Biology subjects

Lichtenstein, L.

Publications and source records attributed to Lichtenstein, L..

4 recordsLinked to original sources

bioRxiv2019

Calling Somatic SNVs and Indels with Mutect2

Mutect2 is a somatic variant caller that uses local assembly and realignment to detect SNVs and indels. Assembly implies whole haplotypes and read pairs, rather than single bases, as the atomic units of biological variation and sequencing evidence, improving variant calling. Beyond local assembly and alignment, Mutect2 is based on several probabilistic models for genotyping and filtering that work well with and without a matched normal sample and for all sequencing depths.

bioinformatics↗

bioRxiv2019

Somatic Truth Data from Cell Lineage

Existing somatic benchmark datasets for human sequencing data use germline variants, synthetic methods, or expensive validations, none of which are satisfactory for providing a large collection of true somatic variation across a whole genome. Here we propose a dataset of short somatic mutations, that are validated using a known cell lineage. The dataset contains 56,974 (2,687 unique) Single Nucleotide Variations (SNV), 6,370 (316 unique) small Insertions and Deletions (Indels), and 144 (8 unique) Copy Number Variants (CNV) across 98 in silico mixed truth sets with a high confidence region covering 2.7 gigabases per mixture. The data is publicly available for use as a benchmarking dataset for somatic short mutation discovery pipelines.

bioinformatics↗

bioRxiv2019

Sphingomyelinase disables Piezo1 channel inactivation to enable sustained response to mechanical force

Piezo1 channels are determinants of vascular responses to fluid flow. They importantly provide sustained response to flow, but this property contrasts with the rapid inactivation that has become a hallmark of the channels in heterologous overexpression studies. Here we reveal a mechanism by which blood vessels disable inactivation to enable sustained physiological response. Creation of a molecular model of Piezo1 channel in defined lipid membranes suggested potential modulation by sphingomyelin and its product ceramide. Biological relevance was indicated by the observation that exogenous sphingomyelinase enhanced Piezo1-mediated Ca2+ entry in cultured endothelial cells. We therefore hypothesised that endogenous sphingomyelinase suppresses channel inactivation. Remarkably, in endothelium freshly-isolated from murine artery, neutral sphingomyelinase inhibitors or genetic disruption of sphingomyelin phosphodiesterase 3 (SMPD3) caused flow- and pressure-activated Piezo1 channels to become inactivating. SMPD3 retained its ability to disable inactivation in cell-free membrane patches, providing evidence for a membrane localised effect. The data suggest that inherent inactivation of Piezo1 channels is disabled by enzymatic control of lipid environment to enable physiological response to mechanical force.

physiology↗

bioRxiv2019

Piezo1 channel activates ADAM10 sheddase to regulate Notch1 and gene expression

Mechanical force has emerged as a determinant of Notch signalling but the mechanisms of force sensing and coupling to Notch are unclear. Here we propose a role for Piezo1 channels, the recently identified mechanosensors of mammalian systems. Piezo1 channel opening in response to shear stress or a chemical agonist led to activation of a disintegrin and metalloproteinase domain-containing protein 10 (ADAM10), a Ca2+-regulated transmembrane sheddase that mediates S2 Notch1 cleavage. Consistent with this observation there was increased Notch1 intracellular domain (NICD) that depended on ADAM10 and the downstream S3 cleavage enzyme, {gamma}-secretase. Endothelial-specific disruption of Piezo1 in mice led to decreased Notch1-regulated gene expression in hepatic vasculature, consistent with prior evidence that Notch1 controls hepatic perfusion. The data suggest Piezo1 as a mechanism for coupling physiological force at the endothelium to ADAM10, Notch1, gene expression and vascular function.

cell biology↗