Biology subjects

Weiss, A.

Publications and source records attributed to Weiss, A..

5 recordsLinked to original sources

bioRxiv2018

Metformin induces lipogenic differentiation in myofibroblasts to reverse mouse and human lung fibrosis

Idiopathic pulmonary fibrosis is a fatal, incurable lung disease in which the intricate alveolar network of the human lung is progressively replaced by fibrotic scars, eventually leading to respiratory failure. Myofibroblasts are the effector cells that lead to abnormal deposition of extracellular matrix proteins and therefore mediate fibrotic disease not only in the lung but also in other organs. Emerging literature suggests a correlation between fibrosis and metabolic alterations in IPF. In this study, we show that the first-line antidiabetic drug, metformin, exerts potent antifibrotic effects in the lung by modulating metabolic pathways, inhibiting TGF{beta}1 action, suppressing collagen formation, activating PPAR{gamma} signaling and inducing lipogenic differentiation in lung myofibroblasts derived from human patients. Using genetic lineage tracing in a murine model of lung fibrosis, we show that metformin alters the fate of myofibroblasts and accelerates fibrosis resolution by inducing myofibroblast-tolipofibroblast transdifferentiation. Detailed pathway analysis showed that the reduction of collagen synthesis was largely AMPK-dependent, whereas the transdifferentiation of myo- to lipofibroblasts occurred in a BMP2-PPAR{gamma}-dependent fashion and was largely AMPK-independent. Our data report an unprecedented role for metformin in lung fibrosis, thus warranting further therapeutic evaluation.

cell biology↗

bioRxiv2018

Switch-like activation of Bruton’s tyrosine kinase by membrane-mediated dimerization

The transformation of molecular binding events into cellular decisions is the basis of most biological signal transduction. A fundamental challenge faced by these systems is that protein-ligand chemical affinities alone generally result in poor sensitivity to ligand concentration, endangering the system to error. Here, we examine the lipid-binding pleckstrin homology and Tec homology (PH-TH) module of Brutons tyrosine kinase (Btk) Using fluorescence correlation spectroscopy (FCS) and membrane-binding kinetic measurements, we identify a self-contained phosphatidylinositol (3,4,5)-trisphosphate (PIP3) sensing mechanism that achieves switch-like sensitivity to PIP3 levels, surpassing the intrinsic affinity discrimination of PIP3:PH binding. This mechanism employs multiple PIP3 binding as well as dimerization of Btk on the membrane surface. Mutational studies in live cells confirm that this mechanism is critical for activation of Btk in vivo. These results demonstrate how a single protein module can institute a minimalist coincidence detection mechanism to achieve high-precision discrimination of ligand concentration.

biophysics↗

bioRxiv2018

Fine-tuning of substrate preferences of the Src-family kinase Lck revealed through a high-throughput specificity screen

To obtain a comprehensive map of the intrinsic specificities of tyrosine kinase domains, we developed a high-throughput method that uses bacterial surface-display and next-generation sequencing to analyze the specificity of any tyrosine kinase against a library of thousands of peptides derived from human tyrosine phosphorylation sites. Using this approach, we identified a difference in the electrostatic recognition of substrates between the cytoplasmic Src-family tyrosine kinases Lck and c-Src. This divergence likely reflects the specialization of Lck to act in concert with the tyrosine kinase ZAP-70 in T cell receptor signaling. The current understanding of substrate recognition by tyrosine kinases emphasizes the role of localization by non-catalytic domains, but our results point to the importance of direct recognition at the kinase active site in fine-tuning specificity. Our method provides a simple approach that leverages next-generation sequencing to readily map the specificity of any tyrosine kinase at the proteome level.

biochemistry↗

bioRxiv2017

Genetic contribution to two factors of neuroticism is associated with affluence, better health, and longer life

Neuroticism is a personality trait that describes the tendency to experience negative emotions. Individual differences in neuroticism are moderately stable across much of the life course1; the trait is heritable2-5, and higher levels are associated with psychiatric disorders6-8, and have been estimated to have an economic burden to society greater than that of substance abuse, mood, or anxiety disorders9. Understanding the genetic architecture of neuroticism therefore has the potential to offer insight into the causes of psychiatric disorders, general wellbeing10, and longevity. The broad trait of neuroticism is composed of narrower traits, or factors. It was recently discovered that, whereas higher scores on the broad trait of neuroticism are associated with earlier death, higher scores on a worry/vulnerability factor are associated with living longer11. Here, we examine the genetic architectures of two neuroticism factors--worry/vulnerability and anxiety/tension--and how they contrast with the architecture of the general factor of neuroticism. We show that, whereas the polygenic load for general factor of neuroticism is associated with an increased risk of coronary artery disease (CAD), major depressive disorder, and poorer self-rated health, the genetic variants associated with high levels of the anxiety/tension and worry/vulnerability factors are associated with affluence, higher cognitive ability, better self-rated health, and longer life. We also identify the first genes associated with factors of neuroticism that are linked with these positive outcomes that show no relationship with the general factor of neuroticism.

genetics↗

bioRxiv2017

Evaluation and Design of Genome-wide CRISPR/Cas9 Knockout Screens

The adaptation of CRISPR/Cas9 technology to mammalian cell lines is transforming the study of human functional genomics. Pooled libraries of CRISPR guide RNAs (gRNAs), targeting human protein-coding genes and encoded in viral vectors, have been used to systematically create gene knockouts in a variety of human cancer and immortalized cell lines, in an effort to identify whether these knockouts cause cellular fitness defects. Previous work has shown that CRISPR screens are more sensitive and specific than pooled library shRNA screens in similar assays, but currently there exists significant variability across CRISPR library designs and experimental protocols. In this study, we re-analyze 17 genome-scale knockout screens in human cell lines from three research groups using three different genome-scale gRNA libraries, using the Bayesian Analysis of Gene Essentiality (BAGEL) algorithm to identify essential genes, to refine and expand our previously defined set of human core essential genes, from 360 to 684 genes. We use this expanded set of reference Core Essential Genes (CEG2), plus empirical data from six CRISPR knockout screens, to guide the design of a sequence-optimized gRNA library, the Toronto KnockOut version 3.0 (TKOv3) library. We demonstrate the high effectiveness of the library relative to reference sets of essential and nonessential genes as well as other screens using similar approaches. The optimized TKOv3 library, combined with the CEG2 reference set, provide an efficient, highly optimized platform for performing and assessing gene knockout screens in human cell lines.

systems biology↗