Multiplexed Single-cell Metabolic Profiles Organize the Spectrum of Cytotoxic Human T Cells, bioRxiv, 2020-01-18

SummaryCellular metabolism regulates immune cell activation, differentiation and effector functions to the extent that its perturbation can augment immune responses. However, the analytical technologies available to study cellular metabolism lack single-cell resolution, obscuring metabolic heterogeneity and its connection to immune phenotype and function. To that end, we utilized high-dimensional, antibody-based technologies to simultaneously quantify the single-cell metabolic regulome in combination with phenotypic identity. Mass cytometry (CyTOF)-based application of this approach to early human T cell activation enabled the comprehensive reconstruction of the coordinated metabolic remodeling of naïve CD8+ T cells and aligned with conventional bulk assays for glycolysis and oxidative phosphorylation. Extending this analysis to a variety of tissue-resident immune cells revealed tissue-restricted metabolic states of human cytotoxic T cells, including metabolically repressed subsets that expressed CD39 and PD1 and that were enriched in colorectal carcinoma versus healthy adjacent tissue. Finally, combining this approach with multiplexed ion beam imaging by time-of-flight (MIBI-TOF) demonstrated the existence of spatially enriched metabolic neighborhoods, independent of cell identity and additionally revealed exclusion of metabolically repressed cytotoxic T cell states from the tumor-immune boundary in human colorectal carcinoma. Overall, we provide an approach that permits the robust approximation of metabolic states in individual cells along with multimodal analysis of cell identity and functional characteristics that can be applied to human clinical samples to study cellular metabolism how it may be perturbed to affect immunological outcomes.

biorxiv immunology 100-200-users 2020

Distinguishing the neural correlates of perceptual awareness and post-perceptual processing, bioRxiv, 2020-01-17

AbstractTo identify the neural correlates of perceptual awareness, researchers often compare the differences in neural activation between conditions in which an observer is or is not aware of a target stimulus. While intuitive, this approach often contains a critical limitation In order to link brain activity with perceptual awareness, observers traditionally report the contents of their perceptual experience. However, relying on observers’ reports is problematic because it makes it difficult to know if the neural responses being measured are associated with conscious perception per se or with post-perceptual processes involved in the reporting task (i.e., working memory, decision-making, etc.). To address this issue, we combined a standard visual masking paradigm with a recently developed “no-report” paradigm. In the visual masking paradigm, observers saw images of animals and objects that were visible or invisible depending on their proximity to masks. Meanwhile, on half of the trials, observers reported the contents of their perceptual experience (i.e., report condition), while on the other half of trials they refrained from reporting about their experiences (i.e., no-report condition). We used electroencephalography (EEG) to examine how visibility interacts with reporting by measuring the P3b event related potential (ERP), one of the proposed canonical “signatures” of conscious processing. Overall, we found a robust P3b in the report condition, but no P3b whatsoever in the no-report condition. This finding suggests that the P3b itself is not a neural signature of conscious processing and highlights the importance of carefully distinguishing the neural correlates of perceptual awareness from post-perceptual processing.Significance statementWhat are the neural signatures that differentiate conscious and unconscious processing in the brain? Perhaps the most well-established candidate signature is the P3b event-related potential (ERP), a late slow wave that appears when observers are aware of a stimulus, but disappears when a stimulus fails to reach awareness. Here, however, we found that the P3b does not track what observers are perceiving but instead tracks what observers are reporting. When observers are aware of simple visual stimuli, the P3b is nowhere to be found unless observers are reporting the contents of their experience. These results challenge the well-established notion of the P3b as a neural marker of awareness and highlight the need for new approaches to the neuroscience of consciousness.

biorxiv neuroscience 0-100-users 2020

Investigating the Genetic Architecture of Non-Cognitive Skills Using GWAS-by-Subtraction, bioRxiv, 2020-01-16

