KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas

Abstract

SummaryDifferentiated derivatives of human pluripotent stem cells in culture are generally phenotypically immature compared to their adult counterparts. Their identity is often difficult to determine with certainty because little is known about their human fetal equivalents in vivo. Cellular identity and signaling pathways directing differentiation are usually determined by extrapolating information from either human adult tissue or model organisms, assuming conservation with humans. To resolve this, we generated a collection of human fetal transcriptional profiles at different developmental stages. Moreover, we developed an algorithm, KeyGenes, which uses this dataset to quantify the extent to which next-generation sequencing or microarray data resemble specific cell or tissue types in the human fetus. Using KeyGenes combined with the human fetal atlas, we identified multiple cell and tissue samples unambiguously on a limited set of features. We thus provide a flexible and expandable platform to monitor and evaluate the efficiency of differentiation in vitro.

Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis

“…Scale bars, 100 mm. f, Heat map visualizing the relative transcriptional identity (score from 0 to 1 determined using the KeyGene algorithm 15 ) of kidney organoids to 13 human fetal tissues. RNA-seq was performed on whole kidney organoids from 4 time points (day 0, 3, 11 and 18 after aggregation) with 3 individual organoids from 1 experiment per time point (see Supplementary Table 2).…”

“…5 and Supplementary Table 2). Transcriptional profiling was performed and compared using an unbiased method with human fetal transcriptional data sets from 21 human fetal organs/tissues from the first and/or second trimester of pregnancy 15 . This analysis clustered kidney organoids at d11 and d18 of culture with first trimester human fetal kidney (Fig.…”

Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells

“…4c) the KeyGenes algorithm 23 was used with a panel of pre-/peri-implantation tissues 21 as training set. Since there were 3 replicates per tissue in the training set, leave-one-out crossvalidation had to be used instead of 10-fold cross-validation.…”

Direct lineage reprogramming via pioneer factors; a detour through developmental gene regulatory networks

“…Such GRN analysis of developmental intermediates will also help identify key transcription factors that regulate both upper-level GRNs and differentiation batteries. A similar computation approach is taken by KeyGenes, which employs a collection of human fetal transcriptional profiles collected from tissues and organs at different developmental stages to assess the cell identity of differentiating human tissues (Roost et al, 2015). To specifically identify pioneer factor activity, a computational method termed 'protein interaction quantitation' (PIQ) helps to identify pioneer factors via assessment of genome-wide DNase I hypersensitivity profiles .…”