Cell Systems

Journal: Cell Systems

Abbreviation

Cell Syst

Publisher

Elsevier

ISSN

2405-4720

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Publications 1 - 10 of 13

Conservation of metabolic regulation by phosphorylation and non-covalent small-molecule interactions
Gruber, Christoph H.; Diether, Maren; Sauer, Uwe (2021)
Cell Systems
Here, we review extant observations of protein phosphorylation and small-molecule interactions in metabolism and ask which of their specific regulatory functions are conserved in Escherichia coli and Homo sapiens. While the number of phosphosites is dramatically higher in humans, the number of metabolite-protein interactions remains largely constant. Moreover, we found the regulatory logic of metabolite-protein interactions, and in many cases also the effector molecules, to be conserved. Post-translational regulation through phosphorylation does not appear to replace this regulation in human but rather seems to add additional opportunities for fine-tuning and more complex responses. The abundance of metabolite-protein interactions in metabolism, their conserved cross-species abundance, and the apparent conservation of regulatory logic across enormous phylogenetic distance demonstrate their relevance for maintaining cellular homeostasis in these ancient biological processes.
A High-Throughput Genome-Integrated Assay Reveals Spatial Dependencies Governing Tcf7l2 Binding
Szczesnik, Tomasz; Chu, Lendy; Ho, Joshua W.K; et al. (2020)
Cell Systems
Predicting where transcription factors bind in the genome from their in vitro DNA-binding affinity is confounded by the large number of possible interactions with nearby transcription factors. To characterize the in vivo binding logic for the Wnt effector Tcf7l2, we developed a high-throughput screening platform in which thousands of synthesized DNA phrases are inserted into a specific genomic locus, followed by measurement of Tcf7l2 binding by DamID. Using this platform at two genomic loci in mouse embryonic stem cells, we show that while the binding of Tcf7l2 closely follows the in vitro motif-binding strength and is influenced by local chromatin accessibility, it is also strongly affected by the surrounding 99 bp of sequence. Through controlled sequence perturbation, we show that Oct4 and Klf4 motifs promote Tcf7l2 binding, particularly in the adjacent ∼50 bp and oscillating with a 10.8-bp phasing relative to these cofactor motifs, which matches the turn of a DNA helix. © 2020 The Authors Transcription factor binding in cells depends on interactions with other proteins. We have developed a high-throughput screening platform to study transcription factor binding strength at thousands of variable sequences in a fixed genomic locus. We find that binding of the Wnt effector Tcf7l2 in mouse embryonic stem cells depends on proximity and phasing that matches the turn of the DNA helix relative to its cofactors Oct4 and Klf4. © 2020 The Authors
Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry
Chevrier, Stéphane; Crowell, Helena L.; Zanotelli, Vito R.T.; et al. (2018)
Cell Systems
The advent of mass cytometry increased the number of parameters measured at the single-cell level while decreasing the extent of crosstalk between channels relative to dye-based flow cytometry. Although reduced, spillover still exists in mass cytometry data, and minimizing its effect requires considerable expert knowledge and substantial experimental effort. Here, we describe a novel bead-based compensation workflow and R-based software that estimates and corrects for interference between channels. We performed an in-depth characterization of the spillover properties in mass cytometry, including limitations defined by the linear range of the mass cytometer and the reproducibility of the spillover over time and across machines. We demonstrated the utility of our method in suspension and imaging mass cytometry. To conclude, our approach greatly simplifies the development of new antibody panels, increases flexibility for antibody-metal pairing, opens the way to using less pure isotopes, and improves overall data quality, thereby reducing the risk of reporting cell phenotype artifacts.
The sound of silence: Transgene silencing in mammalian cell engineering
Cabrera, Alan; Edelstein, Hailey I.; Glykofrydis, Fokion; et al. (2022)
Cell Systems
To elucidate principles operating in native biological systems and to develop novel biotechnologies, synthetic biology aims to build and integrate synthetic gene circuits within native transcriptional networks. The utility of synthetic gene circuits for cell engineering relies on the ability to control the expression of all constituent transgene components. Transgene silencing, defined as the loss of expression over time, persists as an obstacle for engineering primary cells and stem cells with transgenic cargos. In this review, we highlight the challenge that transgene silencing poses to the robust engineering of mammalian cells, outline potential molecular mechanisms of silencing, and present approaches for preventing transgene silencing. We conclude with a perspective identifying future research directions for improving the performance of synthetic gene circuits.
