Characterization of cell fate probabilities in single-cell data with Palantir

Setty, Manu; Kiseliovas, Vaidotas; Levine, Jacob H.; Gayoso, Adam; Mažutis, Linas; Pe’er, Dana

doi:10.1038/s41587-019-0068-4

Cited by 514 publications

(719 citation statements)

References 58 publications

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“…This data representation indicates that enterocytes, Tuft and Goblet together with Paneth cells represent 3 main differentiation trajectories. Next we applied Palantir algorithm to estimate a pseudotime trajectory and branch probability through the data (Setty et al, 2018, 2019). Branch probability assigns to each cell a probability to differentiate into each potential terminal state.…”

Section: Resultsmentioning

confidence: 99%

“…The diffusion components were computed using DiffusionMap function from the destiny R package (Angerer et al, 2016) with a local sigma and the parameter k was set to 500. Pseudo-time and branch probabilities were calculated using the Palantir algorithm (Setty et al, 2019) implemented in python. We used as input for the algorithm the first 4 diffusion components after seeing a significant difference between the DC 4 and DC 5 eigen values.…”

Section: Methodsmentioning

confidence: 99%

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Mitochondria define intestinal stem cell differentiation downstream of a FOXO/Notch axis

Ludikhuize

Meerlo

Pagès-Gallego

et al. 2019

Preprint

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Differential signalling of the WNT and Notch pathways regulates proliferation and differentiation of Lgr5 + cryptbased columnar cells (CBCs) into all cell lineages of the intestine. We have recently shown that high mitochondrial activity in CBCs is key in maintaining stem cell function. Interestingly, while high mitochondrial activity drives CBCs, it is reduced in the adjacent secretory Paneth cells (PCs). This observation implies that during differentiation towards PCs, CBCs undergo a metabolic rewiring involving downregulation of mitochondrial number and activity, through a hitherto unknown mechanism. Here we demonstrate, using intestinal organoids that FoxO transcription factors and Notch signalling functionally interact in determining CBC cell fate. In agreement with the organoid data, combined Foxo1 and 3 deletion in mice increases PC number in the intestine. Importantly, we show that FOXO and Notch signalling converge onto regulation of mitochondrial fission, which in turn provokes stem cell differentiation into the secretory types; Goblet cells and PCs. Finally, mapping intestinal stem cell differentiation based on pseudotime computation of scRNA-seq data further supports the role of FOXO, Notch and mitochondria in determining secretory differentiation. This shows that mitochondria is not only a discriminatory hallmark of CBCs and PCs, but that its status actively determines lineage commitment during differentiation. Together, our work describes a new signalling-metabolic axis in stem cell differentiation and highlights the importance of mitochondria in determining cell fate. 45

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Mitochondria define intestinal stem cell differentiation downstream of a FOXO/Notch axis

Ludikhuize

Meerlo

Pagès-Gallego

et al. 2019

Preprint

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“…We first evaluated the suitability of pseudotime algorithms for modeling axonogenesis and if so, to determine whether separate BC-and SC-fated trajectories can be distinguished. We began with analysis of the early-born MLIs (P0 TMX, 423 cells) using Palantir, a diffusion map-based pseudotime algorithm (Setty et al 2019;Coifman et al 2005). Palantir rendered a trajectory that followed a linear progression, as confirmed through both the default and expert-directed pseudo-timelines ( Figure 6B , which computationally partitions high-dimensional datasets into phenotypically meaningful subpopulations ( Figure 6C).…”

Section: Axon Morphogenesis Can Be Ordered Along a Pseudo-temporamentioning

confidence: 99%

Morphological pseudotime ordering and fate mapping reveals diversification of cerebellar inhibitory interneurons

Wang

Lefebvre

2020

Preprint

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Understanding how diverse neurons are assembled into circuits requires a framework for describing cell types and their developmental trajectories. Here, we combined genetic fate mapping and pseudo-temporal profiling to resolve the diversification of cerebellar inhibitory interneurons based on morphology. The molecular layer interneurons (MLIs) derive from a common progenitor but comprise a diverse population of dendritic-, somatic-, and axon initial segment-targeting interneurons. MLIs are classically divided into two types. However, their morphological heterogeneity suggests an alternate model of one continuously varying population. Through clustering and trajectory inference of 811 MLI reconstructions at maturity and during development, we show that MLIs divide into two discrete classes but also present significant within-class heterogeneity. Pseudotime trajectory mapping uncovered the emergence of distinct phenotypes during migration and axonogenesis, well before neurons reach their final positions. Our study illustrates the utility of quantitative single-cell methods to morphology for defining the diversification of neuronal subtypes. Figure 2. Morphological heterogeneity among MLIs. (A) Left: Immunostaining of MLIs (Parvalbumin, cyan) and PCs (co-labeled by Parvalbumin and Calbindin, cyan and red, respectively) show the ML space in which MLIs reside. PC somata are enveloped by BC axons (white arrowhead). Right: Inverted image of four fluorescently-labelled MLIs. The lower MLI (pink arrowhead) has canonical BC morphologies, including axonal basket terminals around the PC somata (asterisks). The two upper MLIs (teal arrowhead) have canonical SC morphologies and reside within the upper ML. The faintly labelled MLI (blue arrowhead) has SC morphologies but reside within the lower ML. (B) Reconstruction of canonical BC from panel A, with complete dendritic arbor traced in orange, and complete axonal arbor traced in blue. (C) Reconstruction of canonical SC from panel A (cell on far right). (D-F) Representative images of MLIs with mixtures of BC and SC characteristics. Top: inverted fluorescence image; Bottom: reconstruction with dendritic (orange) and axonal (blue) traces. (D) MLI located in the middle ML with SC dendritic features, and a long horizontal axon (arrow) with descending basket collaterals (asterisks). (E) MLI located in the lower ML with SC-like dendritic and axonal arbors. (F) MLI located in the upper ML with a long horizontal axon (arrow) and two descending axon collaterals with basket formations around PC somas (asterisks). All scale bars are 50 μm.

