Biologically Relevant Heterogeneity: Metrics and Practical Insights

Abstract

Heterogeneity is a fundamental property of biological systems at all scales that must be addressed in a wide range of biomedical applications including basic biomedical research, drug discovery, diagnostics and the implementation of precision medicine. There are a number of published approaches to characterizing heterogeneity in cells in vitro and in tissue sections. However, there are no generally accepted approaches for the detection and quantitation of heterogeneity that can be applied in a relatively high throughput workflow. This review and perspective emphasizes the experimental methods that capture multiplexed cell level data, as well as the need for standard metrics of the spatial, temporal and population components of heterogeneity. A recommendation is made for the adoption of a set of three heterogeneity indices that can be implemented in any high throughput workflow to optimize the decision-making process. In addition, a pairwise mutual information method is suggested as an approach to characterizing the spatial features of heterogeneity, especially in tissue-based imaging. Furthermore, metrics for temporal heterogeneity are in the early stages of development. Example studies indicate that the analysis of functional phenotypic heterogeneity can be exploited to guide decisions in the interpretation of biomedical experiments, drug discovery, diagnostics and the design of optimal therapeutic strategies for individual patients.

Using toponomics to characterize phenotypic diversity in alveolar macrophages from male mice treated with exogenous SP-A1

“…The use of TIS to identify CMPs and thereby study the expression patterns of multiple markers and their interactions within the same cellular space provides an important first step in understanding Table 2 for other information on marker numbers and gene names this heterogeneity, appreciating the diversity of the AM population under various conditions, and eventually investigating its impact on different AM functions. Similar heterogeneity and phenotypic diversity is being revealed in numerous systems [52,53] and is likely to be important for many biologically relevant systems. Our results indicate that toponomics may provide a powerful tool for exploring this phenomenon.…”

Digital Assays Part II: Digital Protein and Cell Assays

“…Single-cell assays enable the study of cell heterogeneity in populations, an area of growing interest with implications in disease pathology, immune response, development, differentiation, and general organism function. 59 High-throughput digital cell assays can help statistically quantify genomic or phenotypic differences between cells and, based on that, classify cells into subpopulations. For example, natural microbial populations are composed of many diverse cell types and phenotypes, many of which cannot be cultured individually.…”

Building with intent: Technologies and principles for engineering mammalian cell-based therapies to sense and respond

“…Intercellular variation in device performance can be attributed to external sources, such as sample preparation, cell density, and cell-to-cell contact, as well as internal sources like cell cycle asynchrony, unequal inheritance in cell division, and stochastic fluctuations in gene expression [43,44]. While design goals may be framed using digital metaphors like circuits, ultimately cells operate within a continuum of variation in both component doses and signals, and such variation can limit the extent to which a device reliably performs an engineered function (Figure 1C) [45].…”