Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

[gwaybio]

https://doi.org/10.1016/j.cell.2012.08.023

Authors

Buganim, Y., Faddah, D.A., Cheng, A.W., Itskovich, E., Markoulaki, S., Ganz, K., Klemm, S.L., van Oudenaarden, A., Jaenisch, R.

Year

2012

Abstract

During cellular reprogramming, only a small fraction of cells become induced pluripotent stem cells (iPSCs). Previous analyses of gene expression during reprogramming were based on populations of cells, impeding single-cell level identification of reprogramming events. We utilized two gene expression technologies to profile 48 genes in single cells at various stages during the reprogramming process. Analysis of early stages revealed considerable variation in gene expression between cells in contrast to late stages. Expression of Esrrb, Utf1, Lin28, and Dppa2 is a better predictor for cells to progress into iPSCs than expression of the previously suggested reprogramming markers Fbxo15, Fgf4, and Oct4. Stochastic gene expression early in reprogramming is followed by a late hierarchical phase with Sox2 being the upstream factor in a gene expression hierarchy. Finally, downstream factors derived from the late phase, which do not include Oct4, Sox2, Klf4, c-Myc, and Nanog, can activate the pluripotency circuitry.

[gwaybio]

Experimental Methods

Investigating the reprogramming of induced pluripotent stem cells and Yamanaka factors by Fluidigm array chip (96 cells by 48 genes) and single molecule mRNA FISH (3 genes as validation).

Computational Methods

• PCA of 96 x 48 matrix, visualizing top two components (only ~20 and 5% of variance).
  • Components separate differentiated cells and capture transitioning state cells
• Bayesian hierarchical model of states conditional on key fate deciding genes