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. 2018 Sep;28(9):1285-1295.
doi: 10.1101/gr.233213.117. Epub 2018 Aug 2.

Tracing human stem cell lineage during development using DNA methylation

Lucas A Salas #  1 , John K Wiencke #  2 , Devin C Koestler  3 , Ze Zhang  4   5 , Brock C Christensen #  1   6   7 , Karl T Kelsey #  4   5
Affiliations

Tracing human stem cell lineage during development using DNA methylation

Lucas A Salas et al. Genome Res. 2018 Sep.

Abstract

Stem cell maturation is a fundamental, yet poorly understood aspect of human development. We devised a DNA methylation signature deeply reminiscent of embryonic stem cells (a fetal cell origin signature, FCO) to interrogate the evolving character of multiple human tissues. The cell fraction displaying this FCO signature was highly dependent upon developmental stage (fetal versus adult), and in leukocytes, it described a dynamic transition during the first 5 yr of life. Significant individual variation in the FCO signature of leukocytes was evident at birth, in childhood, and throughout adult life. The genes characterizing the signature included transcription factors and proteins intimately involved in embryonic development. We defined and applied a DNA methylation signature common among human fetal hematopoietic progenitor cells and have shown that this signature traces the lineage of cells and informs the study of stem cell heterogeneity in humans under homeostatic conditions.

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Figures

Figure 1.
Figure 1.
Discovery (A) and replication (B) of the deconvolution algorithm using lineage-invariant, developmentally sensitive CpG loci in newborn and adult peripheral blood leukocytes. Estimated mean percentage (standard deviation [SD]) FCO methylation fractions are 85.4% (6.0) for umbilical cord blood (UCB) and 0.6% (1.7) for peripheral adult blood in A; P = 2.11 × 10−191. In the replication (B), estimated FCO methylation fractions are 89.9% (3.8) for UCB and 2.0% (3.5) for peripheral adult blood; P = 8.35 × 10−81.
Figure 2.
Figure 2.
Developmentally sensitive methylation signature deconvolution in pluripotent, fetal progenitors, and adult CD34+ stem/progenitor cells. Mean (SD) estimated FCO methylation fractions for embryonic/fetal cells are 75.9% (8.5) and 4.4% (5.1) for adult progenitors (bone marrow); P = 1.81 × 10−86. In the boxplots: (1) The box shows the interquartile range (IQR), (2) the whiskers show the inner fences (1.5 × IQR out of the box), (3) the bolded line shows the median of the data, and the notches-horns display the 95% confidence interval of the median. (ESC) Embryonic stem cells; (iPSC) induced pluripotent stem cells; (CD34+ fetal) fresh cord blood cells expressing CD34+; (erythroid fetal) fetal liver CD34+ cells, differentiated ex vivo to express transferrin receptor and glycophorin; (CD34+ adult) bone marrow expressing CD34+ CD38− CD90+ CD45RA−; (MPP) multipotent progenitors; (L-MPP) lymphoid primed multipotent progenitors; (CMP) common myeloid progenitors; (GMP) granulocyte/macrophage progenitors; (MEP) megakaryocyte-erythroid progenitors; (erythroid adult) adult bone marrow CD34+ cells, differentiated ex vivo to express transferrin receptor and glycophorin; (PMC) promyelocyte/myelocyte; (PMN) metamyelocyte/band-myelocyte.
Figure 3.
Figure 3.
FCO methylation signature deconvolution in fetal/embryonic and adult tissues. Panel A compares the estimated FCO methylation fraction between fetal/embryonic and adult tissues. In the boxplots: (1) The box shows the interquartile range (IQR), (2) the whiskers show the inner fences (1.5 × IQR out of the box), (3) the bolded line shows the median of the data, and the notches-horns display the 95% confidence interval of the median. Panel B compares the estimated mean FCO methylation signature in three fetal/embryonic tissues in four gestational periods: Brain and muscle showed a marked reduction of the signature after the 15th week of gestational age. In contrast, fetal/embryonic liver showed a persistently high level of the FCO signature.
Figure 4.
Figure 4.
Candidate CpGs in the FCO methylation signature in the MIRLET7BHG locus on Chromosome 22. Box plots compare the DNA methylation levels (as β-values) at each CpG site for ESC (in yellow), UCB (in orange), adult progenitors (in green), and adult whole blood (in magenta). In the boxplots: (1) The box shows the interquartile range (IQR), (2) the whiskers show the inner fences (1.5 × IQR out of the box), (3) the bolded line shows the median of the data, and the notches-horns display the 95% confidence interval of the median. We rearranged the scale of the boxplots to approximate the different genomic context measured by the probes. Above the boxplots, tracks from the UCSC Genome Browser show the epigenomic features of normal adult CD14+ monocytes including activating histone marks, DNase I hypersensitivity clusters, and transcription factor binding sites. (ORegAnno) Open Regulatory Annotation Database (Lesurf et al. 2016). Differences in DNA methylation between fetal cells (ESC and UCB) and adult cells (adult progenitors and adult whole blood) were statistically significant at P < 2.0 × 10−16 after Bonferroni correction for all five CpG sites. Differences in DNA methylation between ESC and adult progenitors were significant for four out of five CpGs (P < 5.9 × 10−4) after Bonferroni correction (cg03684807 was not significant; P = 0.26).
Figure 5.
Figure 5.
FCO methylation signature deconvolution in blood leukocytes sampled at birth through childhood and adult ages. Panel A shows the loess smoothing curve across different ages ranging from newborn to 101 yr. In the top subplot of the panel is an enlarged depiction of the marked decrease of the fraction of cells showing the FCO signature during the first 18 yr of life. Panel B summarizes the reduction of the FCO signature at different age intervals. In the boxplots: (1) The box shows the interquartile range (IQR), (2) the whiskers show the inner fences (1.5 × IQR out of the box), (3) the bolded line shows the median of the data, and the notches-horns display the 95% confidence interval of the median.
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