, these reports have provided a wealth of exciting new information on the heterogeneity of sensory neurons, correlation with functional types is lacking. Here, we employed retrograde tracing of cutaneous and muscle afferents to examine the variety of mRNA expression profiles of individual, target-specific sensory neurons. In addition, we used an ex vivo skin/nerve/DRG/ spinal cord preparation to record and characterize the functional response properties of individual cutaneous sensory neurons that were then intracellularly labeled with fluorescent dyes, recovered from dissociated cultures and analyzed for gene expression. We found that by using single cell qPCR techniques and a limited set of genes, we can identify transcriptionally distinct groups. We have also used calcium imaging and single cell qPCR to determine the correlation between levels of mRNA expression and functional protein expression and how functional properties correlated with the different transcriptional groups. These studies show that although transcriptomics does map to functional types, within any one functional subgroup, there are highly variable patterns of gene expression. Thus, studies that rely on the expression pattern of one or a few genes as a stand in for physiological experiments, runs a high risk of data misinterpretation with respect to function. Significance statementExpression profiles of unidentified sensory neurons have been recently studied using RNASeq techniques. Here, we utilize a multifactorial approach to target identified cutaneous and muscle afferents to examine expression and functional levels of specific high priority candidate genes using ex vivo electrophysiology, Ca2+ imaging, and single cell qPCR. Using this methodology, we were able to identify specific groups of neurons with distinct functional properties that corresponded to unique transcriptional profiles. This represents the first attempt to relate neuronal phenotype with levels of gene expression in single identified afferents and highlights the importance of combining functional analysis with transcriptomics.

neuroscience↗

bioRxiv2018

Parkinson’s disease genetics: identifying novel risk loci, providing causal insights and improving estimates of heritable risk

We performed the largest genome-wide association study of PD to date, involving the analysis of 7.8M SNPs in 37.7K cases, 18.6K UK Biobank proxy-cases, and 1.4M controls. We identified 90 independent genome-wide significant signals across 78 loci, including 38 independent risk signals in 37 novel loci. These variants explained 26-36% of the heritable risk of PD. Tests of causality within a Mendelian randomization framework identified putatively causal genes for 70 risk signals. Tissue expression enrichment analysis suggested that signatures of PD loci were heavily brain-enriched, consistent with specific neuronal cell types being implicated from single cell expression data. We found significant genetic correlations with brain volumes, smoking status, and educational attainment. In sum, these data provide the most comprehensive understanding of the genetic architecture of PD to date by revealing many additional PD risk loci, providing a biological context for these risk factors, and demonstrating that a considerable genetic component of this disease remains unidentified.

genetics↗

bioRxiv2018

Dynamics of the p53 response to ionizing and ultraviolet radiation

The tumor suppressor protein p53 compiles information about cellular stressors to make decisions on whether the cell should survive or undergo apoptosis. However, the p53 response depends on the source of damage, displaying a digital oscillatory response after ionizing radiation (IR) damage and a proportional non-oscillatory response following UV damage. We propose a mathematical model that qualitatively replicates this observed behavior. The difference in p53 dynamics in the model results from two mechanisms: IR damage is fully detected minutes after exposure while UV damage is detected over several hours; and the p53-controlled transcriptional response is dominated by inactive p53 following UV damage. In particular, we hypothesize that an unidentified positive feedback loop controlled by inactive p53 is required to maintain the qualitative high p53 response to UV damage. This work proposes an explanation for two distinct responses of p53 to DNA damage and how each response can lead to cell cycle arrest or apoptosis.\n\nAuthor summaryWe propose a mathematical model hypothesizing how the tumor suppressor protein p53 produces two contrasting dynamical responses in response to different types of DNA damage. In particular, we predict the existence of a positive feedback loop controlled by the inactive form of p53, which allows the cell to respond to slowly detected damage. The existence of differing dynamic responses by p53 has implications for our understanding of tumor development and possibly p53-related therapeutic strategies.

cancer biology↗