Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping

Abstract

Pleiotropy-when a single mutation affects multiple traits-is a controversial topic with farreaching implications. Pleiotropy plays a central role in debates about how complex traits evolve and whether biological systems are modular or are organized such that every gene has the potential to affect many traits. Pleiotropy is also critical to initiatives in evolutionary medicine that seek to trap infectious microbes or tumors by selecting for mutations that encourage growth in some conditions at the expense of others. Research in these fields, and others, would benefit from understanding the extent to which pleiotropy reflects inherent relationships among phenotypes that correlate no matter the perturbation (vertical pleiotropy). Alternatively, pleiotropy may result from genetic changes that impose correlations between otherwise independent traits (horizontal pleiotropy). We distinguish these possibilities by using clonal populations of yeast cells to quantify the inherent relationships between single-cell morphological features. Then, we demonstrate how often these relationships underlie vertical pleiotropy and how often these relationships are modified by genetic variants (quantitative trait loci [QTL]) acting via horizontal pleiotropy. Our comprehensive screen measures thousands of pairwise trait correlations across hundreds of thousands of yeast cells and reveals ample evidence of both vertical and horizontal pleiotropy. Additionally, we observe that the correlations between traits can change with the environment, genetic background, and cell-cycle position. These changing dependencies suggest a nuanced view of pleiotropy: biological systems demonstrate limited pleiotropy in any given context, but across contexts (e.g., across diverse environments and genetic backgrounds) each genetic change has the potential to influence a larger number of traits. Our method suggests that exploiting pleiotropy for applications in evolutionary medicine would benefit from focusing on traits with correlations that are less dependent on context.

Fitness variation across subtle environmental perturbations reveals local modularity and global pleiotropy of adaptation

“…In principle, we now have advanced tools to measure a large number of phenotypic impacts of a genetic change, for instance through high-throughput microscopy, proteomics, or RNAseq ( Manzoni et al, 2018 ; Ritchie et al, 2015 ; Zhang and Kuster, 2019 ). The conceptual problem is how to define phenotypes given the interconnectedness of biological systems ( Geiler-Samerotte et al, 2020 ; Paaby and Rockman, 2013 ). If a mutation leads to complex changes in cell size and shape, should each change be considered a distinct phenotype?…”

“…For example, perhaps these expression changes are coordinated and reflect the upregulation of a stress-response pathway. Unfortunately, defining the functional units in which a gene product participates remains difficult, especially because these units re-wire across genetic backgrounds, environments, and species ( Geiler-Samerotte et al, 2020 ; Pavličev et al, 2017 ; Sun et al, 2020 ; Zan and Carlborg, 2020 ).…”

“…Further, many measurable phenotypes are related in complex ways (Geiler-Samerotte et al, 2020). Mapping their contribution to fitness requires a complete understanding of how genetic changes lead to molecular changes and how these percolate to higher functional levels and ultimately influence fitness (Kemble et al, 2020).…”

“…This is a challenging problem as the possible number of phenotypes one can measure is effectively infinite, for example the expression level of every gene or the quantity of every metabolite ( Coombes et al, 2019 ; Mehlhoff et al, 2020 ). Further, many measurable phenotypes are related in complex ways ( Geiler-Samerotte et al, 2020 ). Mapping their contribution to fitness requires a complete understanding of how genetic changes lead to molecular changes and how these percolate to higher functional levels and ultimately influence fitness ( Kemble et al, 2020 ).…”

System genetics in the rat HXB/BXH family identifies Tti2 as a pleiotropic quantitative trait gene for adult hippocampal neurogenesis and serum glucose

“…Pleiotropy is widespread among model organisms [9][10][11][12][13] and humans [2,[14][15][16][17] with an estimated median number of around six traits per locus [13]. Pleiotropic mutations can result in genetic covariance among phenotypes [10,12]. Cognition and metabolic homeostasis are both achieved through multiple elementary mechanisms at molecular, cellular, tissue, and inter-organ levels, some of which might be shared.…”