Dataset Information

Using single-cell models to predict the functionality of synthetic circuits at the population scale.

ABSTRACT: SignificanceAt the single-cell level, biochemical processes are inherently stochastic. For many natural systems, the resulting cell-to-cell variability is exploited by microbial populations. In synthetic biology, however, the interplay of cell-to-cell variability and population processes such as selection or growth often leads to circuits not functioning as predicted by simple models. Here we show how multiscale stochastic kinetic models that simultaneously track single-cell and population processes can be obtained based on an augmentation of the chemical master equation. These models enable us to quantitatively predict complex population dynamics of a yeast optogenetic differentiation system from a specification of the circuit's components and to demonstrate how cell-to-cell variability can be exploited to purposefully create unintuitive circuit functionality.

SUBMITTER: Aditya C

PROVIDER: S-EPMC8931247 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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Using single-cell models to predict the functionality of synthetic circuits at the population scale.

Aditya Chetan C Bertaux François F Batt Gregory G Ruess Jakob J

Proceedings of the National Academy of Sciences of the United States of America 20220310 11

SignificanceAt the single-cell level, biochemical processes are inherently stochastic. For many natural systems, the resulting cell-to-cell variability is exploited by microbial populations. In synthetic biology, however, the interplay of cell-to-cell variability and population processes such as selection or growth often leads to circuits not functioning as predicted by simple models. Here we show how multiscale stochastic kinetic models that simultaneously track single-cell and population proce ...[more]

PMID: 35271387

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Project description:Deep generative models, such as variational autoencoders (VAEs) or deep Boltzmann machines (DBMs), can generate an arbitrary number of synthetic observations after being trained on an initial set of samples. This has mainly been investigated for imaging data but could also be useful for single-cell transcriptomics (scRNA-seq). A small pilot study could be used for planning a full-scale experiment by investigating planned analysis strategies on synthetic data with different sample sizes. It is unclear whether synthetic observations generated based on a small scRNA-seq dataset reflect the properties relevant for subsequent data analysis steps. We specifically investigated two deep generative modeling approaches, VAEs and DBMs. First, we considered single-cell variational inference (scVI) in two variants, generating samples from the posterior distribution, the standard approach, or the prior distribution. Second, we propose single-cell deep Boltzmann machines (scDBMs). When considering the similarity of clustering results on synthetic data to ground-truth clustering, we find that the [Formula: see text] variant resulted in high variability, most likely due to amplifying artifacts of small datasets. All approaches showed mixed results for cell types with different abundance by overrepresenting highly abundant cell types and missing less abundant cell types. With increasing pilot dataset sizes, the proportions of the cells in each cluster became more similar to that of ground-truth data. We also showed that all approaches learn the univariate distribution of most genes, but problems occurred with bimodality. Across all analyses, in comparing 10[Formula: see text] Genomics and Smart-seq2 technologies, we could show that for 10[Formula: see text] datasets, which have higher sparsity, it is more challenging to make inference from small to larger datasets. Overall, the results show that generative deep learning approaches might be valuable for supporting the design of scRNA-seq experiments.

Dataset Information

Using single-cell models to predict the functionality of synthetic circuits at the population scale.

Publications

Using single-cell models to predict the functionality of synthetic circuits at the population scale.

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