Elsevier

Methods

Volume 96, 1 March 2016, Pages 3-5
Methods

Integrated, multi-scale, spatial–temporal cell biology – A next step in the post genomic era

https://doi.org/10.1016/j.ymeth.2015.09.007Get rights and content

Abstract

New microscopic approaches, high-throughput imaging, and gene editing promise major new insights into cellular behaviors. When coupled with genomic and other ‘omic information and “mined” for correlations and associations, a new breed of powerful and useful cellular models should emerge. These top down, coarse-grained, and statistical models, in turn, can be used to form hypotheses merging with fine-grained, bottom up mechanistic studies and models that are the back bone of cell biology. The goal of the Allen Institute for Cell Science is to develop the top down approach by developing a high throughput microscopy pipeline that is integrated with modeling, using gene edited hiPS cell lines in various physiological and pathological contexts. The output of these experiments and models will be an “animated” cell, capable of integrating and analyzing image data generated from experiments and models.

Introduction

The emergence and evolution of collaborative activities generating and subsequently analyzing many kinds of large cellular datasets follows in the wake of the enormous success of the human genome project. These “‘omic” efforts include gene expression profiles, proteomics, metabolomics, lipidomics, glycomics, and epigenomics, among others. Most of these activities first collect and catalog data and then mine for novel associations, developing circuits, pathways and network models for the associations that emerge [1], [2], [3], [4]. This useful information, played out most explicitly and robustly with gene expression data, is then used to try to predict cellular behaviors in normal and pathologic contexts.

The jump from genomic, and ‘omic data in general, to cellular phenotypes and behaviors is a large and challenging central goal of cell biology and biomedical research that is not yet in sight. Indeed, few studies even try to integrate different kinds of available ‘omic information, likely because the data are largely incomplete, of varying quality, or done on different cell types and systems. The phenotypic data are also incomplete, usually focusing on one, or a small number of, activities of particular interest.

There is another, larger issue, however. Live cell microscopy reveals the emerging general theme that transient and localized phenomena drive most cellular behaviors. In this context, most of the ‘omic data reflect only a few time points and represent spatial averages across a single cell, or more generally, across a population of cells. In most cells, the cellular machinery, and the signaling complexes that regulates it, are polarized. These localized activities are obvious and dramatic in cells like neurons or skeletal muscle that are high polarized morphologically. But the polarity is also apparent in other cell types like fibroblasts or neutrophils. Under migrating conditions, for example, actin polymerization and branching are largely confined the leading edge. Also, organelle organization is similarly polarized with the nucleus, Golgi, MTs, actin filaments, and ER in stereotyped locations [5].

Activity assays using biosensors in living cells reveal not only a polarity but also the transient nature of cellular activities. For example, fluorescent sensors of PIP3 localization show a highly transient and localized accumulation in response to a chemotactic signal [6]. RhoGTPase signaling is likewise highly polarized and transient at the leading edge of migrating cells [7]. The localized and transient character of signals is important, as diseases like cancer often arises from mislocalized or constitutive signaling. In addition to these examples, nanoscale events, like receptor clustering and the formation of signaling complexes, reflects a localized, transient polarization on a molecular scale.

Thus, understanding cellular behaviors requires live cell image data of cellular organization and activities. While many labs are generating this kind of data, it is usually done studying a single organelle, often in a molecule-by-molecule approach. However, each of the molecular machines, as well as the molecular complexes that regulate them, function as “systems”, and the cell can be viewed as an integrated, complex system of these systems, with poorly characterized interactions among the various different molecular machines and regulatory complexes. Few microcopy efforts have viewed the cell as such an integrated system and attempted to integrate multiple cellular activities.

Section snippets

Microscopy pipelines

A large-scale, high-throughput microscopy program will be required to address the cell as an integrated system. While there are many high-throughput microscopy efforts, particularly in industry, few are devoted to understanding cell behavior, per se. Instead, most are directed toward drug discovery, focusing on high-throughput screens, using robust, relatively large color intensity differences or morphology-based assays with cells growing on microwells. The advantage of these high-throughput,

The time is right

In addition to these high-throughput, “systems” microscopy efforts, other threads are conjoining to place live cell imaging for understanding cellular behavior as a focus for cell biology and next step in the post genomic era. Major advances live cell imaging make feasible quantifying the 3D organization and activities of cells as they execute their characteristic behaviors [15], [16]. These include the low light damage and rapid data accumulation afforded by advances in spinning disk,

The Allen Institute for Cell Science

The Allen Institute for Cell Science will develop a large-scale, high-throughput imaging platform, i.e., a systems microscopy pipeline, using gene-edited hiPS cells. The overarching goal is to localize key cellular molecular machines and regulatory complexes (MMRCs) and activities and then observe their variation in number and localization and how they change in response to alterations in cellular environment, differentiation, mutation (including disease models), drug treatment, infection with

Conclusion

Multi-scale, spatio-temporal cell biology is arguably a major, next step in the postgenomic era, linking ‘omic data to the localized, transient activities that drive cellular behaviors. The recent advances in microscopy and image analysis as well as the focused, high throughput live cell microscopy efforts in the US and Europe point to its feasibility and potential. In implementing this approach, the Allen Institute for Cell Science will make all of its models, data, reagents, and methods

References (18)

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