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“…49 However, although the daughter cells continue to be very similar to their predecessors, 50 in the long term, as further variations get amplified with consecutive cell divisions, 51 the hESC population get established by incremental divergences. These divergences, 52 caused by regulatory mechanisms, noise in the protein expression, etc., create paths 53 through all possible cell states which result in the reported heterogeneity in the stem 54 cell populations [31]. 55 We analyse OCT4 time series from hESCs expressing the fluorescent protein mCherry 56 [29].…”

mentioning

confidence: 99%

Spatio-temporal analyses ofOCT4expression and fate transitions in human embryonic stem cells

Orozco-Fuentes

Wadkin

Neganova

et al. 2020

Preprint

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OCT4 is one of the transcription factors required to maintain an undifferentiated state in human embryonic stem cells (hESCs). Thus, it is crucial to understand how OCT4 transcription is regulated both at the single-cell and colony level. Here we analyse the changes of OCT4-mCherry intensity expression in hESCs in the presence and absence of the BMP4 morphogenetic protein.We show that OCT4 expression is dynamic, reaching a maximum response 10 h after BMP4 treatment. We obtain the stationary probability distributions that govern the hESCs transitions amongst the different cell states in the presence/absence of BMP4 and establish the times at which the hESCs, that lead to differentiated and pluripotent cells, cluster in the colony. Furthermore, by quantifying the similarities between the OCT4 expression amongst neighbouring hESCs, we show that hESCs express, on average, similar values in their local neighbourhood within the first two days of the experiment and before BMP4 treatment. These results are relevant for the development of mathematical and computational models of adherent hESC colonies. Introduction 1 Human pluripotent stem cells (hPSCs), encompassing human embryonic stem cells 2 (hESCs) and human induced pluripotent stem cells (hiPSCs) self-renew indefinitely while 3 maintaining the property to give rise, under differentiation conditions, to almost any cell 4 type in the human body [1,2]. The scientific viewpoint on self-renewal and differentiation 5 of hESCs is established in a regulatory network whose components are a core set of 6 pluripotency transcription factors (TFs) expressed to maintain self-renewal and suppress 7 differentiation [3,4]. Amongst the most important TFs that preserve the undifferentiated 8 1/21 state in hESCs are NANOG, OCT4 and SOX2 [3, 5]. During development, these TFs 9become expressed at different levels and initiate differentiation towards specific cell 10 lineages following signalling cues [6]. 11 Several experiments have been performed to quantify the behaviour and joint influence 12 of each TF in the pluripotent cell [7][8][9][10][11]. Their results indicate that the expression of the 13 TFs proteins are highly variable both at the single-cell (time) and colony-level (space) 14 and are subjected to intrinsic noise due to a finite copy of genes, interactions at the 15 molecular level or due to randomness present in the extracellular environment [12][13][14]. 16 Thus, heterogeneity and stochasticity are inherent properties of pluripotent stem cell 17 populations [13,15,16], that hinder their clonal expansion in culture [17][18][19], but in vivo 18 promote the regionalisation and specification of the early blastocyst stage [20]. 19OCT4, acting in conjunction with other core members of the pluripotent regulatory 20 network, (e.g. SOX2, NANOG), activates both protein-coding genes and non-coding 21 RNAs necessary to maintain pluripotency [9]. Furthermore, besides being an essential 22 TF for the pluripotent state, OCT4 is also key to induce the reprogramming of somatic 23 cells...

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Characterization of cell fate probabilities in single-cell data with Palantir

Cited by 514 publications

References 58 publications

Mitochondria define intestinal stem cell differentiation downstream of a FOXO/Notch axis

Mitochondria define intestinal stem cell differentiation downstream of a FOXO/Notch axis

Morphological pseudotime ordering and fate mapping reveals diversification of cerebellar inhibitory interneurons

Spatio-temporal analyses ofOCT4expression and fate transitions in human embryonic stem cells

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