22 research outputs found
Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images
Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images
of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL
maps are derived through computational staining using a convolutional neural network trained to
classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and
correlation with overall survival. TIL map structural patterns were grouped using standard
histopathological parameters. These patterns are enriched in particular T cell subpopulations
derived from molecular measures. TIL densities and spatial structure were differentially enriched
among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial
infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic
patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for
the TCGA image archives with insights into the tumor-immune microenvironment
Membrane-mediated membrane protein interactions drive membrane protein organization
International audienc
Membrane-mediated protein interactions drive membrane protein organization
International audienceAbstract The plasma membrane’s main constituents, i.e., phospholipids and membrane proteins, are known to be organized in lipid-protein functional domains and supercomplexes. No active membrane-intrinsic process is known to establish membrane organization. Thus, the interplay of thermal fluctuations and the biophysical determinants of membrane-mediated protein interactions must be considered to understand membrane protein organization. Here, we used high-speed atomic force microscopy and kinetic and membrane elastic theory to investigate the behavior of a model membrane protein in oligomerization and assembly in controlled lipid environments. We find that membrane hydrophobic mismatch modulates oligomerization and assembly energetics, and 2D organization. Our experimental and theoretical frameworks reveal how membrane organization can emerge from Brownian diffusion and a minimal set of physical properties of the membrane constituents
Image3_Stabilization of a Membrane-Associated Amyloid-β Oligomer for Its Validation in Alzheimer's Disease.TIF
<p>We have recently reported on the preparation of a membrane-associated β-barrel Pore-Forming Aβ42 Oligomer (βPFO<sub>Aβ42</sub>). It corresponds to a stable and homogeneous Aβ42 oligomer that inserts into lipid bilayers as a well-defined pore and adopts a specific structure with characteristics of a β-barrel arrangement. As a follow-up of this work, we aim to establish βPFO<sub>Aβ42</sub>'s relevance in Alzheimer's disease (AD). However, βPFO<sub>Aβ42</sub> is formed under dodecyl phosphocholine (DPC) micelle conditions—intended to mimic the hydrophobic environment of membranes—which are dynamic. Consequently, dilution of the βPFO<sub>Aβ42</sub>/DPC complex in a detergent-free buffer leads to dispersion of the DPC molecules from the oligomer surface, leaving the oligomer without the hydrophobic micelle belt that stabilizes it. Since dilution is required for any biological test, transfer of βPFO<sub>Aβ42</sub> from DPC micelles into another hydrophobic biomimetic membrane environment, that remains associated with βPFO<sub>Aβ42</sub> even under high dilution conditions, is a requisite for the validation of βPFO<sub>Aβ42</sub> in AD. Here we describe conditions for exchanging DPC micelles with amphipols (APols), which are amphipathic polymers designed to stabilize membrane proteins in aqueous solutions. APols bind in an irreversible but non-covalent manner to the hydrophobic surface of membrane proteins preserving their structure even under extreme dilution conditions. We tested three types of APols with distinct physical-chemical properties and found that the βPFO<sub>Aβ42</sub>/DPC complex can only be trapped in non-ionic APols (NAPols). The characterization of the resulting βPFO<sub>Aβ42</sub>/NAPol complex by biochemical tools and structural biology techniques allowed us to establish that the oligomer structure is maintained even under high dilution. Based on these findings, this work constitutes a first step towards the in vivo validation of βPFO<sub>Aβ42</sub> in AD.</p
Image1_Stabilization of a Membrane-Associated Amyloid-β Oligomer for Its Validation in Alzheimer's Disease.TIF
<p>We have recently reported on the preparation of a membrane-associated β-barrel Pore-Forming Aβ42 Oligomer (βPFO<sub>Aβ42</sub>). It corresponds to a stable and homogeneous Aβ42 oligomer that inserts into lipid bilayers as a well-defined pore and adopts a specific structure with characteristics of a β-barrel arrangement. As a follow-up of this work, we aim to establish βPFO<sub>Aβ42</sub>'s relevance in Alzheimer's disease (AD). However, βPFO<sub>Aβ42</sub> is formed under dodecyl phosphocholine (DPC) micelle conditions—intended to mimic the hydrophobic environment of membranes—which are dynamic. Consequently, dilution of the βPFO<sub>Aβ42</sub>/DPC complex in a detergent-free buffer leads to dispersion of the DPC molecules from the oligomer surface, leaving the oligomer without the hydrophobic micelle belt that stabilizes it. Since dilution is required for any biological test, transfer of βPFO<sub>Aβ42</sub> from DPC micelles into another hydrophobic biomimetic membrane environment, that remains associated with βPFO<sub>Aβ42</sub> even under high dilution conditions, is a requisite for the validation of βPFO<sub>Aβ42</sub> in AD. Here we describe conditions for exchanging DPC micelles with amphipols (APols), which are amphipathic polymers designed to stabilize membrane proteins in aqueous solutions. APols bind in an irreversible but non-covalent manner to the hydrophobic surface of membrane proteins preserving their structure even under extreme dilution conditions. We tested three types of APols with distinct physical-chemical properties and found that the βPFO<sub>Aβ42</sub>/DPC complex can only be trapped in non-ionic APols (NAPols). The characterization of the resulting βPFO<sub>Aβ42</sub>/NAPol complex by biochemical tools and structural biology techniques allowed us to establish that the oligomer structure is maintained even under high dilution. Based on these findings, this work constitutes a first step towards the in vivo validation of βPFO<sub>Aβ42</sub> in AD.</p
