Live cell-lineage tracing and machine learning reveal patterns of organ regeneration

Abstract

Despite the intrinsically stochastic nature of damage, sensory organs recapitulate normal architecture during repair to maintain function. Here we present a quantitative approach that combines live cell-lineage tracing and multifactorial classification by machine learning to reveal how cell identity and localization are coordinated during organ regeneration. We use the superficial neuromasts in larval zebrafish, which contain three cell classes organized in radial symmetry and a single planar-polarity axis. Visualization of cell-fate transitions at high temporal resolution shows that neuromasts regenerate isotropically to recover geometric order, proportions and polarity with exceptional accuracy. We identify mediolateral position within the growing tissue as the best predictor of cell-fate acquisition. We propose a self-regulatory mechanism that guides the regenerative process to identical outcome with minimal extrinsic information. The integrated approach that we have developed is simple and broadly applicable, and should help define predictive signatures of cellular behavior during the construction of complex tissues.

Single cell RNA-Seq reveals distinct stem cell populations that drive sensory hair cell regeneration in response to loss of Fgf and Notch signaling

“…Interestingly, mantle cells express tspan1, and even though not the exact homolog, planarian tspan1 marks a subset of stem cells (neoblasts; An 2018, (Steiner et al, 2014)). Support cells also give rise to mantle cells when mantle cells are ablated (Viader-Llargues et al, 2018) arguing that active and quiescent stem cells can convert back and forth as shown in other systems (Clevers and Watt, 2018). For example, in the intestine slow-cycling, label-retaining stem cells in the +4 position can give rise to stem cells at the bottom of the crypt, which conversely can also give rise to +4 stem cells (Takeda et al, 2011).…”

“…Long term lineage tracing experiments have to be performed to assess if they indeed present stem cells. The second quiescent, long term stem cell population are the mantle cells that give rise to hair cells in long term lineage analyses but that do not respond to acute neomycin-induced hair cell death (Romero-Carvajal et al, 2015;Seleit et al, 2017;Viader-Llargues et al, 2018). Interestingly, mantle cells express tspan1, and even though not the exact homolog, planarian tspan1 marks a subset of stem cells (neoblasts; An 2018, (Steiner et al, 2014)).…”

“…Understanding hair cell production in regenerating species is essential for elucidating how regeneration is blocked in mammals. We and others showed that the zebrafish lateral line system is a powerful in vivo model to study the cellular and molecular basis of hair cell regeneration (Kniss et al, 2016;Lush and Piotrowski, 2014b;Ma and Raible, 2009;Romero-Carvajal et al, 2015;Viader-Llargues et al, 2018). The lateral line is a sensory system that allows aquatic vertebrates to orient themselves by detecting water motion.…”

“…Using time-lapse analyses and tracking of all dividing cells in regenerating neuromasts, coupled with cell fate analyses, we previously identified two major support cell lineages: 1) support cells that divide symmetrically to form two progenitor cells (amplifying divisions); and 2) support cells that divide to form two hair cells (differentiating divisions) (Romero-Carvajal et al, 2015). A recent publication has confirmed these lineages (Viader-Llargues et al, 2018). The two cell behaviors display a striking spatial compartmentalization.…”

Fishing forward and reverse: Advances in zebrafish phenomics

“…To this day the terabyte sizes of imaging and sequence files pose formidable obstacles to the handling and processing of this data (reviewed in Mikut et al, 2013). However, recent advances in segmentation algorithms and increases in computational power have enabled the rapid, sometimes even real-time, identification of individual organs, cells, and organelles from microscopy data (Viader-Llargues et al, 2018; reviewed in Mikut et al, 2013). Additional efforts to thoroughly characterize zebrafish anatomy at the cellular level have already generated online “Atlases”, which provide 3-dimensional, wild-type references for the anatomy of multiple zebrafish organ systems (Randlett et al, 2015; Eames et al, 2013; Castro-Gonzalez et al, 2014).…”