title: Computational methods for direct cell conversion.
abstract: Directed cell conversion (or transdifferentiation) of one somatic cell-type to another can be achieved by ectopic expression of a set of transcription factors. Since the experimental identification of transcription factors for transdifferentiation is extremely time-consuming and expensive, there are still relatively few transdifferentiations achieved in comparison to the number of human cell-types. However, the growing volume of transcriptional data available and the recent introduction of data-driven algorithmic approaches that predict factors for transdifferentiation holds great promise for accelerating this field. Here we review those computational methods whose in-silico predictions have been experimentally validated, highlighting differences and similarities. Our analysis reveals that the factors predicted by each method tend to be different due to varying source cells used, gene expression quantification and algorithmic steps. We show these differences have an impact on the regulatory influences downstream, with some methods favoring transcription factors regulating developmental progression and others favoring factors regulating mature cell processes. These computational approaches offer a starting point to predict and test novel factors for transdifferentiation. We argue that collecting high-quality gene expression data from single-cells or pure cell-populations across a broader set of cell-types would be necessary to improve the quality and consistency of the in-silico predictions.
authors.affiliation: a Cardiovascular and Metabolic Disorders, Duke-NUS Medical School , Singapore.
authors.forename: Uma S
authors.initials: US
authors.lastname: Kamaraj
authors.affiliation: b Department of Computer Science , University of Bristol , Bristol , UK.
authors.forename: Julian
authors.initials: J
authors.lastname: Gough
authors.affiliation: c Anatomy and Developmental Biology, Monash University , Clayton , Victoria , Australia.
authors.forename: Jose M
authors.initials: JM
authors.lastname: Polo
authors.affiliation: a Cardiovascular and Metabolic Disorders, Duke-NUS Medical School , Singapore.
authors.forename: Enrico
authors.initials: E
authors.lastname: Petretto
authors.affiliation: a Cardiovascular and Metabolic Disorders, Duke-NUS Medical School , Singapore.
authors.forename: Owen J L
authors.initials: OJ
authors.lastname: Rackham
mesh_terms: D000818:Animals; D054338:Cell Transdifferentiation; D002477:Cells / Q000378:metabolism*; D065150:Cellular Reprogramming; D019295:Computational Biology / Q000379:methods*; D005786:Gene Expression Regulation; D006801:Humans; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors
keywords: algorithm; prediction; transcription factor; transdifferentiation