AbstractEducational attainment (EA) is influenced by cognitive abilities and by other characteristics and traits. However little is known about the genetic architecture of these “non-cognitive” contributions to EA. Here, we use Genomic Structural Equation Modelling and results of prior genome-wide association studies (GWASs) of EA (N = 1,131,881) and cognitive test performance (N = 257,841) to estimate SNP associations with variation in EA that is independent of cognitive ability. We identified 157 genome-wide significant loci and a polygenic architecture accounting for 57% of genetic variance in EA. Phenotypic and biological annotation revealed that (1) both cognitive and non-cognitive contributions to EA were genetically correlated with socioeconomic success and longevity; and (2) non-cognitive contributions to EA were related to personality, decision making, risk-behavior, and increased risk for psychiatric disorders; (3) non-cognitive and cognitive contributions to EA were enriched in the same tissues and cell types, but (4) showed different associations with gray-matter neuroimaging phenotypes.

biorxiv genetics 100-200-users 2020

The structure and global distribution of the endoplasmic reticulum network is actively regulated by lysosomes, bioRxiv, 2020-01-16

AbstractThe endoplasmic reticulum (ER) comprises morphologically and functionally distinct domains, sheets and interconnected tubules. These domains undergo dynamic reshaping, in response to changes in the cellular environment. However, the mechanisms behind this rapid remodeling within minutes are largely unknown. Here, we report that ER remodeling is actively driven by lysosomes, following lysosome repositioning in response to changes in nutritional status. The anchorage of lysosomes to ER growth tips is critical for ER tubule elongation and connection. We validate this causal link via the chemo- and optogenetically driven re-positioning of lysosomes, which leads to both a redistribution of the ER tubules and its global morphology. Lysosomes sense metabolic change in the cell and regulate ER tubule distribution accordingly. Dysfunction in this mechanism during axonal extension may lead to axonal growth defects. Our results demonstrate a critical role of lysosome-regulated ER dynamics and reshaping in nutrient responses and neuronal development.

biorxiv cell-biology 100-200-users 2020

Theoretical and empirical quantification of the accuracy of polygenic scores in ancestry divergent populations, bioRxiv, 2020-01-16

AbstractPolygenic scores (PGS) have been widely used to predict complex traits and risk of diseases using variants identified from genome-wide association studies (GWASs). To date, most GWASs have been conducted in populations of European ancestry, which limits the use of GWAS-derived PGS in non-European populations. Here, we develop a new theory to predict the relative accuracy (RA, relative to the accuracy in populations of the same ancestry as the discovery population) of PGS across ancestries. We used simulations and real data from the UK Biobank to evaluate our results. We found across various simulation scenarios that the RA of PGS based on trait-associated SNPs can be predicted accurately from modelling linkage disequilibrium (LD), minor allele frequencies (MAF), cross-population correlations of SNP effect sizes and heritability. Altogether, we find that LD and MAF differences between ancestries explain alone up to ~70% of the loss of RA using European-based PGS in African ancestry for traits like body mass index and height. Our results suggest that causal variants underlying common genetic variation identified in European ancestry GWASs are mostly shared across continents.

biorxiv genetics 0-100-users 2020

A behavioral polymorphism caused by a single gene inside a supergene, bioRxiv, 2020-01-15

AbstractBehavioral evolution relies on genetic changes, yet few social behaviors can be traced to specific genetic sequences in vertebrates. Here, we show experimental evidence that differentiation of a single gene has contributed to divergent behavioral phenotypes in the white-throated sparrow, a common North American songbird. In this species, one of two alleles of ESR1, encoding estrogen receptor α (ERα), has been captured inside a differentiating supergene that segregates with an aggressive phenotype, such that ESR1 expression predicts aggression. Here, we show that the aggressive phenotype associated with the supergene is prevented by ESR1 knockdown in a single brain region. Next, we show that in a free-living population, aggression is predicted by allelic imbalance favoring the supergene allele. Cis-regulatory variation between the two alleles affects transcription factor binding sites, DNA methylation, and rates of transcription. This work provides a rare illustration of how genotypic divergence has led to behavioral phenotypic divergence in a vertebrate.

biorxiv neuroscience 0-100-users 2020