Neighborhood Impact Factor to Study Cell-Fate Decision-Making in Cellular Communities

Methods Mol Biol. 2021;2258:17-28. doi: 10.1007/978-1-0716-1174-6_2.

Abstract

Cell-fate determination is a function of cell-intrinsic and -extrinsic signaling cues. Understanding the design principles governing fate control in multicellular systems remains difficult to understand and analyze. To address the current challenges of spatial analysis of potential signaling events, we have developed a pipeline for assessment of the neighboring cells at defined areas in the vicinity of target cells using a newly defined concept of Neighborhood Impact Factor. We have used our pipeline to interrogate cellular decision-making in a genetically derived multi-lineage liver organoid from induced pluripotent stem cells. We examined endothelial versus hepatocyte fate determination for cells with similar expression level of an engineered driver gene circuit. Our analysis suggests that the relative level of gene expression to the neighbor population can control the final fate choice in our engineered liver multicellular system.

Keywords: Cell fate; Cell state; Gene regulatory network; Multicellular; Neighborhood impact factor; Organoids.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Cell Communication
  • Cell Culture Techniques
  • Cell Lineage* / genetics
  • Cell Tracking*
  • Cells, Cultured
  • Gene Expression Regulation, Developmental
  • Gene Regulatory Networks
  • Humans
  • Image Processing, Computer-Assisted*
  • Induced Pluripotent Stem Cells / physiology*
  • Microscopy, Fluorescence*
  • Morphogenesis
  • Organoids
  • Signal Transduction
  • Software Design*
  • Spheroids, Cellular
  • Stem Cell Niche