Showing papers by "Dennis Vitkup published in 2018"

Protein Stability and Avoidance of Toxic Misfolding Do Not Explain the Sequence Constraints of Highly Expressed Proteins

Abstract: The avoidance of cytotoxic effects associated with protein misfolding has been proposed as a dominant constraint on the sequence evolution and molecular clock of highly expressed proteins. Recently, Leuenberger et al. developed an elegant experimental approach to measure protein thermal stability at the proteome scale. The collected data allow us to rigorously test the predictions of the misfolding avoidance hypothesis that highly expressed proteins have evolved to be more stable, and that maintaining thermodynamic stability significantly constrains their evolution. Notably, reanalysis of the Leuenberger et al. data across four different organisms reveals no substantial correlation between protein stability and protein abundance. Therefore, the key predictions of the misfolding toxicity and related hypotheses are not supported by available empirical data. The data also suggest that, regardless of protein expression, protein stability does not substantially affect the protein molecular clock across organisms.

Quantifying spatiotemporal dynamics and noise in absolute microbiota abundances using replicate sampling

Abstract: Metagenomic sequencing has enabled detailed investigation of diverse microbial communities, but understanding their spatiotemporal dynamics remains an important challenge. Here we present DIVERS, a widely applicable method based on replicate sampling and spike-in sequencing that quantifies the contributions of temporal dynamics, spatial sampling variability and technical noise to the variances and covariances of absolute bacterial abundances. Using high resolution time series profiling, we apply DIVERS to the human gut microbiome. Our method reveals complex spatiotemporal dynamics of individual gut bacteria and unmasks key features of their behavior hidden from previous analyses.

Receptor-Based Mechanism of Cell Memory and Relative Sensing in Mammalian Signaling Networks

Abstract: Detecting relative rather than absolute changes in external signals enables cells to make decisions in fluctuating environments and diverse biological contexts. However, how mammalian signaling networks store the memories of past stimuli and use them to compute relative signals is not well understood. Using the growth factor-activated PI3K-Akt signaling pathway, we develop computational and analytical models, and experimentally validate a novel mechanism of relative sensing in mammalian cells. This non-transcriptional mechanism relies on a new form of cellular memory, where cells effectively encode past stimulation levels in the abundance of cognate receptors on the cell surface. We show the robustness and specificity of the relative sensing for two physiologically important ligands, epidermal growth factor (EGF) and hepatocyte growth factor (HGF), and across wide ranges of background stimuli. The described memory and sensing mechanism could play a role in multiple other sensory cascades where stimulation leads to a proportional reduction in the abundance of cell surface receptors.

Exons as units of phenotypic impact for truncating mutations in autism

Abstract: Autism spectrum disorders (ASD) are a group of related neurodevelopmental diseases displaying significant genetic and phenotypic heterogeneity1-4. Despite recent progress in understanding ASD genetics, the nature of phenotypic heterogeneity across probands remains unclear5,6. Notably, likely gene-disrupting (LGD) de novo mutations affecting the same gene often result in substantially different intellectual quotient (IQ) phenotypes. Nevertheless, we find that truncating mutations that affect the same exon frequently lead to strikingly similar intellectual phenotypes in unrelated ASD probands. Analogous patterns are observed for two independent probands’ cohorts and several important ASD phenotypes. These results suggest that exons, rather than genes, often represent a unit of effective phenotypic impact for truncating mutations in autism. We find that phenotypic effects are likely mediated by nonsense-mediated decay (NMD) of splicing isoforms, and that autism phenotypes are usually triggered by relatively mild (15-30%) decreases in overall gene dosage. For genes with recurrent truncating mutations, predicted expression changes can be used to infer phenotypic consequences in individual ASD probands. We further demonstrate that LGD mutations in the same exon usually lead to similar expression changes across human tissues. Therefore, analogous phenotypic patterns may be also observed in other developmental genetic disorders.

