Hidden heterogeneity and circadian-controlled cell fate inferred from single cell lineages

Abstract

The origin of lineage correlations among single cells and the extent of heterogeneity in their intermitotic times (IMT) and apoptosis times (AT) remain incompletely understood. Here we developed single cell lineage-tracking experiments and computational algorithms to uncover correlations and heterogeneity in the IMT and AT of a colon cancer cell line before and during cisplatin treatment. These correlations could not be explained using simple protein production/degradation models. Sister cell fates were similar regardless of whether they divided before or after cisplatin administration and did not arise from proximity-related factors, suggesting fate determination early in a cell’s lifetime. Based on these findings, we developed a theoretical model explaining how the observed correlation structure can arise from oscillatory mechanisms underlying cell fate control. Our model recapitulated the data only with very specific oscillation periods that fit measured circadian rhythms, thereby suggesting an important role of the circadian clock in controlling cellular fates.

Automated deep lineage tree analysis using a Bayesian single cell tracking approach

“…We observed moderate correlations (Pearson and Spearman rank coefficients of 0.43 and 0.51, respectively) between 11,696 reference and mother cell pairs (Figure 4D), which represents an order of magnitude higher, yet still relatively low, mother-daughter correlation compared to previously shown trends 4,7,8 . The correlations continued to decrease with increasing ancestor distance all the way to a cell's great-great-grandmother (0.24, 0.10, 0.17 for Pearson and 0.25, 0.07, 0.14 for Spearman rank coefficients).…”

“…For example, the observed distribution of cell cycle durations in a population of cells is governed either by stochastic processes, inherited in a deterministic fashion, or some combination of both [3][4][5][6] (Figure 1A). Previous studies have shown poor correlations within lineages when observing direct ancestral relationships, but remain correlated with immediate relatives 4,7,8 . However, these studies have been performed using manually annotated data, which is laborious to acquire and limits the depth and statistical power to study more distant relationships amid noisy data.…”

“…generational depth compared to the reference cell ( Figure 4A). In doing so, we were able to analyse orders of magnitude greater numbers and significantly greater depth of lineage trees then in previous studies 4,7,8 . Our ancestral analysis comprised 11,696 mother, 4,667 grandmother, 1,002 great-grandmother, 109 great-great-grandmother and 10 great-great-greatgrandmother comparisons (Figure 4).…”

“…Previous studies suggested that cell cycle durations within lineages show poor correlation when observing the direct ancestral cell pairs (mother-daughter and grandmother-granddaughter), but remain highly correlated when examining intra-generational relationships (sister and cousin cells) 4,7,8 . However, due to lack of deep datasets, the analysis has traditionally focussed on immediate cell relatives, including mother, grandmother, sister and first cousin relationships 4,7 and less frequently on more remote family members, such as greatgrandmothers or second cousins 8 . We have extended previous studies using the enhanced depth (up to eight generations), breadth (up to fourth cousin distance from reference cell), and number of lineages (5,032 trees) from our automatically reconstructed lineage tree pool ( Figure 4A).…”

A model for the regulation of the timing of cell division by the circadian clock in the cyanobacterium Synechococcus elongatus

“…Correlations in generation times along cell lineages have been used to study systems from cyanobacteria to cancer cells [22, 30, 32]. In particular, the relations between the parent-child, sibling-sibling, and cousin-cousin correlations in generation times ( ρ md , ρ ss , ρ cc , respectively) inform how division timing might be inherited from the parent cell or affected by an underlying clock-like process.…”