Image2_Stabilization of a Membrane-Associated Amyloid-β Oligomer for Its Validation in Alzheimer's Disease.TIF
<p>We have recently reported on the preparation of a membrane-associated β-barrel Pore-Forming Aβ42 Oligomer (βPFO<sub>Aβ42</sub>). It corresponds to a stable and homogeneous Aβ42 oligomer that inserts into lipid bilayers as a well-defined pore and adopts a specific structure with characteristics of a β-barrel arrangement. As a follow-up of this work, we aim to establish βPFO<sub>Aβ42</sub>'s relevance in Alzheimer's disease (AD). However, βPFO<sub>Aβ42</sub> is formed under dodecyl phosphocholine (DPC) micelle conditions—intended to mimic the hydrophobic environment of membranes—which are dynamic. Consequently, dilution of the βPFO<sub>Aβ42</sub>/DPC complex in a detergent-free buffer leads to dispersion of the DPC molecules from the oligomer surface, leaving the oligomer without the hydrophobic micelle belt that stabilizes it. Since dilution is required for any biological test, transfer of βPFO<sub>Aβ42</sub> from DPC micelles into another hydrophobic biomimetic membrane environment, that remains associated with βPFO<sub>Aβ42</sub> even under high dilution conditions, is a requisite for the validation of βPFO<sub>Aβ42</sub> in AD. Here we describe conditions for exchanging DPC micelles with amphipols (APols), which are amphipathic polymers designed to stabilize membrane proteins in aqueous solutions. APols bind in an irreversible but non-covalent manner to the hydrophobic surface of membrane proteins preserving their structure even under extreme dilution conditions. We tested three types of APols with distinct physical-chemical properties and found that the βPFO<sub>Aβ42</sub>/DPC complex can only be trapped in non-ionic APols (NAPols). The characterization of the resulting βPFO<sub>Aβ42</sub>/NAPol complex by biochemical tools and structural biology techniques allowed us to establish that the oligomer structure is maintained even under high dilution. Based on these findings, this work constitutes a first step towards the in vivo validation of βPFO<sub>Aβ42</sub> in AD.</p
Image3_Stabilization of a Membrane-Associated Amyloid-β Oligomer for Its Validation in Alzheimer's Disease.TIF
<p>We have recently reported on the preparation of a membrane-associated β-barrel Pore-Forming Aβ42 Oligomer (βPFO<sub>Aβ42</sub>). It corresponds to a stable and homogeneous Aβ42 oligomer that inserts into lipid bilayers as a well-defined pore and adopts a specific structure with characteristics of a β-barrel arrangement. As a follow-up of this work, we aim to establish βPFO<sub>Aβ42</sub>'s relevance in Alzheimer's disease (AD). However, βPFO<sub>Aβ42</sub> is formed under dodecyl phosphocholine (DPC) micelle conditions—intended to mimic the hydrophobic environment of membranes—which are dynamic. Consequently, dilution of the βPFO<sub>Aβ42</sub>/DPC complex in a detergent-free buffer leads to dispersion of the DPC molecules from the oligomer surface, leaving the oligomer without the hydrophobic micelle belt that stabilizes it. Since dilution is required for any biological test, transfer of βPFO<sub>Aβ42</sub> from DPC micelles into another hydrophobic biomimetic membrane environment, that remains associated with βPFO<sub>Aβ42</sub> even under high dilution conditions, is a requisite for the validation of βPFO<sub>Aβ42</sub> in AD. Here we describe conditions for exchanging DPC micelles with amphipols (APols), which are amphipathic polymers designed to stabilize membrane proteins in aqueous solutions. APols bind in an irreversible but non-covalent manner to the hydrophobic surface of membrane proteins preserving their structure even under extreme dilution conditions. We tested three types of APols with distinct physical-chemical properties and found that the βPFO<sub>Aβ42</sub>/DPC complex can only be trapped in non-ionic APols (NAPols). The characterization of the resulting βPFO<sub>Aβ42</sub>/NAPol complex by biochemical tools and structural biology techniques allowed us to establish that the oligomer structure is maintained even under high dilution. Based on these findings, this work constitutes a first step towards the in vivo validation of βPFO<sub>Aβ42</sub> in AD.</p
Imaging longitudinal changes in articular cartilage and bone following doxycycline treatment in a rabbit anterior cruciate ligament transection model of osteoarthritis
Results and lessons learned from the sbv IMPROVER metagenomics diagnostics for inflammatory bowel disease challenge
Abstract A growing body of evidence links gut microbiota changes with inflammatory bowel disease (IBD), raising the potential benefit of exploiting metagenomics data for non-invasive IBD diagnostics. The sbv IMPROVER metagenomics diagnosis for inflammatory bowel disease challenge investigated computational metagenomics methods for discriminating IBD and nonIBD subjects. Participants in this challenge were given independent training and test metagenomics data from IBD and nonIBD subjects, which could be wither either raw read data (sub-challenge 1, SC1) or processed Taxonomy- and Function-based profiles (sub-challenge 2, SC2). A total of 81 anonymized submissions were received between September 2019 and March 2020. Most participants’ predictions performed better than random predictions in classifying IBD versus nonIBD, Ulcerative Colitis (UC) versus nonIBD, and Crohn’s Disease (CD) versus nonIBD. However, discrimination between UC and CD remains challenging, with the classification quality similar to the set of random predictions. We analyzed the class prediction accuracy, the metagenomics features by the teams, and computational methods used. These results will be openly shared with the scientific community to help advance IBD research and illustrate the application of a range of computational methodologies for effective metagenomic classification