Quantification of human gut microbiota variability using replicate sampling and spike-in sequencing

Abstract: 16S rRNA amplicon sequencing has enabled detailed investigation of the spatiotemporal dynamics of the human gut microbiome and their corresponding alterations during disease. However, the contributions of temporal changes, spatial sampling location and technical sources of variability in gut microbiome studies remain poorly understood. Commonly used sequencing approaches are further limited by compositional biases due to relative abundance measurements. Here, we combine mathematical modeling with an experimental workflow based on replicate sampling and spike-in sequencing to separately quantify the major sources of gut microbiota variability measured in absolute abundances. We apply this framework to the healthy human gut microbiome and find substantial and distinct contributions to measured abundance variability associated with time, spatial sampling location and technical noise. Notably, our approach allows us to identify a critical abundance threshold (~0.01% in average taxa relative abundance) above which variability primarily results from temporal changes and below which technical noise predominates. Furthermore, we find a large contribution (~20%) to measured microbiota variability resulting from different spatial sampling locations. Across all taxa, we observe that overall patterns of temporal and spatial variability in the human gut microbiome follow closely those in other diverse ecosystems, but we also identify specific taxa whose behavior are largely associated with either underlying temporal or spatial sources. Finally, we use our approach to show that temporal factors can largely explain the significant changes in total bacterial densities observed in the gut and the abundance correlations of individual bacterial taxa. Collectively, our results highlight important pitfalls of current fecal profiling practices and provide a general framework to facilitate future quantitative ecological analysis of the human gut microbiome and other complex microbial communities.

Macroecological relationships in the dynamics of gut microbiota

Abstract: The gut microbiome is now widely recognized as a dynamic ecosystem that plays an important role in health and disease1. While current sequencing technologies make it possible to estimate relative abundances of host-associated bacteria over time2,3, the biological processes governing their dynamics remain poorly understood. Therefore, as in other ecological systems4,5, it is important to identify quantitative relationships describing global aspects of gut microbiota dynamics. Here we use multiple high-resolution time series data obtained from humans and mice6–8 to demonstrate that despite their inherent complexity, gut microbiota dynamics can be characterized by several robust scaling relationships. Remarkably, these patterns are highly similar to those previously observed across diverse ecological communities and economic systems, including the temporal fluctuations of animal and plant populations9–12 and the performance of publicly traded companies13. Specifically, we find power law relationships describing short-and long-term changes in gut microbiota abundances, species residence and return times, and the connection between the mean and variance of species abundances. The observed scaling relationships are altered in mice receiving different diets and affected by context-specific perturbations in humans. We use these macroecological relationships to reveal specific bacterial taxa whose dynamics are significantly affected by dietary and environmental changes. Overall, our results suggest that a quantitative macroecological framework will be important for characterizing and understanding complex dynamical processes in the gut microbiome.

Intellectual phenotypes in autism strongly correlate with gene dosage changes and exon locations of truncating mutations

Abstract: Autism spectrum disorders (ASD) are a group of related neurodevelopmental diseases displaying significant genetic and phenotypic heterogeneity. Despite recent progress in understanding ASD genetics, the nature of phenotypic heterogeneity across probands is currently unclear. It is also unknown how autism-associated mutations affect specific disorder phenotypes or whether similar genetic insults lead to similar phenotypic consequences. Likely gene-disrupting (LGD) de novo mutations affecting the same gene often result in substantially different intellectual quotient (IQ) phenotypes. Nevertheless, we find that truncating mutations affecting the same exon frequently lead to strikingly similar intellectual phenotypes in unrelated simplex ASD probands. Analogous patterns are observed for several other important ASD phenotypes. These findings suggest that exons, rather than genes, often represent a unit of effective phenotypic impact for truncating mutations. Our analysis shows that similar phenotypic effects are likely mediated by similar perturbations to the expression of splicing isoforms and corresponding gene dosage changes. For genes with recurrent truncating mutations, predicted changes in expression dosage strongly correlate with relative phenotypic consequences. Further analysis demonstrates that LGD mutations in the same exon often lead to similar perturbations of gene and isoform expression across human tissues. Therefore, analogous phenotypic patterns may be also observed in other developmental disorders triggered by highly penetrant genetic insults.