Computational Strategies for Niche-Dependent Cell Conversion to Assist Stem Cell Therapy

The field of regenerative medicine has blossomed in recent decades. However, the ultimate goal of tissue regeneration – replacing damaged or aged cells with healthy functioning cells – still faces a number of challenges. In particular, better understanding of the role of the cellular niche in shapin...

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Bibliographic Details
Published in:Trends in biotechnology (Regular ed.) 2019-07, Vol.37 (7), p.687-696
Main Authors: del Sol, Antonio, Okawa, Satoshi, Ravichandran, Srikanth
Format: Article
Language:English
Subjects:
cellular niche
Computation
computational cell conversion strategy
Computer applications
Conversion
Epigenetics
Explicit knowledge
Gene expression
Genotype & phenotype
Growth factors
Medicine
Phenotypes
Proteins
Regeneration (physiology)
Regenerative medicine
rejuvenation
stem cell
Stem cells
Tissue engineering
Transplantation
Transplants & implants
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Summary:The field of regenerative medicine has blossomed in recent decades. However, the ultimate goal of tissue regeneration – replacing damaged or aged cells with healthy functioning cells – still faces a number of challenges. In particular, better understanding of the role of the cellular niche in shaping stem cell phenotype and conversion would aid in improving current protocols for stem cell therapies. In this regard, the implementation of novel computational approaches that consider the niche effect on stem cells would be valuable. Here we discuss current problems in stem cell transplantation and rejuvenation, and we propose computational strategies to control niche-dependent cell conversion to overcome them. Cellular niche shapes stem cell phenotype and conditions cell conversion. Therefore, stem cell conversion should be considered a niche-specific process. Current computational methods for cell conversion do not consider the niche effect and therefore are not able to predict niche-dependent cell conversion factors. Single-cell RNA-seq allows the gene expression profiling of cell subpopulations in a given niche and therefore enables the modeling of niche-specific cell conversion. We propose a computational strategy for the development of single-cell-based methods for niche-dependent cell conversion and its application to stem cell transplantation and rejuvenation.
ISSN:0167-7799
1879-3096
DOI:10.1016/j.tibtech.2019.01.005