Perfect adaptation in biology
Khammash, Mustafa Hani (2021)
Cell Systems
A distinctive feature of many biological systems is their ability to adapt to persistent stimuli or disturbances that would otherwise drive them away from a desirable steady state. The resulting stasis enables organisms to function reliably while being subjected to very different external environments. This perspective concerns a stringent type of biological adaptation, robust perfect adaptation (RPA), that is resilient to certain network and parameter perturbations. As in engineered control systems, RPA requires that the regulating network satisfy certain structural constraints that cannot be avoided. We elucidate these ideas using biological examples from systems and synthetic biology. We then argue that understanding the structural constraints underlying RPA allows us to look past implementation details and offers a compelling means to unravel regulatory biological complexity.
Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry
Schulz, Daniel; Zanotelli, Vito R.T.; Fischer, Jana R.; et al. (2018)
Cell Systems
Statistical modeling and analysis of cell counts from multiplexed imaging data
Bost, Pierre; Casanova, Ruben; Mor, Uria; et al. (2025)
Cell Systems
The rapid development of multiplexed imaging technologies has enabled the spatial cartography of various healthy and tumor tissues. However, adequate statistical models are still lacking to compare tissue compositions across sample groups. Here, we developed two statistical models that accurately describe the distributions of cell counts in an imaging mass cytometry dataset comprising tissues from a lymph node, COVID-19-affected lung samples, and Hashimoto disease. The parameters of these distributions are directly linked to the field of view size and to cellular properties, including density and spatial aggregation. We identified statistical tests that improved statistical power for differential abundance testing compared with the commonly used rank-based test. Our analysis revealed spatial aggregation as the main determinant of statistical power and that high numbers of fields of view are required when cells are highly aggregated. To overcome this challenge, we propose a stratified sampling strategy that considerably reduces the required sample size.
Programming cells to sniff in digital
Müller, Marius; Fussenegger, Martin (2017)
Cell Systems
Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer
Goncalves, Emanuel; Fragoulis, Athanassios; Garcia-Alonso, Luz; et al. (2017)
Cell Systems
Copy-number variations (CNVs) are ubiquitous in cancer and often act as driver events, but the effects of CNVs on the proteome of tumors are poorly understood. Here, we analyze recently published genomics, transcriptomics, and proteomics datasets made available by CPTAC and TCGA consortia on 282 breast, ovarian, and colorectal tumor samples to investigate the impact of CNVs in the proteomes of these cells. We found that CNVs are buffered by post-transcriptional regulation in 23%–33% of proteins that are significantly enriched in protein complex members. Our analyses show that complex subunits are highly co-regulated, and some act as rate-limiting steps of complex assembly, as their depletion induces decreased abundance of other complex members. We identified 48 such rate-limiting interactions and experimentally confirmed our predictions on the interactions of AP3B1 with AP3M1 and GTF2E2 with GTF2E1. This study highlights the importance of post-transcriptional mechanisms in cancer that allow cells to cope with their altered genomes.
A Simple and Flexible Computational Framework for Inferring Sources of Heterogeneity from Single-Cell Dynamics
Dharmarajan, Lekshmi; Kaltenbach, Hans-Michael; Rudolf, Fabian; et al. (2019)
Cell Systems
Single-cell time-lapse data provide the means for disentangling sources of cell-to-cell and intra-cellular variability, a key step for understanding heterogeneity in cell populations. However, single-cell analysis with dynamic models is a challenging open problem: current inference methods address only single-gene expression or neglect parameter correlations. We report on a simple, flexible, and scalable method for estimating cell-specific and population-average parameters of non-linear mixed-effects models of cellular networks, demonstrating its accuracy with a published model and dataset. We also propose sensitivity analysis for identifying which biological sub-processes quantitatively and dynamically contribute to cell-to-cell variability. Our application to endocytosis in yeast demonstrates that dynamic models of realistic size can be developed for the analysis of single-cell data and that shifting the focus from single reactions or parameters to nuanced and time-dependent contributions of sub-processes helps biological interpretation. Generality and simplicity of the approach will facilitate customized extensions for analyzing single-cell dynamics.

Publications 1 - 10 of 13

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